title: Total PolII (N20) mouse ES

status: Public on Jun 12 2012

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

data_processing:
Pre-processing and pipeline  All DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the  mouse 2007 (mm9, build 37) or human (hg18, build 36.1) genomes using the integrated Eland  software. The Eland output files provide tag sequences, scores and coordinates. For  experiments with multiple sequencing lanes (technical replicates), these files were directly  merged and then processed as described. As pre-filtering steps, only non-ambiguously mapped  tags were used for further processing. A threshold based on the number of sequenced tags  (Nseq) has been set up as Nseq/7,000,000. All regions with a number of repeated tags (with  identical sequences/coordinates) above this threshold were filtered out to remove possible  sequencing and/or alignment artefacts. Remaining tags were processed using a custom R  pipeline, employing the ShortRead library.
Tag extension and Wiggle file generation  In order to accurately represent and further process the ChIP-seq and input control signals, the  Watson and Crick strand tags need to be merged after elongation/size extension to the gel  purified fragment size. The optimal elongation size of each ChIP-seq experiment was estimated  in-silico by employing a step-wise 10bp chromosomal sequence tag shifting and score  multiplication. Tag coordinates were subsequently elongated according to this estimated DNA  fragment size, corresponding to the tag shift maximizing the score. Then, a nucleotide score  representing the genome-wide overlap of elongated tags was computed across both strands.  Wiggle files for genome-wide scores were generated following a binning step, calculating the  average score every 50bp.
ChIP-Seq artefact removal, normalization and input subtraction  Due to the size of the genome and relative low frequencies of binding events, we assume that  more than 90% of the obtained scores from the ChIP-seq experiments represent a background  (BG) level. We therefore used the genome-wide average score in each experiment to estimate  the BG level. Using these average scores, it is possible to rescale the scores accordingly, acting  as normalization and reducing the inter-experiment differences due to effects of different  sequencing depths and/or fragment sizes.  Furthermore we employed an input subtraction step for each experiment using the normalized  file for the input control. This not only allows for correction of overrepresentations of certain  genomic regions due to possible (un-) favorable events during sonication and/or DNA  sequencing, but also serves to reduce the signal/noise ratio especially for experiments with low  enrichment values.
Genome_build: Human samples : HG18
Genome_build: Mouse samples : MM9
Supplementary_files_format_and_content: 50bp binned WIG files generated with a custom R pipeline represent the average local enrichment in the genome of studied feature. A specific pipeline (previously described) has been used to generate midpoint wig files from Mnase experiments. For TSS RNA, strand specific transcripts were separated prior to wig generation.

source_name: Mouse ES-cells

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS),  100U/ml penicillin, 100mg/ml streptomycin and 2mM L-glutamine (Gibco/Invitrogen) at 37°C and  5% CO2. For the removal of Pol II, cells were treated with 2.5 μg/ml of α-amanitin for the  indicated time points for the WT Raji cells. We checked for cell survival that was still above 90%  that was still above 90% after 36h of treatment.  For primary thymocytes, thymuses were  extracted from wild-type C57BL/6 mice (5-6 weeks) and kept on ice in RPMI 1640 medium  (Invitrogen, USA) with 10% FCS for a maximum of one hour. Animals were sacrificed in  accordance with our institutional as well as European guidelines. Single cell suspensions were  obtained by filtering through a 70μm nylon mesh (BD Biosciences, USA). Murine Bruce4 ES  cells (Bl6) were grown as described(1) on a layer of mouse embryonic fibroblasts feeder cells  (PMEF) in the presence of leukemia inhibitory factor (LIF) on gelatinised plates.

extract_protocol: Chromatin Preparation (ChIP):  EDTA-free protease inhibitors (Roche, France) were added to all washing buffers to a final  concentration of 1x together with 0.2mM PMSF and 1μg/ml pepstatin. Aliquots of 5x107 cells  were lysed after resuspension in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA  pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at  4°C. Chromatin was collected by centrifugation for 5 minutes at 4°C and 1.350g in a tabletop  centrifuge, and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8,  10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was collected,  resuspended in 1.5ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM  NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000  (Misonix Inc, USA) sonicator for 10 cycles in the case of thymocytes, 12 cycles for ES cells and  14 cycles in the case of Raji cells (30 seconds on, 30 seconds off, amplitude 40) with the tubes  submerged in ice-cold sonication solution (500mM NaCl, 20% ethanol). After the addition of  Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at  20.000g and 4°C for 20 minutes. For batch processing, supernatants were combined, mixed  thoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at  -80°C until use and 50μl aliquots were taken to serve as input controls.  Inputs were combined with an equal volume of 2x elution buffer (100mM Tris pH 8, 20mM EDTA  pH 8, 2% SDS) and incubated overnight in a water bath at 65°C for 13-15 hours. SDS was then  diluted by the addition of an equal volume of TE (10mM Tris pH 8, 1mM EDTA pH 8) and RNA  was digested by RNase A at a final concentration of 0.2μg/ml at 37°C for 2 hours. Samples  were subsequently Proteinase K treated at 55°C for two hours at a final concentration of  0.2μg/ml. DNA was purified by two subsequent phenol:chloroform:isoamylalcohol (25:24:1, pH  8) extractions and followed by a Qiaquick purification (PCR purification columns, Qiagen,  Germany). To ensure greater DNA purity, columns were washed twice with PE buffer and eluted  in 50μl H2O. DNA concentration was measured using a Nanodrop 1000 (Thermo Scientific,  France) and 500ng were run on 2% agarose gels to verify sonication efficiencies or alternatively  2ng using High Sensitivity DNA chips on a 2100 Bioanalyzer.  ChIP-Seq:  All experiments were performed using Dynabeads (Invitrogen, USA) coated with Protein-G. For  biological replicates, all steps were repeated using a biologically independent sample as  described above. Beads were washed 3x with 1ml and subsequently resuspended in 250μl of  blocking solution (0.5% BSA in 1x DPBS). After the addition of the antibody, the beads were  incubated at 4°C overnight on a rotating wheel. Unbound antibodies were removed through  three further washes with 1ml of blocking solution. Beads were resuspended in 100μl of  blocking solution, extracts were added and the mix was incubated overnight at 4°C on a rotating  wheel.  EDTA-free protease inhibitors (Roche) were added to all washing buffers to a final concentration  of 1x together with 0.2mM PMSF and 1μg/ml pepstatin. Beads were washed 8 times in RIPA  buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA pH 8, 1% NP-40, 0.7% Na-  Deoxycholate) and once in TE+ (10mM Tris pH 8, 1mM EDTA pH 8, 50mM NaCl).  Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps  at 65°C for 15 and 10 minutes in 110μl and 100μl of elution buffer (50mM Tris pH 8, 10mM  EDTA pH 8, 1% SDS) respectively. The two eluates were combined and incubated at 65°C  overnight (13-15 hours) for crosslink reversal. DNA was purified as described for the input (see  Supplemental Table 1 for a summary of ChIP conditions for each experiment).  Prior to sequencing, ChIP DNA was quantified using the picogreen method (Invitrogen, USA)  using input dilutions as standards, or by running 20% of the ChIP material on a High Sensitivity  DNA chip on a 2100 Bioanalyzer. At least 1ng of ChIP or input DNA was used for library  preparation according to the Illumina ChIP-seq protocol (see Supplemental Table 1 for  quantities obtained for each experiment). After end-repair and adapter ligation, fragments were  size-selected (cut) on an agarose gel prior to preamplification and clustering. The size-selected  and preamplified fragments were verified on a 2100 Bioanalyzer (Agilent, USA) before  clustering and 36 cycle sequencing on a Genome Analyzer II (Illumina, USA) according to  manufacturer’s instructions.

treatment_protocol: Raji cells were directly crosslinked in 25ml of growth medium and thymocytes were  resuspended in 25ml of DPBS. ES cells were trypsynised and separated from feeders prior to  crosslinking. For RNA-seq experiments, the crosslinking and quenching steps were omitted.  Crosslinking was performed with the addition of 1/10th volume of crosslinking solution (11%  formaldehyde, 100mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 50mM Hepes pH 7.8) for a  final formaldehyde concentration of 1% for 10 minutes at room temperature. The reaction was  quenched with the addition of 250mM glycine and incubation at room temperature for 5 minutes.  Cells were washed twice with cold DPBS and counted using a Vi-CELL cell counter (Beckman  Coulter, France). Cells were snap-frozen in liquid nitrogen in aliquots of 5x107cells/pellet.  T-cells were sorted using the AutoMACS (Miltenyi, France) system. After labelling with anti-CD8  antibodies coupled to PE (Miltenyi, France), cells were incubated with anti-PE multisort  magnetic beads (Miltenyi, France) according to manufacturer’s instructions. Sorting was  performed using a single positive selection. Cells were released and incubated with anti-CD4  magnetic beads (Miltenyi, France) according to manufacturer’s instructions. After a subsequent  single positive selection, sorting efficiency was verified through flow cytometry analysis. Sorted  CD4+/CD8+ thymocytes were counted and snap-frozen in liquid nitrogen in aliquots of 5x107  cells/pellet for further processing.

tag: passages

tag: developmental stage

value: PolII

tag: vendor/catalog#

value: Santa Cruz/sc-899x


title: Fragment 2 4C PCR of tL(UAA)B2 tRNA replaced with SUP4-1 containing MspI fragment

status: Public on Jun 14 2012

type: SRA

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description:
PCR Product: Nested inverse PCR primers were designed to amplify out of the "bait" MspI fragments that contained the intact tL(UAA)B2 or tL(CAA)G3 tRNA genes and the SUP4-1 replacement mutants.
Circular chromosome conformation capture of wildtype and two tRNA replacement mutants
Processed data file: yPH499-yDP77_dat_and_datcomb.txt
Processed data file: yPH77-yDP84_dat_and_datcomb.txt

library_source: genomic

data_processing:
Sequences were mapped onto the S. cerevisiae S288c genome sequence [June 2008 (SGD/sacCer2) assembly] using Topography v1.19. For analysis Fragment 1 and Fragment 2 need to be concatenated for each mutant and the unknown sequence ligated to the forward primer of fragment 1 needs to be re assigned to the forward primer of fragment 2. The same needs to be performed for the reverse primer of fragment 2 needs to be re-assigned to the reverse primer of fragment 1. This is because the SUP4-1 element which has replaced the wild type tRNA is a repetitive element meaning that during the Topography program analysis the 4C fragment cannot be uniquely positioned upon the reference genome without these reassignments.
Processed data file type: Alignment - Topography 1.19 Proprietary Software Output (see supplementary files on the Series record).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: S. cerevisiae strains (i.e. WT: yPH499, Mutants: yDP77 and yDP84) were grown (30oC, 160 rpm) to an OD600 = 0.6 in synthetic complete media containing amino acid supplements and glucose (2% w/v).

