title: WT_Flag_leaf_rep3

tag: genotype/variation

tag: cultivar

tag: Stage


title: Yale_ChipSeq_MEL_H3K4me3_IgG-Yale (superseded by GSM1003753)

status: Public on Sep 20 2011

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
****************************
GSM798324 record metadata submitted on Sep 19 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSM1003753
****************************

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: MEL

tag: lab

value: Yale-m

tag: lab description

value: Weissman - Yale University

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

tag: cell sex

value: M

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal

tag: antibody targetdescription

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: IgG-Yale

tag: control description

value: Input signal from Mouse IgG ChIP-seq prepared at Yale

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

value: MEL/None/Input/IgG-Yale

tag: replicate

tag: replicate description

value: tier 1

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: WT_Flag_leaf_rep2

status: Public on Sep 23 2011

city: Davis

first: Dario

last: Cantu

address: One Shields Ave

department: Plant Sciences

institute: UC Davis

library_source: transcriptomic

data_processing: Low quality sequences and vector contaminants were removed using custom scripts available from http://code.google.com/p/atgc-illumina/. High quality reads were aligned with Bowtie to wheat transcripts (454 assembled sequences, TSA project 59945 - accession numbers: HP608076-HP639668)

molecule: total RNA

organism: Triticum aestivum

growth_protocol: Transgenic plants for the NAM RNAi construct  were grown under long-days (LD, 16 h light 8 h dark)

extract_protocol: Amplified cDNA synthesis was performed according to mRNA sequencing protocol  from Illumina (Part # 1004898 Rev. D) and using 10 µg total RNA as starting material

treatment_protocol: At anthesis, spikes were labelled and after 12 days, flag leaves samples from four plants were pooled and used for RNA extraction.

tag: tissue

value: flag leaf

tag: genotype/variation

value: wild type

tag: cultivar

value: Bobwhite

tag: Stage

value: 12 Days Post Anthesis


title: u87_adar_kd

status: Public on Sep 21 2011

city: Los Angeles

first: Gang

last: Li

address: 611 Charles E. Young Drive Rm. 660

institute: UCLA

description: cDNA with ADAR siRNA treatment

data_processing: The sequence reads are aligned to the genome and transcriptome using blat, bowtie and tophat allowing at most 12 mismatches. Unique pair of the alignments of a pair of reads is accepted if both ends have less than 6 mismatches.

organism: Homo sapiens

source_name: Glioblastoma

growth_protocol: U87MG cells were maintained in DMEM high glucose medium supplemented with pyruvate, L-glutamine, and 10% fetal bovine serum (FBS).

extract_protocol: We used the standard Illumina protocol to prepare libraries for RNA-Seq (http://www.illumina.com/support/documentation.ilmn). Briefly, 10ug total RNA was first processed via poly-A selection and fragmentation. We generated first-strand cDNA using random hexamer-primed reverse transcription and subsequently used it to generate second-strand cDNA using RNase H and DNA polymerase. Sequencing adapters were ligated using the Illumina Paired-End sample prep kit. Fragments of ~200 bp were isolated by gel electrophoresis, amplified by 15 cycles of PCR and sequenced.

treatment_protocol: 50ng of ADAR1 siRNA and control siRNA were transfected respectively with lipofectamine RNAiMAX into 5x104 U87MG cells per single well of 6-well plate via reverse transfection and cells were harvested 48h following transfection. Total RNA was isolated using the RNeasy micro kit.

tag: cell line

value: ADAR1 siRNA


title: GPC_RNAi_Flag_leaf_rep1


title: Yale_ChipSeq_MEL_Input_DMSO_2.0pct_IgG-Yale

tag: lab

value: Yale-m

tag: lab description

value: Weissman - Yale University

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

tag: cell sex

value: M

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: 5 d with 2% DMSO (Weissman)


title: chd1del_MNase

status: Public on Sep 16 2011

city: Dundee

first: Triantafyllos

last: Gkikopoulos

state: Angus

address: Dow Street

department: College of Life Sciences

country: United Kingdom

institute: University of Dundee

description:
processed data file build: sacCer1, Oct, 2003
mono-nucleosomes

data_processing:
The average DNA length of paired-end samples is 150 bp +/- 40 bp.
Read sequences for each sample were received as two FASTQ files one for each fragment. These sequences were aligned to the Yeast SGD database (obtained from the SGD site as FASTA files dated Nov 2006) using Bowtie 0.12.3 as unique matched paired reads (5) as unique matched paired reads with maximum fragment length of 500bp to create a SAM file. A BAM file was created using samtools and once sorted was subsequently used to create a BED coverage file. The BAM file was then used to create a BigWig file.

organism: Saccharomyces cerevisiae

source_name: Mnase digested chromatin

growth_protocol: Liquid suspension cultures were inoculated from starter cultures and grown O/N in YPAD at 30C.

extract_protocol: Yeast suspension cultures were grown in rich media (YPAD) at 30oC O/N to a cell density of 1-4 x107 nucleated cells/ml. Cells were cross-linked by addition of formaldehyde to a final concentration of 1% v/v for 10 minutes at room temperature (RT). Crosslinking was quenched with addition of 2.5 M glycine to a final concentration of 0.125 M and cells were further incubated for another 5 min at RT.  Crosslinked cells were washed 3x with ice cold TBS (20mM Tris pH 7.5, 120 mM NaCl) and finally resuspended in 1M Sorbitol. Spheroplast preparation and micrococcal nuclease digestion of chromatin were carried out as previously described (3). Nucleosomal fragments were gel purified from 1.5% agarose gels run in TBE and DNA was extracted with QIAGEN gel extraction kits and subject to paired end sequencing using the Illumina platform

tag: strain

tag: library selection

value: gel purified mononucleosomes


title: Chd1_ChIP

description:
processed data file build: sacCer1, Oct, 2003
sonicated DNA

source_name: ChIP

extract_protocol: Yeast cultures at a density of between 0.5 x 107 and 2 x 107 cells/ml were treated with 1 % formaldehyde for 20 min at room temperature.  Cross-linking was quenched by addition of 2.5 M glycine to a final concentration of 0.125 M. Cross-linked cells were washed three times with ice cold TBS and resuspended in 300 ul lysis buffer (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate and a mixture of protease inhibitors) and agitated with glass beads for 25 minutes at 4 0C. Chromatin sonication was carried out using an Ultrasonic cell disruptor, Bioruptor (Diagenode) to produce sheared chromatin with an average fragment size of 300 bp. Immunoprecipitation was performed using magnetic beads (Dynal) (2 x 107) per sample. Dynabeads coated with rat monoclonal anti-mouse IgG were used for immunoprecipitation of myc tagged proteins using the 9E10monoclonal (Upstate). The immunoprecipitation reactions as well as washing steps were carried out as described previously (Strahl-Bolshinger et al 1997)

value: ChIP

tag: chip antibody

value: 9E10-anti myc, Millipore cat no:05-419


title: VPA, 16 hrs, ChIP-seq

status: Public on Sep 17 2011

city: Jerusalem

first: Eran

last: Meshorer

address: Edmond J. Safra campus

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: VPA 16 hr

data_processing: Sequence reads were mapped to the mouse mm9 (July, 2007) genome sequence using Bowtie 0.12.5, allowing up to 2 mismatches. Only uniquely mapped reads were reported.

source_name: ES cells, VPA, 16hrs, H3K9ac ChIP

growth_protocol: Cells were grown on mitomycin-C-treated primary embryonic fibroblasts, with ES cell medium with 15% FBS and leukemia inhibitory factor.

extract_protocol: Chromatin was cross-linked with 1% formaldehyde (10 min, 37°C), incubated with glycine (125 mM, 10 min, room temp.), and washed with cold PBS. Cells were harvested and sonicated to generate DNA fragments of 100 to 500 bp. Chromatin was immunoprecipitated with 1 μg of H3K9ac-specific antibody. Cross-linking was reversed by incubation for 4 hrs at 65°C under high-salt conditions. The DNA was extracted with phenol-chloroform, precipitated with ethanol, and dissolved in TE. Preparation of sequence libraries and SOLiD sequencing were performed according to the manufacturer’s instructions and kits (Applied Biosystems) at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

treatment_protocol: 0.5mM VPA was added to the cell medium in the indicated samples for either 4 or 16 hrs.

tag: cell type

value: embryonic stem cells (ESCs)

tag: treatment

value: valproic acid (VPA)

tag: time

value: 16 hours

tag: antibody vendor

value: Millipore/Upstate

tag: antibody catalog #

tag: antibody lot#


title: HCC1954-methylC-Seq

city: Dallas

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

description:
bisulfite-converted genomic DNA
Instrument models: both Illumina Genome Analyzer IIx and Illumina HiSeq 2000 were used.

data_processing:
MethylC-Seq reads were mapped as previously described (Lister et al., Nature, 2009). Briefly, reads were trimmed until encountering a base with PHRED score <= 2 and bases near the 3â end were trimmed if the adapter sequence was included. For the purpose of mapping, all cytosines were computationally converted to thymines, to be reverted back to their original state after mapping. The Bowtie program(Langmead et al. 2009) was then used to align these computationally converted reads to computationally converted copies of hg18. Non-uniquely mapping reads were discarded.
Genome build: hg18

source_name: breast cancer cells

extract_protocol: 5.5 Âµg of genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Biorupter (Diagenode, Woburn, MA) to 100-300 bp, followed by end repair and addition of a 3' A base. Single-end cytosine-methylated adapters were ligated to the sonicated DNA and 150-350bp fragments were purified from a 2% agarose gel. Adapter-ligated DNA (~450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 5 cycles of PCR with PfuTurboCx Hotstart DNA polymerase (Stratagene). The reaction products were purified with a 2% agarose gel.

