title: 2_Untreated_6hrs_Control

status: Public on Feb 04 2012

city: New Haven

first: Frank

middle: J

last: Slack

address: 266 Whitney Ave

department: MCDB

institute: Yale University

data_processing:
The raw data were aligned to the C. elegans genome (genome build WormBase WS190) using the SOAP program (ver. 1.10 Li, R. et al., Bioinformatics 24: 713-714. 2008) with the following command options:  –S 3 –A TCGTATGCCGTCTTCTGCTTGT (maximum 2 base pair mismatches were allowed as a default option). Then, the number of times of each read sequenced was examined.
The *Processed.txt files represent aligned, unique sequencing reads, and their counts observed.
Genome Build:
2_Untreated_6hrs_Control_Processed.txt: WormBase WS190

source_name: untreated young adult animals (6 hrs)

growth_protocol: spe-9(hc88, a sterile mutant) hermaphrodites were maintained for a few generations without starvation at 15°C to collect embryos. After embryos were harvested, they were incubated at 23°C without a food source in M9 buffer for 24 hrs with rotating to arrest their growth at the L1 stage. Synchronized animals were exposed to each stress when they were young adult (Day 0-1 post-L4 molt. More specifically, 66 hrs after synchronized L1 animals were placed on bacterial plates)

extract_protocol: Total RNAs were prepared using the mirVana miRNA Isolation kit (Ambion), and 10 μg of total RNAs were used for cDNA library preparation for small RNAs using the DGE-Small RNA Sample Prep Kit ver. 1.0 (Illumina) according to the manufacturers' instructions.

treatment_protocol: Animals were exposed to each stress condition, including heat shock (32°C, 6 hrs), Hypoxia (0.01% oxygen, 6 hrs), Oxidation (Juglone 750microM, 6 hrs) and Starvation (complete food deprivation, 12 hrs). Total RNAs were purified from animals just after stress treatment. Also, for recovery from heat shock, animal exposed to heat stress (32°C, 6 hrs) were placed at 23°C for 6 hrs, and then used for RNA isolation. In addition, RNAs were prepared from normally cultured, untreated animals at three time points, 0 hr (baseline), 6 hrs (as controls for heat shock, hypoxia and oxidation) and 12 hrs (as controls for heat shock recovery and starvation) after starting stress exposure.

tag: gender

value: hermaphrodites

tag: developmental stage

value: Day 0-1 post-L4 molt (young adult stage. Specifically, 66 hrs after synchronized L1 stage animals were placed bacterial plates)

tag: growth condition

tag: stress conditions

value: Untreated for 6 hrs


title: 6_Starvation

type: SRA

state: CT

country: USA

library_source: transcriptomic

data_processing:
The raw data were aligned to the C. elegans genome (genome build WormBase WS190) using the SOAP program (ver. 1.10 Li, R. et al., Bioinformatics 24: 713-714. 2008) with the following command options:  –S 3 –A TCGTATGCCGTCTTCTGCTTGT (maximum 2 base pair mismatches were allowed as a default option). Then, the number of times of each read sequenced was examined.
The *Processed.txt files represent aligned, unique sequencing reads, and their counts observed.
Genome Build:
6_Starvation_Processed.txt: WormBase WS190

molecule: total RNA

organism: Caenorhabditis elegans

source_name: young adult animals exposed to complete food deprivation

tag: strain

value: Complete food deprivation for 12 hrs


title: 3_HeatShock

data_processing:
The raw data were aligned to the C. elegans genome (genome build WormBase WS190) using the SOAP program (ver. 1.10 Li, R. et al., Bioinformatics 24: 713-714. 2008) with the following command options:  –S 3 –A TCGTATGCCGTCTTCTGCTTGT (maximum 2 base pair mismatches were allowed as a default option). Then, the number of times of each read sequenced was examined.
The *Processed.txt files represent aligned, unique sequencing reads, and their counts observed.
Genome Build:
3_HeatShock_Processed.txt: WormBase WS190

source_name: young adult animals exposed to heat shock

value: Heat shock at 32°C for 6 hrs


title: C24 methylC

status: Public on Feb 05 2012

city: Canberra

first: Jennifer

last: Taylor

address: Clunies Ross St

department: Plant Industry

country: Australia

institute: CSIRO

library_source: genomic

data_processing:
Sequence reads were mapped using the BSMAP analysis pipeline (Xi and Li, 2009) using default values.  Mapping was accomplished by using a reiterative single nucleotide trimming of the read until either a successful hit was found or 30 bases had been removed.  An error rate was determined by the number of uniquely mapped methylated C’s to the number of uniquely mapped C’s on the Chloroplast genome.  This equated to above 98% conversion rate. BSMAP output files and README included.
Genome Build:
C24.bsp: TAIR 9

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: C24 methylC

growth_protocol: grown in a 16 hour day cycle at 22°C/18°C (day/night)

extract_protocol: Genomic DNA was extracted using the Dneasy Plant Mini Kit (Qiagen). DNA underwent sonication, end repair and ligation with methylated adapters as per Illumina recommendations for methylSeq. Bisulfite conversion used the Methyl Easy Xceed Kit (Human Genetic Signatures). Bisulfite treated samples were enriched by 18 cycles of PCR.

treatment_protocol: Bisulfite converted DNA using  Methyl Easy Xceed Kit (Human Genetic Signatures)

tag: tissue

value: Unopened buds


title: HSF/D.mel_PB-seq_Rep2_seqA

status: Public on Feb 06 2012

city: Farmington

first: Michael

middle: Joseph

last: Guertin

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

data_processing: The PB-seq reads were aligned to the Drosophila Genome (BDGP R5/DM3) using BWA (v 0.5.8c)

organism: Drosophila melanogaster

source_name: HSF IP

growth_protocol: Prior to DNA extraction S2 were cultured as previously described (PMID: 20844575).

extract_protocol: We performed an in vitro binding experiment with purified HSF and naked, sheared genomic Drosophila S2 DNA (PB-seq), to derive an accurate set of potential HSF binding sites in the Drosophila genome.  HSF-bound DNA was specifically eluted and detected by high throughput sequencing.  Drosophila HSF was N-terminally tagged with glutathione s-transferase and a tobacco etch virus (TEV) protease cleavage site.  The C-terminus of the recombinant HSF was fused to the 3xFLAG epitope.  Recombinant HSF was purified from E. coli with glutathione resin as previously described (PMID: 20078429) , with the following modifications:  HSF-3xFLAG elution was achieved by addition of 6xHistidine tagged TEV protease and TEV protease was cleared from the HSF preparation using a Nickel-NTA column.  We incubated 600pM HSF and 2500ng genomic DNA (sonicated to 100-600bp fragment size as previously described in PMID: 20844575) in 1500μl final volume of 1xHSF binding buffer and let it come to equilibrium for an hour at room temperature.  We added 20μl ANTI-FLAG M2 affinity gel for 10 minutes, washed 8 times with 1xHSF binding buffer to remove unbound DNA; 3xFLAG peptide was added to a final concentration of 200ng/μl to specifically elute HSF and HSF-bound DNA.  The mock IP was done in the absence of recombinant HSF.

tag: library strategy

value: PB-Seq

tag: library selection

value: immunoprecipitation

tag: library source

tag: antibody

value: Anti-FLAG M2


title: 4_Juglone

data_processing:
The raw data were aligned to the C. elegans genome (genome build WormBase WS190) using the SOAP program (ver. 1.10 Li, R. et al., Bioinformatics 24: 713-714. 2008) with the following command options:  –S 3 –A TCGTATGCCGTCTTCTGCTTGT (maximum 2 base pair mismatches were allowed as a default option). Then, the number of times of each read sequenced was examined.
The *Processed.txt files represent aligned, unique sequencing reads, and their counts observed.
Genome Build:
4_Juglone_Processed.txt: WormBase WS190

source_name: young adult animals exposed to oxidation

value: Juglone (oxidative stress) 750 μM for 6 hrs


title: HSF/D.mel_PB-seq_Rep1_seqB

value: naked, sheared genomic Drosophila S2 DNA


title: 1_Baseline_0hrs_Control

data_processing:
The raw data were aligned to the C. elegans genome (genome build WormBase WS190) using the SOAP program (ver. 1.10 Li, R. et al., Bioinformatics 24: 713-714. 2008) with the following command options:  –S 3 –A TCGTATGCCGTCTTCTGCTTGT (maximum 2 base pair mismatches were allowed as a default option). Then, the number of times of each read sequenced was examined.
The *Processed.txt files represent aligned, unique sequencing reads, and their counts observed.
Genome Build:
1_Baseline_0hrs_Control_Processed.txt: WormBase WS190

source_name: untreated young adult animals (baseline)

value: Untreated for 0hrs


title: iMN-ESCs without Dox treatment, rep2

status: Public on Feb 03 2012

city: Brockport

first: Rongkun

last: Shen

state: New York

address: 350 New Campus Dr

department: Biology

institute: SUNY Brockport

description: In iMN-ESCs, Isl1-Lhx3 expression is induced upon treatment with doxycycline. iMN-ESCs are derived from mouse ESCs.