extract_protocol: Circular Chromosome Conformation Capture (4C): Cells were cross-linked (2% v/v formaldehyde, 10 mins, room temperature, with stirring) and quenched (0.125M glycine). Samples (residuals of 108 cells in 52.6ul) were digested (37°C, 2hr) with MspI (100U, Fermentas) in a final volume of 100 ml.  MspI was inactivated by the addition of 1% SDS (final v/v) and incubation (65°C, 20mins). Reactions were diluted in 2ml T4 ligation buffer (NEB) containing 1% Triton X-100. T4 DNA Ligase (20U, Invitrogen) was added and the reaction incubated (16°C, 2hrs). Samples were reverse cross-linked (65°C, O/N) in the presence of Proteinase K (7-11ug, Roche), 20ul EDTA (0.5M), 12ul NaCl (5M), 1.2ul Tris-HCl (1M).  RNase (20ug) was added and incubated (37°C, 15mins) prior to three Phenol:Chloroform (1:1) extractions.  Samples were purified by ethanol precipitation using LPA as a carrier. Nested inverse PCR primers were designed to amplify out of the "bait" MspI fragments that contained the intact tL(UAA)B2 or tL(CAA)G3 tRNA genes and the SUP4-1 replacement mutants. PCR conditions were as follows 1) first round (95°C, 2:00 min; 35x [95°C, 0:30 sec; 59°C, 0:30 sec; 72°C, 2:00 sec]; 72°C, 5:00) and 2) nested second round (95°C, 2:00 min; 35x [95°C, 0:30 sec; 62°C, 0:30 sec; 72°C, 2:00 sec]; 72°C, 5:00). The primer annealing temperatures for fragment 1 and 2 of the yDP77 strain were 68.1°C and 60°C, respectively. Nested primers contained unique 6 bp tags (TCTCTG [yPH499 wild type arrangement of the yDP84 strain], TGATGC [yDP84 fragment 1], and AGCACG [yDP84 fragment 2], AGAGAC [yPH499 wild type arrangement of the yDP77 strain], ACAGAG [yDP77 fragment 1], TAGATC [yDP77 fragment 2]) to enable pooling of the 4C PCR products for sequencing (100 bp paired end) on an Illumina Genome Analyser (Allan Wilson Centre, Massey University).

tag: strain

tag: genotype/variation

value: Mutant

tag: unique 6 bp tags to enable pooling of 4c pcr products for sequencing

value: TAGATC


title: MnaseSeq mouse ES

data_processing:
Pre-processing and pipeline  All DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the  mouse 2007 (mm9, build 37) or human (hg18, build 36.1) genomes using the integrated Eland  software. The Eland output files provide tag sequences, scores and coordinates. For  experiments with multiple sequencing lanes (technical replicates), these files were directly  merged and then processed as described. As pre-filtering steps, only non-ambiguously mapped  tags were used for further processing. A threshold based on the number of sequenced tags  (Nseq) has been set up as Nseq/7,000,000. All regions with a number of repeated tags (with  identical sequences/coordinates) above this threshold were filtered out to remove possible  sequencing and/or alignment artefacts. Remaining tags were processed using a custom R  pipeline, employing the ShortRead library.
Tag extension and Wiggle file generation  In order to accurately represent and further process the ChIP-seq and input control signals, the  Watson and Crick strand tags need to be merged after elongation/size extension to the gel  purified fragment size. The optimal elongation size of each ChIP-seq experiment was estimated  in-silico by employing a step-wise 10bp chromosomal sequence tag shifting and score  multiplication. Tag coordinates were subsequently elongated according to this estimated DNA  fragment size, corresponding to the tag shift maximizing the score. Then, a nucleotide score  representing the genome-wide overlap of elongated tags was computed across both strands.  Wiggle files for genome-wide scores were generated following a binning step, calculating the  average score every 50bp. In order to score for the nucleosome midpoint, we performed a shift  for the extreme 5’ and 3’ tag scores based on half of the estimated elongation size. The  nucleotide score is only taking in account the first base of sequenced tags. For the RNA-Seq  experiment, the elongation step was omitted and separate Wiggle files for the Watson and Crick  strand were generated using 50bp bins.
ChIP-Seq artefact removal, normalization and input subtraction  Due to the size of the genome and relative low frequencies of binding events, we assume that  more than 90% of the obtained scores from the ChIP-seq experiments represent a background  (BG) level. We therefore used the genome-wide average score in each experiment to estimate  the BG level. Using these average scores, it is possible to rescale the scores accordingly, acting  as normalization and reducing the inter-experiment differences due to effects of different  sequencing depths and/or fragment sizes.  Furthermore we employed an input subtraction step for each experiment using the normalized  file for the input control. This not only allows for correction of overrepresentations of certain  genomic regions due to possible (un-) favorable events during sonication and/or DNA  sequencing, but also serves to reduce the signal/noise ratio especially for experiments with low  enrichment values.
Genome_build: Human samples : HG18
Genome_build: Mouse samples : MM9
Supplementary_files_format_and_content: 50bp binned WIG files generated with a custom R pipeline represent the average local enrichment in the genome of studied feature. A specific pipeline (previously described) has been used to generate midpoint wig files from Mnase experiments. For TSS RNA, strand specific transcripts were separated prior to wig generation.

organism: Mus musculus

extract_protocol: Prior to sequencing, DNA was quantified using the picogreen method (Invitrogen, USA)  using input dilutions as standards, or by running 20% of the DNA on a High Sensitivity  DNA chip on a 2100 Bioanalyzer. At least 1ng of Mnase digested DNA material was used for library  preparation according to the Illumina  protocol. After end-repair and adapter ligation, fragments were  size-selected (cut) on an agarose gel (146 plus the size of adapters) prior to preamplification and clustering. The size-selected  and preamplified fragments were verified on a 2100 Bioanalyzer (Agilent, USA) before  clustering and 36 cycle sequencing on a Genome Analyzer II (Illumina, USA) according to  manufacturer’s instructions.

treatment_protocol: For sequencing of nucleosomal DNA, 2.E7 cells were resuspended in 50μl Solution I (150mM sucrose, 80mM KCl, 5mM K2HPO4, 5mM MgCl2, 0.5mM CaCl2, 35mM HEPES pH 7.4) and NP40 was added to a final concentration of 0.2%. Cell membranes were permeabilized for one minute at 37°C. For nucleosomal digestion, either 10U, 20U or 40U, for thymocytes, murine ES cells and Raji cells respectively, of MNase was added with 0.5ml of Solution II (150mM sucrose, 50mM Tris pH 8, 50mM NaCl, 2mM CaCl2) and incubated for 30 minutes at room temperature. The reactions were stopped with the addition of EDTA to a final concentration of 10mM. The cells were lyzed using 1.45ml of SDS Lysis Buffer (1% SDS, 10mM EDTA pH 8, 50mM Tris pH 8), with a 10 minute incubation at 4°C. A 200μl aliquot was taken for purification and the remaining extract was stored at -80°C. at -80C. An equal volume of TE (200ul) was added to the aliquot, followed by subsequent 2 hour treatments with each 0.2ug/ml final concentrations of Rnase A and Proteinase K at 37C and 55C respectively. DNA was extracted by two subsequent phenol:chloroform:isoamylalcohol (25:24:1) extractions, further purified using QIAquick PCR purifications colums (Qiagen, Germany) and eluted in 50μl of water. Nucleosomal digestion was verified by running 500ng of DNA on a 2% agarose gel as well as on DNA high-sensitivity 2100 Bioanalyzer chips (Agilent, USA). After library preparation, DNA fragments corresponding to mononucleosomes were cut from an agarose gel and subsequently clustered and sequenced using 36 cycles on a Genome Analyzer II (Illumina, USA) according to manufacturer’s instructions.

tag: cell type

value: ES


title: Mouse Genomic DNA

data_processing:
Pre-processing and pipeline  Genomic samples were sequenced on an Illumina Genome Analyzer and aligned against the  mouse 2007 (mm9, build 37) genome using the integrated Eland  software. The Eland output files provide tag sequences, scores and coordinates. For multiple sequencing lanes (technical replicates), these files were directly  merged and then processed as described. As pre-filtering steps, only non-ambiguously mapped  tags were used for further processing. A threshold based on the number of sequenced tags  (Nseq) has been set up as Nseq/7,000,000. All regions with a number of repeated tags (with  identical sequences/coordinates) above this threshold were filtered out to remove possible  sequencing and/or alignment artefacts. Remaining tags were processed using a custom R  pipeline, employing the ShortRead library.
Tag extension and Wiggle file generation  In order to accurately represent and further process the ChIP-seq and input control signals, the  Watson and Crick strand tags need to be merged after elongation/size extension to the gel  purified fragment size. The optimal elongation size of each ChIP-seq experiment was estimated  in-silico by employing a step-wise 10bp chromosomal sequence tag shifting and score  multiplication. Tag coordinates were subsequently elongated according to this estimated DNA  fragment size, corresponding to the tag shift maximizing the score. Then, a nucleotide score  representing the genome-wide overlap of elongated tags was computed across both strands.  Wiggle files for genome-wide scores were generated following a binning step, calculating the  average score every 50bp.
ChIP-Seq artefact removal, normalization and input subtraction  Due to the size of the genome and relative low frequencies of binding events, we assume that  more than 90% of the obtained scores from the ChIP-seq experiments represent a background  (BG) level. We therefore used the genome-wide average score in each experiment to estimate  the BG level. Using these average scores, it is possible to rescale the scores accordingly, acting  as normalization and reducing the inter-experiment differences due to effects of different  sequencing depths and/or fragment sizes.  Furthermore we employed an input subtraction step for each experiment using the normalized  file for the input control. This not only allows for correction of overrepresentations of certain  genomic regions due to possible (un-) favorable events during sonication and/or DNA  sequencing, but also serves to reduce the signal/noise ratio especially for experiments with low  enrichment values.
Genome_build: Mouse samples : MM9
Supplementary_files_format_and_content: 50bp binned WIG files generated with a custom R pipeline represent the average local enrichment in the genome of studied feature. A specific pipeline (previously described) has been used to generate midpoint wig files from Mnase experiments. For TSS RNA, strand specific transcripts were separated prior to wig generation.

source_name: genomic DNA from Promega

extract_protocol: See chipseq library protocol

treatment_protocol: Genomic mouse DNA was obtained commercially (Promega, France) and sonicated in TE  (100ng/μl) using in a final volume of 50μl for 16 cycles (30s on/30s off) in a Bioruptor  (Diagenode, Belgium) on medium power. The resulting sheared DNA displayed an average of  200bp fragments as verified on an agarose gel. The sample was used for library preparation  and sequencing as described for the ChIP-Seq and MNase-Seq samples.