tag: cell line

value: breast cancer cells


title: Control, ChIP-seq

description: Control

source_name: ES cells, untreated, H3K9ac ChIP

value: untreated


title: VPA, 4 hrs, ChIP-seq

description: VPA 4 hr

source_name: ES cells, VPA, 4hrs, H3K9ac ChIP

value: 4 hours


title: Input, ChIP-seq

description: Input

source_name: ES cells, untreated, input


title: chd1del_isw1del_MNase


title: HCC1954: chromatin IP against H3K27me3, bisulfite treated

extract_protocol: To isolate chromatin, formaldehyde-cross-linked nuclei were sonicated using a Branson 450 Sonifier (Branson, Danbury, CT). Following ChIP performed with Dynal beads (Invitrogen, Carlsbad, CA), ChIP DNA was subjected to end repair, A-tailing, adaptor ligation with methylated adaptors, and gel purification. Following bisulfite conversion and PCR amplification for 20 cycles, the final library underwent gel purification.


title: HCC1954-mRNA-Seq

description: polyA-selected RNA

data_processing:
mRNA-Seq reads were mapped with the TopHat program with default parameters.
Genome build: hg18

molecule: polyA RNA

extract_protocol: Total RNA from 2 million cells was extracted with TRIZOL (Invitrogen, Carlsbad, CA) using manufacturer's instructions, followed by mRNA purification with Dynabeads Oligo (dT)25 (Invitrogen, Carlsbad, CA). First strand synthesis was performed with SuperScriptÂ® III First-Strand Synthesis System (Invitrogen, Carlsbad, CA), followed by purification with Sephadex G50 beads (medium) (GE Healthcare, UK) and second strand synthesis with dUNTPs. cDNA was sonicated with a Bioruptor (Diagenode, Woburn, MA) followed by end repair, addition of a 3' base, and ligation of adaptors. Fragments were purified on a 2% agarose gel and the second strand was degraded with AmpErase UNG (Applied Biosystems, Foster City, CA). Samples were amplified with between 7 and 10 cycles of PCR, followed by gel purification.

value: breast cancer


title: HCC1954: input DNA

description: input

data_processing:
We mapped ChIP-Seq reads using the Bowtie program, keeping only those reads that mapped uniquely to hg18 with at most 3 mismatches. Specifically, the parameters used were: "--solexa1.3-quals -v 3 -m 1 --best --strata -S ". PCR duplicates for each library were removed with the Picard program(Picard 2011). All biological replicates were combined and compressed/indexed by the SAMtools suite into BAM format(Li et al. 2009).
Genome build: hg18

extract_protocol: To isolate chromatin, formaldehyde-cross-linked nuclei were sonicated using a Branson 450 Sonifier (Branson, Danbury, CT). Following ChIP performed with Dynal beads (Invitrogen, Carlsbad, CA), ChIP DNA was subjected to end repair, A-tailing, adaptor ligation, and gel purification. Following PCR amplification for 18 cycles, the final library underwent gel purification.

value: input


title: HCC1954: chromatin IP against H3K36me3, bisulfite treated


title: HCC1954: chromatin IP against H3K9me3, bisulfite treated


title: chd1del_isw1del_isw2del_MNase


title: WT_Mnase


title: HMEC-mRNA-Seq

description: polyA-selected RNA

source_name: mammary epithelial cells

value: HMEC

value: primary human mammary epithelial cells


title: HCC1954: chromatin IP against H3K27me3

description:
H3K27me3
Instrument models: both Illumina Genome Analyzer IIx and Illumina HiSeq 2000 were used.


title: HMEC-methylC-Seq

description: bisulfite-converted genomic DNA


title: HCC1954: chromatin IP against H3K27ac


title: HCC1954: chromatin IP against H3K36me3

description:
H3K36me3
Instrument models: both Illumina Genome Analyzer IIx and Illumina HiSeq 2000 were used.


title: HCC1954: chromatin IP against H3K4me3


title: HCC1954: chromatin IP against H3K4me1


title: 12_hr

status: Public on Sep 15 2011

city: Cambridge

first: Olivia

last: Rissland

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: small RNAs from cells that, after being starved by serum withdrawal for 48 hours, were released synchronously into the cell cycle for 12 hours by the addition of serum

data_processing:
The processed files are complete 36-nt reads collapsed to unique sequences (1 line per sequence); the second (numeric) value in each column is the number of times each unique sequence was sequenced.
The processed files were generated using internal, home-made scripts. For the Day_0/3/5 files, no filtering was applied. For the 0/12/16/20/24_hr files, the default Illumin pipline quality filter was used (with a threshold of CHASTITY>=0.6).

source_name: synchronous release after serum starvation_12h

growth_protocol: NIH-3T3 cells were passaged in DMEM with 10% DCS and P/S

extract_protocol: Small-RNA cDNA libraries were prepared as described in Grimson et al. (2008).

treatment_protocol: For serum starvation experiments, cells were serum-starved for 2 days; media containing 20% serum was then added, and cells were harvested 0, 12, 16, 20 and 24 hours after the re-addition of serum. For contact inhibition experiments, cells were plated at 12% confluency and grown (with media being replaced) for 5 days.

tag: cell cycle arrest

value: Serum starvation

tag: cell cycle phase

value: Fibroblast


title: 0_hr

description: small RNAs from cells were starved by serum withdrawal for 48 hours

source_name: synchronous release after serum starvation_0h


title: 0_day

description: small RNAs from cells that had been arrested by contact inhibition for 0 days (I.e. asynchronous cells)

source_name: cell-cycle arrest by contact inhibition_0d

value: Contact inhibition

value: Asynchronous


title: 16_hr

description: small RNAs from cells that, after being starved by serum withdrawal for 48 hours, were released synchronously into the cell cycle for 16 hours by the addition of serum

source_name: synchronous release after serum starvation_16h

value: S


title: 3_day

description: small RNAs from cells that had been arrested by contact inhibition for 3 days

source_name: cell-cycle arrest by contact inhibition_3d


title: 20_hr

description: small RNAs from cells that, after being starved by serum withdrawal for 48 hours, were released synchronously into the cell cycle for 20 hours by the addition of serum

source_name: synchronous release after serum starvation_20h


title: HCC1954: chromatin IP against H3K9me3

description:
H3K9me3
Instrument models: both Illumina Genome Analyzer IIx and Illumina HiSeq 2000 were used.


title: human_neutrophil

first: Andrew

middle: D

last: Smith

address: 1050 Childs Way

department: Molecular and Computational Biology

institute: University of Southern California

description: Bisulfite converted

data_processing:
Each Sample contains processed data file corresponding to the hypomethylated_regions, cpg_methylation_levels, and cpg_read_coverages
Alignment: Mapping bisulfite treated reads was done with methods described by Smith et al. (2009) using tools from the RMAP package (Smith et al., 2009).
HMR detection: Hypomethylated regions (HMRs) were identified using a hidden Markov model as described in Molaro et al. (Cell 146, 1-13, September 16, 2011).

source_name: Neutrohphil

extract_protocol: Bisulfite sequencing libraries were generated by previously described methods (Hodges et al., 2009) and on the manufacturer's instructions (Illumina) but with several additional modifications. Briefly, following each enzymatic step, genomic DNA was recovered by phenol:chloroform extraction and ethanol precipitation. Adenylated fragments were ligated to Illumina-compatible paired-end adaptors synthesized with 5'-methyl-cytosine and, when necessary, adaptors were diluted 100-1000x to compensate for low-input libraries and maintain an approximate 10-fold excess of adaptor oligonucleotides. Following ligation, DNA fragments were purified and concentrated on MinElute columns (Qiagen). The standard gel purification step for size selection was excluded from the protocol. Fragments were denatured and treated with sodium bisulfite using the EZ DNA Methylation Gold kit according to the manufacturer's instructions (Zymo). Lastly, the sample was desulfonated and the converted, adaptor-ligated fragments were PCR enriched using paired-end adaptor-compatible primers 1.0 and 2.0 (Illumina) and the Expand High Fidelity Plus PCR system (Roche). Paired-end Illumina sequencing was performed on bisulfite converted libraries for 76-100 cycles each end. Average insert length were 150-200bp.

tag: developmental stage

value: mature granulocyte


title: human_cd133hsc

description: Bisulfite converted

value: progenitor (umbilical cord blood)


title: human_hspc

description: Bisulfite converted

source_name: HSPC

value: progenitor


title: human_bcell

description: Bisulfite converted

source_name: B cell

value: mature lymphocyte


title: WCE_1

first: Xinchen

last: Wang

address: 32 Vassar St, D514

institute: MIT

description: Whole chromatin extract

data_processing: ChIP-seq reads were aligned to the human hg19 genome assembly using Bowtie (Langmead et al., 2009) and peaks were called using QuEST (Valouev et al., 2008) with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).

source_name: H9 hESCs

growth_protocol: H9 hESCs were cultured under two different conditions (using feeder cells or Matrigel) to promote self-renewal. H9 ESCs were also cultured in micropatterned chambers of 200um2, 400um2 and 800um2 to control colony size, which previously has been shown induce differentiation along endoderm, mesoderm and neural-specified lineages, respectively

extract_protocol: Library construction performed according to steps given by Schmidt et al. Methods 48 (2009) 240-248.

value: H9 hESCs


title: WCE_2

description: Whole chromatin extract


title: IgG control RIP-seq

city: Boston

first: Mark

middle: L

last: Borowsky

address: 185 Cambridge Street

department: Molecular Biology

institute: MGH

description:
IgG control RIP
RIP-Seq

data_processing:
Image processing and base calling were performed using the Illumina pipeline.
Preprocessing: 3' adapter sequences were identified using cross_match and trimmed if a match of at least 5 bp was found.  Reads matching mtDNA or rRNA sequences, reads < 12 bp long, reads containing N's, and homopolymer reads were removed.
Alignment: reads were aligned to the mouse genome (mm9) using shortQueryLookup with a maximum of 1 error and no indels.