data_processing:
Reads were aligned to the mouse mm9 genome using TopHat. BAM and SAM files were generated as the output files. DEXSeq was used to count the reads per gene based on mm9 RefSeq annotation.
Genome Build:
3doxN.sam.count.txt: mm9

organism: Mus musculus

source_name: iMN-ESCs, no Dox

growth_protocol: Mouse iMN-ESCs were trypsinized and grown in ESC growth medium with LIF in suspension as cell aggregates for 2 d.

extract_protocol: The standard Illumina TruSeq RNA Sample Preparation protocol was used with index tags, allowing multiplexing.

treatment_protocol: The ESC aggregates (Ebs) were first treated with all-trans RA (0.5uM) alone for 2 d. Then, RA along-treated Ebs were cultured without or with doxycycline (2ug/mL) in the presence of RA for another 2-3 d.

tag: background strain

tag: cell type

value: inducible motor neurons-embryonic stem cells (iMN-ESCs)

tag: treatment


title: iMN-ESCs with Dox treatment, rep1

data_processing:
Reads were aligned to the mouse mm9 genome using TopHat. BAM and SAM files were generated as the output files. DEXSeq was used to count the reads per gene based on mm9 RefSeq annotation.
Genome Build:
2doxP.sam.count.txt: mm9

source_name: iMN-ESCs, Dox

value: doxycycline


title: 7_Untreated_12hrs_Control

data_processing:
The raw data were aligned to the C. elegans genome (genome build WormBase WS190) using the SOAP program (ver. 1.10 Li, R. et al., Bioinformatics 24: 713-714. 2008) with the following command options:  –S 3 –A TCGTATGCCGTCTTCTGCTTGT (maximum 2 base pair mismatches were allowed as a default option). Then, the number of times of each read sequenced was examined.
The *Processed.txt files represent aligned, unique sequencing reads, and their counts observed.
Genome Build:
7_Untreated_12hrs_Control_Processed.txt: WormBase WS190

source_name: untreated young adult animals (12 hrs)

value: Untreated for 12 hours


title: 5_Hypoxia

data_processing:
The raw data were aligned to the C. elegans genome (genome build WormBase WS190) using the SOAP program (ver. 1.10 Li, R. et al., Bioinformatics 24: 713-714. 2008) with the following command options:  –S 3 –A TCGTATGCCGTCTTCTGCTTGT (maximum 2 base pair mismatches were allowed as a default option). Then, the number of times of each read sequenced was examined.
The *Processed.txt files represent aligned, unique sequencing reads, and their counts observed.
Genome Build:
5_Hypoxia_Processed.txt: WormBase WS190

source_name: young adult animals exposed to low oxygen condition

value: 0.01% oxygen (hypoxia) for 6 hrs


title: H3R2me2sK4me3 ChIP-seq

status: Public on Feb 02 2012

city: Boston

first: Mark

middle: L

last: Borowsky

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: MGH

description:
Sample 2
H3R2me2sK4me3 custom antibodies was raised in the lab.

data_processing:
FASTQ files were processed to remove identical duplicate reads and aligned to the mouse mm9 reference genome sequence with at most 1 mismatch using imperfectLookupTable (ILT; Batzoglou et al. 2002). ILT alignments were converted to BED format using a custom program.
Genome Build:
s_2.distinct.bed: mm9

source_name: Pro-B_H3R2me2sK4me3 ChIP-seq

growth_protocol: RAG2-/- Abelson-transformed pro-B cells were routinely cultured on uncoated plastic in RPMI1640 medium supplemented with 10% FBS.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments between 100 and 500 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: RAG2-/- Abelson-transformed pro-B cells

tag: chip antibody


title: H3R2me2s ChIP-seq

description:
Sample 1
H3R2me2s custom antibody was raised in the lab.

data_processing:
FASTQ files were processed to remove identical duplicate reads and aligned to the mouse mm9 reference genome sequence with at most 1 mismatch using imperfectLookupTable (ILT; Batzoglou et al. 2002). ILT alignments were converted to BED format using a custom program.
Genome Build:
s_3.distinct.bed: mm9

source_name: Pro-B_H3R2me2s ChIP-seq


title: H3K4me3 ChIP-seq

description: Sample 3

data_processing:
FASTQ files were processed to remove identical duplicate reads and aligned to the mouse mm9 reference genome sequence with at most 1 mismatch using imperfectLookupTable (ILT; Batzoglou et al. 2002). ILT alignments were converted to BED format using a custom program.
Genome Build:
s_1.distinct.bed: mm9

source_name: Pro-B_H3K4me3 ChIP-seq

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#

tag: chip antibody lot #


title: 8_Recovery_post-HeatShock

data_processing:
The raw data were aligned to the C. elegans genome (genome build WormBase WS190) using the SOAP program (ver. 1.10 Li, R. et al., Bioinformatics 24: 713-714. 2008) with the following command options:  –S 3 –A TCGTATGCCGTCTTCTGCTTGT (maximum 2 base pair mismatches were allowed as a default option). Then, the number of times of each read sequenced was examined.
The *Processed.txt files represent aligned, unique sequencing reads, and their counts observed.
Genome Build:
8_Recovery_post-HeatShock_Processed.txt: WormBase WS190

source_name: young adult animals recovered from heat shock exposure

tag: gender

value: hermaphrodites

value: Day 0-1 post-L4 molt (young adult stage. Specifically, 66 hrs after synchronized L1 stage animals were placed bacterial plates)

value: Recovery (23°C for 6 hrs) from heat shock treatment


title: kidney-CTL-3

first: Zhenqiang

last: Su

address: 22 Thomson Place

department: IP & Science

institute: Thomson Reuters

description: RNA-Seq

data_processing: 30,941 unique rat RefSeq RNAs downloaded from NCBI blast database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/refseq_rna.tar.gz) on November 30, 2009 as the reference annotation. The aligners used were bowtie-0.10.1 (http://sourceforge.net/projects/bowtie-bio/files/bowtie/), blastn/megablast (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.21/), and GeneSifter (http://www.geospiza.com/Products/AnalysisEdition.shtml).  For bowtie, the default options were used to control the behavior of the aligner for sequence alignment except for options “-5 4 -3 10 -l 12”.  The “-5 4” option trims four bases from the high-quality (left) end of each read before alignment, the “-3 10” controls the length of bases trimmed from the low-quality (right) end of reads, and the “-l 12” option controls the length of seeds which are the first 12 bases on the high-quality end of sequence reads.  The maximum number of mismatches allowed in seeds is the default 2.  For blastn, we used the default options except for the expectation value of 0.001; for megablast, we used an expectation value of 0.001 and word size of 12.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: vehicle control

growth_protocol: six-week-old Big Blue rats were gavaged with 10 mg/kg body weight AA five times a week for 12 weeks and were sacrificed one day after of the last treatment.  The animal tissues were isolated, frozen quickly in liquid nitrogen, and stored at -80°C.

extract_protocol: Libraries were prepared according to Illumina's instructions for mRNA sequencing. Briefly, poly-A tailed mRNA was purified from total RNA with Sera-Mag Magnetic Oligo (dT) beads, and then was fragmented into small pieces using divalent cations under elevated temperature.  Using reverse transcriptase and random primers, the cleaved RNA fragments were then used to synthesize the first and second strand cDNAs.  The cDNA was treated in “end repair” reaction with T4 DNA polymerase and Klenow DNA polymerase to blunt ends.  An “A” base was then added to the 3’ end of the blunt phosphorylated DNA fragments, and an Illumina adapter with a single “T” base overhang at its 3’ end was then ligated to the end of the DNA fragment, preparing it to be hybridized in a single read flow cell.  After the ligation reaction, a size range of cDNA templates was selected and these fragments were amplified on a cluster station with single-read cluster generation kit v2.  Finally, cDNA template clusters were sequenced on the Genome Analyzer II with SBS Sequencing Kit v3.  Each RNA sample was sequenced in one lane, generating over 16 million reads of 36 bases long per sample.  Images taken during the sequencing reactions were analyzed with Illumina software pipelines with base-calling done by Bustard, and sequence analysis performed with Gerald.

value: kidney


title: kidney-AA-3

description: RNA-Seq

source_name: aristolochic acid treated


title: kidney-CTL-1

description: RNA-Seq


title: kidney-CTL-2

description: RNA-Seq


title: kidney-AA-2

description: RNA-Seq


title: kidney-AA-1

description: RNA-Seq


title: kidney-CTL-4

description: RNA-Seq


title: wild type replicate 2

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

data_processing:
reads_r4s1.txt; genome build: miRBase Release 16
Small RNA sequences were mapped to mature miRNA sequences annotated in miRBase Release 16 (miRBase, http://www.mirbase.org/). The mapping was performed using NextGenMap (FJ Sedlazeck, S Tauber, GB Ewing, and A von Haeseler, submitted) and allowed for up to two mismatches.