tag: sample type

value: reference


title: H3K27me3 mouse DP

source_name: DP T-cells

tag: tissue

value: Thymus

value: Double Positive Thymocytes

tag: antibody


title: input_ChIP-Seq_2

status: Public on Jun 04 2012

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

country: Italy

institute: EMBL

description: Chromatin IP against sonicated genomic DNA

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the human 2006 (hg18) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates.
For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described.
As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out at a threshold of 1 per 7 million tags to remove possible sequencing and/or alignment artefacts.
Remaining tags were processed using a custom R pipeline, employing the ShortRead library.
Genome_build: hg18
Supplementary_files_format_and_content: The processed data files are provided in wig format. The wig files are fixed step and thus contain scores representing 50 nucleotides according to the binning method we used

organism: Homo sapiens

source_name: Raji-cells

extract_protocol:
CTD mutants carry 48 consensus repeats (Con48), or have replaced Thr4 residues in all consensus repeats by alanine (Thr4/Ala) were induced for 24h and then treated with α-amanitin (2μg/ml) for 48h. Wild-type or stable-transfected Raji cells were crosslinked at room temperature with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 25 8.0, 50mM Hepes pH 7.8) in growth medium for 10min. The reaction was quenched with the addition of 250mM glycine for 5min. Cells were washed twice with cold DPBS and 5x107 cells/aliquot were pelleted. Final concentrations of 1x phosphatase inhibitors, 1x EDTA-free protease inhibitors  (Roche), 0.2mM PMSF and 1μg/ml pepstatin were added to all LB buffers. Centrifugations and lysis steps were carried out at 4°C. Each cell aliquot was lysed in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 1% NP-40, 0.5% Triton X-100) for 20min on a rotating wheel. Chromatin was collected by centrifugation for 5min at 1.350g and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 10mM Tris pH 8.0) for 20 minutes. Chromatin was collected, resuspended in 1.5ml of LB3 (1mM EDTA pH 8.0, 0.5mM EGTA pH 8, 10mM Tris pH 8.0, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% Nlauroylsarcosine) and sonicated using a Misonix 4000 (Misonix Inc.) sonicator for 14 cycles (30sec on, 30sec off, amplitude 40). After the addition of Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at 20.000g for 20min a 50μl aliquot was taken to serve as input control. The input was combined with an equal volume of 2x elution buffer (100mM Tris pH 8.0, 20mM EDTA pH 8.0, 2% SDS) and incubated overnight at 65°C for 13-15h. SDS was diluted by the addition of an equal volume of TE (10mM Tris pH 8.0, 1mM EDTA pH 8.0), followed by 2h of RNase A (0.2μg/ml) and 2h of Proteinase K (0.2μg/ml) digestions at 37°C and 55°C, respectively. DNA was purified by two subsequent phenol:chloroform:isoamylalcohol (25:24:1, pH 8) extractions, followed by a PCR purification column (Qiagen). DNA was eluted using 50μl H2O and the concentration was measured on a Nanodrop 1000 (Thermo Scientific). To verify DNA fragmentation, 500ng were run on a 2% agarose gel.
EDTA-free protease inhibitors (Roche, France) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1µg/ml pepstatin. Phosphatase inhibitors (Roche, France) were added to a final concentration of 1x for Pol II phospho-serine ChIPs. Aliquots of 5x107 cells were lysed after resuspension in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at 4°C. Chromatin was collected by centrifugation for 5 minutes at 4°C and 1.350g in a tabletop centrifuge, and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was collected, resuspended in 1.5ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000 (Misonix Inc, USA) sonicator for 14 cycles (30 seconds on, 30 seconds off, amplitude 40) with the tubes submerged in ice-cold sonication solution (500mM NaCl, 20% Ethanol). After the addition of Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at 20.000g and 4°C for 20 minutes. For batch processing, supernatants were combined, mixed thoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at -80°C until use and 50µl aliquots were taken to serve as input controls.  All experiments were performed using Dynabeads (Invitrogen, USA) coated with Protein-G. For biological replicates, all steps were repeated using a biologically independent sample. Beads were washed 3x with 1ml and subsequently resuspended in 250µl of blocking solution (0.5% BSA in 1x DPBS). After the addition of the antibody, the beads were incubated at 4°C overnight on a rotating wheel. Unbound antibodies were removed through three further washes with 1ml of blocking solution. Beads were resuspended in 100µl of blocking solution, extracts were added and the mix was incubated overnight at 4°C on a rotating wheel.  EDTA-free protease inhibitors (Roche) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1µg/ml pepstatin. Phosphatase inhibitors (Roche) were added to a final concentration of 1x in the case of Pol II phospho-serine ChIPs. Beads were washed 8 times in RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 10 mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in TE+ (10mM Tris pH8, 1mM EDTA pH 8, 50mM NaCl). Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps at 65°C for 15 and 10 minutes in 110µl and 100µl of elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) respectively. The two eluates were combined and incubated at 65°C overnight (13-15 hours) for crosslink reversal.

tag: cell line

value: Raji-cells

value: consensus T48

value: Burkitt's lymphoma

tag: ChIP


title: MnaseSeq mouse DP

value: T-cells


title: PolII_HA_ChIP-Seq_1

description: Chromatin IP against PolII

extract_protocol: EDTA-free protease inhibitors (Roche, France) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1µg/ml pepstatin. Phosphatase inhibitors (Roche, France) were added to a final concentration of 1x for Pol II phospho-serine ChIPs. Aliquots of 5x107 cells were lysed after resuspension in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at 4°C. Chromatin was collected by centrifugation for 5 minutes at 4°C and 1.350g in a tabletop centrifuge, and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was collected, resuspended in 1.5ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000 (Misonix Inc, USA) sonicator for 14 cycles (30 seconds on, 30 seconds off, amplitude 40) with the tubes submerged in ice-cold sonication solution (500mM NaCl, 20% Ethanol). After the addition of Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at 20.000g and 4°C for 20 minutes. For batch processing, supernatants were combined, mixed thoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at -80°C until use and 50µl aliquots were taken to serve as input controls.  All experiments were performed using Dynabeads (Invitrogen, USA) coated with Protein-G. For biological replicates, all steps were repeated using a biologically independent sample. Beads were washed 3x with 1ml and subsequently resuspended in 250µl of blocking solution (0.5% BSA in 1x DPBS). After the addition of the antibody, the beads were incubated at 4°C overnight on a rotating wheel. Unbound antibodies were removed through three further washes with 1ml of blocking solution. Beads were resuspended in 100µl of blocking solution, extracts were added and the mix was incubated overnight at 4°C on a rotating wheel.  EDTA-free protease inhibitors (Roche) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1µg/ml pepstatin. Phosphatase inhibitors (Roche) were added to a final concentration of 1x in the case of Pol II phospho-serine ChIPs. Beads were washed 8 times in RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 10 mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in TE+ (10mM Tris pH8, 1mM EDTA pH 8, 50mM NaCl). Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps at 65°C for 15 and 10 minutes in 110µl and 100µl of elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) respectively. The two eluates were combined and incubated at 65°C overnight (13-15 hours) for crosslink reversal.

value: Chromatin IP against PolII


title: ChIP_Seq_p300_H1

status: Public on May 10 2012

city: LA JOLLA

first: Nisha

last: Rajagopal

state: CA

address: 9106 REGENTS RD APT F

country: USA

institute: UCSD

data_processing:
base-calling using Illumina software with output as Fastq files
Sample 1 and 2:alignment and mapping with Bowtie with seed length 32bp,maximum matches 1 and maximum mismatches 2.Output was bowtie_output or BAM file.; Sample 3: alignment and mapping with Illumnia's ELAND software using seed length of 25bp and maximum number of mismatches 2
Bed files were created using custom perl scripts. Read length of 36bp was used and only reads that mapped uniquely were used. Polyclonal reads were reduced to one instance.
Genome_build: hg18
Supplementary_files_format_and_content: bed files

source_name: Embryonic Stem Cells

value: p300 [Manufacturer:Santa Cruz, Catalog:SC-585XS, Lot#: E2209]

value: Embryonic Stem Cells


title: KSHV LANA_ChIPSeq

status: Public on Jun 02 2012

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description: KSHV

data_processing:
Alignment: Alignment was performed using Bowtie software on both the human HG18 genome downloaded from the UCSC browser site and the viral genome HQ404500BAC36 with a 35 repeat added to terminal.
Wiggle files were created using moving average of raw reads at each base. Peaks were identified on wiggle profile based on Mathematical maxima in local regions.
Supplementary_files_format_and_content: WIG: Single-column UCSC Wiggle file format.
Supplementary_files_format_and_content: BED: Six-column peak bed format.
Genome_build: HQ404500BAC36 with 35 repeat added to terminal

organism: Human gammaherpesvirus 8

source_name: BCBL1 pleural effusion lymphoma, KSHV LANA ChIP

growth_protocol: BCBL1 cells were grown to 1x10^6 cells/ml in RPMI with 10% FBS supplemented with Glutamax and Penn/Strep.

extract_protocol: Lysates were clarified from sonicated nuclei, and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions.

treatment_protocol: According to the publication "Chromatin immunoprecipitation and microarray-based analysis of protein location" from the Natural Protocol (PMID 17406303).

value: KSHV-infected pleural effusion lymphoma cells

tag: chip antibody

value: rat anti-KSHV LANA

tag: antibody vendor

value: Advanced Biotechnologies

tag: antibody catalog #

tag: antibody lot#


title: Input mouse DP


title: SIRT7.rep2

status: Public on May 07 2012

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

description: chromatin IP against SIRT7

data_processing: Reads are mapped to genome (hg18) using ELAND with up to 2 mismatches allowed.

source_name: Leukemia

extract_protocol:
Lysates were clarified from sonicated nuclei, and histone-DNA complexes were isolated with a non-commercial antibody (Michishita, E., Park, J. Y., Burneskis, J. M., Barrett, J. C. & Horikawa, I. Evolutionarily conserved and nonconserved cellular localizations and functions of human SIRT proteins. /Mol Biol Cell/*16*, 4623-4635 (2005).)
single-end, 27-mer or 34-mer sequencing using standard protocol

tag: genotype

value: Wide type

tag: sequencing protocol

value: single-end, 27-mer sequencing


title: 2-6hr Embryo (Replicate 1) extraction1_seq1 aliquote 1

status: Public on Aug 10 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

description: small RNAs

library_source: transcriptomic

data_processing: raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt

molecule: total RNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster 2-6hr embryo

extract_protocol: total RNA from 2-6hr embryo, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: Stage

value: 2-6hr embryo


title: Heat treated HT-2

status: Public on Mar 31 2012

city: Shanghai

first: Yu-ke

last: He

address: 300 Fenglin Road

country: China

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing: The adaptor sequences in Illumina sequencing reads were removed using âvectorshipâ in the EMBOSS package. The small RNA with length of 9~36 nt were mapped to chloroplast genomes (GenBank accession number: DQ231548) and nuclear genomic sequences (BRAD, Brassica Database, http://brassicadb.org/brad/) of Chinese cabbage (Brassica rapa ssp. chinensis) and nuclear, chloroplast, mitochondrial genomes of Arabidopsis (http://www.arabidopsis.org).

organism: Brassica rapa subsp. chinensis

source_name: Chinese cabbage (B. rapa ssp. chinensis)

extract_protocol: Chinese cabbage and Arabidopsis total RNA samples were sent to Keygene N.V., Wageningen, the Netherlands and Zhejiang-California Nanosystems Institute, China respectively, where the samples were prepared and sequenced on Illumina GAII sequencer, according to the manufacturer's protocol.

treatment_protocol: 46â 1 hour for heat treatment, 22â 1 hour as control

value: above-ground portions of the seedlings

tag: treatment

value: heat treated

tag: age

tag: breed

value: Heat-sensitive inbred line Wu-12

tag: organelle

value: Chloroplast


title: Control MT-1

value: moderate temperature control

value: Heat-sensitive inbred line Wu-13


title: Control MT-2

value: Heat-sensitive inbred line Wu-14


title: Ler

source_name: Arabidopsis thaliana

value: Whole seedlings

value: Landsberg erecta ecotype


title: Heat treated HT-1

value: Heat-sensitive inbred line Wu-11


title: 2-6hr Embryo (Replicate 2) extraction2_seq1 aliquote 1

description: small RNAs


title: control.rep2

description: Genomic Input

value: single-end, 34-mer sequencing


title: Log Unfixed Narrow Mnase-seq

status: Public on Apr 24 2012

city: Buffalo

first: Michael

last: Buck

state: NY

address: 701 Ellicott St

department: Biochemistry

institute: SUNY at Buffalo

description: Mnase-seq for unfixed Log phase Pombe with narrow band excised

data_processing: Sequencing reads were aligned to the August, 2008, build of the S. pombe genome (http://www.sanger.ac.uk/Projects/S_pombe/) using the BowTie algorithm ( http://bowtie-bio.sourceforge.net/index.shtml), allowing only unique matches with up to two possible mismatches.