source_name: embryonic stem cells

growth_protocol: mouse embryonic stem cells were routinely growed and maintained in T25 or T75 flasks with LIF supplemented in the culture medium.

extract_protocol: Cell nuclei were isolated, nuclear lysate was prepared and incubated with normal rabbit IgG. Afterwards, the RNA-protein complexes were immunoprecipitated with protein A agarose beads and the RNA fraction was extracted using Trizol reagent. Template switching method was used for the library construction per manufacturer's recommendation (Clontech's SMART cDNA Library Construction Manual).

value: embryonic stem cells

value: IgG


title: FOXP1_ChIP-Seq_2

description: ChIP against FOXP1 (both isoforms)

tag: chip antibody vendor

value: Abcam

tag: chip antibody lot#

tag: chip antibody catalog#


title: FOXP1_ChIP-Seq_1

description: ChIP against FOXP1 (both isoforms)


title: dcr1Delta [2]

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description: Schizosaccharomyces pombe small RNA library from total RNA isolations

data_processing: All samples were barcoded at the 3'end of the 5'adapter using a hamming distance two code with a 3' cytosine (AAAC,ACCC,AGGC,ATTC,CACC,CCGC,CGTC,CTAC,GAGC,GCTC,GGAC,GTCC,TATC,TCAC,TGCC,TTGC) and sequenced (with other samples) in one lane of an Illumina GA2 instrument. Individual reads were assigned to their sample based on the first 4 nucleotides containing the barcode. The 3' adapter was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least 7 or 10 bases respectively. Low complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). All the reads that were shorter than 14 nucleotides were removed.

organism: Schizosaccharomyces pombe

extract_protocol: Total RNA was isolated from cells harvested at OD600=0.5 using the hot phenol method (Leeds, 1991) and subjected to size fractionation using RNeasy Midi columns (QIAGEN) as previously described (Buhler, 2006). 17-30nt small RNAs were PAGE purified and were cloned based upon the preactivated, adenylated linkering method described previously (Lau, 2001) using a mutant T4 RNA ligase (Rnl21-249) (Ho, 2004). Bar coded linkers suitable for Solexa sequencing were used for multiplexing and sequencing using an Illumina Genome Analyzer 2 (GA2).


title: exon 18b siRNAs

description: RNA-Seq performed on polyadenylated RNA

data_processing: The sequence reads were aligned to human genomic sequence (NCBI Genome Assembly Build #36) using Bowtie (Langmead et al., Genome Biol. 2009 10).

source_name: H9 hESCs transfected with an siRNA pool targeting exon 18b

extract_protocol: Total RNA from two independent transfections were pooled and submitted to Illumina Inc. for polyA+ isolation and mRNA sequencing.

treatment_protocol: H9 hESCs were transfected with a control, non-targeting siRNA pool (Dharmacon) or with siRNA pools targeting FOXP1 exon 18 or exon 18b sequences using DharmaFECT reagent following the manufacturer recommendations. Two days after transfection, H9 hESCs were transfected again and total RNA was isolated after an additional two days of culture using TRI reagent (Sigma-Aldrich).

value: hESC cells


title: rIgG ChIP-seq

status: Public on Sep 14 2011

city: Helsinki

first: Olli

middle: A.

last: Jänne

department: Inst. of Biomedicine/Physiology

country: Finland

institute: University of Helsinki

description: Chromatin IP against rabbit IgG

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (Feb, 2009) genomes using the Illumina Genome Analyzer Pipeline (ELAND) or BOWTIE. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) and peaks were assigned to nearest Refseq gene using a transcription factor associtaion strength (TFAS) approach (Ouyang et al., 2009). Overlapping peaks present in both biological replicates are shown in the peak file [The TTFAS_peak files are provided as Series supplementary file]. The DHS- seq data was analyzed using F-seq algorithm (http://www.genome.duke.edu/labs/furey/software/fseq/).

source_name: rIgG ChIP-seq

growth_protocol: LNCaP-1F5 cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 10 mM HEPES supplemented with antibiotics (penicillin and streptomycin).

extract_protocol: Lysates were clarified from sonicated nuclei and DNA-protein complexes were isolated with respective antibodies. Libraries were prepared according to Illumina's instructions. 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 (3' to 5' 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 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. The DNaseI-hypersensitivity assay and deep sequencing was performed as described by Song and Crawford (2010).

treatment_protocol: FoxA1 depletion was done using siRNA smartpool specific to FoxA1 mRNA. Both parental and FoxA1 depleted cells were treated with 100 nM DHT (or 100 nM DEX) for 2 hours followed by Chromatin Immunoprecipitation or DNaseI-Hypersensitivity mapping.

value: Prostate epithelial cells derived from metastatic prostate carcinoma

tag: genotype/variation

value: genetically engineered to express rat glucocorticoid receptor (Cleutjens et al., 1997).

tag: passages

value: rabbit IgG

tag: antibody vendor, cat. number

value: Santa Cruz, sc-2027


title: Control siRNAs

description: RNA-Seq performed on polyadenylated RNA

source_name: H9 hESCs transfected with a control, non targeting siRNA pool


title: exon 18 siRNAs

description: RNA-Seq performed on polyadenylated RNA

data_processing:
The sequence reads were aligned to human genomic sequence (NCBI Genome Assembly Build #36) using Bowtie (Langmead et al., Genome Biol. 2009 10).
Raw file corresponding to H9_ex18_2_tag.txt.fa.bowtie is unavailable.

source_name: H9 hESCs transfected with an siRNA pool targeting exon 18


title: GR-siFoxA1_ChIP-seq

description: Chromatin IP against GR in siFoxA1 cells

tag: chip antibody

value: GR

value: non-commercial (Widen et al, 2000)


title: GR_ChIP-seq

description: Chromatin IP against GR in parental cells

tag: cell type


title: DHS-seq_siFoxA1

description: DNaseI-hypersensitivity sites sequencing in siFoxA1 cells


title: FoxA1_ChIP-seq_siFoxA1_rep2

description: Chromatin IP against FoxA1 in siFoxA1 cells

value: Abcam, ab23738


title: FoxA1_ChIP-seq_siFoxA1_rep1


title: DHS-seq

description: DNaseI-hypersensitivity sites sequencing in parental cells

source_name: DHS-seq


title: FoxA1_ChIP-seq_rep2

description: Chromatin IP against FoxA1 in parental cells


title: H3K4me2_ChIP-seq

description: Chromatin IP against H3K4me2 in parental cells

value: Millipore, 07-030


title: H3K4me2_ChIP-seq_siFoxA1

description: Chromatin IP against H3K4me2 in siFoxA1 cells


title: FoxA1_ChIP-seq_rep1


title: INPUT_Seq

city: New York

first: Katerina

last: Hatzi

state: NY

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

institute: WCMC

description: INPUT DNA

data_processing: Alignment: 36bp sequence reads were obtained and mapped using ELAND to the human genome (hg18) by Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

source_name: Input, human CML cell line

growth_protocol: JURL-MK1 cells were maintained in Roswell Park Memorial Institute medium (RPMI-1640, Invitrogen, Carlsbad, CA) with GlutaMAX containing 20% fetal bovine serum, 100 IU/ml penicillin and 100 μg/ml streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Lysates were purified from crosslinked sonicated nuclei and BCL6-DNA complexes were isolated with BCL6 antibody (N3,Santa Cruz). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 11257047). 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 (3' to 5' 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 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No treatment

value: none (control)


title: BCL6_ChIPSeq

description: Chromatin IP against BCL6

source_name: ChIPSeq, human CML cell line

value: anti-BCL6 antibody (N3)

value: Santa Cruz


title: AR_ChIP-seq_siFoxA1_rep2

description: Chromatin IP against AR in siFoxA1 cells

value: AR

value: non-commercial (Kang et al, 2004)


title: AR_ChIP-seq_siFoxA1_rep1


title: AR_ChIP-seq_rep2

description: Chromatin IP against AR in parental cells


title: RPKM value for R5

first: Bill

last: Wong

institute: Whitehead Institute

description: RNA-seq expression value for R5 cells

data_processing: MAQ was used for mapping reads to the mouse mm9 genome. Gene expression values were calculated as Reads Per Kilobase of Exon Model Per Million Mapped Reads (RPKM)

source_name: R5 cells

growth_protocol: The RNA is extracted directly from the sorted cells without in vitro culture

extract_protocol: Total RNA was extracted using an RNeasy kit (Qiagen) from freshly sorted cells. The library preparation was performed using polyA enriched RNA according to the manufacturer's instructions (Illumina) and then sequenced on a Solexa sequencing cell.

value: fetal liver cells


title: AR_ChIP-seq_rep1


title: RPKM value for R4

description: RNA-seq expression value for R4 cells

source_name: R4 cells


title: wild-type

source_name: wild-type

tag: strain


title: H3K36me3_mLSC_ChIPSeq

status: Public on Sep 13 2011

first: Amit

last: Sinha

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Chromatin IP against H3K36me3

data_processing: Sequence reads were aligned to the mouse genome assembly mm8 or human genome assembly hg18 using Bowtie. ChIP-Seq signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.

source_name: murine L-GMP

growth_protocol: GMP-like leukaemic cells (L-GMP) were isolated by flow cytometry from GMP derived MLL-AF9 primary leukemias.

extract_protocol: ChIP DNA libraries were made following the Illumina ChIP-seq library preparation kit.

treatment_protocol: Cells were subjected to ChIP-Seq using an antibody specific for H3K4me3, H3K27me3, H3K36me3, H3K79me2 or streptavidin beads (for biotinylated MLL-AF9 targets).