source_name: female E11.5 whole embryo

extract_protocol: Female mouse embryos were dissected on E11.5, homogenized and total RNA was extracted using peqGOLD TriFast reagent according to manufacturer's instructions (PEQLAB Biotechnologie GmbH, Erlangen, Germany). DNA for genotyping was extracted from the remaining amnions and sex determination was performed as described (Lambert et al. 2000). Total RNA was enriched for small RNAs (<200 nucleotides) using the mirVana miRNA Isolation Kit (Ambion, Applied Biosystems). Small RNAs were 5'-end labeled with 20Î¼Ci [Î³-32P] ATP using T4 polynucleotide kinase (Fermentas). Radiolabeled RNA was separated on 15% 19:1 AA:bisAA gels (8M UREA in 1xTBE) and exposed to X-ray films. RNA bands between 19-25 nucleotides were cut out and eluted in 400ul elution buffer (500mM NH4OAc, 0.2%SDS, 100mM EDTA) at room temperature over night. Eluted samples were purified over Sephadex G-25 spin-columns and precipitated. The size selected RNA was ligated to a 5' pre-adenylated and 3' blocked 3'-end adapter (5'-Appp- UCGUAUGCCGUCUUCUGCUUGUidT-3') using truncated T4 RNA Ligase 2, (New England Biolabs) with the supplied buffer and a final concentration of 20% PEG6000. Ligations were incubated for 6 hours at room temperature followed by 4C over night. Ligation products were purified on a 10% denaturing PAGE next to radiolabeled markers and ligated to the 5'adapter (5'-GUUCAGAGUUCUACAGUCCGACGAUC- 3') using T4 RNA Ligase 1 (New England Biolabs) with the supplied buffer and 20% PEG. Again, the ligation product was purified on a denaturing PAGE. The final product was reverse transcribed using RevertAid H Minus Reverse Transcriptase (Fermentas) using RT primer 5'-CAAGCAGAAGACGGCATACGA-3' following manufacturer's instructions. The cDNA was used as template for 15 cycles of PCR amplification (forward primer: 5'- AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA-3', reverse primer: 5'-CAAGCAGAAGACGGCATACGA3') using Phusion High-Fidelity DNA Polymerase (Finnzymes) according to manufacturer's protocol. PCR products were separated on a non-denaturing 6% AA TBE gel and stained with ethidiumbromide in 1x TBE. Bands of approximately 100bp corresponding to the final mature miRNA library were cut out and eluted in 400 ul elution buffer (0.5M NH4OAc, 1mM EDTA, pH 8.1) over night at room temperature. DNA was precipitated and subsequently resuspended in 10ul 1x TE.

value: female

tag: genotype/variation

value: wild type

value: whole embryo

tag: developmental stage

tag: replicate #


title: LXR ChIP-seq T09 treated

city: Olsztyn

first: Carsten

last: Carlberg

address: ul. Trylińskiego 18

department: Food Research

country: Poland

institute: Polish Academy of Sciences

description: Chromatin IP against LXR

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome (hg19) using Bowtie.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

organism: Homo sapiens

source_name: THP-1 cells

growth_protocol: THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 Â°C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
PMA-differentiated THP-1 cells (per condition nine 175 cm2-flasks, each 2x107 cells, density of 1x106 cells/ml) were treated for 60 min with 1 µM T09 or vehicle (DMSO) and nuclear proteins were cross-linked to DNA by adding formaldehyde directly to the medium to a final concentration of 1% following incubation for 10 min at room temperature on a rocking platform. Cross-linking was stopped by adding glycine to a final concentration of 0.15 M and incubating at room temperature for 10 min on a rocking platform. The cells were collected by centrifugation and washed twice with ice cold PBS (140 mM NaCl, 2.7 mM KCl, 1.5 mM KH2PO4, 8.1 mM Na2HPO4.2H2O). Nuclear extraction was performed by adding 500 µl PIPES buffer (5 mM Pipes pH 8.0, 0.85 mM KCl, 0.5% Nonidet P-40, protease inhibitors), incubating for 10 min on ice and removing cytoplasmatic components by centrifugation. Nuclear pellets were dissolved in 500 µl SDS lysis buffer (1% SDS, 10 mM EDTA, protease inhibitors, 50 mM Tris-  HCl, pH 8.1) and incubated 10 min on ice. Lysates were sonicated at high power with 22x30 s pulses in a Bioruptor (Diagenode, Liège, Belgium) to result in DNA fragments of 100 to 600 bp. Cellular debris were removed by centrifugation. Aliquots of 100 µl of the lysate were diluted 1:10 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl, protease inhibitors, 16.7 mM Tris-HCl, pH 8.1) and 2 µg of anti-LXR antibody (Jakobsson et al. 2009) or non-specific anti-IgG rabbit (sc-2027, Santa Cruz Biotechnologies, Santa Cruz, CA, USA) were added and the samples were incubated for overnight at 4 °C on a rotating platform. The immunocomplexes were collected using 60 µl of BSA-coated protein A agarose beads slurry (Millipore) for 3 h at 4 °C with rotation. The beads were washed sequentially for 4 min in rotating platform with 1 ml of the following buffers: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 8.1), high sa  lt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, 20 mM Tris-HCl, pH 8.1) and LiCl wash buffer (0.25 M LiCl, 1% Nonidet P-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1). Finally, the beads were washed twice with 1 ml TE buffer (1 mM EDTA, 10 mM Tris-HCl, pH 8.0) and the immune complexes were eluted twice using 250 µl elution buffer (1% SDS, 100 mM NaHCO3) for 15 min at room temperature with rotation. The supernatants were combined and the immune complexes were reverse cross-linked overnight at 65 °C in the presence of proteinase K (Fermentas) in a final concentration of 40 µg/ml. DNA was extracted with the ChIP DNA Clean & Concentrator Kit (Zymo Research Cooperation, HiSS Diagnostics, Freiburg, Germany) according to manufacturer's instructions and eluted in 40 µl nuclease-free H2O. The ChIP templates were sequenced using a Solexa Gene Analyzer II platform (Illumina) at 36 bp read length using standard manufacturer protocols at the Genomics Co  re Facility in Heidelberg, Germany.
The anti-LXR antibody used was established in: Jakobsson T, Venteclef N, Toresson G, Damdimopoulos AE, Ehrlund A, Lou X, Sanyal S, Steffensen KR, Gustafsson JA, Treuter E. 2009. GPS2 is required for cholesterol efflux by triggering histone demethylation, LXR recruitment, and coregulator assembly at the ABCG1 locus. Mol Cell 34: 510-518.

treatment_protocol: For differentiation into macrophages the cells were incubated for 3 days with 20 nM PMA. Prior to stimulation with 1 ÂµM of the synthetic LXR ligand T09 (Sigma-Aldrich) or vehicle (DMSO), final concentration 0.1%) the medium was replaced by RPMI 1640 supplemented with 5% lipid-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and 20 nM PMA.

value: LXR


title: ADAR2-/- replicate 2

data_processing:
reads_r4s2.txt; genome build: miRBase Release 16
Small RNA sequences were mapped to mature miRNA sequences annotated in miRBase Release 16 (miRBase, http://www.mirbase.org/). The mapping was performed using NextGenMap (FJ Sedlazeck, S Tauber, GB Ewing, and A von Haeseler, submitted) and allowed for up to two mismatches.

tag: strain


title: ADAR2-/-/ADAR1-/- replicate 2

data_processing:
reads_r4s3.txt; genome build: miRBase Release 16
Small RNA sequences were mapped to mature miRNA sequences annotated in miRBase Release 16 (miRBase, http://www.mirbase.org/). The mapping was performed using NextGenMap (FJ Sedlazeck, S Tauber, GB Ewing, and A von Haeseler, submitted) and allowed for up to two mismatches.

tag: tissue


title: ADAR2-/- replicate 3

data_processing:
reads_r5s2.txt; genome build: miRBase Release 16
Small RNA sequences were mapped to mature miRNA sequences annotated in miRBase Release 16 (miRBase, http://www.mirbase.org/). The mapping was performed using NextGenMap (FJ Sedlazeck, S Tauber, GB Ewing, and A von Haeseler, submitted) and allowed for up to two mismatches.


title: ADAR2-/-/ADAR1-/- replicate 3

data_processing:
reads_r5s3.txt; genome build: miRBase Release 16
Small RNA sequences were mapped to mature miRNA sequences annotated in miRBase Release 16 (miRBase, http://www.mirbase.org/). The mapping was performed using NextGenMap (FJ Sedlazeck, S Tauber, GB Ewing, and A von Haeseler, submitted) and allowed for up to two mismatches.