organism: Schizosaccharomyces pombe

source_name: Log phase Pombe

growth_protocol: The cells were grown in minimal medium at 25Â°C with 200-rpm agitation to either log phase (5-8Ã106 cells/ml ) or stationary phase (1-2Ã108 cells/ml), as required.

extract_protocol: Cryoground isolated nuclei were digested with MNase at 25C at various concentrations.  The DNA was isolated and size selected by agarose gel.  The band representing mono-nucleosomal DNA was isolated, purified, and processed for sequencing using the standard Illumina protocol.

treatment_protocol: Fixed samples were prepared by adding 0.0423 volumes of 37% w/w formaldehyde (Fisher Scientific # F79-500) to each volume of culture, to achieve a final (taking the added volume into account) concentration of 1.5% formaldehyde, then allowing incubation to continue with rotary agitation for 15 minutes.

tag: strain

tag: plasmid

tag: growth phase

value: Log Phase

tag: fixation

value: Unfixed

tag: band excised

value: narrow


title: Log Fixed Broad Mnase-seq

description: Mnase-seq for Fixed Log phase Pombe with broad band excised

value: Fixed

value: broad


title: Log Fixed Narrow Mnase-seq

description: Mnase-seq for Fixed Log phase Pombe with narrow band excised


title: Oryza sativa L. ssp. japonica Nipponbare panicles sRNA

status: Public on Mar 30 2012

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

description: high-throughput sequencing of small RNA

data_processing: The raw data was acquired by Illumina base calling, all the reads containing ambiguous 'N' were eliminated from raw data, remained data was submitted to our following bioinformatics study, including sRNA annotation, phasiRNA prediction and motif analysis etc.

organism: Oryza sativa

source_name: young panicles (4cm)

growth_protocol: The rice 93-11 and Nipponbare seedlings were grown on Murashige and Skoog medium with a daylength of 16h and a night of 8h at 25 centigrade. And the panicles were collected from plants which were grown on field.

extract_protocol: Total RNA was extracted from seedling and panicles using Trizol reagent (Invitrogen). The low molecular weight (LMW) RNA was enriched by adding equal volume of 8M LiCl, incubating on ice for 1 hour and centrifuging at 12,000 rpm for 5 min at 4°C. Approximately 150µg of low molecular weight RNA was resolved in formamide and loaded into 15% PAGE gel with 7M urea and 1×TBE buffer. The gel fragments ranging between 15-30 nt were excised from gel for further purification. The purified small RNA was then ligated with a 5’ adaptor GUUCAGAGUUCUACAGUCCGACGAUC using T4 RNA ligase (NEB) at 20℃ for 6 hours and the ligation product ranging between 40-60 nt was purified again. The purified product was further ligated to the 3’ adaptor pUCGUAUGCCGUCUUCUGCUUGidT, which has a phosphate group in the 5’ terminal and an inverted deoxythymidine in the 3’ terminal, using T4 RNA ligase. The 2nd ligation product between 60-90 nt was separated within 10% Urea-PAGE gel and the purified product was reverse transcription (RT) using primer CAAGCAGAAGACGGCATACGA. The RT product was then amplified by PCR using p5 (AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA) and p7 (CAAGCAGAAGACGGCATACGA) primers for 15 cycles. The amplified products (90-95 nt) was excised from a 6% PAGE gel without urea and purified eventually. The purified product was resolved in 1×TE buffer and submitted to SBS sequencing after quality control (QC) assay in Beijing Genomics Institution.

treatment_protocol: Collected materials were ground into a fine powder in liquid nitrogen and processed following with Trizol reagent (Invitrogen) kit to extract total RNA.

tag: genotype/variation

value: Wild-type

tag: tissue

value: panicles


title: Oryza sativa L. ssp. indica 93-11 panicles sRNA

description: high-throughput sequencing of small RNA


title: Ko Nkx2-5cre, Ezh2f/f E12.5 apx

status: Public on Mar 15 2012

city: Boston

last: Hsing

state: MA

address: 300 Longwood Ave.

department: Cardiology

institute: Children's Hospital Boston

data_processing: All p-values were corrected for multiple concurrent hypothesis testing using the Benjamini-Hochberg method. We used the false discovery rate < 1% and fold change of greater than 50% as the significance threshold.

source_name: embryonic cardiomyocytes at E12.5

extract_protocol: Full-length transcript RNA-seq library preparation kit

tag: cell type

value: cardiomyocyte

value: Ko Nkx2-5cre, Ezh2f/f E12.5 apx


title: control.rep1

description: Genomic Input

tag: cell line

value: Wide type

tag: chip antibody


title: Oryza sativa L. ssp. indica osdcl4-1 seedlings sRNA

description: high-throughput sequencing of small RNA

source_name: young seedlings

value: seedlings


title: Het Nkx2-5cre, Ezh2f/+ E12.5 apex

tag: genotype

value: Het Nkx2-5cre, Ezh2f/+ E12.5 apex


title: Oryza sativa L. ssp. indica 93-11 seedlings sRNA

description: high-throughput sequencing of small RNA


title: Forebrain_Embryonic day 10_Technical replicate_2

status: Public on Jun 26 2012

first: Maojin

last: Yao

address: 320# Yueyang Road

department: Neural circuit development

institute: Institute of Neurosciecne

data_processing: After removing low quality reads according to the criteria of Solexa, the full length unique small RNA tag were counted as their expression abundances. Those identical RNA tag were mapped to genome of Rat by SOAP software (Short Oligonucleotide Alignment Program) (http://soap.genomics.org.cn) to analyze their expression and distribution on the genome. Small RNA tags were aligned to the miRNA precursor and mature sequence from miRbase 14.0 (www.miRBase.org) to obtain the known miRNA counts and get rid of matched tags from unannotated tags. Then small RNA tags were aligned with the sequences of non-coding RNAs (rRNA, tRNA, scRNA,snRNA, snoRNA) from Rfam  http://www.sanger.ac.uk/software/Rfam) and the GenBank (http://www.ncbi.nlm.nih.gov/) to get rid of matched tags from unannotated tags. In addition, all sequences were searched for piRNA in NCBI database with screening program developed by Beijing Genomics Institute.To identify potential novel miRNA candidates, software Mireap (http://sourceforge.net/projects/mireap) developed by BGI was used to predict novel miRNA by exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the unannotated small RNA tags which could be mapped to genome. In briefly, the sequence length should be between 18-26 nt, maximal free energy allowed for a miRNA precursor was -18 kcal/mol, maximal space between miRNA and miRNA* was 35 nt, and flank sequence length of miRNA precursor should be 10 nt. After filtering in above analysis pipeline, unannotated small RNA tags were aligned with mature miRNAs from miRBase14.0 to detect miRNA editing allowing one mismatch on certain position miRNAs.

organism: Rattus norvegicus

source_name: Forebrain

extract_protocol: Rat cortical tissues of various developmental stages (E10-P28) were dissected and total RNA was then extracted with TRIzol. Size-fractionation was performed on 15% polyacrylamide gel electrophoresis (PAGE) to collect the 16-35 nt fraction. Libraries were prepared according to Illumina's instructions. In briefly, adapters were ligated to the 5’ and 3’ termini of these small RNAs, which then were used as templates for cDNA synthesis. After producing libraries via PCR amplification, the purified PCR products were then sequenced using Illumina genome Analyzer II

value: Forebrain

value: Embryonic day 10

value: Sprague Dawley


title: SIRT7.rep1

description: chromatin IP against SIRT7

tag: sequencing protocol

value: single-end, 27-mer sequencing


title: Oryza sativa L. ssp. indica osdcl4-1 panicles sRNA

description: high-throughput sequencing of small RNA


title: Somatosensory cortex_Postnatal day 28_Technical replicate_1

source_name: cortex

value: cortex

value: Postnatal day 28


title: THP1-LPS-1-BWA-RNAPII

status: Public on Mar 07 2012

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

country: Denmark

institute: National Genome Center

data_processing: Sequence reads were 35 bases or longer but truncated to 35 bases to ensure base quality over the entire read. Reads were aligned to the human reference genome (GRCh37/hg19) with Burrows-Wheeler Alignment tool (BWA) (Li H and Durbinv R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform.

growth_protocol: THP-1 cells (monocyte cell line) (ATCC , Manassas, VA, USA) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 1mM sodium pyruvate , 100 units/ml penicillin and 100 μg/ml streptomycin at 37°C with 5% CO2. For differentiation of THP-1 cells into macrophages a protocol using conditioned media as previously described by Whatling et al was used. To confirm differentiation of THP-1 monocytes into macrophages CD11b expression was measured using FACS and quantitative polymerase chain reaction (qPCR).

extract_protocol: DNA-protein complexes were eluted, treated with RNaseA (USB,Cleveland, OH, USA) for 4-6 hours at 45°C and Proteinase K (USB, Cleveland, OH, USA) overnight at 65°C. DNA was extracted by phenol/chloroform/isoamyl alcohol extraction, purified and resuspended in water. library construction: Illumina core center, standard protocol

treatment_protocol: THP-1 macrophages were then either left unstimulated (control) or stimulated with 1ug/ml LPS (LPS-stimulated) from Escherichia coli O55:B5 for 2 hours (Sigma Chemical Co., St. Louis, MO, USA) to induce an acute inflammatory response. To confirm an induction of the inflammatory response in the THP-1 macrophages, TNF mRNA levels were measured in control and LPS-stimulated samples.

tag: agent

value: LPS

tag: sample pair

value: RNA Pol II (phospho S5)


title: THP1-LPS-2-BWA-H3K9/K14Ac


title: THP1-control-2-BWA-H3K9/K14Ac


title: THP1-LPS-1-BWA-SP1


title: THP1-LPS-2-BWA-SP1


title: THP1-LPS-2-BWA-RNAPII


title: THP1-control-1-BWA-RNAPII


title: THP1-control-2-BWA-RNAPII


title: THP1-control-2-BWA-SP1


title: Stationary Unfixed Narrow Mnase-seq

description: Mnase-seq for unfixed stationary phase Pombe with narrow band excised

source_name: Stationary Phase Pombe

value: Stationary Phase

value: Unfixed

value: narrow


title: input-BWA


title: THP1-control-1-BWA-H3K9/K14Ac


title: THP1-LPS-1-BWA-H3K9/K14Ac


title: input

data_processing: Sequence reads were 35 bases or longer but truncated to 35 bases to ensure base quality over the entire read. Reads were aligned to the human reference genome (GRCh37/hg19) with Burrows-Wheeler Alignment tool (BWA) (Li H and Durbinv R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 (14): 1754-60), and only uniquely mapped reads with a maximum of 2 mismatched bases were considered for further analysis. The sequence tag density generated from the input library (total DNA) was used as background.

growth_protocol: THP-1 cells (monocyte cell line) (ATCC , Manassas, VA, USA) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 1mM sodium pyruvate , 100 units/ml penicillin and 100 Î¼g/ml streptomycin at 37Â°C with 5% CO2. For differentiation of THP-1 cells into macrophages a protocol using conditioned media as previously described by Whatling et al was used. To confirm differentiation of THP-1 monocytes into macrophages CD11b expression was measured using FACS and quantitative polymerase chain reaction (qPCR).