tag: genotype

tag: cell origin

value: MLL-AF9 Leukemic Stem Cell (IL-7R-Lin-Sca-1-c-Kit+CD34+FcgammaII/III+) from GMP-derived leukemia


title: H3K79me2_normal_karyotype_huAML_ChIPSeq

description: Chromatin IP against H3K79me2

source_name: human leukemic blasts

growth_protocol: A sample from an adult MLL-AF9 AML patient was provided by the German-Austrian AML study Group (AMLSG) with patient consent according to the Declaration of Helsinki and IRB approval of all participating institutions.

value: diagnostic sample (pre-treatment)


title: H3K79me2_MLL-AF9_huAML_ChIPSeq

description: Chromatin IP against H3K79me2


title: H3K36me3_mHSC_ChIPSeq

description: Chromatin IP against H3K36me3

source_name: murine HSC

growth_protocol: LSK cells were isolated by flow cytometry from bone marrow of wild type C57BL/6 (6-8 wks).

value: wild type

tag: age

value: 6-8 weeks

value: murine LSK cells (IL-7R-Lin-Sca-1+c-Kit+)


title: H3K36me3_mGMP_ChIPSeq

description: Chromatin IP against H3K36me3

source_name: murine GMP

growth_protocol: GMP cells were isolated by flow cytometry from bone marrow of wild type C57BL/6 (6-8 wks).

value: murine GMP cells (IL-7R-Lin-Sca-1-c-Kit+CD34+FcgammaII/IIIhi)


title: H3K79me2_mLSC_ChIPSeq

description: Chromatin IP against H3K79me2


title: H3K79me2_mGMP_ChIPSeq

description: Chromatin IP against H3K79me2


title: H3K79me2_mHSC_ChIPSeq

description: Chromatin IP against H3K79me2


title: H3K27me3_mGMP_ChIPSeq

description: Chromatin IP against H3K27me3


title: H3K27me3_mLSC_ChIPSeq

description: Chromatin IP against H3K27me3


title: eri-6(mg379)_embryo

status: Public on Sep 25 2011

first: Taiowa

last: Montgomery

address: 185 Cambridge Street, CPZN-7250

institute: Massachusetts General Hospital

data_processing: Raw datasets are fastq files generated by Illumina.  For processed datasets, small RNA sequences were parsed from fastq files using CASHX v. 2.0 with a Q value threshold of 20.  Sequences were not filtered for alignment to any genome.  Tab delimited files containing unique sequences and corresponding read counts were generated using custom perl scripts.

organism: Caenorhabditis elegans

source_name: Embryos

growth_protocol: C. elegans were grown at 20C on OP50

extract_protocol: Total RNA was isolated from synchronized worms and small RNAs were size selected, tobacco acid pyrophosphatase (TAP) treated to remove 5'di- and triphosphate groups, ligated to 5'and 3'adapters and subjected to RT-PCR.

value: embryo


title: 24_hr

description: small RNAs from cells that, after being starved by serum withdrawal for 48 hours, were released synchronously into the cell cycle for 24 hours by the addition of serum

source_name: synchronous release after serum starvation_24h

value: Serum starvation

value: Fibroblast


title: H3K27me3_mHSC_ChIPSeq

description: Chromatin IP against H3K27me3


title: 5_day

description: small RNAs from cells that had been arrested by contact inhibition for 5 days

source_name: cell-cycle arrest by contact inhibition_5d

value: Contact inhibition


title: MLL-AF9_ChIPSeq

description: Chromatin IP using streptavidin beads against biotinylated MLL-AF9

source_name: MLL-AF9 transformed blasts

growth_protocol: Murine bone marrow cells were transformed with biotinylated MLL-AF9, harvested after two rounds of replating.

value: 5-FU treated BM cells transduced with HA-Bio-MLL-AF9 and BirA

value: streptavidin beads


title: H3K4me3_mHSC_ChIPSeq

description: Chromatin IP against H3K4me3


title: H3K4me3_mGMP_ChIPSeq

description: Chromatin IP against H3K4me3


title: ergo-1(tm1860)_embryo


title: RPKM value for R2

description: RNA-seq expression value for R2 cells

source_name: R2 cells


title: RPKM value for R3

description: RNA-seq expression value for R3 cells

source_name: R3 cells


title: Wild type_embryo


title: H3K4me3_mLSC_ChIPSeq

description: Chromatin IP against H3K4me3


title: dcr1-SHSS


title: RNA Capture sequencing 3 (454)

status: Public on Sep 12 2011

city: Sydney

first: Tim

middle: R.

last: Mercer

state: New South Wales

address: 384 Victoria Street Darlinghurst NSW 2010

country: Australia

institute: Garvan

data_processing: Roche 454 reads were firstlycombined and aligned to the human genome (hg19) using Blat (http://www.soe.ucsc.edu/~kent) with the following non-default parameters; minIdentity=90, minScore=100. Resultant *.psl files were converted into *.sam files using bedTools and samtools.

source_name: Foot (c45) fibroblasts

growth_protocol: Primary human female fetal lung fibroblasts and human male foot fibroblasts in DMEM supplemented with 10% FBS at 37 Â°C with 5% CO2 as previously described (J. L. Rinn et. al., PLoS Genet, 2006).

extract_protocol: 454 GS-FLX Titanium Sequencing libraries from c45 and FL fibroblast cDNA were constructed using the 454 LifeSciences GSFLX Titanium Kit according to manufacturers instructions. All single-stranded DNA product from library preparation was utilized as template in a Pre-Hybridization Linker Mediated PCR reaction to ensure that the plurality of the molecules contained adapters on both sides of the putative cDNA inserts. The amplified material was recovered with a Qiaquick column and DNA evaluated electrophoretically by an Agilent Bioanalyzer 2100.  Library fragment sizes were found to be between 500-700 bp. Samples were purified and combined with C0T-1 DNA, enhancing oligos, NimbleGen hybridization buffer and Component A prior to capture. Hybridisation and post-hybridisation LMPCR were performed with identical conditions. The resulting post capture enriched sequencing libraries were sequenced on 454 Genome Sequencer FLX System using Titanium chemistry.

value: Primary foot fibroblasts

tag: sample type

value: RNA Capture sequencing


title: RNA Capture sequencing (Illumina)

data_processing: Reads were aligned to the human genome (hg19) using TopHat with the following non-default parameters; -r 242 --min-isoform-fraction 0.001 -G RefSeq.gtf (downloaded from UCSC hg19 October 2010). .bam files were converted to .wig files using in house scripts.

extract_protocol: Illumina paired-end libraries were constructed from array captured or input double stranded cDNA using Illuminaâs PE Kit according to manufacturers instructions with the following modifications: prescribed Agarose gel excision was performed at 350-300 base pairs to produce libraries with an approximate insert size of 340bp. Illumina RNAseq libraries were used in cluster formation on an Illumina cBot and paired end sequencing was done using the Genome Analyzer IIX. Both cluster formation and 76bp paired-end sequencing were performed using the manufacturers provided protocols.

value: primary foot fibroblast


title: RNA Capture sequencing 12 (454)

source_name: Fetal lung (FL) fibroblasts

value: Primary fetal lung fibroblasts


title: RNA Capture sequencing 1 (454)


title: RNA Capture sequencing 7 (454)


title: RNA Capture sequencing 8 (454)


title: RNA Capture sequencing 9 (454)


title: RNA Capture sequencing 11 (454)


title: RNA Capture sequencing 10 (454)


title: RNA Capture sequencing 4 (454)


title: Wild type_adult

source_name: Whole worms

value: adult


title: RNA Capture sequencing 6 (454)


title: eri-1(mg366)_embryo


title: RNA sequencing (Illumina)

value: RNA sequencing


title: RNA Capture sequencing 5 (454)


title: DNA Capture sequencing 4 (454)

value: DNA Capture sequencing


title: eri-7(mg369)_embryo


title: DNA Capture sequencing 2 (454)


title: dcr1Deltaloop2


title: eri-7(mg369)_adult


title: RNA Capture sequencing 2 (454)


title: YJS329_RNA-seq

status: Public on Sep 10 2011

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

data_processing: After removing reads containing sequencing adapters and reads of low quality (the percentage of the low quality bases of quality value </= 5 is more than 50% in a read), the clear reads were aligned to the S. cerevisiae S288c genes (ftp://ftp.ncbi.nih.gov/genomes/Fungi/Saccharomyces_cerevisiae_uid128) and genes using SOAPAligner.Mismatches no more than 2 bases were allowed in the alignment. Alignment file build: sacCer2

source_name: Yeast S. cerevisiae strain YJS329

growth_protocol: Yeast cells were cultured in 25mL YPD medium (1g/L yeast extract, 2g/L peptone, and 2g/L glucose) with an initial OD600 of 0.05.

extract_protocol: The total RNA was extracted at early-stationary phase by the hot phenol method and then treated with RNase-free DNase I (TaKaRa) for 30 min according to the manufacturer’s protocols.  The poly (A) containing mRNA molecules were puriﬁed and the cDNA libraries were prepared according to the manufacturer’s instructions (Illumina). The cDNA library products were sequenced on the Illumina HiSeq™ 2000.

value: Wide type

tag: application

value: Bioethanol strain


title: DNA Capture sequencing 1 (454)


title: DNA Capture sequencing 3 (454)


title: chimp_1_MspI

status: Public on Sep 09 2011

first: Dario

last: Boffelli

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

description:
MspI digest
MethylSeq

data_processing: Alignment ('_bwtout.txt' files): sequencing data were quality-filtered using the Illumina Pipeline CHASTITY filter with default parameter (0.6) and aligned using Bowtie v0.9.9.2 (bowtie-bio.sourceforge.net) to their respective reference genomes. Parameters used to run bowtie: --all -m 1. These parameters allow up to 2 mismatches in  the first 28nt. In v 0.9.9.2, hits are "stratified" by default: if a read has 1 zero mismatch hit, and 2 1-mismatch hits, the 1 zero mismatch hit is reported when-m 1 is specified.