title: iMN-ESCs with Dox treatment, rep2

data_processing:
Reads were aligned to the mouse mm9 genome using TopHat. BAM and SAM files were generated as the output files. DEXSeq was used to count the reads per gene based on mm9 RefSeq annotation.
Genome Build:
4doxP.sam.count.txt: mm9


title: LXR ChIP-seq vehicle treated

description: Chromatin IP against LXR

value: vehicle


title: IgG control

description: Chromatin IP against IgG

value: pooled

value: IgG


title: iMN-ESCs without Dox treatment, rep1

data_processing:
Reads were aligned to the mouse mm9 genome using TopHat. BAM and SAM files were generated as the output files. DEXSeq was used to count the reads per gene based on mm9 RefSeq annotation.
Genome Build:
1doxN.sam.count.txt: mm9

value: inducible motor neurons-embryonic stem cells (iMN-ESCs)


title: ADAR2-/- replicate 1

data_processing:
reads_r3s2.txt; genome build: miRBase Release 16
Small RNA sequences were mapped to mature miRNA sequences annotated in miRBase Release 16 (miRBase, http://www.mirbase.org/). The mapping was performed using NextGenMap (FJ Sedlazeck, S Tauber, GB Ewing, and A von Haeseler, submitted) and allowed for up to two mismatches.


title: wild type replicate 3

data_processing:
reads_r5s1.txt; genome build: miRBase Release 16
Small RNA sequences were mapped to mature miRNA sequences annotated in miRBase Release 16 (miRBase, http://www.mirbase.org/). The mapping was performed using NextGenMap (FJ Sedlazeck, S Tauber, GB Ewing, and A von Haeseler, submitted) and allowed for up to two mismatches.


title: ADAR2-/-/ADAR1-/- replicate 1

data_processing:
reads_r3s3.txt; genome build: miRBase Release 16
Small RNA sequences were mapped to mature miRNA sequences annotated in miRBase Release 16 (miRBase, http://www.mirbase.org/). The mapping was performed using NextGenMap (FJ Sedlazeck, S Tauber, GB Ewing, and A von Haeseler, submitted) and allowed for up to two mismatches.


title: +3 long day (LD) B

status: Public on Feb 01 2012

city: Köln

first: George

last: Coupland

address: Carl-von-Linne-Weg 10

department: Plant Developmental Biology

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description: For replicate A and B: whole transcriptome shotgun; For replicate C: ready-to-run library

data_processing:
Analysis of short-sequence reads from Illumina-Solexa sequencing
-Trimming and Filtering
The data were initially filtered using “Seqclean” (release dated 2005-08-18). This program trims matches against user-specified target sequences, which here were the primer sequences
(GACGGCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGG
and CCAGCATACAGATCTCCCTATAGTGAGTCGTATTACAATTCACTGGCCGTC), as well as the UniVec_Core database (dated 2008-10-08), poly-A tails and ends rich in undetermined bases. After trimming, a read may be removed entirely for one of 3 reasons: (a) the sequence is shorter than the minimum length specified via the "-l" parameter (here, 30), (b) the percentage of undetermined bases is greater than 3%, and (c) less than 40nt of the sequence is left unmasked by the "dust" low-complexity filter.
-Mapping the reads
Each dataset of reads was converted into a blast database using “formatdb”. To identify matches to known genes, the TAIR8 cDNA collection (TAIR8_cdna_20080325) was then compared to the read databases using Megablast (settings: -v 2000 -b 500 -a 4 -W16 -p 0.6 -e 1 -D3).
The initial runs were performed using the Megablast version BLASTN 2.2.13 [Nov-27-2005]; the last runs were done with BLASTN 2.2.21 [Jun-14-2009].
-Determining raw expression counts of genes (loci)
The Megablast output was converted to an expression count by the following 4 steps, in this order:
(1) discard a match if its bitscore is 5 or more below the best bitscore that is reached by the respective read
(2) discard a match if it is shorter than 20 bp, or if its edit distance (number of gaps + number of mismatches) is 4 or more, or if the match does not start within the first 3 bases of the read (rationale for the last condition: sequencing quality is best at the 5' end, therefore a true match should cover the 5' end)
(3) discard all matches involving reads that map to more than a single locus (note that a locus can encompass more than a single transcript (cDNA))
(4) for each locus, count the number of different reads that map to it (a single read can map multiple times to a locus if the locus has multiple transcripts: yet, the read will be counted only once at this step)
The count of step (4) is output as a raw expression count.
-Identifying differentially expressed genes
The count data was normalized with edgeR and the package's exact test for the negative binomial distribution was used to compute p-values

source_name: laser dissected shoot apical meristems

growth_protocol:
short days condition (8 hours light, 16 hours darkness)
long days condition (16 hours light, 8 hours darkness)

extract_protocol: RNA extraction, RNA amplification, cDNA synthesis with random primers.

value: after 3 LD induction

value: shoot apical meristems


title: wild type replicate 1

data_processing:
reads_r3s1.txt; genome build: miRBase Release 16
Small RNA sequences were mapped to mature miRNA sequences annotated in miRBase Release 16 (miRBase, http://www.mirbase.org/). The mapping was performed using NextGenMap (FJ Sedlazeck, S Tauber, GB Ewing, and A von Haeseler, submitted) and allowed for up to two mismatches.


title: kidney-AA-4

description: RNA-Seq


title: +3 long day (LD) C


title: +1 long day (LD) B

value: after 1 LD induction


title: +1 long day (LD) C


title: +1 long day (LD) A


title: +0 long day (LD) C

value: before induction


title: +0 long day (LD) A


title: +3 long day (LD) A


title: brain

city: Cambridge

first: Sidi

last: Chen

institute: MIT

description: Trizol-chloroform-Qiagen

data_processing: raw reads only

source_name: dissected whole brains

growth_protocol: standard cornmeal

extract_protocol: standard Illumina mRNA-seq library prep Kit

tag: Stage

value: 1-7d adult

value: whole brains


title: MB_2

description: Trizol-chloroform-Qiagen

source_name: dissected mushroom bodies

value: mushroom bodies


title: MB_1

description: Trizol-chloroform-Qiagen


title: RZd7

city: Durham

first: Jenny

last: Tung

state: NC

address: 125 Science Drive

institute: Duke University

data_processing:
Reads were mapped to the rhesus macaque genome (rhemac2) using the software bismark (http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/) and methylation status at each CpG site was obtained using the bismark methylation_extractor function (masking data from the first three base pairs).
Columns for the bed file represent, respectively: 1) chromosome; 2) base pair coordinate; 3) base pair coordinate + 1; 4) methylated CpGs for individual REm6; 5) total coverage for REm6; 6) methylated CpGs for RGs6; 7) total coverage for RGs6; 8) methylated CpGs for RNf4; 9) total coverage for RNf4; 10) methylated CpGs for RNf6; 11) total coverage for RNf6; 12) methylated CpGs for RZd7; 13) total coverage for RZd7; 14) methylated CpGs for RZp6; 15) total coverage for RZp6.
Note also that coverage for each CpG site integrates both forward reads of that site and reverse reads for the same site.

organism: Macaca mulatta

source_name: PBMC_low ranking individual

extract_protocol: PBMCs were purified using a standard Ficoll gradient and DNA was extracted using the Gentra PureGene kit. Standard Illumina protocol for constructing DNA libraries

tag: rank

tag: age

value: adult

value: peripheral blood mononuclear cells


title: testis_1

description: Trizol-chloroform-Qiagen

source_name: dissected testis

value: testis


title: RZp6

source_name: PBMC_high ranking individual

value: female


title: RGs6


title: RNf4


title: REm6


title: VCS2 AR DHT 4h

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

country: Canada

institute: UNIVERSITY HEALTH NETWORK

description: Chromatin IP against androgen receptor

data_processing:
bed: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the "Model-based Analysis for ChIP-Seq(MACS)" algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: prostate cancer Cells

extract_protocol: Lysates were clarified from digested chromatin and AR-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 200~300 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.

treatment_protocol: Cells were incubated in DMEM supplemented with 5%  charcoal/dextran-treated FBS for 3 days, and then treated with 10nM DHT or Ethanol for 4h

value: DHT for 4h

tag: passages

value: AR

tag: cell line

tag: chip antibody manufacturer

value: Santa Crus

tag: chip antibody catalog #


title: VCaP AR DHT 4h

description: Chromatin IP against androgen receptor

tag: treatment

tag: chip antibody

value: VCaP


title: Ring1B ChIPSeq

city: London

first: Ines

middle: de

last: Santiago

address: Hammersmith Hospital Campus

department: Epigenetics

country: United Kingdom

institute: MRC Clinical Sciences Centre

data_processing:
Ring1B.bw; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using Illumina Eland extended software allowing 2 mismatches and unique reads only. Multiple sequencing runs were merged and used to create bedgraph and bigwig (bw) summary files.

source_name: Undifferentiated ES cells

growth_protocol: Mouse ES-OS25 cells were grown on 0.1% gelatin-coated surfaces in GMEM-BHK21 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 1% MEM non-essential amino acids, 1 mM sodium pyruvate (all from Gibco), 50 μM 2-mercaptoethanol, 1000 U/ml of human recombinant leukaemia inhibitory factor (Chemicon) and 0.1 mg/ml Hygromycin (Roche).