title: THP-1-LPS-2

tag: antibody vendor

value: Upstate, Charlottesville, VA, USA

tag: antibody catalog number

tag: antibody lot number


title: K_late

status: Public on Mar 13 2012

city: Guangzhou

first: Hui-Run

last: Huang

state: Guangdong

address: Xingke Road 723

institute: South China Botanical Garden, Chinese Academy of Sciences

data_processing: Illumina pipeline was used for off-instrument data processing, including image analysis, base calling and tag counting. Adaptor tags, low quality tags and tags of copy number = 1 were filtered.

organism: Capsella bursa-pastoris

source_name: Capsella bursa-pastoris late-flowering sample K

growth_protocol: Seeds were stored at 4℃ for 4 days in distilled water to break seed dormancy, and then sterilized using 75% ethanol and 0.1% HgCl2. For each plant the surface-sterilized seeds were sown on an 0.8% agar plate with Murashige and Skoog medium, subsequently the plates were placed randomly in a growth chamber under long-day conditions as stated above (16/8 h photoperiod, 23℃).

extract_protocol: RNA was extracted from frozen seedlings using RNAiso Plus and RNAiso-mate for Plant Tissue (TaKaRa Biotechnology Co., Ltd.) according to the manufacturer's protocols. RNA integrity and concentration were evaluated by Agilent 2100 Bioanalyzer (Agilent Technologies).Total RNA was incubated with magnetic oligo(dT) beads to capture mRNA. First- and second-strand cDNA was synthesized and bead-bound cDNA was subsequently digested with NlaIII. GEX NlaIII adapter 1 was ligated at the site of NlaIII cleavage. This adapter contains a restriction site for MmeI that cuts 17 bp downstream from the NlaIII site, thus creating 21 bp tags starting with the NlaIII recognition sequence, CATG. After digestion, the fragments detached from the beads, and GEX NlaIII adapter 2 was ligated at the site of MmeI cleavage. The adapter-ligated cDNA tags were subsequently enriched using PCR-primers that anneal to the adapter ends. The resulting 85 bp fragments were purified from 6% acrylamide gels, and integrity of the tagged sequence was confirmed using the Agilent 2100 Bioanalyzer. Cluster generation was performed after applying 6 pmol of cDNA to the individual lanes of Illumina 1G flowcell, and sequencing by synthesis was performed using Illumina Genome Analyzer.

treatment_protocol: Two-week-old seedlings were sampled and immediately flash-frozen in liquid nitrogen. Three seedlings representing each sample were pooled together for RNA extraction.

tag: flowering ecotype

value: late

tag: developmental stage

value: two-week-old seedling

tag: sample source

value: Harbin,Heilongjiang,China


title: G_late

source_name: Capsella bursa-pastoris late-flowering sample G

value: Taibai Mt.,Shaanxi,China


title: THP1-control-1-BWA-SP1


title: C_early

source_name: Capsella bursa-pastoris early-flowering sample C

value: early

value: Pingxiang,Jiangxi,China


title: I_late

source_name: Capsella bursa-pastoris late-flowering sample I

value: Handan,Hebei,China


title: H_late

source_name: Capsella bursa-pastoris late-flowering sample H

value: Qingdao,Shandong,China


title: THP-1-control-2


title: THP-1-control-1


title: D_early

source_name: Capsella bursa-pastoris early-flowering sample D

growth_protocol: Seeds were stored at 4℃for 4 days in distilled water to break seed dormancy, and then sterilized using 75% ethanol and 0.1% HgCl2. For each plant the surface-sterilized seeds were sown on an 0.8% agar plate with Murashige and Skoog medium, subsequently the plates were placed randomly in a growth chamber under long-day conditions as stated above (16/8 h photoperiod, 23℃).

value: WH,Hubei,China


title: THP-1-LPS-1


title: E_early

source_name: Capsella bursa-pastoris early-flowering sample E

value: Haishiwan,Gansu,China


title: J_late

source_name: Capsella bursa-pastoris late-flowering sample J

value: Zhangye,Gansu,China


title: L_late

source_name: Capsella bursa-pastoris late-flowering sample L

value: Dalian,Liaoning,China


title: B_early

source_name: Capsella bursa-pastoris early-flowering sample B

value: Guiyang,Guizhou,China


title: Col0-CMV∆2b_rep1_CMV_matches

status: Public on Mar 01 2012

city: Riverside

first: JUAN

last: JOVEL

address: 3401 Watkins Drive

department: Plant Pathology

institute: University of California Riverside

data_processing:
Reads were extracted using the Illumina pipeline.  Trimming of adapters and down-stream analyses were carried out with in-house Perl scripts, except alignments of short reads to Arabidopsis or CMV sequences, which were performed with bowtie (no mistmatches were allowed).
All sequences containing perfect match 5' barcode (ATC/CGT/TAC) and at least 6 sucessive perfect-matched nucleotides of the 3' linker were kept for later analysis. The barcode and linker sequences were computationally removed by in-house perl scripts. All trimmed sequences in length of 18-30nt were aligned with CMV genome and the perfect matched reads were used for all further analysis.

organism: Arabidopsis thaliana

source_name: Systemically-infected leaves

growth_protocol: Arabidopsis plants were grown in our glass houses under stardard conditions.

extract_protocol:
Low molecular weight RNAs extracted by Trizol (Invitrogen) from the systemically infected leaves 14 days after inoculation with CMV-Δ2b were purified from 15% denatured polyacrylamide gel. Purified small RNAs were directly ligated to the 3′-linkers for miRNA cloning (Integrated DNA Technology) by T4 RNA ligase 2Tr (New England Biolabs). The ligation products were purified and ligated to a suitable 5′ Solexa linker by T4 RNA ligase I (New England Biolabs). The final ligation products were reverse transcribed using a primer targeting the 3′-linker and the cDNA pool was amplified by PCR and sequenced by the Solexa technology (Illumina) in our campus facility. Duplicate libraries were constructed from two independent RNA samples.
immunoprecipitation: Three g systemic leaves from FLAG-AGO1 or HA-AGO2 plants infected with CMV-Δ2b were ground to powder in liquid nitrogen and supplied with 10 ml of extraction buffer [20 mM Tris•HCl, pH 7.5/300 mM NaCl/5 mM MgCl2/5 mM DTT/1% plant protease inhibitor mixture (Sigma)].  The suspension was clarified by centrifugation (10 min, 4ºC, 14,000 rpm) and the supernatant filtered through cheesecloth. The filtered supernatant was incubated with anti-FLAG M2 agarose (Sigma-Aldrich) or anti-HA affinity matrix (Roche), according to manufacturers’ protocols, for 4h at 4ºC.  The beads were then washed twice with extraction buffer supplemented with 0.5% Nonidet P-40 and the AGO-bound RNA extracted with TRIzol.

tag: source

value: Total RNA


title: FLAG-AGO1-CMV∆2b_total_At_matches

tag: genotype reference

value: Baumberger & Baulcombe 2005. PNAS 102(33):11928-33.


title: rdr6-CMV∆2b_rep2_CMV_matches


title: rdr6-CMV∆2b_rep2_At_matches


title: HA-AGO2-CMV∆2b_total_At_matches


title: rdr6-CMV∆2b_rep1_CMV_matches


title: rdr6-CMV∆2b_rep1_At_matches


title: Col0-CMV∆2b_rep1_At_matches


title: F_early

source_name: Capsella bursa-pastoris early-flowering sample F


title: H1_shRNA_DNMT3B_p60_RRBS

status: Public on Feb 21 2012

city: Munich

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

country: Germany

institute: Max Planck Institute of Psychiatry

description: reduced representation bisulfite sequencing

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using MAQ bisulfite alignment mode.
References: Smith, Z. D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput bisulfite sequencing in mammalian genomes. Methods 48, 226-232, doi:S1046-2023(09)00111-X
Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7, 133-136, doi:nmeth.1414
Genome Build:
RRBS_cpaMethylation_H1_shRNA_DNMT3B_11_p60.RRBS.bed: hg18
RRBS_cpcMethylation_H1_shRNA_DNMT3B_11_p60.RRBS.bed: hg18
RRBS_cptMethylation_H1_shRNA_DNMT3B_11_p60.RRBS.bed: hg18

source_name: hES H1 passage 60 infected with control shRNA against DNMT3B

growth_protocol: The pluripotent cell lines were grown in human ES media consisting of KO-DMEM (Invitrogen), 10% KOSR (Invitrogen), 10% plasmanate (Talecris), 1% glutamax or L-glutamin, nonessential amino acids, penicillin/streptomycin, 0.1% 2-mercaptoethanol and 10–20 ng/ml bFGF. All pluripotent cells were grown on a monolayer of irradiated CF1-MEFs (GlobalStem) and passaged using trypsin (0.05%) or dispase (Invitrogen). Before collection of DNA and RNA for analysis, ES and iPS cells were either isolated using trypsin (0.05%) or dispase, or plated on matrigel (BD Biosciences) for one passage and fed with human ES media conditioned in CF1-MEFs for 24 hr. The material from the rectal mucosa, rectal smooth muscle, skeletal muscle and stomach smooth muscle was obtained from MGH Pathology under the REMC project.  human blood CD19 and CD34 samples were obtained from Shelly Heimfeld’s lab. Pancreatic islet samples were retrieved from the islet donor network and supplied by Stuart Schreibers Group.

extract_protocol: RRBS was performed according to a previously published protocol (Smith et al., 2009) with some optimizations for small cell numbers (Gu et al., 2010)


title: A_early

source_name: Capsella bursa-pastoris early-flowering sample A

value: Boluo,Guangdong,China


title: FLAG-AGO1-CMV∆2b_total_CMV_matches


title: H1_shRNA_DNMT3A_p60_RRBS

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using MAQ bisulfite alignment mode.
References: Smith, Z. D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput bisulfite sequencing in mammalian genomes. Methods 48, 226-232, doi:S1046-2023(09)00111-X
Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7, 133-136, doi:nmeth.1414
Genome Build:
RRBS_cpgMethylation_H1_shRNA_DNMT3A_7_p60.RRBS.bed: hg18
RRBS_cpaMethylation_H1_shRNA_DNMT3A_7_p60.RRBS.bed: hg18
RRBS_cpcMethylation_H1_shRNA_DNMT3A_7_p60.RRBS.bed: hg18
RRBS_cptMethylation_H1_shRNA_DNMT3A_7_p60.RRBS.bed: hg18

source_name: hES H1 passage 60 infected with control shRNA against DNMT3A


title: Col0-CMV∆2b_rep2_CMV_matches


title: HA-AGO2-CMV∆2b_total_CMV_matches


title: H1_shRNA_DNMT3A_1_ctrl_p60_RRBS

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using MAQ bisulfite alignment mode.
References: Smith, Z. D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput bisulfite sequencing in mammalian genomes. Methods 48, 226-232, doi:S1046-2023(09)00111-X
Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7, 133-136, doi:nmeth.1414
Genome Build:
RRBS_cpgMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed: hg18
RRBS_cpaMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed: hg18
RRBS_cpcMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed: hg18
RRBS_cptMethylation_H1_shRNA_DNMT3A_1_ctrl_p60.RRBS.bed: hg18

source_name: hES H1 passage 60 infected with control shRNA against GFP


title: HUES48_p15_RRBS

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using MAQ bisulfite alignment mode.
References: Smith, Z. D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput bisulfite sequencing in mammalian genomes. Methods 48, 226-232, doi:S1046-2023(09)00111-X
Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7, 133-136, doi:nmeth.1414
Genome Build:
RRBS_cpgMethylation_HUES48_p15.RRBS.bed: hg18
RRBS_cpaMethylation_HUES48_p15.RRBS.bed: hg18
RRBS_cpcMethylation_HUES48_p15.RRBS.bed: hg18
RRBS_cptMethylation_HUES48_p15.RRBS.bed: hg18

source_name: hES HUES48 p15


title: RNA Pol II siRNA Control (reanalysis)

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing: Raw sequences generated from Illumina/Solexa sequencer were aligned using ELAND software to NCBI Build 36.1 (UCSC hg18) of the human genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple sequences mapped to the same genomic position, a maximum of two reads mapping to the same position were used. The sequenced reads represent only the ends of each immunoprecipitated fragments instead of the precise protein-DNA binding sites. To illustrate the entire DNA fragment, the 3’ end of each read was extended 200 bp. The reference genome was partitioned into 25 bp bins and the total reads (including partial reads) in each bin were summed and used to generate the visualization file in wiggle (WIG) format. The complete set of RefSeq genes was downloaded from the UCSC table browser on December 1, 2010. A custom annotated RefSeq gene list was generated by merging the all TSSs for each gene that were within 500 bases of each other. Then TSSs within 1000 bp of each other (6% of the total number) were removed from the list. This list was used for further analyses. A genomic coordinate file was compiled by extending the 3’ end of each original sequence to a total of 200 bp. The number of reads within 10,000 bases of the TSS of each gene in the custom gene list was tabulated. Similar analysis was applied to the location of center of peaks generated from the peak finding algorithm for the region within 500 bp relative to the TSS. Heat maps were generated using the program R. Genes were rank ordered based on the sequence density for RNAP II from -2K to +2K from the TSS. Using this order, basepair resolution sequence density for RNAP II and Gdown1 for the top 20,000 genes was displayed without binning. A peak finding algorithm (ChIP-Seq Peak) was designed to examine the data within individual WIG files and determine precise position and height of each significant peak. This algorithm assumes that each 200 bp immunoprecipitated DNA fragment is sequenced randomly from either end and that typical peaks would be approximately 400 bases wide at the base. Peaks less than 250 bp wide were eliminated and the center of each remaining peak was determined using Gaussian curve fitting. The height was determined by the area under each peak.

source_name: RNA Pol II siRNA Control

growth_protocol: HeLa cells were maintained at 5% CO2 and 37°C in DMEM plus 10% FBS (Hyclone). Cells were grown in T-150 flasks to 90% confluence and treated for 5 or 60 minutes with Flavopiridol (final concentration 1 μM with 0.1% DMSO) or 0.1% DMSO alone for control.

extract_protocol: For each immunoprecipitation, 5 x 10^7-1 x 10^8 cells were used. 1/10 volume of fresh 11% paraformaldehyde solution was added directly into the plates and cells were cross-linked for 15 minutes at room temperature. Cross-linking was stopped by adding glycine. Cells were washed and pelleted in PBS and resuspended in ice cold Lysis Buffer 1 for 10 minutes, then pelleted and resuspended in ice cold Lysis buffer 2 for another 10 minutes, and then the cells were pelleted and resuspended in ice cold Lysis buffer 3. After sonication, DNA fragments (<500 bp) were spun to pellet debris. For each immunoprecipitation 100 μL of Protein G Dynabeads (Invitrogen) were used. The beads were washed with Block Solution three times and resuspended in 250 μL Block Solution. The beads were incubated with 10 μg of RNAP II antibody at 4°C overnight. For ChIP-Seq, the N-20 antibody (Santa Cruz, sc-899) was used which recognizes the N-terminus of Rpb1. Then the beads were washed with Block Solution three times, resuspended in 100 μL of Block Solution, and incubated with the sonicated cell lysate at 4°C overnight. After the incubation, beads were washed four times with RIPA buffer, once with a buffer containing TE and 50 mM NaCl. Immunocomplexes were eluted for 30 minutes at 65°C with Elution buffer and the beads were removed with a magnetic concentrator. Reverse crosslinking was performed for both the immunoprecipitated DNA and for the input DNA samples by an incubation at 65°C for a minimum of six hours. DNA was purified through ethanol precipitation and then used for ChIP-Seq. The DNA fragments were isolated from an agarose gel, blunt-ended, ligated to the Solexa adaptors, and sequenced using the Illumina 1G Genome Analyzer.

value: HeLa

value: N-20 antibody (Santa Cruz, sc-899)

tag: treatment


title: RNA Pol II siRNA Gdown1 (reanalysis)

source_name: RNA Pol II siRNA Gdown1

value: Gdown1 siRNA treatment


title: Chicken_muscle

status: Public on Feb 20 2012

first: Tingting

address: 38 Xueyuan Rd

department: Medical informatics

institute: Peking University

description: chicken muscle RNA-seq

data_processing: Here we used TopHat to map the sequence reads to the UCSC chicken genome galGal3 with the following parameters: --mate-inner-dist = 50; --mate-std-dev = 1000. The remaining parameters were set to the default values. From reads distribution we found that more than half of reads are from Chr1. Checking the reads distribution in details we found that one ribosomal RNA RN28S1 might account for this abnormal reads number distribution. After removing reads located in this region (Chr1:104451000-104485000) and reads located in ChrM, 3 million reads were left.

organism: Gallus gallus

source_name: Skeletal muscle

growth_protocol: Chicken eggs (White Leghorn) were incubated at 37.5°C for 10 days (E10), 12 days (E12), 14 days (E14), 18 days (E18). All embryonic manipulations were conducted in accordance with the protocols of the Chinese Academy of Medical Sciences and the Institutional Animal Care and Use Committee of Peking Union Medical College.

extract_protocol: Skeletal muscles (pectoralis) were collected from chicken embryo incubated at 10 days (E10), 12 days (E12), 14 days (E14), 18 days (E18). All muscle samples were immediately frozen in liquid nitrogen and stored at -80Â°C until RNA isolation. Total RNA was isolated from skeletal muscles using the TRIzol reagent (Invitrogen) and fractionated by 6% denaturing polyacrylamide gel containing 7M urea (urea-PAGE). A RNA fraction with length ranging from 300-1600 nt were recovered from urea-PAGE.

value: embryo

tag: age

tag: tissue

value: muscle


title: RNA Pol II Flavo 5min (reanalysis)

source_name: RNA Pol II Flavo 5min

tag: cell line

value: 5min flavopiridol treatment


title: RNA Pol II Flavo 60min (reanalysis)

source_name: RNA Pol II Flavo 60min

tag: chip antibody

value: 60min flavopiridol treatment


title: RNA Pol II Control (reanalysis)

source_name: RNA Pol II Control


title: HUES48_shDNMT_control_p23_RRBS

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using MAQ bisulfite alignment mode.
References: Smith, Z. D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput bisulfite sequencing in mammalian genomes. Methods 48, 226-232, doi:S1046-2023(09)00111-X
Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7, 133-136, doi:nmeth.1414
Genome Build:
RRBS_cpgMethylation_HUES48_shDnmt_control_p23.RRBS.bed: hg18
RRBS_cpaMethylation_HUES48_shDnmt_control_p23.RRBS.bed: hg18
RRBS_cpcMethylation_HUES48_shDnmt_control_p23.RRBS.bed: hg18
RRBS_cptMethylation_HUES48_shDnmt_control_p23.RRBS.bed: hg18

source_name: hES HUES48 passage 23 infected with control shRNA against GFP

tag: cell type


title: HUES48_shDNMT3A_p23_RRBS

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using MAQ bisulfite alignment mode.
References: Smith, Z. D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput bisulfite sequencing in mammalian genomes. Methods 48, 226-232, doi:S1046-2023(09)00111-X
Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7, 133-136, doi:nmeth.1414
Genome Build:
RRBS_cpgMethylation_HUES48_shDnmt3a_7_p23.RRBS.bed: hg18
RRBS_cpaMethylation_HUES48_shDnmt3a_7_p23.RRBS.bed: hg18
RRBS_cpcMethylation_HUES48_shDnmt3a_7_p23.RRBS.bed: hg18
RRBS_cptMethylation_HUES48_shDnmt3a_7_p23.RRBS.bed: hg18

source_name: hES HUES48 passage 23 infected with control shRNA against DNMT3A


title: Gdown1 Flavo (reanalysis)

source_name: Gdown1 Flavo

value: Gdown1 antibody (in-house)


title: Gdown1 Control (reanalysis)

source_name: Gdown1 Control


title: Total RNA from Ipomoea batatas, initial tuberous roots

status: Public on Feb 18 2012

city: Chengdu

first: Yinghong

last: Gu

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

description: Illumina DGE tag profiling.

data_processing: Counts: 3' adaptor sequence removal: since tags are only 21nt long while the sequencing reads are 35nt long, raw sequences are with 3' adaptor sequences; Empty reads removal (reads with only 3' adaptor sequences but no tags); Low quality Tags removal (Tags with unknown sequences ‘N'); Removal of Tags which are too long or too short, leaving Tags of 21nt long; Removal of Tags with a copy number of 1 (probably a sequencing error); Generate Clean Tags.

organism: Ipomoea batatas

source_name: initial tuberous roots

growth_protocol: Stem cuts of sweet potato [I. Batatas (L.) Lam. cv. Xushu 18] were planted in June, 2009, and grown under normal conditions in Chengdu, Sichuan Province of China. Tissues of young leaves (YL), mature leaves (ML), and stems (Stem) were collected at 1.5 months after planting, and fibrous roots (FR), initial tuberous roots (ITR), expanding tuberous roots (ETR) and harvest tuberous roots (HTR) were collected at 1, 1.5, 3 and 5 months after planting, respectively.

extract_protocol: Total RNAs were extracted using the Trizol® Reagent (Invitrogen, USA), and treated with DNase I (Fermentas, USA) according to the manufacturer’s instructions. RNA integrity was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Double-stranded cDNA was synthesized using oligo (dT) beads. The cDNA was then digested with an anchoring restriction enzyme Nla III, which recognizes and cuts 3’ ‘CATG’. The digested cDNA samples were ligated to Illumina specific adapter A, containing a recognition site for enzyme Mme I. Following Mme I digestion, the Illumina specific adapter B containing a 2 bp degenerated 3’ overhangs was ligated. The adapter-ligated cDNA tag library was then enriched by PCR primers annealing to the adaptor ends. The PCR program was as follows: 30 s at 98 °C, followed by 15 cycles of 98 °C for 10 s, 60 °C for 30 s and 72 °C for 15 s, and then 72 °C for 5 min. After gel-purification, cDNA was used for cluster generation on separated flow cell lane. Sequencing by synthesis was performed using the Illumina Genome Analyzer II according to the manufacture’s protocol. Image analysis, base calling, extraction of tags and tag counting were performed using the Illumina pipeline.

value: initial tuberous roots

value: 1.5 months after planting


title: Total RNA from Ipomoea batatas, stems

description: Illumina DGE tag profiling.

source_name: stems

value: stems


title: Total RNA from Ipomoea batatas, mature leaves

description: Illumina DGE tag profiling.

source_name: mature leaves

value: mature leaves


title: Total RNA from Ipomoea batatas, fibrous roots

description: Illumina DGE tag profiling.

source_name: fibrous roots

value: fibrous roots

value: 1 month after planting


title: asbestos exposed SCC 54

status: Public on Jan 30 2012

type: RNA

city: Concord

first: Casey

middle: M

last: Wright

state: NSW

address: Gate 3, Hospital Road

country: Australia

institute: ADRI

description: Lung tumour from asbestos exposed individual (>20AB/gww)

hyb_protocol: Standard Illumina hybridisation protocols were used.

scan_protocol: Standard Illumina scanning protocols were used.

data_processing: Data was normalised using the 75th percentile algorithm in GeneSpring version 9.0 and missing values filled using the K-Nearest Neighbour algorithm.

source_name: Lung Tumour Tissue

label_protocol: Biotinylated cRNA was generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

extract_protocol: Total RNA was extracted from fresh-frozen tissue using TRIZOL (Invitrogen) and miRNEASY (QIAGEN) clean-up and quality assessed using the Agilent Bioanalyzer.

tag: sex

value: F

tag: smoking pack per year

tag: smoking status

value: Smoker

tag: tnm stage

value: IB

tag: self-reported asbestos exposure

value: Unknown

tag: asbestos count

tag: exposure

value: asbestos exposed individual (>20AB/gww)

value: lung tumor


title: non-exposed SCC 48

description: Lung tumour from non-exposed individual (0AB/gww)

value: M

value: non-exposed individual (0AB/gww)


title: asbestos exposed SCC 53

value: No


title: asbestos exposed SCC 51


title: non-exposed SCC 52

value: IIIB

value: Yes


title: non-exposed SCC 45

value: IIB


title: Total RNA from Ipomoea batatas, expanding tuberous roots

description: Illumina DGE tag profiling.

source_name: expanding tuberous roots

value: expanding tuberous roots

value: 3 months after planting


title: non-exposed SCC 46


title: non-exposed SCC 56


title: asbestos exposed SCC 39

value: IIA

value: unknown


title: non-exposed SCC 49

value: IA


title: asbestos exposed SCC 43


title: asbestos exposed SCC 47


title: non-exposed SCC 55


title: non-exposed SCC 42

value: F


title: asbestos exposed SCC 50

value: Smoker


title: non-exposed SCC 38

value: IB


title: non-exposed SCC 40


title: Total RNA from Ipomoea batatas, harvest tuberous roots

description: Illumina DGE tag profiling.

source_name: harvest tuberous roots

value: harvest tuberous roots

value: 5 months after planting


title: Total RNA from Ipomoea batatas, young leaves

description: Illumina DGE tag profiling.

source_name: young leaves

value: young leaves

value: 1.5 months after planting


title: asbestos exposed SCC 44

value: Never

value: asbestos exposed individual (>20AB/gww)

value: lung tumor


title: H3K27ac_ChIPSeq

city: Oxford

first: Monika

middle: S

last: Kowalczyk

state: Oxfordshire

address: Headley Way

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine, University of Oxford

description: Chromatin IP against H3K27ac

data_processing: The reads were aligned to the mm9 mouse genome build using bowtie (version 0.12.3) with indices on m2 (map twice to the genome).  Before downstream analysis duplicate reads of the same chromosome and start position were collapsed to a single representative read to exclude overrepresented PCR products. All aligned reads starts were summed in sliding windows of 300 bp to create summary windows.

source_name: sorted erythroid cells (Ter119+)

extract_protocol:
ChIPs were performed according to the Millipore ChIP protocol, as described previously (De Gobbi et al., 2007). For ChIP-Seq experiments, Ter119+ cells were fixed with 1% formaldehyde for 10 minutes at RT and chromatin was sonicated to a size <500 bp. Immunoprecipitations were performed, after an overnight incubation with the appropriate antibody, with protein A agarose (Millipore). A sample containing no antibody was used as a negative control. Immunoprecipitations were performed after an overnight incubation with the appropriate antibody with protein A agarose (Millipore). A sample containing no antibody was used as a negative control. Input and immunoprecipitated DNA were purified by phenol and chloroform extraction followed by ethanol precipitation. Subsequently the material was analysed by real time PCR (ABI Prism 7000 Sequence Detection System, Applied Biosystems) using a series of PCR amplicons and 5'FAM-3'TAMRA probes across the alpha-globin locus.
The library was constructed using Illumina protocol. The library was amplified prior to size selection (150-200bp).

treatment_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: erythroid cells

tag: strain

value: antiH3K27ac [Abcam ChIP grade ab 4729 lot730178]


title: M. truncatula-control

status: Public on May 09 2012

first: Tianzuo

last: Wang

address: No.20 Nanxincun, Xiangshan

department: State Key Laboratory of Vegetation and Environmental Change

institute: Institute of Botany, the Chinese Academy of Sciences

data_processing: Sequences of small RNAs were BLAST-matched to the Version MT3.0 of M. truncatula genome.

organism: Medicago truncatula

source_name: control

growth_protocol: Four M. truncatula (cv Jemalong A17) seedlings were grown in a pot (diameter 10 cm) filled with vermiculite: peat soil (2:1) under controlled conditions (26â day/ 20â night, 14-h photoperiod, and 50% relative humidity).

extract_protocol: To construct small RNA libraries, total RNA was extracted from control (CK) and drought stress (DS) shoots using the Trizol (Invitrogen) according to the manufacturerâs protocols. For each sample, the 18-30 nt small RNAs were ligated with 5' and 3' RNA adapter by T4 RNA ligase (TaKaRa) after they were purified by electrophoretic separation on a 15% TBE-urea denaturing PAGE gel, and at each step purified by urea PAGE gel electrophoretic separation. The RNA was subsequently transcribed to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen). Thereafter the cDNA was used as templates for double-stranded cDNA synthesis by PCR amplification using primers that anneal to adapters. The purified DNA was sequenced on a Solexa sequencer (Illumina).

treatment_protocol: Drought stress was initiated by withholding water supply to 3-week-old seedlings for varying periods after seedlings were fully watered until the severely wilted leaves appeared on the 14th day after water withholding. The soil water content was reduced from approx. 60% to 8.1% during the drought stress. Shoots under drought stress were harvested after withholding of water for 6, 8, 10 and 12 d, and mixed averagely as drought treatment materials (DS). The relative water content for leaves collected after 6, 8, 10 and 12 d drought stress was 87.4%, 78.8%, 75.2% and 68.3%, respectively. At the same time, shoots of M. truncatula seedlings grown under normal watering conditions were also harvested as control (CK). The relative water content for control leaves was 91.4%.

value: shoots


title: M. truncatula-drought stress

source_name: drought stress


title: asbestos exposed SCC 35

value: M

value: IIB

value: Yes


title: asbestos exposed SCC 31

value: No


title: asbestos exposed SCC 36

value: F

value: IIIA


title: non-exposed SCC 22

value: Smoker

value: IIIB

value: unknown

value: non-exposed individual (0AB/gww)


title: non-exposed SCC 27

value: IB


title: non-exposed SCC 25


title: asbestos exposed SCC 34

value: Never


title: non-exposed SCC 30


title: non-exposed SCC 33


title: non-exposed SCC 24

value: IA


title: asbestos exposed SCC 14

value: asbestos exposed individual (>20AB/gww)

value: lung tumor


title: asbestos exposed SCC 18


title: asbestos exposed SCC 15


title: non-exposed SCC 23


title: non-exposed SCC 12


title: asbestos exposed SCC 29


title: non-exposed SCC 20


title: non-exposed SCC 21


title: non-exposed SCC 10

value: IIA


title: non-exposed SCC 41


title: non-exposed SCC 19


title: asbestos exposed SCC 16


title: non-exposed SCC 17


title: asbestos exposed SCC 13


title: non-exposed SCC 11


title: H3K27me3_ChIPSeq

description: Chromatin IP against H3K27me3

extract_protocol:
ChIPs were performed according to the Millipore ChIP protocol, as described previously (De Gobbi et al., 2007). For ChIP-Seq experiments, Ter119+ cells were fixed with 1% formaldehyde for 10 minutes at RT and chromatin was sonicated to a size <500 bp. Immunoprecipitations were performed, after an overnight incubation with the appropriate antibody, with protein A agarose (Millipore). A sample containing no antibody was used as a negative control. Immunoprecipitations were performed after an overnight incubation with the appropriate antibody with protein A agarose (Millipore). A sample containing no antibody was used as a negative control. Input and immunoprecipitated DNA were purified by phenol and chloroform extraction followed by ethanol precipitation. Subsequently the material was analysed by real time PCR (ABI Prism 7000 Sequence Detection System, Applied Biosystems) using a series of PCR amplicons and 5'FAM-3'TAMRA probes across the alpha-globin locus.
The library was constructed using Illumina protocol. The library was amplified prior to size selection (150-200bp).
Model- GAIIx  Chemistry-SBS v4  cBot single generation kit with v4 flow cell  SCS 2.8  RTA 1.8  Recipe v7.4

value: erythroid cells

value: antiH3K27me3 Millipore (used to be Upstate) catalog number 07-449 lot DAM1641103


title: RNAP2_ChIPSeq

description: Chromatin IP against RNAP2

value: antiRNAP2 Santa Cruz catalog number H-224 lot K1709


title: non-exposed SCC 9

value: M

value: IIB


title: DNAse-Seq

source_name: erythroid cells

extract_protocol:
Nuclei from 5x107 mature primary erythroid cells, obtained from the spleen of a phenylhydrazine-treated adult mice as described (Spivak et al., 1973), were digested with increasing concentrations (10, 20, 40, 80U) of DnaseI (Roche 10776785001) and DNA was extracted by phenol/chloroform (Higgs et al., 1990). Since, as a general rule, the DHSs are not all equally intense and more than one concentration of DnaseI is required to detect them, 1.5 mg of DNA from each of digestion (10, 20, 40, 80U) was pooled and blunt-ended with T4 DNA Polymerase (NEB), and prepared for Illumina-Solexa sequencing following the manufacture's protocol. The DnaseI -digested material was amplified using PCR primer PE1.0 and PE2.0 for 10 cycles. A short extension time (15 seconds) was used to allow amplification of only the short fragments generated by the DnaseI digestion. Finally, the 200-500 bp window library was gel purified.
Model- GAIIx  Chemistry-SBS v4  cBot single generation kit with v4 flow cell  SCS 2.8  RTA 1.8  Recipe v7.4

treatment_protocol: DNAse I hypersensititivity digestion was performed on mouse primary erythroid cells were obtained from the spleens of acetylphenylhydrazine-treated mice  (Spivak et al., 1973; Vernimmen et al., 2009).


title: H3K4me1_ChIPSeq

description: Chromatin IP against H3K4me1

value: antiH3K4me1 Millipore catalog number 07-436 lot DAM1687548


title: non-polyA_RNASeq

description: wild type

data_processing: The reads were aligned to the mm9 mouse genome build using bowtie (version 0.12.3) with indices on m2 (map twice to the genome).  Before downstream analysis duplicate reads of the same chromosome and start position were collapsed to a single representative read to exclude overrepresented PCR products. The sam file was split into forward and reverse strand based on the sam biwise FLAG. All aligned reads starts were summed in sliding windows of 600 bp (increment of movement 60 bp) to create summary windows.

extract_protocol:
Total RNA was prepared using Trizol reagent (Sigma) and DNaseI treated (Ambion). The total RNA quality was assessed using Agilent Bioanalyser. RNA with overall RIN score >9 was used for further procedures. poly(A)- fraction was separated from mRNA (or poly(A)+) using PolyA selection kit (Promega) according to the manufacturer's protocol with the modification of keeping the poly(A)- fraction. poly(A)- fraction was depleted of ribosomal transcripts by using RiboMinus Eukaryote Kit for RNA-sequencing (Invitrogen) according to the manufacturer's protocol followed by RNA purification on RiboMinus Concentration Module (Invitrogen). The quality of obtained RNA samples was assessed using PicoChip (Agilent). The library was prepared according to DGE Small RNA Sample Prep kit (Illumina). Size selection 100-350bp
Model- GAIIx  Chemistry-SBS v4  cBot single generation kit with v4 flow cell  SCS 2.8  RTA 1.8  Recipe v7.4


title: asbestos exposed SCC 7

value: F


title: H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

value: antiH3K4me3 Millipore catalog number 05-745R clone 15-10C-E4 lot DAM1605007


title: Cel mixed N2 dsRNA GA2

status: Public on Jan 26 2012

city: Los Angeles

first: Fan

address: 675 Charles E Young Drive South

department: Pediatrics

institute: University of California Los Angeles

description: 3' adapter sequence: ATCTCGTATGCCGTCTTCTGCTTG

data_processing:
Abundance info of NR-seqs (*info.txt file): All reads are reduced to non-redundant (NR) sequences at first to minimize the computational requirement for subsequent analysis steps. Only NR-seqs that can map to the D. melanogaster (UCSC, dm3) or C. elegans (UCSC, ce6) genomes are shown (either trimmed or untrimmed).
NR-seq after trimming of 3'-adapters (*seq.fasta file): In order to detect 3'-adapter sequences, all NR-sequences are aligned to the Illumina 3'-adapter version 1.5 sequence using the "cross-match" program. The alignment parameters for cross-match are carefully tuned to maintain all alignments with less than 6% mis-matches. The cross-match alignment results are parsed using in-house Perl scripts. All NR-sequences that align to â¥ 6 bp of the 3'-adapter sequence at their 3' end are defined as short and are subsequently trimmed at the adapter-sequence boundary. The remaining NR-sequences (without detectable 3'-adapters) remain "untrimmed". Only NR-seqs that can map to the D. melanogaster (UCSC, dm3) or C. elegans (UCSC, ce6) genomes are shown (either trimmed or untrimmed).
Alignment (*loc.txt file): All trimmed and untrimmed NR-sequences are aligned to the D. melanogaster (UCSC, dm3) or C. elegans (UCSC, ce6) genomes using cross-match, with the program parameters set to guarantee all sequences that align with 6% mis-matches to the respective genome. Alignment results for trimmed or untrimmed inputs are then parsed independently using in-house Perl scripts. More specifically, alignments for trimmed sequences are required to extend to the ends of the query sequences, whereas alignments for untrimmed sequences are only required to extend to the imaginary positions of undetectable 3'-adapters (< 6 bp from the 3' end of the sequence). The true lengths of the untrimmed sequences are also determined in this step by the most-frequent aligned length of all possible alignments to the respective genome. At last, trimmed and untrimmed NR-sequences, as well as their genome loci information, are combined to form the final dataset using in-house Perl scripts. The smRNA libraries are pre-processed by this balanced pipeline as well.

organism: Caenorhabditis elegans

source_name: mixed stage N2 worms, dsRNA

extract_protocol: Total RNA was subjected to two rounds of rRNA depletion (Ribominus, Invitrogen (Carlsbad, CA)), and then treated with a single-strand specific ribonuclease (RNase One, Promega (Madison, WI)) for dsRNA-seq or with a double-strand specific ribonuclease (RNase V1, ABI (Foster City, CA)) for ssRNA-seq, all per manufacturer's instructions. The RNA samples are then used as the substrate for sequencing library construction using the Small RNA Sample Prep v1.5 kit (Illumina, San Diego, CA) as per manufacturer's instructions.

tag: target molecules

value: double-stranded RNA (dsRNA)

value: whole organism

tag: rnase treatment

value: ssRNase (RNase One)


title: Dme DL1 dsRNA Hiseq

source_name: DL1 cells, dsRNA


title: Cel mixed N2 smRNA GA2

source_name: mixed stage N2 worms, smRNA

value: small RNA (smRNA)


title: Dme DL1 smRNA GA2

source_name: DL1 cells, smRNA


title: Cel mixed N2 ssRNA GA2

source_name: mixed stage N2 worms, ssRNA

value: single-stranded RNA (ssRNA)

value: dsRNase (RNase V1)


title: Dme DL1 ssRNA GA2

source_name: DL1 cells, ssRNA


title: Dme DL1 ssRNA Hiseq


title: Cel mixed N2 ssRNA Hiseq


title: asbestos exposed SCC 8

value: Smoker

value: unknown

value: asbestos exposed individual (>20AB/gww)


title: Dme DL1 dsRNA GA2


title: non-exposed SCC 5

value: IB

value: No

value: non-exposed individual (0AB/gww)

value: lung tumor


title: Cel mixed N2 dsRNA Hiseq


title: non-exposed SCC 4

value: M


title: asbestos exposed SCC 6

value: IA

value: Yes


title: asbestos exposed SCC 2


title: asbestos exposed SCC 1


title: Input

status: Public on Jan 12 2012

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing: Sequence reads were compiled and mapped to the mouse genome (mm9) using Illumina pipeline software. Peaks were called using the QuEST software at a threshold of 15 against "input.extended.txt". Threshold was raised post-QuEST to attain an FDR of at most 1%.

source_name: pre-B cell, pro-B cell

growth_protocol: IRF-4,8-/- pre-B cells were cultured in Opti-MEM (Invitrogen) media supplemented with 5% FCS and 5 ng/mL of IL-7.

extract_protocol: 100 ng of immunoprecipitated DNA was blunt ended and adaptor ligated. 0.05 l of undiluted the Illumina adaptors were ligated per library preparation and amplified via PCR. Fragments were then gel purified using Qiagen Minelute kit.

treatment_protocol: Chromatin was isolated from IRF-4,8-/- pre-B cells cultured with 0.1 ng/mL of IL-7 for 48 hr. The chromatin was sonicated to obtain DNA fragments ranging in size from 100 to 500 bp. Chromatin fragments were immunoprecipitated using anti-FoxO1 or anti-Pax5. After reversal of formaldehyde crosslinks, specific DNA sequences were assessed by quantitative real-time PCR for verifying ChIP efficiency.

value: IRF-4,8-/- pre-B cell; Rag2-/- pro-B cell

tag: antibody

value: none, input


title: FoxO1_ChIPseq

source_name: pre-B cell

value: IRF-4,8-/- pre-B cell

tag: antibody vendor

value: Abcam

tag: antibody catalog #


title: Pax5_ChIPseq

value: Santa Cruz


title: asbestos exposed SCC 3

tag: age

tag: tissue


title: mouse_testes.B

status: Public on Jan 05 2012

city: Cambridge

first: Robert

middle: K

last: Bradley

address: 77 Massachusetts Avenue, 68-223A

department: Biology

institute: MIT

data_processing:
Alignment: The files human.nagnag.junctions.gff and mouse.nagnag.junctions.gff (see Series supplementary files) give the intron-proximal and intron-distal splice junctions of all NAGNAG splicing events analyzed in this study. The 'start' field specifies the last base of the upstream exon and the 'end' field specifies the first base of the downstream exon (upstream and downstream defined with respect to the gene). For each NAGNAG, we extracted the transcript sequence flanking the proximal and distal 3' splice sites and used Bowtie version 0.12.7 to map reads to these two sequences. We required that short reads have at least 6 nt on either side of the splice junction (an "overhang" of 6 nt), and furthermore that there be no mismatches within the overhang region.
Human genome build: hg19
Mouse genome build: mm9

molecule: polyA RNA

source_name: testes

extract_protocol:
Human: RNA-Seq libraries are from the Body Map 2.0 dataset distributed by Illumina, available at the ENA archive with accession number ERP000546.
Mouse: Tissues from a 10-week-old male were extracted immediately after death and stored in RNAlater per the manufacturerâs instructions (Ambion). Tissue was lysed in Trizol and RNA was extracted with Qiagen miRNeasy mini columns. Using 5ug of total RNA, we performed polyA selection and prepared strand-specific libraries for Illumina sequencing following the dUTP protocol and the SPRIworks Fragment library system (Beckman Coulter). We obtained final insert sizes of approximately 160 bp. We sequenced these libraries using the Illumina HiSeq 2000 and the GAIIx machines.

tag: library type

value: paired-end

tag: read length

tag: insert size

tag: insert standard deviation


title: mouse_spleen.A

source_name: spleen


title: mouse_brain.A

source_name: brain


title: mouse_skeletal_muscle.A

source_name: skeletal muscle


title: mouse_kidney.A

source_name: kidney


title: mouse_lung.A

source_name: lung


title: mouse_skeletal_muscle.B


title: Flag-Evi1 input DNA

status: Public on Jan 15 2012

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description: DNA from chromatin before ChIP

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, hg18) using Eland software with maximal 2 mis-matches.
The sequencing data were mapped to the human reference genome (NCBI v36, hg18), peaks were called and fold change of ChIP DNA versus input DNA was calculated for each peak as described previously (Chen et al., 2008)

source_name: SKOV-3 cells

growth_protocol: SKOV-3 cells (ATCC, HTB-77) were grown at 37degres in 10%FBS RPMI. They were passaged every 3-4 days. P8, P9, P10, P11 in the sample names refer to the cell passage number.

extract_protocol:
SKOV3 cells were crosslinked with 1% formaldehyde for 10min at room temperature. Cells were resuspended in lysis buffer (50 mM Hepes KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate) supplemented with 0.1% SDS. After 15min incubation, the nuclei pellet was obtained by centrifugation and washed once with the same 0.1% SDS lysis buffer. The nuclei pellet was then incubated for 15min in lysis buffer supplemented with 1% SDS to break the nuclear membranes. The chromatin was pulled-down by centrifugation at 47,000g for 30min. The supernatant (nucleoplasm) was removed and the chromatin pellet was resuspended in lysis buffer with 0.5% SDS. Sonication was used to generate fragments of 200-500 bp. The chromatin was diluted with 3 volumes of Dilution buffer (50 mM Hepes pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% NP40) and precleared 3hrs to overnight with Dynabeads Protein G (Invitrogen). The chromatin after preclear was used as input DNA and  for the ChIP.
10ng of ChIP material, respectively, as per manufacturers protocol. Briefly, using the Solexa ChIP Seq DNA sample preparation kit universal linkers were added to the chromatin fragments and DNA was PCR amplified for 15 cycles. DNA was gel-purified and fragments between 200-300bp were selected for sequencing

treatment_protocol: SKOV-3 cells were transfected with pCMV-Flag-Evi1 plasmid 3 days before harvest. Then the cells were fixed in 1 % formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 125mM glycine before chromatin extract preparation

tag: cell type

value: ovarian carcinoma cell line

tag: cell line

value: SKOV-3 cells

tag: chip sample

value: Flag-Evi1 input

tag: chip antibody

value: (ATCC, HTB-77)


title: mouse_testes.A


title: Flag-Evi1 ChIP DNA

description: ChIP was performed using Flag M2 antibody (Sigma)

value: Flag-Evi1 ChIP


title: non-exposed SCC 28

source_name: Lung Tumour Tissue

tag: sex

tag: smoking pack per year

tag: smoking status

value: Smoker

tag: tnm stage

value: IIIA

tag: self-reported asbestos exposure

value: No

tag: asbestos count

tag: exposure


title: mouse_spleen.B

tag: strain


title: mouse_liver.B

source_name: liver


title: mouse_kidney.B


title: mouse_colon.B

source_name: colon


title: mouse_lung.B