organism: Pan troglodytes

source_name: whole blood

growth_protocol: Whole-blod samples were obtained from healthy, young adult males.

extract_protocol: Neutrophils were isolated immediately after phlebotomy with CD-16 microbeads. An aliquot of each specimen was Wright-Giemsa stained and examined microscopically; all specimens contained >99% neutrophils. DNA was extracted by standard methods, and digested overnight with the methylation-insensitive enyzme MspI (in contrast to HpaII, MspI cuts CCGG sites independently of their methylation state). MspI fragments of 50-300Â bp in length were  isolated from an agarose gel, and used to construct single read sequencing libraries using the standard Illumina protocol.

value: neutrophil

tag: gender

value: male

value: young adult


title: BYZ1_RNA-seq

source_name: Yeast S. cerevisiae strain BYZ1

value: BYZ1(MATa/MATalpha his3delta1/his3delta1 leu2delta0/leu2delta0 lys2delta0/+ met15delta0/+ ura3delta0/ura3delta0)

value: Labortory strain


title: human_1_MspI

description:
MspI digest
MethylSeq


title: human_2

description: HpaII digest

data_processing:
Alignment ('_bwtout.txt' files): sequencing data were quality-filtered using the Illumina Pipeline CHASTITY filter with default parameter (0.6) and aligned using Bowtie v0.9.9.2 (bowtie-bio.sourceforge.net) to their respective reference genomes. Parameters used to run bowtie: --all -m 1. These parameters allow up to 2 mismatches in  the first 28nt. In v 0.9.9.2, hits are "stratified" by default: if a read has 1 zero mismatch hit, and 2 1-mismatch hits, the 1 zero mismatch hit is reported when-m 1 is specified.
Determination of metylation status ('_metmap.wig' files): reads that aligned to HpaII sites (CCGG) were analyzed with MetMap (http://www.cs.berkeley.edu/~meromit/MetMap) to infer methylation states. Results are reported for each CCGG site that can generate a sequenceable fragment (ie, the fragment is of a length that can pass the size selection step during library construction). Results are expressed as the probability p(U) that the site in unmethylated, and vary between 0 (methylated site) and 1 (unmethylated site).
Processed data file build: hg18

extract_protocol: Neutrophils were isolated immediately after phlebotomy with CD-16 microbeads. An aliquot of each specimen was Wright-Giemsa stained and examined microscopically; all specimens contained >99% neutrophils. DNA was extracted by standard methods, and digested overnight with the methylation-sensitive enyzme HpaII (HpaII cuts CCGG sites when the central C is unmethylated). HpaII fragments of 50-300 bp in length were  isolated from an agarose gel, and used to construct single read sequencing libraries using the standard Illumina protocol.


title: orang

description: HpaII digest

data_processing:
Alignment ('_bwtout.txt' files): sequencing data were quality-filtered using the Illumina Pipeline CHASTITY filter with default parameter (0.6) and aligned using Bowtie v0.9.9.2 (bowtie-bio.sourceforge.net) to their respective reference genomes. Parameters used to run bowtie: --all -m 1. These parameters allow up to 2 mismatches in  the first 28nt. In v 0.9.9.2, hits are "stratified" by default: if a read has 1 zero mismatch hit, and 2 1-mismatch hits, the 1 zero mismatch hit is reported when-m 1 is specified.
Determination of metylation status ('_metmap.wig' files): reads that aligned to HpaII sites (CCGG) were analyzed with MetMap (http://www.cs.berkeley.edu/~meromit/MetMap) to infer methylation states. Results are reported for each CCGG site that can generate a sequenceable fragment (ie, the fragment is of a length that can pass the size selection step during library construction). Results are expressed as the probability p(U) that the site in unmethylated, and vary between 0 (methylated site) and 1 (unmethylated site).
Processed data file build: ponAbe2

organism: Pongo pygmaeus

value: leukocyte


title: chimp_1

description: HpaII digest

data_processing:
Alignment ('_bwtout.txt' files): sequencing data were quality-filtered using the Illumina Pipeline CHASTITY filter with default parameter (0.6) and aligned using Bowtie v0.9.9.2 (bowtie-bio.sourceforge.net) to their respective reference genomes. Parameters used to run bowtie: --all -m 1. These parameters allow up to 2 mismatches in  the first 28nt. In v 0.9.9.2, hits are "stratified" by default: if a read has 1 zero mismatch hit, and 2 1-mismatch hits, the 1 zero mismatch hit is reported when-m 1 is specified.
Determination of metylation status ('_metmap.wig' files): reads that aligned to HpaII sites (CCGG) were analyzed with MetMap (http://www.cs.berkeley.edu/~meromit/MetMap) to infer methylation states. Results are reported for each CCGG site that can generate a sequenceable fragment (ie, the fragment is of a length that can pass the size selection step during library construction). Results are expressed as the probability p(U) that the site in unmethylated, and vary between 0 (methylated site) and 1 (unmethylated site).
Processed data file build: PanTro2


title: chimp_2

description: HpaII digest


title: human_1

description: HpaII digest


title: human_3

description: HpaII digest


title: H4IIE_TCF7L2

city: San Antonio

first: Luke

last: Norton

address: 7703 Floyd Curl Dr

institute: UTHSCSA

description: Chromatin IP against TCF7L2

data_processing: Raw reads were imported into CLC Genomics Workbench and mapped to the RN4 reference using a mismatch cost of 1 and a limit of 2. ChIP peak detection was performed using CLC Genomics Workbench, with a window size of 250 bp and a FDR of 1%. Peaks were further filtered based on the spatial distribution of forward and reverse reads, with threshold P value set at 0.001.

organism: Rattus norvegicus

source_name: H4IIE cells

growth_protocol: H4IIE cells were grown in standard DMEM (4.5 mM glucose) supplemnted with 10% FBS. Cells were used up to passage 35.

extract_protocol: We used an Mnase based protocol (SimpleChIP Enzymatic Magnetic kit from Cell Signaling Technology, CST #9003) to generate fragmented genomic DNA-protein complexes. IP's were performed with the antibody stated above and libraries were constructed using the Illumina ChIP prep kit. The only modification was that a 1:30 ratio of adapters was used and a 1:2 dilution of primers was used in the final amplification step.

treatment_protocol: Basal. Cells were not treated prior to ChIP assay

tag: passage


title: H4IIE_input

description: Input


title: MCF7_PFKFB3_inhibitor

status: Public on Sep 08 2011

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

description: cells treated with 10 μM 3-(3-pyridinyl)-1-(4-pyridinyl)-2-propen-1-one dissolved in DMSO for 46 hours

data_processing: Sequencing was carried out at the Wistar Institute. Processed data files include columns for tag sequences and frequencies.

source_name: cell line MCF7

growth_protocol: Cells were plated at 3,000,000 cells per P150 (for inhibitor/DMSO treatments) or at 2,800,000 cells per P150 (for siRNAs transfection) and were cultured at 37°C with 5% CO2 in growth medium (50% DMEM/F12 + 10% FBS, 50% Medium 171 + HuMEC supp. for SUM159PT; RPMI + 10% FBS + 10 μg/mL insulin for Hs 578T and MCF7).

extract_protocol: 1,000,000 cells of each sample were used to prepare SAGE-Seq libraries according to a detailed protocol (http://research4.dfci.harvard.edu/polyaklab/protocols_linkpage.php).

treatment_protocol: Cells were treated the day after plating with individual inhibitors or DMSO only or transfected the day after plating with either STAT3 siRNAs from Dharmacon (siGENOME SMARTpool composed of GGAGAAGCAUCGUGAGUGA, CCACUUUGGUGUUUCAUAA, UCAGGUUGCUGGUCAAAUU, and CGUUAUAUAGGAACCGUAA) or non-targeting siRNAs #2 from Dharmacon. Transfection mixes were removed from transfected cells the day after transfection.

tag: cell line

tag: treatment

value: PFKFB3 inhibitor

tag: supplier

value: ATCC


title: Hs_578T_PFKFB3_inhibitor

source_name: cell line Hs 578T

value: Hs 578T


title: MCF7_JAK_inhibitor

description: cells treated with 2 μM JAK Inhibitor I dissolved in DMSO for 46 hours

value: JAK inhibitor


title: Hs_578T_HAS1_inhibitor

description: cells treated with 1 mM 4-methylumbelliferone dissolved in DMSO for 46 hours

value: HAS1 inhibitor


title: Hs_578T_NQO1_inhibitor

description: cells treated with 50 μM 1,4-dimethoxy-2-methylnaphthalene dissolved in DMSO for 46 hours

value: NQO1 inhibitor


title: MCF7_NQO1_inhibitor


title: Hs_578T_JAK_inhibitor


title: MCF7_CXCR2_inhibitor

description: cells treated with 1.5 μM N-(2-Hydroxy-4-nitrophenyl)-N′-(2-bromophenyl)urea dissolved in DMSO for 46 hours

value: CXCR2 inhibitor


title: MCF7_HAS1_inhibitor


title: MCF7_PTGIS_inhibitor

description: cells treated with 1 mM tranylcypromine dissolved in DMSO for 46 hours

value: PTGIS inhibitor


title: Hs_578T_non-targeting_siRNAs

description: cells transfected with 0.1 μM non-targeting siRNAs #2 0.1 μM with DharmaFECT 1 for 45 hours

value: non-targeting siRNAs


title: Hs_578T_STAT3_siRNAs

description: cells transfected with 0.1 μM STAT3 siRNAs 0.1 μM with DharmaFECT 1 for 45 hours