extract_protocol: ChIP-seq libraries were prepared from 10 ng DNA (quantified by Qubit) according to Illumina protocols (Part #11257047 Rev A), with some modifications. Samples were PCR amplified prior to size selection on an agarose gel. Libraries were quantified by Qubit (Invitrogen) and qPCR, and library size was assessed by Bioanalyzer (Agilent).

tag: modification

value: OS25 ES cells

tag: chromatin

value: Fixed

tag: beads

value: Magnetic beads


title: RNAPII S5P Repeat ChIPSeq

data_processing:
RNAPII_S5PRepeat.bw; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using Illumina Eland extended software allowing 2 mismatches and unique reads only. Multiple sequencing runs were merged and used to create bedgraph and bigwig (bw) summary files.

value: RNAPII S5P

value: CTD4H8 (MMS-128P, Covance)

value: Covance

value: Sepharose beads


title: HIF-1beta

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

institute: University of Oxford

description: ChIP DNA

data_processing:
5472_HIF1B_hg18.bigWig; genome build: hg18
Sequences were mapped to NCBI build 36 (hg18) using ELAND software. Subsequent assessment, 2-sample peak finding, motif analysis, and mapping of RCGTG motifs were undertaken using the CisGenome software suite (http://www.biostat.jhsph.edu/~hji/cisgenome/)

source_name: 786-O clear cell renal carcinoma cells

growth_protocol: 786-O cells were purchased from ATCC. Cell lines were grown in Dulbecco’s modified Eagle’s Medium, 100U/ml penicillin, 100μg/ml streptomycin and 10% fetal bovine serum (Sigma).

extract_protocol: Lysates were clarified from sonicated whole cells and immunoprecipitated with andtibodies against HIF-2a (PM9), HIF-1beta (Novus Biologicals, NB100-110), or pre-immune serum. Libraries were prepared from immunoprecipitated chromatin using the Illumina ChIP-Seq kit.

treatment_protocol: Fixed with 1% formaldehyde for 10 minutes at 25 C, followed by 125 mM Glycine for 5 minutes at 25 C.

value: 786-O clear cell renal carcinoma cells


title: HIF-2alpha

description: ChIP DNA

data_processing:
5180_HIF2A_hg18.bigWig; genome build: hg18
Sequences were mapped to NCBI build 36 (hg18) using ELAND software. Subsequent assessment, 2-sample peak finding, motif analysis, and mapping of RCGTG motifs were undertaken using the CisGenome software suite (http://www.biostat.jhsph.edu/~hji/cisgenome/)

value: HIF-2alpha (PM9)


title: RNf6

tag: gender

value: adult

tag: cell type


title: RNAPII S5P ChIPSeq

data_processing:
RNAPII_S5P.bw; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using Illumina Eland extended software allowing 2 mismatches and unique reads only. Multiple sequencing runs were merged and used to create bedgraph and bigwig (bw) summary files.


title: +0 long day (LD) B

tag: developmental stage

value: before induction

value: shoot apical meristems


title: H2Aub1 ChIPSeq

data_processing:
H2Aub1.bw; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using Illumina Eland extended software allowing 2 mismatches and unique reads only. Multiple sequencing runs were merged and used to create bedgraph and bigwig (bw) summary files.

value: E6C5 (Upstate)

value: Upstate

value: Native


title: H3K36me3 ChIPSeq

data_processing:
H3K36me3.bw; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using Illumina Eland extended software allowing 2 mismatches and unique reads only. Multiple sequencing runs were merged and used to create bedgraph and bigwig (bw) summary files.


title: Control MockIP

data_processing:
Control.bw; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using Illumina Eland extended software allowing 2 mismatches and unique reads only. Multiple sequencing runs were merged and used to create bedgraph and bigwig (bw) summary files.

value: Control


title: Pre-immune control

description: ChIP DNA

data_processing:
5179_control_hg18.bigWig; genome build: hg18
Sequences were mapped to NCBI build 36 (hg18) using ELAND software. Subsequent assessment, 2-sample peak finding, motif analysis, and mapping of RCGTG motifs were undertaken using the CisGenome software suite (http://www.biostat.jhsph.edu/~hji/cisgenome/)

value: control


title: RNAPII 8WG16 ChIPSeq

data_processing:
RNAPII_8WG16.bw; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using Illumina Eland extended software allowing 2 mismatches and unique reads only. Multiple sequencing runs were merged and used to create bedgraph and bigwig (bw) summary files.

value: RNAPII 8WG16

value: OS25 ES cells

value: 8WG16 (MMS-126R, Covance)


title: Infiltrative tumor 8, lane 1

first: Christopher

last: Heffelfinger

state: Ct

address: 333 Cedar Street

description: Tumor was extracted via mohs surgery. Total RNA was extracted via mirVana total RNA extraction kit

data_processing: miRExpress was used to collapse raw fastq files into unique tags and number of appearances, and trim adapter sequences from each unique tag (see *merge.trim.txt files). Data table for raw expression was created by aligning sequences to annotated miRNA precursor sequences in miRBase ver 15.0 then the number of hits on each annotated miRNA was calculated.

source_name: Infiltrative Basal Cell Carcinoma

extract_protocol: Illumina Small RNA version 1.5 protocol

value: Basal Cell Carcinoma, infiltrative


title: RNAPII S7P ChIPSeq

data_processing:
RNAPII_S7P.bw; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using Illumina Eland extended software allowing 2 mismatches and unique reads only. Multiple sequencing runs were merged and used to create bedgraph and bigwig (bw) summary files.

**Correction (Mar 14, 2012):
Due to curation error, runs for SRX112177 and SRX112179 switched, specifically,
Run SRR391034.1 was removed from experiment SRX112177 (GSM850468) and added to experiment SRX112179 (GSM850470) as SRR391034.3
Run SRR391040.1 was removed from experiment SRX112179 (GSM850470) and added to experiment SRX112177 (GSM850468) as SRR391040.3

value: RNAPII S7P

value: Fixed

value: Magnetic beads


title: Infiltrative tumor 6, lane 2


title: Infiltrative tumor 5, lane 2


title: Infiltrative tumor 7, lane 1


title: Infiltrative tumor 5, lane 1


title: Infiltrative tumor 4, lane 1


title: Infiltrative tumor 6, lane 1


title: Infiltrative tumor 3, lane 1


title: Infiltrative tumor 1, lane 2


title: Infiltrative tumor 2, lane 1


title: Infiltrative tumor 1, lane 1


title: Infiltrative tumor 3, lane 2


title: Infiltrative tumor 4, lane 2


title: Infiltrative tumor 2, lane 2


title: RNAPII S2P ChIPSeq

data_processing:
RNAPII_S2P.bw; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using Illumina Eland extended software allowing 2 mismatches and unique reads only. Multiple sequencing runs were merged and used to create bedgraph and bigwig (bw) summary files.

**Correction (Mar 14, 2012):
Due to curation error, runs for SRX112177 and SRX112179 switched, specifically,
Run SRR391034.1 was removed from experiment SRX112177 (GSM850468) and added to experiment SRX112179 (GSM850470) as SRR391034.3
Run SRR391040.1 was removed from experiment SRX112179 (GSM850470) and added to experiment SRX112177 (GSM850468) as SRR391040.3

value: RNAPII S2P

value: H5 (MMS-129R, Covance)

value: Covance


title: Infiltrative tumor 7, lane 2


title: Nodular tumor 4, lane 2

source_name: Nodular basal cell carcinoma

value: Basal Cell Carcinoma, nodular


title: Nodular tumor 6, lane 1


title: Nodular tumor 7, lane 2


title: Nodular tumor 2, lane 2


title: Nodular tumor 2, lane 1


title: Nodular tumor 6, lane 2


title: Nodular tumor 8, lane 1


title: Nodular Tumor 1, lane 2


title: Nodular tumor 4, lane 1


title: Nodular tumor 7, lane 1


title: Nodular tumor 3, lane 2


title: Nodular Tumor 1, lane 1


title: RNAPolII ChIP LXRdKO T0901317 replicate 2

status: Public on Jan 31 2012

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: LXR alpha/beta double knockout

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_LXRdKO_T09_repl2.bed: mm9

source_name: C57BL/6 LXRdKO mouse liver

extract_protocol: Chromatin was prepared from snap frozen livers, homogenized in PBS and cross-linked in 1% formaldehyde (10 min, RT). Cross-linked material was added 1M glycine to a final concentration of 0.125 M and incubated for 10 min rotating at RT, pelleted by centrifugation at 400xg for 2 min at 4°C, washed 2x in cold PBS and resuspended in lysis buffer (1% triton, 0.1% SDS, 150 mM NaCl, 2 mM EDTA, 1 mM EGTA, 20 mM Tris, pH 8.0) (200 μl/10 mg chromatin) before sonication according to the manufacturer’s protocol using the Diagenode Bioruptor twin (2x20 cycles, 30 sec. on/off, max. level). Samples were centrifuged for 2 min at 10.000xg and supernatant used for subsequent chromatin IP performed according to standard protocol. ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina).