value: STAT3 siRNAs


title: MCF7_non-targeting_siRNAs


title: MCF7_DMSO_only

description: cells treated with DMSO only for 46 hours

value: DMSO only


title: Hs_578T_DMSO_only


title: SUM159PT_STAT3_siRNAs

source_name: cell line SUM159PT

value: Dr. Steve Ethier, University of Michigan


title: MCF7_STAT3_siRNAs


title: SUM159PT_non-targeting_siRNAs


title: Hs_578T_CXCR2_inhibitor


title: SUM159PT_DMSO_only


title: Hs_578T_PTGIS_inhibitor


title: SUM159PT_NQO1_inhibitor


title: SUM159PT_JAK_inhibitor


title: SUM159PT_PFKFB3_inhibitor


title: SUM159PT_HAS1_inhibitor


title: SUM159PT_PTGIS_inhibitor


title: SUM159PT_CXCR2_inhibitor


title: 2hrKCl-Input-sampleB2

city: Brookline

first: Harrison

middle: Wren

last: Gabel

address: 7 Linden St Apt 3

department: Neurobiology

institute: Harvard Medical School

data_processing: Reads were mapped to mm9 using the large genomes matching pipeline from Life Technolofies with parameters -e 3 -t 35 -z 10.  BigWig files were generated for uniquely mapped reads of IP samples; reads were extended to 150 bps, corresponding to the estimated fragmen length of the DNA. If multiple reads were mapped to the same starting base and strand, only one of those reads was retained.

source_name: cultured cortical neurons E16+7DIV

growth_protocol: Dissociated cortical cultures (E16+7DIV) grown in neurobasal media supplemented with B27, glutamine, and pen/strep.

extract_protocol: Samples were crosslinked, chromatin was fragmented and immunoprecipitation was performed using the indicated antibodies. IP'd DNA was decrosslinked and purified. qPCR was used to validate successful IP before proceeding with library preparation. Input samples were taken after fragmentation, but before IP. Sequencing libraries were constructed by cloning fragments of ~125-175bp  using the SOLiD Fragment Library Adaptor kit Module 1-16 (PN4444836)

treatment_protocol: neuronal cultures were pre-treated with 1 ÂµM tetrodotoxin (TTX) and 100 ÂµM D-APV (Tocris Bioscience) overnight to reduce endogenous neuronal activity prior to stimulation and then left unstimulated or membrane depolarized for 2hrs with 55 mM extracellular KCl by addition of 0.5 volumes of prewarmed depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl2, 10 mM HEPES pH7.5)

tag: sample

tag: ip antibody

tag: condition

value: 2 hour KCl depolarized

tag: fragmentation method

value: sonication


title: 0hrKCl-Input-sampleB2

value: Unstimulated


title: 0hrKCl-MeCP2IP-sampleB2

value: Custom Anti-MeCP2 c-terminal antibody


title: 2hrKCl-pS421MeCP2IP-sampleB2

value: Custom Anti-pS421 MeCP2 antibody


title: 2hrKCl-MeCP2IP-sampleB2


title: 2hrKcl-Input-sampleB1

value: sonication+Mnase digestion


title: 0hrKCl-MeCP2IP-sampleB1


title: Chromatin IP against H3K9me3 - wild type ovary

first: Prashanth

last: Rangan

state: New York

address: 540 1st Aveune

department: Developmental genetics

institute: NYU/HHMI

description: Chromatin IP against H3K9me3

data_processing: Sequence aligns (35 bases) were extended in silico at their 3â ends to a length of 110 bp, which is the average fragment length in the size-selected library, and assigned to 32 nt bins along the genome. The resulting histograms were stored in BAR (Binary Analysis Results) files. Sequences (36 nt reads) were aligned to the Drosophila dm5 (Flybase r5.22) genome using bowtie analysis.

organism: Drosophila melanogaster

source_name: Chromatin IP against H3K9me3

growth_protocol: 25 degrees C

extract_protocol: Chromatin was isolated by adding lysis buffer, followed by disruption with a motor pestle.  Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Genomic DNA regions of interest were isolated using an antibody against H3K9me3.  After incubation at 4Â°C overnight, protein A or G agarose beads were used to isolate the immune complexes

treatment_protocol: Wild-type ovaries were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.

tag: tissue

value: ovary


title: Th2-WT-H3K4me3 [Methyl-Seq]

status: Public on Sep 07 2011

city: Memphis

first: Brian

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

description: Methyl-Seq

data_processing: Reads were aligned against genome build mm8 using ELAND

source_name: T-helper 2 cells

growth_protocol: DP cells are separated from WT and GATA3-knockout mice respectively.

extract_protocol: Following standard ChIP-seq protocol

tag: genotype/variation

value: WT

tag: cell type

value: T-helper 2 cells

tag: antibody

value: anti-H3K4me3 (Millipore 17-614)


title: Th2-WT-H3K4me1 [Methyl-Seq]

description: Methyl-Seq

tag: strain

value: anti-H3K4me1 (Abcam Ab8895-100)


title: 0hrKCl-Input-sampleB1


title: Nrd1 HTB Glucose Depletion with Arc Lamp Crosslinking

city: Baltimore

first: Jeff

last: Corden

state: MD

address: 725 N Wolfe Street

department: Molecular Bio and Gen

institute: JHU

description: Adaptation of PAR-ClIP

data_processing: Alignment: Bowtie short read aligner was used to map the samples to the yeast genome (SGD Oct 2010). Alignments allowed up to one mismatch and only one unique alignment.

extract_protocol: RNA library was prepared using tandem-affinity purification of a tagged protein covalently crosslinked to RNA. The 6xHis and Biotinylation site tags were used for protein purification. RNA was then prepared using a protocol adapted from Hafner et al (2010) for yeast (Jamonnak et al. submitted Mar 2011).

tag: crosslinking device

value: UV Power-Shot 1100 Lamp


title: Nab3 HTB with Stratalinker Crosslinking

description: Adaptation of PAR-ClIP

source_name: Nab3 HTB with Stratalinker Crosslinking

value: Stratalinker


title: Nrd1 HTB with Stratalinker Crosslinking

description: Adaptation of PAR-ClIP

source_name: Nrd1 HTB with Stratalinker Crosslinking


title: TF68_RNA

city: Yesan

first: Fu-Hao

last: Lu

address: 314, Plant Resources Department

country: South Korea

institute: Kongju National University

description: Trancriptome profiling of red pepper TF68 accession, muture fruit

data_processing: The de novo sequence assembly was analyzed to identify all contiguous sequences (contigs) and singletons using GS De Novo Assembler software (version 2.3, Roche, Korea), a tool for processing larger, more complex genomes and transcriptomes.

organism: Capsicum annuum

source_name: Camsicum annuum L. TF68 obtained by crossing YCM334 Ã Taean

growth_protocol: Plants were grown under 16h light.

extract_protocol: To isolate total RNA, approximately 100 mg of red pepper fruit were snap-frozen in liquid nitrogen, ground into a powder, and then subjected to genome DNA isolation using an RNeasy Plant Mini Kit (Qiagen, Seoul, Korea) following the manufacturerâs instructions. Messenger RNA (mRNA) was purified using the PolyATract mRNA Isolation System IV (Promega, Seoul, Korea), and then the purified products were used to synthesize the full-length cDNAs using a ZAP-cDNA Synthesis Kit (Stratagene, Seoul, Korea). Finally, cDNA was fragmented by nebulization for library construction. Approximately 1 Î¼g of cDNA was used to generate a single strand cDNA (sstDNA) library for use with the Genome Sequencer (GS) - FLX Titanium system (Roche, Mannheim, Germany) following standard procedures.

value: mature fruit


title: Sen1 HTB with Arc Lamp Crosslinking

description: Adaptation of PAR-ClIP

source_name: Sen1 HTB with Arc Lamp Crosslinking


title: Rpb2 HTB with Arc Lamp Crosslinking

description: Adaptation of PAR-ClIP

source_name: Rpb2 HTB with Arc Lamp Crosslinking


title: Nrd1 HTB with Arc Lamp Crosslinking

description: Adaptation of PAR-ClIP

source_name: Nrd1 HTB with Arc Lamp Crosslinking


title: 2hrKCl-MeCP2IP-sampleB1


title: H3K36me3 ChIP-seq in SSA treated  cells

status: Public on Sep 05 2011

city: Aurora

first: David

last: Bentley

state: CO

institute: UCHSC

description:
Chromatin IP against H3K36me3
barcode: GTT

data_processing: Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5

source_name: Hela

growth_protocol: cells were grown in DMEM 10% FCS

extract_protocol: IPs from 2 mg of cross-linked extract were immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina PE primers using Phusion DNA polymerase.

treatment_protocol: Cells were treated with spliceostatin A (20ng/ml) for 12 hr

tag: growth protocol

value: DMEM 10% FCS, 20ng/ml spliceostatin A for 12hr

tag: chip antibody

value: rabbit antibody (homemade) against peptide NH2-ATGGVKme3KPHRYC-COOH (rabbits immunized with peptide coupled to KLH)


title: RNA pol II ChIP-seq in SSA treated cells

description:
Chromatin IP against RNA pol II
barcode: GTT

value: rabbit anti pan CTD (Schroeder et al. Genes Dev. 14:2435, 2000)


title: H3K36me3 ChIP-seq

description:
Chromatin IP against H3K36me3
barcode: TAT

value: DMEM 10% FCS, methanol solvent control 1/5000


title: p300 sequencing in estradiol (E2) treated MCF-7 cells

city: Singapore

first: Guoliang

last: Li

address: 60 Biopolis Street, #02-01, Genome

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description: p300 sequencing, after E2 treatment.