treatment_protocol: Female C57BL/6 wild-type and LXRα/β-deficient mice (13 weeks of age) were treated by oral gavage once daily for 14 days with the RXR agonist bexarotene (100 mg/kg body weight [mpk], in 1% carboxymethylcellulose), the LXR agonist T0901317 (T09, 30 mpk) or vehicle alone.

tag: strain

value: female

tag: genotype/variation

value: LXRdKO

value: liver

tag: ChIP

value: RNA Polymerase II

tag: antibody catalog #

tag: antibody vendor/provider

value: Diagenode


title: RNAPolII ChIP LXRdKO Control replicate 2

description: LXR alpha/beta double knockout

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_LXRdKO_Control_repl2.bed: mm9

value: Control

tag: tissue


title: RNAPolII ChIP LXRdKO Bexarotene replicate 2

description: LXR alpha/beta double knockout

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_LXRdKO_Bexa_repl2.bed: mm9

value: Bexarotene


title: RNAPolII ChIP LXRdKO Bexarotene replicate 1

description: LXR alpha/beta double knockout

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_LXRdKO_Bexa_repl1.bed: mm9


title: RNAPolII ChIP LXRdKO T0901317 replicate 1

description: LXR alpha/beta double knockout

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_LXRdKO_T09_repl1.bed: mm9


title: OS25 cells mRNA-Seq

data_processing:
mRNA_ESC_OS25.bw; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using RNA implementation of CASAVA 1.6 software allowing 2 mismatches and unique reads only. Multiple sequencing runs per sample were merged and used to create wiggle and bigwig(bw) summary files.

extract_protocol: Total RNA was prepared from ES-OS25 cells by TRIzol extraction using Phase Lock Gel tubes and 8 µg prepared for mRNA sequencing. Quality of total RNA was assessed by bioanalyser before library preparation. The mRNA-seq library was prepared according to Illumina’s instructions (#1004898 Rev A) with some modifications. After selection of polyA-containing mRNA molecules, RNA was further depleted for ribosomal RNA (rRNA) using the Ribominus kit (Invitrogen). The library was quantified by Qubit, and library size was assessed by Bioanalyzer before high-throughput sequencing.

tag: cell line

value: OS25 ES cells


title: P_furiosus_total_small_RNAs

first: Brenton

middle: R

last: Graveley

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

description: Total RNA extracted using standard Trizol extraction. Total RNA fractionated on 10% polyacrylamide gel and size selected to enrich for RNAs of 20-70 nt, treated with thermosensitive alkaline phosphatase, and ligated to a 3' adaptor. Gel purified ligated products were then treated with T4 polynucleotide kinase and ligated to a 5' adaptor. The ligated RNAs were reverse transcribed, treated with RNaseH, and amplified by 16 cycles of PCR.  Samples were sequenced on an Illumina Genome Analyzer IIx for 76 cycles.

data_processing: Reads were trimmed to remove 3' linker sequence and aligned to the reference genome using bowtie-0.12.0-beta1 with parameters -m 1 -v 2 to identify uniquely mapping reads. Plus and minus strand wiggle tracks (bedGraphs) were made from the uniquely aligned reads. Reference genome: pyrFur2

organism: Pyrococcus furiosus

source_name: Cultured organisms

tag: cell

value: Cultured organisms


title: RNAPolII ChIP WT T0901317 replicate 1

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_WT_T09_repl1.bed: mm9

source_name: C57BL/6 wild type mouse liver

value: wild type


title: P_furiosus_Cmr2-associated_small_RNAs

description: RNA was extracted from Cmr2-immunopurified complexes using standard Trizol extraction. Total RNA fractionated on 10% polyacrylamide gel and size selected to enrich for RNAs of 20-70 nt, treated with thermosensitive alkaline phosphatase, and ligated to a 3' adaptor. Gel purified ligated products were then treated with T4 polynucleotide kinase and ligated to a 5' adaptor. The ligated RNAs were reverse transcribed, treated with RNaseH, and amplified by 16 cycles of PCR.  Samples were sequenced on an Illumina Genome Analyzer IIx for 76 cycles.


title: RNAPolII ChIP LXRdKO Control replicate 1

description: LXR alpha/beta double knockout

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_LXRdKO_Control_repl1.bed: mm9


title: RNAPolII ChIP WT Bexarotene replicate 1

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_WT_Bexa_repl1.bed: mm9


title: Nodular tumor 5, lane 1


title: RNAPolII ChIP WT Control replicate 2

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_WT_Control_repl2.bed: mm9


title: RXR ChIP LXRdKO T0901317

description: LXR alpha/beta double knockout

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RXR_dKO_T09.bed: mm9
RXR_dKO_T09_peaks.bed: mm9

value: RXR

value: Santa Cruz


title: RNAPolII ChIP WT Control replicate 1

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_WT_Control_repl1.bed: mm9


title: Nodular tumor 3, lane 1


title: RXR ChIP LXRdKO Bexarotene

description: LXR alpha/beta double knockout

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RXR_dKO_Bexa.bed: mm9
RXR_dKO_Bexa_peaks.bed: mm9


title: RXR ChIP WT Bexarotene

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RXR_WT_Bexa.bed: mm9
RXR_WT_Bexa_peaks.bed: mm9


title: RXR ChIP LXRdKO Control

description: LXR alpha/beta double knockout

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RXR_dKO_Control.bed: mm9
RXR_dKO_Control_peaks.bed: mm9


title: LXR ChIP WT T0901317

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
LXR_WT_T09.bed: mm9
LXR_WT_T09_peaks.bed: mm9

value: LXR

value: Jakobsson et al. 2009


title: RXR ChIP WT T0901317

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RXR_WT_T09.bed: mm9
RXR_WT_T09_peaks.bed: mm9


title: LXR ChIP WT Control

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
LXR_WT_Control.bed: mm9
LXR_WT_Control_peaks.bed: mm9


title: PPARalpha ChIP WT Control

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
PPARa_WT.bed: mm9
PPARa_WT_peaks.bed: mm9

value: PPARalpha


title: LXR ChIP WT Bexarotene

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
LXR_WT_Bexa.bed: mm9
LXR_WT_Bexa_peaks.bed: mm9


title: RNAPolII ChIP WT T0901317 replicate 2

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_WT_T09_repl2.bed: mm9


title: Snyder_CES1_GFP_L3_rep1 extraction1_seq1 aliquote 1

first: DCC

last: modENCODE

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

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: eGFP;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
The current ChIP Protocol is modified from Ercan et al., Nature Genetics 39: 403-408 (2007). Worm samples are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents. The cellular debris is removed by centrifugation and the supernatant containing any formaldehyde crosslinked chromatin is saved for preparing input DNA and collecting immunocomplexes. 10% (or 50 ul) of the above supernatant from each sample is saved as input sample (control). Input sample (also known as whole cell extract) represents the total genomic DNA and is processed later (treated with RNAase A, proteinase K and reverse crosslink steps) along with the ChIPed samples to isolate genomic DNA (input DNA). The remaining supernatant is incubated with affinity-purified anti-GFP antibodies and Protein G-sepharose beads to collect the immunocomplexes containing a targeted transcription factor that is C-terminally tagged with GFP and its genomic binding fragments. Alternatively, the 8WG16 mouse monoclonal antibodies and Protein A-sepharose beads are used to collect the immunocomplexes containing RNA polymerase II. After extensive washing, any immunocomplexes are eluted and the protein-DNA crosslinks are reversed. The degree of sonication is assessed by running a small aliquot of DNA on a 2% agarose gel. Quantitative PCR is used to check if the ChIPed sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

value: OP174(official name :OP174 genotype :unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by :S. Kim )

tag: genotype

tag: Sex

value: Hermaphrodite


title: Snyder_GEI-11_GFP_L3_rep1 extraction1_seq1 aliquote 1

description: ChIP DNA;Antibody information listed below: official name: Anti-eGFP;target name: Enhanced Green Fluorescent Protein;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.;

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS190

value: OP179(official name :OP179 genotype :unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by :R. Waterston )


title: Snyder_CES1_GFP_L3_rep2 extraction1_seq1 aliquote 1

value: unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119)


title: RNAPolII ChIP WT Bexarotene replicate 2

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RNAPII_WT_Bexa_repl2.bed: mm9

value: female

tag: treatment

value: liver


title: Snyder_GEI-11_Input_L3_rep2 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_CES1_Input_L3_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_GEI-11_GFP_L3_rep2 extraction1_seq1 aliquote 1


title: Snyder_CES1_Input_L3_rep2 extraction1_seq1 aliquote 1

description: input DNA


title: Mutant ΔMCS-P6MCS-R3-/- Murine erythroid cells mRNA-seq

status: Public on Jan 30 2012

first: Monika

middle: S

last: Kowalczyk

state: Oxfordshire

address: Headley Way

department: MRC Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine, University of Oxford

description: instrument model: Model- GAIIx  Chemistry-SBS v4  cBot single generation kit with v4 flow cell  SCS 2.8  RTA 1.8  Recipe v7.4

data_processing: Bcl conversion to Qseq files using OLB v1.8.0  Gerald- using Eland alignment to produce sequence and export files (carried out by CASAVA 1.7.0)  Reads were mapped to the mm9 mouse genome build using TopHat 1.1.1b .  Transcript abundances and differential expression were tested using Cufflinks and Cuffdiff using current Ensembl transcript ID and Refseq gene annotation. Gene ontology analysis was performed using DAVID (http://david.abcc.ncifcrf.gov/content.jsp?file=functional_annotation.html#intro).