data_processing: Alignment: Sequence reads were obtained and mapped to the human (hg18) genome using the Illumina Genome Analyzer II Pipeline. The ELAND program provided with the 1G analyzer software package and in-house (Genome Institute of Singapore) computational tools were used for mapping the sequence tags to the reference genome hg18 and clustering short sequences. In order to avoid potential PCR amplification bias, tags that shared the same mapping location on the same strand were removed. The uniquely-mapped reads with at most 2-mismatches were kept for further processing.

source_name: MCF-7 breast cancer cells, E2-treated, p300 ChIP

growth_protocol: MCF-7 cancer cells were grown to 70-80% confluence in D-MEM/F-12 (Invitrogen/Gibco)  supplemented with 10% FBS (Hyclone) in 150 mm dishes. In preparation for the 17 beta-estradiol (âestrogen/E2â, Sigma) treatment, cells were then split into 1:3 into serum starving medium [phenol red-free D-MEM/F-12 medium (Invitrogen/Gibco) supplemented with 5% charcoal-dextran stripped FBS (Hyclone)] and cultured for 72 hours to 70-80% confluence.

extract_protocol: All DNA samples were processed as per the Illumina Solexa ChIP-seq sample processing methods.  10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by picogreen assay and subjected to Solexa sequencing according to the manufacturerâs instructions.

treatment_protocol: Hormone-depleted cells were treated with E2 to a final concentration of 10 nM for 45 mins before the ChIP procedure.  The control cells were treated with an equal volume and concentration of vehicle, DMSO (Merck), for 4 5mins. For a ChIP experiment, we routinely used approximately 1 x 10^8 cells from 5-6, 150 mm diameter cell culture plates.

value: breast cancer cells

value: estradiol (E2)

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog number

tag: antibody lot number


title: RNA pol II ChIP-seq in control cells

description:
Chromatin IP against RNA pol II
barcode: CTT

value: DMEM 10% FCS, no methanol


title: p300 sequencing in non-treated (DMSO as vehicle) MCF-7 cells

description: p300 sequencing, vehicle only treatment.

source_name: MCF-7 breast cancer cells, untreated, p300 ChIP

tag: cell line

tag: treatment


title: GATA3 sequencing in non-treated (DMSO as vehicle) MCF-7 cells

description: GATA3 sequencing, vehicle only treatment.

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (hg18) genome using the Illumina Genome Analyzer II Pipeline. The ELAND program provided with the 1G analyzer software package and in-house (Genome Institute of Singapore) computational tools were used for mapping the sequence tags to the reference genome hg18 and clustering short sequences. In order to avoid potential PCR amplification bias, tags that shared the same mapping location on the same strand were removed. The uniquely-mapped reads with at most 2-mismatches were kept for further processing.

Peaks: The oriented 25-36 bp DNA reads (depending on the library) were extended to 200 bp regions to count clusters of overlapping sequences. The enrichment peaks for corresponding libraries were identified using the ChIP-seq peak calling algorithm MACS (Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W, Liu XS. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol 9:R137.)

source_name: MCF-7 breast cancer cells, untreated, GATA3 ChIP


title: GATA3 sequencing in estradiol (E2) treated MCF-7 cells

description: GATA3 sequencing, after E2 treatment.

source_name: MCF-7 breast cancer cells, E2-treated, GATA3 ChIP


title: Sed_Tric

status: Public on Sep 03 2011

city: Rochester

first: Stephen

last: Welle

address: 601 Elmwood Avenue

institute: University of Rochester

data_processing: 50-base reads were mapped to the mouse genome (mm9) with default settings of Bioscope v1.3 software. Reads mapping to exons of Refseq transcripts were counted with Bioscope v1.3 software. Exon-level data were consolidated to gene-level read counts and summarized for all 8 samples in a single table. Data were normalized so that the trimmed column means (excluding values above 97.5 %ile and below 2.5 %ile) were the same for all samples. The 13 protein-coding mtDNA transcripts were mapped to xxxx and counted separately, then normalized to the trimmed mean of the non-mitochondrial transcripts.

source_name: skeletal muscle

growth_protocol: Until 6 months of age, all mice housed 2-3 per cage with ad lib access to food and water and 12 h dark cycle (6PM-6AM)

extract_protocol: RNA was extracted with Trizol reagent and polyadenylated RNA was extracted from 8 total RNA pools (each pool from one muscle group of 3 sedentary or 7 active mice) by binding to oligo-dT. The polyA-RNA was eluted, ligated to adapters, converted to cDNA, amplified, and barcoded with the Applied Biosystems whole transcriptome library preparation kit according to instructions provided with the kit.

treatment_protocol: At 6 months of age, 7 of 10 mice transferred to individual cages with running wheels for a 12 week period.

tag: activity level

value: sedentary

value: triceps


title: Sed_Tib

value: tibialis anterior


title: Active_Mstn_deficient_1

data_processing: 65-base reads were mapped to the mouse genome (mm9) with default settings of CASAVA software. Reads mapping to exons of Refseq transcripts were counted with CASAVA software. Exon-level data were consolidated to gene-level read counts and summarized for all 12 samples in a single table. Data were normalized so that the trimmed column means (excluding values above 95th %ile and below 5th %ile) were the same for all samples. The 13 protein-coding mtDNA transcripts were mapped to NC_005089.1 and counted separately, then normalized to the trimmed mean of the non-mitochondrial transcripts.

source_name: triceps brachii muscle

growth_protocol: Until 6 months of age, all mice housed 2-3 per cage with ad lib access to food and water and 12 h dark cycle (6PM-6AM). From four to six months of age, regular chow was replaced with chow containing 0.025% (w/w) tamoxifen except for two 1-wk breaks with regular chow, for total of 6 weeks of tamoxifen feeding. Tamoxifen feeding depleted myostatin only in mice with floxed myostatin genes.

extract_protocol: RNA was extracted with Trizol reagent as directed by Invitrogen. Polyadenylated RNA was extracted, converted to cDNA, and amplified with an Illumina TruSeq RNA library preparation kit as directed by the vendor.

treatment_protocol: At 6 months of age, 6 of 12 mice (3 of each genotype) transferred to individual cages with running wheels for a 12 week period.

value: active

value: triceps brachii

tag: myostatin genotype

value: Mstn exon 3 floxed


title: Active_Mstn_deficient_3


title: Active_control_2

value: normal


title: Active_control_3


title: Sedentary_Mstn_deficient_3


title: Sed_Gast

value: gastrocnemius


title: Active_control_1


title: Active_Tib


title: Sed_Quad

value: quadriceps


title: Sedentary_control_3


title: Active_Quad


title: Active_Gast


title: Sedentary_control_2


title: Sedentary_control_1


title: Active_Mstn_deficient_2


title: TCF7L1_ChIP_seq

status: Public on Sep 02 2011

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

description: against TCF7L1

data_processing: Peaks: Peak detection was performed with the Global Identifier of Target Regions (GLITR) algorithm (http://web.me.com/kaestnerlab1/GLITR/).

source_name: 3T3-L1 cells

growth_protocol: Murine 3T3-L1 cells were maintained in DMEM (Invitrogen) supplemented with 10% FBS (Tissue Biologicals) and 1% penicillin/streptomycin (Invitrogen).

extract_protocol: 3T3-L1 cells treated for 24 hours with DMI were crosslinked with 1% formaldehyde (Fisher) for 10 minutes and quenched for 5 min with 100 mM of glycine (Fisher). After harvesting and spinning cells in cold PBS, cells were lysed in hypotonic buffer, nuclear pellet was resuspended in SDS-based lysis buffer, and DNA was fragmented at âHighâ in Bioruptor for 30 seconds on and 30 seconds off for 1 round of 7.5 minutes. TCF7L1 antibody (Santa Cruz) was used to immunoprecipitate protein bound DNA. Multiple pooled immunoprecipitations for TCF7L1 were amplified, size selected (approximately 170 bp in length +/- 30 bp), and labeled as per Illlumina. Deep sequencing was performed using Illumina platform. Unique reads were mapped to Feb. 2006 mm8 Mouse Genome Assembly. Running average between each group of 3 neighboring GLTR regions were used to determine regions where there was amplification or duplication in the cell line. Regions with running average less than 10,000 bp were discarded for final analysis.

treatment_protocol: Low passage 3T3-L1 cells were grown to confluency and maintained in growth media for 2 days. Post-confluent 3T3-L1 cells were treated with adipogenic stimuli (1 µM dexamethasone, 500 µM 3-isobutyl-1-methylxanthine, and 10 µg/ml insulin).

value: 24 hours of adipogenic stimuli

tag: passage

value: 5 though 12


title: HF-TAC_H3K27me3_ChIPSeq

first: Wen-Hui

last: Lien

address: 1230 York Ave Box#300

department: Mammalian cell biology and development

institute: The Rockefeller Unoversity

description: Chromatin IP against H3K27me3

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program. Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification using software MACS.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm

source_name: Mouse back skins

growth_protocol: HF-SCs and TACs were FACS-purifed from the back skins of indicated ages of mice

extract_protocol: 3 million of sorted cells were used for each ChIP-seq run. Sorted cells were cross-linked by addition of 1/10th volume of fresh 11% formaldehyde solution for 10 minutes at room temperature and then rinsed twice with 1X phospho-buffered saline (PBS) prior to freezing in liquid nitrogen and storing at -80C. Before ChIP, cells were resuspended, lysed and sonicated to solubilize and shear cross-linked DNAs. For sonication, lysates were treated with Triton X-100 to 1% and then subjected to a Bioruptor Sonicator (Diagenode, UCD-200) according to a 30X regiment of 30 seconds sonication followed by 60 second rest. The resulting whole cell extract was incubated overnight at 4C with 10 ul of Dynal Protein G magnetic beads (Invitrogen) which had been pre-incubated with ~5 ug of the appropriate Ab. 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 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 25 cycles and library fragments of 150-300 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.