source_name: erythroid cells (fetal liver culture)

growth_protocol: Erythroid cells were grown from fetal livers following published protocol (Dolznig et al., 2001).

extract_protocol:
Total RNA was prepared using Trizol reagent (Sigma) and DNaseI treated (Ambion). The RNA quality was assessed using Agilent Bioanalyser. RNA with overall RIN score >9 was used for further procedures. poly(A)+ mRNA was isolated from total RNA using PolyA selection kit (Promega) according to the manufacturer’s protocol. poly(A)+ mRNA from erythroid cells was depleted of globin transcripts using GlobinClear (Ambion). The quality of obtained RNA samples was assessed using PicoChip (Agilent).
cDNA libraries were prepared from poly(A)+ mRNA from ΔMCS-P6MCS-R3-/- erythroid cells (fetal liver culture) and wild-type Ter119+ cells using the mRNA-Seq pair-end kit (Illumina) and then sequenced using massively parallel sequencing (Illumina, GAII) with 50 base paired-end reads.

value: CBA/C57BL/6 mixed

value: erythroid cells (fetal liver culture)


title: wild type Murine Ter119+ mRNA-seq

source_name: Ter119 positive Cells

growth_protocol: Mouse primary erythroid cells were sorted from the spleens of acetylphenylhydrazine-treated mice based on the expression of Ter119 (Spivak et al., 1973; Vernimmen et al., 2009).

value: Wild type


title: RXR ChIP WT Control

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RXR_WT_Control.bed: mm9
RXR_WT_Control_peaks.bed: mm9

value: Control


title: Sample6

status: Public on Jan 25 2012

city: Leiden

first: Anastasios

last: Mastrokolias

address: LUMC, Building 2 Einthovenweg 20 2333 ZC Leiden

country: Netherlands

institute: Leiden University Medical Center

data_processing: The FASTQ files were analysed using the open source GAPSS_B(v2) pipeline (www.lgtc.nl\GAPSS). All sequences were trimmed to 17 base pairs to remove the first lower quality base pair from the 3' end of the sequences. After trimming, the NlaIII recognition site (CATG) was added to the 5' end of the sequence to create the complete 21-22mer nucleotide sequences. Sequences were aligned using the Bowtie short read aligner (version 0.12.7) against the UCSC hg19 reference genome, allowing for a maximum of one mismatch and a maximum of two possible positions in the genome (options: -k 1 -m 2 -n 1 --best --strata –solexa1.3-quals).A custom Perl script was used to create reference region files from the SAGE region files that were composed of the overlapping tags from all samples. A second Perl script was then used to link all individual region files to the reference region file, reporting the number of tags in each individual region of the reference region file. Finally, the reference region file was annotated with transcript information using BIOMART (Ensembl build 60). For all reported downstream statistical and biological analysis only sequences aligned to known exons were used.  Analyses were performed at the gene level, and in case of multiple SAGE tags per gene, e.g. as a consequence of alternative polyadenylation, tags were summed.

source_name: untreated whole blood

growth_protocol: Samples from six healthy individuals of Caucasian decent  (4 females, 2 males) aged from 39 to 70 years old were collected after informed consent and with ethical approval. Whole blood was drawn into PAX gene tubes (Qiagen, Venlo, The Netherlands) and inverted 10 times. Samples were allowed to equilibrate at room temperature for 2 hours, placed at -20oC overnight and stored at -80oC until further processing. Before total RNA extraction, samples were thawed overnight at 4oC and total RNA was isolated using the PAX RNA isolation kit following the manufacturer’s instructions, including DNAse treatment. RNA quality and the RIN values were determined using the RNA Nano LabChip assay (Agilent Technologies, Santa Clara, CA, USA). The concentration of each sample was validated using the Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA)

extract_protocol: SAGE libraries were produced according to the Illumina protocol for digital gene expression tag profilling with Nlaii.  In short, after hybridization of 1μg total RNA to polydT magnetic beads (Dynabeads, Invitrogen Life Technologies, Carlsbad, CA, USA), first and second strand synthesis was performed. The beads attached to the double stranded DNA were digested with NlaIII restriction endonuclease to produce short double stranded constructs starting at the most 3’ CATG of the transcript. After ligation of the GEX adapter 1, the construct was digested with MmeI to create a 21 base pair fragment downstream of the GEX adapter 1. This fragment was then ligated to GEX adapter 2 to complete the cassette. The adaptor ligated constructs were amplified by 15 cycles of PCR and the products were loaded on 6% Novex TBE precast acrylamide gels (Invitrogen). The 96 base band corresponding to the NlaIII construct was excised and purified from the gel slice using the soak and crush method followed by ethanol precipitation. Sample quality was checked on a DNA 1000 LabChip (Agilent). Sequencing was performed at the Leiden Genome Technology Center on Illumina GA2 sequencer (Illumina, San Diego, CA, USA). Purified samples were diluted to 10nM and loaded on a single lane of the flow cell where, after cluster amplification, samples were put through an ultra short 18 cycle sequencing run.

treatment_protocol: From each sample, 1.5 µg of RNA was treated using the GLOBINclear™ Human Kit (Ambion, Austin, TX, USA) according the manufacturer’s instructions. The kit contains 10 globin sequence specific biotinylated oligonucleotides (http://www.freepatentsonline.com/y2006/0257902.html). Transcripts hybridized to the oligonucleotides are removed through streptavidin magnetic beads. Concentration and quality of the samples were checked as described above.

value: whole blood


title: Sample6Reduced

source_name: globin reduced blood


title: Sample4Reduced


title: Sample5


title: Sample4


title: Sample1Reduced


title: Sample5Reduced


title: Sample3


title: Sample2Reduced


title: Sample2


title: Sample3Reduced


title: Snyder_GEI-11_Input_L3_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: AtLerCentralCell_wildtype_1

status: Public on Jan 26 2012

city: Glarus

first: Marc

middle: William

last: Schmid

address: Hauptstrasse 34

country: Switzerland

institute: MWSchmid GmbH

data_processing: In short: alignment of the reads to the genome, files are TopHat output. Potential sequencing errors were corrected using the SOLiD Accuracy Enhancement Tool (solidsoftwaretools.com). The corrected reads were aligned to the Arabidopsis thaliana reference genome (TAIR10) using TopHat (version 1.2, DOI:10.1093/bioinformatics/btp120), which is designed to identify previously undescribed splice junctions. To avoid a potential underestimation of expression levels of gene family members with similar transcript sequences we allowed up to ten alignments per read. The alignments of those reads were then weighted based on the number of uniquely aligned reads in the neighborhood. We used the total number of hits mapping to the transcripts of a locus as expression value for the locus. Hits mapping to more than one locus (ambiguous hits) were proportionally distributed based on the number of unambiguous hits. Loci with transcripts having less than five hits or no hit located within the 250 bps at the 3â end were discarded, the others declared as being expressed. [see publication for details]

source_name: central cells isolated with LAM

extract_protocol: DOI:10.1038/NMETH.1315. In short, mRNA is reverse transcribed to cDNA with poly(T)-primers fused to anchor sequences for PCR amplification. After PCR amplification, cDNA is sheared and amplified again after the ligation of the sequencing adapters.

tag: ecotype

value: Landsberg erecta

value: mature female gametophyte

value: central cell


title: AtLerCentralCell_wildtype_2


title: Sample1


title: LIN9_ChIPSeq_HeLa_Rep1

first: Subhashini

last: Sadasivam

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Insitute

description: Chromatin IP DNA

data_processing:
Base calling and mapping of the 36-bp reads to the human genome (Build 37, hg19) was done using Bowtie using very strict alignment criteria: only perfect matches (-n 0) and only unique alignments (-m 1). Enriched genomic regions from ChIP-Seq experiments were determined using CisGenome version 1.2 by two-sample analysis using the Input signal as negative control.
The ChIP-Seq libraries were used for cluster generation and single-end sequencing (36-bp reads) using the Genome Analyzer II (Illumina) following the manufacturer's protocol.