tag: gender

value: Female

tag: age

tag: sorting markers

value: GFP, integrin alpha 6, ephrinB1

value: H3K27me3 (Millipore, 07-449)


title: HF-TAC_H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

value: H3K4me3 (Abcam, ab1012)


title: Sedentary_Mstn_deficient_1

tag: tissue


title: Active_Tric


title: Sedentary_Mstn_deficient_2


title: HF-TAC_H3K79me2_ChIPSeq

description: Chromatin IP against H3K79me2

value: H3K79me2 (Abcam, ab3594)


title: HF-TAC_input DNA

description: input DNA


title: aHF-SC_H3K27me3_ChIPSeq

description: Chromatin IP against H3K27me3

value: GFP, integrin alpha 6 and CD34


title: aHF-SC_input DNA

description: input DNA


title: aHF-SC_H3K79me2_ChIPSeq

description: Chromatin IP against H3K79me2


title: aHF-SC_H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3


title: yMA1322_pKN3050

city: Irvine

first: Suzanne

last: Sandmeyer

address: University

department: Biological Chemistry

institute: University of CA, Irvine

description: total DNA was used as the template to amplify insertion sites using inverse PCR

data_processing:
HTS image files were converted to fastq files using Illumina pipeline software.   Sequence began with the last 17 nts of the Ty3 LTR.  HTS reads that did not initiate with this sequence was discarded. For remaining sequences, the LTR barcode was filtered and the genomic sequence was extracted. Fastq files with less than 19 nts of genomic sequence were also excluded from further analysis.  Retained reads were mapped to the yeast genome sequence downloaded from the UCSC Genome Browser (build sacCer2 June2008) (Rhead et al.) using Bowtie (v 0.9.8.1) (Langmead et al. 2009). Only reads with no mismatches were kept for further analysis. Reads that matched multiple genomic loci were tagged for separate analysis.
Mapped sequence reads were converted to insertion sites deï¬ned by chromosome number, strand (Watson or Crick), and coordinate. Read density of an insertion site was defined as the number of reads that mapped to that site. Insertion sites with densities less than ï¬ve in either dataset were excluded from further analysis. Neighboring insertion sites were linked into clusters by aggregating any two sites that were no more than 10 nts apart, regardless of strandedness. The read density of a cluster is the sum of the read densities of the insertion sites in the cluster. The event density of a cluster is the number of unique insertion sites associated with the cluster.

source_name: Ty3 transposition in wt cells

growth_protocol: Yeast were cultured using standard procedures.  Transformants of yMA1356 (MATα ura3-52 trp1-∆63 his3-∆200 ade2-101 lys2o leu2-∆1, rad52∆) or yMA1322 (MATα ura3-52 trp1-∆63 his3-∆200 ade2-101 lys2o leu2-∆1) transformed with a high-copy URA3-marked plasmid bearing a galactose-inducible Ty3 element with a HIS3 insertion downstream of the POL3 open reading frame (Ty3HIS3 on pKN3050) were inoculated into 3 ml of SR (synthetic complete medium containing raffinose as a carbon source) -ura, -his or SR -ura medium at 24°C for 24 h. Five hundred microliters of the over-night culture was diluted with 9.5 ml of fresh SR -ura, -his or SR -ura and cells were grown at 24°C for 24 h. Two million transformants were plated onto each of ten SG (synthetic galactose) -ura, -his plates per sample and incubated for 3 d at 24°C in order to induce expression of Ty3.  Cultures were replica-plated onto 1% yeast extract-2% peptone-2% dextrose (YPD), and incubated at 30°C for 24 h. Cells from YPD plates were then replica-plated onto SD -his medium supplemented with 0.1% of 5-fluoro-orotic acid (5FOA) {Boeke, 1984 #1096} to select for cells that had lost the URA3-marked donor plasmid but contained Ty3 HIS3 chromosomal integrants, which conferred the His+ phenotype. Approximately 10,000 colonies each for yMA1322 carrying pKN3050 and yMA1356 carrying pKN3050 cultures were scraped from plates. All harvested cells were inoculated in 10 ml SD (synthetic dextrose) -his at 30°C on a rotating wheel for 24 h.  Genomic DNA (gDNA) was extracted using standard procedures.

extract_protocol: DNA preparation. Cells from both induced and uninduced cultures were harvested DNA was extracted. Nucleic acid samples were treated with RNAse A (0.2 µg/ µl) and purified afterward using Microspin-30 columns (BioRad, Hercules, CA). DNA concentrations were measured on a NanoDrop-1000 (Thermal Scientific Inc., NanoDrop products, Wilingtons, DE). High-throughput sequence (HTS) analysis on the Illumina GAIIX.  Two experimental sample sets were prepared for HTS to evaluate Ty3 target sites relative to the 3' LTR. Samples were processed as follows: (1)  yeast total DNA was extracted and digested with three different 4 bp-cutters independently in this step as well as subsequent steps prior sequencing, (2) cleaved DNA was circularized in a ligation reaction; (3) samples were amplified by inverse PCR (iPCR) using primers that annealed within Ty3; and (4) samples were submitted to the Genetics Department Sequence Facility, Washington University (St. Louis, MO) for HTS using the Illumina GA system.  Digestion: Each digest, 1µg of Ty3HIS3 integrant gDNA was cut for 3 h at 37°C and for 20 min at 65°C to deactivate the enzyme. Four-base cutters Csp6I, HaeIII, and HpyCH4V (5-10 units/each) (New England Biolabs, USA) were used to digest gDNA. Complete digestion products were fractionated by electrophoresis in 0.7% agarose resulting in a smear from 300 bp to 10 kb. Digested gDNAs were purified using QAIquick Spin Columns 50 (Qiagen Inc., Germany) and eluted with 30 µl of sterile water. Self-ligation: Digested DNA at a concentration of 1 ng/microl was ligated at 15°C for more than 12 h. One µg of digested DNA was self-ligated using 18 Weiss units of T4 DNA ligase, 40 µl of 10x ligase buffer in 400 µl reaction (New England Biolabs, USA). Self-ligated DNA was ethanol precipitated. Inverse PCR: Both forward and reverse primers contained Ty3 unique sequences and Illumina adaptors. The forward primer also contained a sequence which was used as a GAIIx sequencing primer. Five ng or one µg of circularized DNA was used as template for iPCR. The final concentration of all PCR components per 50-µl reaction was 0.5 x RedTaq buffer, 0.2 mM of each dNTPs, 1 M Betaine, 0.5 µM of each primer, 2 units or 4 units of RedTaq DNA polymerase, 5 ng or 1 µg circularized DNA and water. Thermal cycler settings included 1 cycle at 93°C for 3 min, 32 cycles (93°C for 30 sec, 60°C for 6 min), and 1 cycle holding indefinitely at 4°C. Five µl of PCR products were ran on 0.7% agarose gel. Product size from iPCR was from 200 bp to 2 kb but on average about 400 bp. The PCR product was purified using QAIquick Spin Columns 50 (Qiagen Inc., Germany) and eluted with 30 µl of sterile water. Ten nM iPCR stock was prepared based on an estimation for a 200 bp DNA fragment (10nM is equivalent to 1.32 ng/ µl). Equal amounts of iPCR from three different restriction enzyme digests of the same sample were combined and submitted for HTS.

treatment_protocol: see growth protocol

tag: genotype/variation


title: qHF-SC_input DNA

description: input DNA

tag: strain

value: integrin alpha 6 and CD34


title: yMA1356_pKN3050

source_name: Ty3 transposition in rad52 deletion cells

value: MATα ura3-52 trp1-∆63 his3-∆200 ade2-101 lys2o leu2-∆1, rad52∆


title: qHF-SC_H3K79me2_ChIPSeq

description: Chromatin IP against H3K79me2


title: qHF-SC_H3K27me3_ChIPSeq

description: Chromatin IP against H3K27me3


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: H3K4me3 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC02 (A03478) using Illumina HiSeq 2000
library name: A03478
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 73-291 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM707009_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K4me3.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03478-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 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.8186
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,750,906
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
FINDPEAKS_SCORE: 0.6905
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.6889
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9991
IROC_PERCENTILE: 38
POISSON_SCORE: 0.6921
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707009_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K4me3.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03478-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 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.8206
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: NGED H3K4me3 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me3 Donor HuFNSC02 Library A03478-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,750,906
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
FINDPEAKS_SCORE: 0.6905
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.6889
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9991
IROC_PERCENTILE: 38
POISSON_SCORE: 0.6921
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: NA

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

extract_protocol: library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: female

tag: body site

value: Brain

tag: histological type

value: Ganglionic eminence neurosphere culture

tag: is tumor

value: No

value: primary cell culture

tag: cell type


description:
design description: H3K27me3 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC02 (A03480) using Illumina HiSeq 2000
library name: A03480
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 78-372 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00241
****************
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: GSM707011_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K27me3.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03480-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 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.8197
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,269,834
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.0094
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.0455
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.816
IROC_PERCENTILE: 9
POISSON_SCORE: 0.2138
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707011_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K27me3.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03480-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 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.8217
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: NGED H3K27me3 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 Donor HuFNSC02 Library A03480-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,269,834
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.0094
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.0455
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.816
IROC_PERCENTILE: 9
POISSON_SCORE: 0.2138
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: H3K9me3 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC02 (A03479) using Illumina HiSeq 2000
library name: A03479
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 74-346 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0042
****************
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: GSM707010_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K9me3.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03479-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 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.8205
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,306,288
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.1051
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1546
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8545
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3605
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707010_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K9me3.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03479-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 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.8225
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: NGED H3K9me3 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 Donor HuFNSC02 Library A03479-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,306,288
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.1051
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1546
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8545
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3605
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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