source_name: HeLa cell line

growth_protocol: Asynchronously growing HeLa cells

extract_protocol:
ChIP protocol is modified from Rayman et al, 2002. The purification and extraction of ChIP DNA from the IPs is described in the protocol (pdf file) attached to the Series record. Briefly, it involves purification using the Qiagen QiaQuick PCR purification columns (Cat. No. 28104). The LIN9 antibody used in ChIP was manufactured in-house in collaboration with Bethyl labs. The B-Myb antibody used in ChIP was from Bethyl labs, Cat. No. A301-656A. The average insert size of the ChIP-Seq libraries was 150-300 bp including adapters, 50-150 without adapters, as determined by running 1 ul of the library on the Agilent BioAnalyzer.
Chromatin from HeLa cells was used to immunoprecipitate B-Myb or LIN9 using specific antibodies. From ~30 ng of chromatin IPed DNA or input DNA, libraries were prepared using Illumina's ChIP-Seq sample prep kit. ChIP-Seq DNA libraries were quantified using Nanodrop (Thermo-Scientific) and a sharp peak at 200-400 nt was confirmed on the BioAnalyzer (Agilent) before sequencing. Diluted libraries were used for cluster generation and single-end sequencing using the Genome Analyzer II (Illumina).

value: HeLa cell line

tag: chip antibody


title: BMyb_ChIPSeq_HeLa_Rep1

description: Chromatin IP DNA

value: B-Myb


title: BMyb_ChIPSeq_HeLa_Rep2

description: Chromatin IP DNA


title: LIN9_ChIPSeq_HeLa_Rep2

description: Chromatin IP DNA


title: Input_ChIPSeq_HeLa_Rep1

description: Chromatin IP DNA


title: Input_ChIPSeq_HeLa_Rep2

description: Chromatin IP DNA


title: UNC_FaireSeq_HeLa-S3_IFNg4h

status: Public on Jan 24 2012

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

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

tag: datatype

value: FaireSeq

tag: datatype description

value: FAIRE-seq Open Chromatin

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_HelaS3,p-value cutoff:0.05

tag: replicate

tag: cell organism

value: human

tag: cell description

value: cervical carcinoma

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: Interferon gamma treatment - 4 hours with 5 ng/ml (Crawford)

value: align_on_cluster_bwa.pl v 1

tag: replicate description

value: tier 1


title: UNC_FaireSeq_GM12878

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

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_GM12878,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: normal

value: mesoderm


title: total amplified RNA, globular Col/Ler embryos, sample # MC_ColLer_2

data_processing: 50 base reads generated by SOLiD v3 were aligned to the TAIR8.0 version of the Arabidopsis Col genome using the SOLiD™ System Analysis Pipeline Tool (Corona Lite 4.0r2.0, Applied Biosystems, USA), allowing up to 4 color-space mismatches with the additional rule “count valid adjacent errors as single errors”. For transcriptome profiles, reads were excluded if they mapped to more than one genomic position, mapped at splice junctions or were partially overlapping. Consequently, full-length reads uniquely mapping inside a transcript were taken.

source_name: embryos (dissected)

growth_protocol: Plants were grown under 16h light.

extract_protocol: 1-RNA extraction: PicoPure RNA Isolation Kit (Arcturus). 2-RNA amplification: WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies, USA) producing single-stranded cDNA. 3- Second strand synthesis: poly-A tails added using Terminal Transferase (New England Biolabs, USA) in presence of dATPs (1 PCR cycle using Ex Taq Polymerase , (TaKaRa, Japan), and oligo(dT)12-18   primers (Invitrogen).  4-Library preparation:  from 500 ng ds cDNA, Covaris S2 system (Covaris, Inc.),  sheared into 80–130 bp   fragments , DNA ends were repaired and ligated to SOLiD P1 and P2 adaptors, followed by enrichment by PCR (7 cycles) and a size selection on gel

tag: Stage

value: globular embryo stage with suspensor (partial)

tag: maternal strain

value: Columbia_0 (Col0)

tag: maternal genotype/variation

value: wildtype

tag: paternal strain

value: Landsberg erecta (Ler)

tag: paternal genotype/variation


title: UNC_FaireSeq_GM19239

tag: datatype

value: FaireSeq

value: FAIRE-seq Open Chromatin

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: M


title: UNC_FaireSeq_HeLa-S3_IFNa4h

tag: datatype description

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_HelaS3,p-value cutoff:0.05

value: human

value: cervical carcinoma

value: cancer

value: ectoderm

value: F

tag: treatment

value: 4 hours of 500 U/ml Interferon alpha (Crawford)


title: UNC_FaireSeq_HepG2

value: hepatocellular carcinoma

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_HepG2,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: liver carcinoma

value: endoderm

value: align_on_cluster_bwa.pl v 1

value: tier 1


title: UNC_FaireSeq_Medullo

source_name: Medullo

value: FaireSeq

value: FAIRE-seq Open Chromatin

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.1

tag: replicate

tag: cell organism

value: medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997)

value: U


title: UNC_FaireSeq_GM18507

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,1% ENCODE array platform validation tests,p-value cutoff:0.1

value: human

tag: cell description

value: lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: mesoderm

value: M


title: UNC_FaireSeq_Urothelia

source_name: Urothelia

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_female,p-value cutoff:0.1

value: primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene

tag: cell karyotype

value: normal

value: F


title: UNC_FaireSeq_K562

value: baseAlignCounts.pl v 1,1% ENCODE array platform validation tests,p-value cutoff:0.05,fseq v 1.84, iff_K562

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: cancer

tag: cell lineage

tag: cell sex


title: UNC_FaireSeq_NH-A

source_name: NH-A

tag: lab

value: UNC

tag: lab description

value: Lieb - University of North Carolina

value: FaireSeq

value: FAIRE followed by sequencing

tag: cell

value: NH-A

value: astrocytes (also called Astrocy)

value: ectoderm

value: align_on_cluster_bwa.pl v 1

tag: replicate description

value: tier 1


title: UNC_FaireSeq_PanIslets

source_name: PanIslets

value: FAIRE-seq Open Chromatin

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,Lieb Lab peaks

value: human

value: pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005)

value: endoderm

value: M


title: UNC_FaireSeq_GM12891

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.1

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: mesoderm


title: UNC_FaireSeq_A549

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: cancer


title: UNC_FaireSeq_H1-hESC

growth_protocol: missing

value: FaireSeq

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: embryonic stem cells

value: normal

value: inner cell mass


title: UNC_FaireSeq_Urothelia_UT189

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_female,p-value cutoff:0.1

value: primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene

value: F

tag: treatment description

value: UT189 E.Coli treatment 1 hour, followed by 24 hour incubation

value: align_on_cluster_bwa.pl v 1

value: tier 1


title: UNC_FaireSeq_HeLa-S3

value: FAIRE-seq Open Chromatin

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_HelaS3,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: human

value: cervical carcinoma

value: ectoderm


title: PPARalpha ChIP LXRdKO Control

description: LXR alpha/beta double knockout

data_processing:
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4  with the parameters -subpeaks 0.1 and -trim-peaks 0.3.  All peaks with less than 10 overlapping reads were discarded.
Genome Build:
PPARa_dKO.bed: mm9
PPARa_dKO_peaks.bed: mm9

tag: strain

tag: gender

value: female

tag: genotype/variation

value: LXRdKO

value: Control

tag: tissue

value: liver

tag: ChIP

value: PPARalpha

tag: antibody catalog #

tag: antibody vendor/provider

value: Santa Cruz


title: UNC_FaireSeq_HTR8svn

tag: datatype

value: FaireSeq

tag: datatype description

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_female,p-value cutoff:0.1

tag: replicate

tag: cell organism

value: trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo

value: normal


title: UNC_FaireSeq_K562_OHUrea

treatment_protocol: OHUrea

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_K562,p-value cutoff:0.1

tag: cell description

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

tag: cell karyotype

value: cancer

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: treatment

value: OHUrea

value: 100 uM Hydroxyurea for 72 hours

value: align_on_cluster_bwa.pl v 1


title: UNC_FaireSeq_GM12892

value: FAIRE-seq Open Chromatin

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_female,1% ENCODE array platform validation tests,p-value cutoff:0.1

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

tag: replicate description

value: tier 1


title: UNC_FaireSeq_Gliobla

source_name: Gliobla

value: FaireSeq

value: Gliobla/Input

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_H54,p-value cutoff:0.1

value: glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID:7252524)

value: ectoderm

value: U


title: UNC_FaireSeq_K562_NaBut

treatment_protocol: NaBut

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_K562,p-value cutoff:0.1

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: cancer

value: NaBut

tag: treatment description

value: 0.5 mM Sodium Butyrate for 72 hours


title: Reference Epigenome: ChIP-Seq Input from BMP4 Mesendoderm Cells; renlab.Input.BMP4M.04.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK312
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11185
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11184
****************
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: GSM864802_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Input.AK312.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.BMP4M.04.01.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK312, 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.12849
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,989,073
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.1083
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2888
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8719
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4296
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM864802_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Input.AK312.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.BMP4M.04.01.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK312, 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.12858
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 7
BROWSER_TRACK_NAME: HBDM Input 12
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK312 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,989,073
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.1083
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2888
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8719
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4296
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.Input.BMP4M.04.01

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

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

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

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

tag: passage

tag: medium

tag: Sex

value: Male

tag: batch

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms