title: HCT116_H3K27ac

status: Public on Jun 12 2012

city: Columbus

first: rui

last: wang

state: OHIO

address: 212 Biomedical Research Tower,460 West 12th Ave

institute: Ohio State University

description: 2 replicates

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat with default parameters
ChIP-seq sequence reads were aligned to the UCSC human genome assembly HG19 using the Eland pipeline (Illumina).
ChIP-seq peaks were called using Solesearch (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) with the following settings: 250 bp fragments, alpha-value=0.0001, FDR=0.001, histone modification analysis.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peak files in gff format, peaks are called from the merged of all replicated samples.

source_name: Human colorectal cancer cell-line HCT116

growth_protocol: Thawing Cells:  1. Thaw vial immediately in 37º C water bath. Keep O ring above the water surface to prevent contamination. Thaw content with slight  shake until only small ice is left in vial. It usually takes 1 min. Spray vial with 70% ethanol all over and wipe its surface with clean tissue in the hood.  2. Open the vial and transfer the content to a 15 ml Falcon tube already containing 5 ml of fresh medium.  3. Spin down at 1000 rpm or 200g for 3 to 5 mins at 4º C. Aspirate supernatant.  4. Resuspend cells in fresh medium and transfer to 150mm x 25mm tissue culture dish.  5. Check the cells under microscope.  6. Cells are cultured in CO2 incubator and medium is changed about every 3 days.  7. It usually takes 3 days or more for cells to recovery from freezing. After cell culture reaches  80-85%  confluence, subculture is conducted. Subculture ratio is about 1:3 or 1:4.  Passaging Cells:  1. Observe cells to see how confluent they are, whether the cells are alive, whether the cells are contaminated, and whether the cells have the correct morphology. After cell culture reaches 80 to 85% confluence, subculture is conducted  2. Remove media from dish  3. Wash 1x with 10 ml of PBS  4. Add 5 ml of Trypsin and trypsinize for 3 min at 37C. Whack hard – you should see the cells coming down. (Important: never overtrypsinize the cells, so work quickly)  5. Add 5 ml of media and use it to rinse the dish to detach the cells off (4 to 5 times)  6. Spin down at 1000rpm for 3 to 5 min at room temperature. Aspirate supernatant  7. Add 15 ml of media to 15ml tube containing cell pellet, and pipette up and down to mix  8. Add 15 ml of media to each new 150mm x 25mm tissue culture dish (we split 1 dish into 3 to 4 dishes)  9. Add 5mls of cell culturecontaining media to each tissue culture dish. Make sure the media covers the entire area of the dish. Put the cells into 37C with 5% CO2.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10-14 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell-line

tag: passage


title: T47D_E2_R1

status: Public on Jun 13 2012

type: SRA

city: Huntsville

first: Jason

last: Gertz

state: AL

address: 601 Genome Way

country: USA

institute: HudsonAlpha Institute

library_source: transcriptomic

data_processing:
To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value

molecule: polyA RNA

organism: Homo sapiens

source_name: Breast cancer cell line

growth_protocol: Both ECC-1 and T-47D were grown on phenol red-free RPMI-1640 supplemented with 10% dextran/charcoal treated fetal bovine serum for five days.  RNA lysate was harvested from 100 mm dishes

extract_protocol: mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment.  Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41.

treatment_protocol: Cells were treated with either 10 nM 17β-estradiol, 100 nM genistein, 100 nM bisphenol A or 0.02% DMSO (vehicle control) for 8 hours before harvesting.

tag: treatment

value: 8 hour 10 nM 17β-estradiol

tag: replicate

tag: cell line


title: Phenantroline Raji WT

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

library_source: genomic

data_processing:
Pre-processing and pipeline  Phenantroline samples were sequenced on an Illumina Genome Analyzer and aligned against the human (hg18, build 36.1) 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: Human samples : HG18
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.

molecule: genomic DNA

source_name: Human Raji WT

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.

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 phenantroline 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: A total of 2.E7 Raji cells was resuspended in Solution I and permeabilized using NP40 as described for MNase digestion. Instead of MNase, we added 80μM CuCl2, 0.4mM 10,1- phenantroline (stock in absolute ethanol), 3.2mM ascorbic acid and 320μM H2O2 with Solution II, similar to concentrations used previously(2). Reactions were incubated for 2h at room temperature and stopped with the addition of EDTA to a final concentration of 10mM. Cells were then lyzed and purified as for the MNase experiments. 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: tissue

value: Burkitt's lymphoma

tag: passages

value: Raji

value: 0.4mM 10,1- phenantroline


title: middle-age donor

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description: Whole genome bisulphite sequencing.

data_processing:
Read mapping: Two reference sequences were prepared based on the hg19 human reference; referenceC2T had the C residues replaced by T's, and referenceG2A had the G's replaced by A's. Two sets of reads were generated in the same way; setC2T with the C's replaced by T's, and setG2A with the G's replaced by A's.  Both sets of reads were aligned to each of the two references, producing four sets of mappings. This mapping strategy allowed reads to be aligned irrespective of the methylation status of any C residues.  The alignment was performed using the GEM alignment software allowing up to 4 mismatches in high quality bases (bases with quality scores > 25). Uniquely mapping read pairs were used to generate an empirical distribution of insert sizes of each of the libraries, and this is information was used to select read pairs with unique compatible mappings.
The bisulfite conversion followed by a PCR step generates 4 different strands; the original + and - strands along with their complements.  Reads derived from the original + strand (and its complement) will align to referenceC2T, while reads from the original - strand (and complement) will align to referenceG2A.  Both members of a read pair are derived from the same original strand, and >99% of mapped reads could have the original strand assigned unambiguously. By keeping the information on the original strand origin of each read pair, the methylation status of C residues on either of the two original strands can be inferred along with the underlying genotypes, because any conversion due to the bisulphite treatment will only be seen on read pairs deriving from one of the two original strands.

Methylation call files were generated using Bismark methylation call procedure from the bam aligned files and then processed as a bed files with columns showing : Chromosome, initial and end position of this Cpg and its methylation value

source_name: middle-age donor

extract_protocol: For normal BS-seq library constructing, 10μg genomic DNA was fragmented using a Covaris sonication system (Covaris S2). Following fragmentation, libraries were constructed using the Illumina Paired-End protocol consisting of end repair, <A> base addition and methylated-adaptor ligation. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size were excised from the same lane of a 2% TAE agarose gel. Normally, three bands are excised corresponding to DNA insert sizes of 80–100 bp, 100–120 bp to 120–150bp. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. PCR was carried out in a final reaction volume of 50μl consisting of 20μl purified DNA, 4μl 2.5 mM dNTP, 5 μl 10X buffer, 0.5 μl JumpStart™ Taq DNA polymerase, 2μl 10uM PCR primers and 37.5 μl ΜltraPure TM Water and the following thermal cycling program: 94ºC 30 s, 10 cycles of 94ºC 30 s, 60ºC 30 s, 72ºC 30 s then prolong with 1 min at 72ºC. PCR products were sequenced with a HiSeq2000. The alignment was performed using GEM.

treatment_protocol: Peripheral blood was obtained from a healthy donor (age 26). Peripheral blood mononuclear cells (PBMCs) were extracted using a Ficoll gradient. To separate CD19-positive cells, CD19 MicroBeads Kit (Miltenyi Biotec) was applied following the manufacturer's instructions.  DNA was extracted using Phenol:Chloroform:Isoamylalcohol (Sigma).

tag: age

value: 26 years

tag: disease status

value: healthy

tag: source tissue

value: peripheral blood

tag: cell type

value: mononuclear cells


title: MnaseSeq + a-amanitin36hrs Raji WT

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.

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: 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.

value: 2.5 ug/ml of alpha-amanitin for 36 hrs


title: MnaseSeq + a-amanitin24hrs Raji WT

value: 2.5 ug/ml of alpha-amanitin for 24 hrs


title: ECC1_GEN_R1

source_name: Endometrial cancer cell line

value: 8 hour 100 nM genistein


title: T47D_BPA_R2

value: 8 hour 100 nM bisphenol A


title: MCF7_H3K4me1

description: 3 replicates

source_name: Human breast adenocarcinoma cell-line MCF7

tag: chip antibody

value: H3K4me1 (CellSignalingTechnologies, 9723S, lot#1)


title: MCF7_H3K9me3

description: 3 replicates

value: H3K9me3 (CellSignalingTechnologies, 9754S, lot#1)


title: MCF7_H3K27me3

description: 3 replicates

value: H3K27me3 (CellSignalingTechnologies, 9733S, lot#5)


title: MCF7_H3K27ac

description: 2 replicates


title: MnaseSeq Raji WT


title: HCT116_H3K4me1

description: 2 replicates


title: Total PolII (N20) Raji WT

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.

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: antibody

value: PolII

tag: vendor/catalog#

value: Santa Cruz/sc-899x


title: Input Raji WT


title: Total PolII (N20) + a-amanitin36hrs Raji WT


title: Input mouse ES

organism: Mus musculus

source_name: Mouse ES-cells

value: ES

tag: strain

tag: developmental stage


title: V5-tagged REX1 pulldown

city: Rotterdam

first: Eskeatnaf

last: Mulugeta Achame

state: Rotterdam

address: Dr Molewaterplein 50

department: Reproduction and Development

country: Netherlands

institute: Erasmusmc

data_processing:
Basecalling , Illumina pipeline 1.7.0
Read Alignment, Eland, Illumina pipeline 1.7.0
import, filter,  normalize and coverage calculation, using R based bioconductor packages (Shortread and ChIP-Seq packages)
peak calling using using R based bioconductor package(MACS)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: V5-tagged REX1_ESCs

growth_protocol: Female ESCs expressing V5-tagged REX1 and control wild-type ESCs were grown without feeders to 80% confluence (3·107 cells per ChIP or 1·108 cells per ChIP-seq).

extract_protocol: Purified ChIP-DNA was prepared for sequencing on a HiSeq 2000 sequencer using Illumina standerd protocol.

treatment_protocol: For ChIP-seq the cells were treated for 3 h with proteasome inhibitor (15uM, MG132, Sigma) before chromatin was cross-linked for 10 min at RT with 1% formaldehyde. The cross-linking reaction was stopped by addition of 0.125 M glycine.

value: Cast/Eij /129/Sv

tag: genotype/variation

value: expressing V5-tagged REX1

value: Embryonic stem cell (ESC)

value: Anti-V5 Agarose Affinity Gel antibody produced in mouse purified    immunoglobulin, clone V5-10

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat. #

tag: chip antibody lot #


title: TSS RNA mouse DP

data_processing: Pre-processing and pipeline  Samples were sequenced on an Illumina Genome Analyzer. We obtained the raw sequences and detected and removed the adapter  sequences using the MIRO pipeline (http://seq.crg.es/main/bin/view/Home/MiroPipeline). The  obtained reads were aligned against the mouse genome using the GEM aligner  (http://gemlibrary.sourceforge.net). Only unambiguously aligned tags were used for further  analysis.

molecule: total RNA

source_name: DP T-cells

growth_protocol: 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).

extract_protocol: Small RNAs were purified from a 10% denaturing urea polyacrylamide gel, essentially as  described in the Illumina Small RNA Rev. B protocol with some minor modifications (see treatment section) to yield directional short RNAseq profiling.

treatment_protocol: Total RNA was extracted using TRIzol (Invitrogen, USA) according to the manufacturer’s  instructions with some modifications to ensure higher recovery rates of small RNAs. In brief,  sorted CD4+/CD8+ cells were divided into 1x107 aliquots and 1ml of TRIzol was added. Cells  were lysed with vigorous vortexing and pipetting. Homogenized samples were incubated at  room temperature for 5 minutes and 0.2ml of chloroform was added. Samples were vigorously  shaken and incubated at room temperature for an additional 5 minutes. Phase separation was  carried out by centrifugation at 4°C and 12,000g in a tabletop centrifuge for 15 minutes. The  aqueous phase was transferred to fresh tubes and 1.5 volumes (approximately 1ml) of  isopropanol together with 10μg of linear acrylamide (Ambion, USA) were added. Samples were  vortexed and incubated at room temperature for 15 minutes. The precipitated RNA was pelleted  by centrifugation at 4°C and 12,000g in a tabletop centrifuge for 20 minutes. Pellets were  washed with 80% ethanol, vortexed and centrifuged at 4°C and 7,500g in a tabletop centrifuge  for 10 minutes. Pellets were allowed to air-dry and resuspended in nuclease-free water  (Ambion, USA). DNA was digested using the rigorous Turbo DNase (Ambion, USA) treatment  as per manufacturer’s instructions. RNA quantity was measured on a Nanodrop 1000 and the  quality was verified using RNA Nano chips on a 2100 Bioanalyzer (Agilent, USA).  Small RNAs were purified from a 10% denaturing urea polyacrylamide gel, essentially as  described in the Illumina Small RNA Rev. B protocol with some minor modifications.  Approximately 10μg of total RNA was run at 200V for 1 hour, until the blue front reached the  bottom of the gel. We used 21G needles to puncture holes into the bottom of two 0.5ml and  placed them into 2ml eppendorf tubes. RNA corresponding to 15nt-70nt was cut from the gel,  diagonally cut in half and separately transferred into the 0.5ml tubes. The gel was crushed into  the 2ml tubes by a two minute centrifugation at 14,000rpm. For gel elution by soaking, 0.4ml of  0.3M NaCl was added to each tube, before a 4 hour rotation at room temperature. After removal  of gel particles using 0.22μm cellulose acetate filters, 10μg of linear acrylamide (Ambion, USA)  and 2.5 volumes (approximately 1ml) of ice-cold absolute ethanol were added. After a 30 minute  incubation at -80°C, the eluted RNA was precipitated by centrifugation at 4°C and maximum  speed for 45 minutes. The pellet was washed with 1ml of room temperature 80% ethanol and  resuspended in 5.7μl of water. This PAGE purification step was repeated after both the 5’ and 3’  adapter ligations, which were carried out according to the protocol. The resulting cDNA was  purified with the QIAquick Gel Extraction kit (Qiagen, Germany) using the DNA cleanup protocol  modification in order to retain DNA fragments as low as 70bp. The DNA was quantified using a  Nanodrop 1000 (Thermo Scientific, France) and verified using DNA High Sensitivity 2100  Bioanalyzer chips (Agilent, USA). The library was clustered and sequenced using 76 cycles on  a Genome Analyzer II (Illumina, USA) according to manufacturer’s instructions.

value: Thymus

value: Double Positive Thymocytes


title: HistoneH3 mouse DP


title: PSU_ChipSeq_Erythrobl_H3K36me3

status: Public on Jun 11 2012

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

source_name: Erythrobl

tag: lab

value: PSU-m

tag: lab description

value: Hardison - Penn State University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: Erythrobl

tag: cell organism

value: mouse

tag: cell description

value: Erythroblast, ter119+ cells from liver

tag: cell sex

value: B

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: age description

value: Embryonic day 14.5

tag: control

tag: control description

value: No special treatment or protocol applies

tag: controlid

tag: replicate

tag: strain description

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: PSU_ChipSeq_Erythrobl_H3K9me3

tag: lab

tag: lab description

tag: antibody

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

tag: age

tag: strain


title: PSU_ChipSeq_CH12_H3K4me1

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: B-cell lymphoma (GM12878 analog)

value: F

value: rabbit polyclonal. Antibody Target:H3K4me1

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

value: immortalized

value: Immortal cells

value: Input

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

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: PSU_ChipSeq_Erythrobl_H3K27me3

value: PSU-m

value: Hardison - Penn State University

value: ChipSeq

value: Chromatin IP Sequencing

value: Erythrobl

value: mouse

value: Erythroblast, ter119+ cells from liver

tag: cell sex

value: B

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid


title: PSU_ChipSeq_CH12_H3K9me3

value: B-cell lymphoma (GM12878 analog)

value: F

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

value: Abcam

tag: age description

tag: control

tag: control description

value: No special treatment or protocol applies

tag: controlid

tag: replicate


title: PSU_ChipSeq_Megakaryo_H3K36me3

source_name: Megakaryo

tag: lab

value: PSU-m

tag: lab description

value: Megakaryo

value: Megakaryocyte

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K36me3

value: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.

tag: age

value: Embryonic day 14.5

tag: strain description

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: Wild type

tag: strain

value: Cast/Eij /129/Sv

tag: genotype/variation

value: wild type

tag: cell type

value: Embryonic stem cell (ESC)


title: PSU_ChipSeq_CH12_H3K27me3

value: Hardison - Penn State University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27me3

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

value: Millipore

value: immortalized

value: Immortal cells

value: Input

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

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: PSU_ChipSeq_Erythrobl_Input

value: PSU-m

value: Erythrobl

value: Erythroblast, ter119+ cells from liver

value: B

tag: antibody description

tag: age description

value: Embryonic day 14.5

tag: control

tag: control description

tag: controlid


title: PSU_ChipSeq_G1E-ER4_H3K9me3

tag: lab

tag: lab description

value: Hardison - Penn State University

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: M

tag: antibody

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

tag: antibody targetdescription

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: age

value: Embryonic day 0 (stem cell)

value: No special treatment or protocol applies

tag: replicate

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_Erythrobl_H3K4me1

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

value: rabbit polyclonal. Antibody Target:H3K4me1

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

tag: strain

tag: strain description

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: PSU_ChipSeq_Megakaryo_H3K9me3

value: PSU-m

value: Megakaryo

tag: cell description

value: Megakaryocyte

tag: cell sex

value: B

tag: antibody antibodydescription

tag: age description

tag: control


title: PSU_ChipSeq_Megakaryo_Input

tag: lab

tag: lab description

value: Hardison - Penn State University

tag: antibody

value: Input

tag: antibody description

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

value: Embryonic day 14.5

tag: control description

tag: controlid


title: PSU_ChipSeq_G1E-ER4_H3K27me3

tag: datatype

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: M

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: age

value: Embryonic day 0 (stem cell)

tag: replicate


title: PSU_ChipSeq_G1E_H3K9me3

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Gata1- erythroid progenitor

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

value: Abcam

value: No special treatment or protocol applies

tag: strain

tag: strain description

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_G1E-ER4_H3K4me1

tag: lab

value: PSU-m

tag: lab description

value: Hardison - Penn State University

tag: cell sex

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me1

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

tag: age description

tag: control


title: Total PolII (N20) + a-amanitin24hrs Raji WT

tag: tissue

value: Burkitt's lymphoma

tag: passages

tag: cell line

value: Raji

tag: antibody

value: PolII

tag: vendor/catalog#

value: Santa Cruz/sc-899x

tag: treatment

value: 2.5 ug/ml of alpha-amanitin for 24 hrs


title: PSU_ChipSeq_G1E_H3K4me3

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: M

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: antibody targetdescription

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

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: age

value: Embryonic day 0 (stem cell)

value: Input

tag: control description

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

tag: controlid

tag: replicate


title: PSU_ChipSeq_G1E_H3K4me1

tag: lab

value: PSU-m

tag: lab description

value: Hardison - Penn State University

tag: cell organism

value: mouse

tag: cell description

value: Gata1- erythroid progenitor

tag: cell sex

tag: antibody antibodydescription

value: Abcam

tag: age description

tag: control

tag: strain

tag: strain description

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_CH12_H3K36me3

tag: datatype

tag: datatype description

tag: cell

value: B-cell lymphoma (GM12878 analog)

value: F

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.

value: immortalized

value: Immortal cells

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: PSU_ChipSeq_G1E_H3K36me3

value: ChipSeq

value: Chromatin IP Sequencing

value: M

tag: antibody vendorname

tag: antibody vendorid

tag: age

tag: control description

tag: controlid


title: PSU_ChipSeq_Megakaryo_H3K4me3

tag: lab

tag: lab description

value: Megakaryo

tag: cell organism

tag: cell description

value: Megakaryocyte

value: B

value: rabbit polyclonal. Antibody Target:H3K4me3

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

value: Millipore

value: Embryonic day 14.5

value: Input

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

tag: replicate

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: PSU_ChipSeq_CH12_H3K4me3

value: PSU-m

value: Hardison - Penn State University

value: mouse

value: B-cell lymphoma (GM12878 analog)

tag: cell sex

value: F

tag: antibody antibodydescription

tag: age description

tag: control

tag: strain


title: PSU_ChipSeq_Megakaryo_H3K4me1

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me1

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

value: Abcam

tag: strain description


title: PSU_ChipSeq_G1E-ER4_H3K36me3

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: B

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.

tag: antibody vendorname

tag: antibody vendorid

tag: age

value: Embryonic day 0 (stem cell)

tag: control description

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_Megakaryo_H3K27me3

tag: lab

tag: lab description

value: Megakaryo

tag: cell organism

tag: cell description

value: Megakaryocyte

value: rabbit polyclonal. Antibody Target:H3K27me3

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

value: Millipore

value: Embryonic day 14.5

value: No special treatment or protocol applies

tag: controlid

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: PSU_ChipSeq_Erythrobl_H3K4me3

value: PSU-m

value: Hardison - Penn State University

value: ChipSeq

value: Chromatin IP Sequencing

value: Erythrobl

value: mouse

value: Erythroblast, ter119+ cells from liver

tag: cell sex

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

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

tag: age description

tag: control

tag: replicate


title: PSU_ChipSeq_CH12_Input

tag: datatype

tag: datatype description

tag: cell

value: B-cell lymphoma (GM12878 analog)

value: F

tag: antibody

value: Input

tag: antibody description

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

value: immortalized

value: Immortal cells

tag: strain

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: Arabidopsis rdr2-1 mutant inflorescence

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
Sample name: rdr2
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
rdr2_adapters_trimmed.txt: TAIR9

organism: Arabidopsis thaliana

source_name: immature inflorescence

extract_protocol: Small RNA libraries  were constructed as previously described (Lu et al. 2007 PMID:17889797) and sequenced on an Illumina GAIIx instrument at University of Delaware.

tag: background

tag: genotype/variation

value: rdr2-1 mutant

tag: tissue

value: immature inflorescence


title: Arabidopsis nrpd1a-4 mutant (Pol IV mutant) inflorescence

description:
Sample name: nrpd1
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
nrpd1_adapters_trimmed.txt: TAIR9

value: nrpd1a-4 mutant (Pol IV mutant)


title: Arabidopsis dms3-1 mutant inflorescence

description:
Sample name: dms3-1
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
dms3_adapters_trimmed.txt: TAIR9

value: dms3-1 mutant


title: Arabidopsis rdm1-4 mutant inflorescence

description:
Sample name: rdm1-4
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
rdm1_adapters_trimmed.txt: TAIR9

value: rdm1-4 mutant


title: PSU_ChipSeq_G1E_H3K27me3

tag: lab

value: PSU-m

tag: lab description

value: Hardison - Penn State University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: Gata1- erythroid progenitor

value: M

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: age

value: Embryonic day 0 (stem cell)

tag: control description

tag: strain description

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_G1E-ER4_H3K4me3

tag: datatype

tag: datatype description

value: mouse

tag: cell description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

tag: cell sex

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

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

tag: age description

tag: control

value: Input

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

tag: controlid

tag: replicate


title: PSU_ChipSeq_G1E_Input

tag: lab

value: PSU-m

tag: lab description

tag: cell

tag: antibody

tag: antibody description

tag: strain


title: Arabidopsis dms4-1 mutant inflorescence

description:
Sample name: dms4-1
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
dmS4_adapters_trimmed.txt: TAIR9

tag: background

tag: genotype/variation

value: dms4-1 mutant

tag: tissue

value: immature inflorescence


title: Arabidopsis drd1-1 mutant inflorescence

description:
Sample name: drd1-1
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
drd1_adapters_trimmed.txt: TAIR9

value: drd1-1 mutant


title: Arabidopsis control plant inflorescence, control for dms4-1, drd1-1, dms3-1, and rdm1-4 mutants

description:
Sample name: Wt (T+S)
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
wtedt_adapters_trimmed.txt: TAIR9

value: wildtype (control for dms4-1, drd1-1, dms3-1, and rdm1-4 mutants previously described in Kanno et al. 2004 Current Biology, PMID:15120073)


title: Arabidopsis nrpd1b-1 (Pol V) mutant inflorescence, barcoded with 5' "AG" - biological replicate 2

description:
Sample name: nrperep2
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
nrpe_2_adapters_trimmed.txt: TAIR9

value: nrpd1b-1 (Pol V) mutant


title: Arabidopsis nrpd1b-1 (Pol V) mutant inflorescence, barcoded with 5' "AG" - biological replicate 3

description:
Sample name: nrperep3
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
nrpe_3_adapters_trimmed.txt: TAIR9


title: Arabidopsis wildtype Col-0 inflorescence, barcoded with 5' "AG" - biological replicate 3

description:
Sample name: Colrep3
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
Col_3_adapters_trimmed.txt: TAIR9

value: wildtype


title: Arabidopsis wildtype Col-0 inflorescence, barcoded with 5' "AG" - biological replicate 2

description:
Sample name: Colrep2
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
Col_2_adapters_trimmed.txt: TAIR9


title: Arabidopsis wildtype Col-0 inflorescence, barcoded with 5' "AG"-biological replicate 1

description:
Sample name: Colrep1
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
Col_1_adapters_trimmed.txt: TAIR9


title: female liver RNA-Seq

city: Bethesda

first: Pavel

middle: P

last: Khil

state: MD

address: 5 Memorial Dr.

institute: NIDDK

data_processing:
Basecalls were performed using CASAVA versions 1.7.0-1.8.0
Alignment to MonDom5 assembly of Monodelphis domestica genome was performed using BWA 0.5.9rc1 with default parameters.
Genome_build: MonDom5
Supplementary_files_format_and_content: bedGraph files were created from BAM files using genomeCoverageBed (part of bedtools package v. 2.15.0). BAM files were generated using BWA 0.5.9rc1. Only "properly-paired"  reads (0x2 SAM flag) were used

organism: Monodelphis domestica

source_name: adult liver

extract_protocol: Total RNA was extracted from opossum brain and liver using Trizol and further purified using QIAGEN RNAEasy mini kit. Library was constructed using strand-specific protocol (Nucleic Acids Res. 2009:e123) with the exception that total RNA was used instead of polyA+ fraction. In the resultant library reads originate on complementary strand relative to source RNA.

value: liver

tag: Sex

value: female


title: CHCC5086

status: Public on Jun 10 2012

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

data_processing:
The sequencing was done using the Illumina HiSeq2000 technology for 90-bp paired-end reads according to protocol. Results were 13 million qualified paired-end transcriptome sequence reads in FASTQ format with an insert size of 180-250 bp. For the analysis the complete genome sequence of S. thermophilus LMG 18311 (Accession number: CP000023) was downloaded in FASTA format from GenBank http://www.ncbi.nlm.nih.gov/genbank/. Genomic Workbench 3 (CLC bio, Aarhus, Denmark) was used for the subsequent sequence analysis.  The Illumina Genome Analyzer Pipeline Version 1.5 software was used to qualify reads based on the quality scores assigned to each base call. The qualified reads were exported to the CLC Genomic Workbench for the RNA-Seq algorithm followed by Expression analysis.  The RNA-Seq analysis transforms the lists of reads into a list of genes with an expression value. The expression value was measured as RPKM (reads per kb of exon model per million mapped reads) which estimates the abundance of transcripts based on their depth of coverage in the mapping.
The Illumina Genome Analyzer Pipeline Version 1.5 software was used to qualify reads based on the quality scores assigned to each base call. The qualified reads were exported to the CLC Genomic Workbench for the RNA-Seq algorithm followed by Expression analysis.
The RNA-Seq analysis transforms the lists of reads into a list of genes with an expression value. The expression value was measured as RPKM (reads per kb of exon model per million mapped reads; Mortazavi et al., 2008) which estimates the abundance of transcripts based on their depth of coverage in the mapping.

organism: Streptococcus thermophilus

source_name: Streptococcus thermophilus

growth_protocol: grown at 37ºC in M17 broth media (Oxoid A/S, Greve, Denmark) supplemented with 2% lactose. Stationary cultures (16-18 hours) were used to inoculate 9.5% boiled skimmed milk powder (Arla Foods, Viby, Denmark) supplemented with 0.05% sterile tryptone (Oxoid A/S, Greve, Denmark). The inoculation level was 1%, i.e. an optical density (OD600) of 0.03. pH in the milk was recorded over time using the PC-logger AAC-216 (INTAB Interface-Teknik AB, Sweden).

extract_protocol: Cells were harvested at pH 5.7 and total RNA was extracted, quantified, and checked for quality using the RNA 6000 Nano Kit on the Bioanalyzer 2100 (Agilent Technologies, CA). Ten micrograms of total RNA was sent for whole transcriptome sequencing at BGI-HONGKONG (Shenzhen, China). The pre-treatment protocol at BGI included mRNA enrichment using Ribo-Zero™ rRNA Removal Kit for Gram-positive bacteria (EPICENTRE Technologies Corporation). The sequencing was done using the Illumina HiSeq2000 technology for 90-bp paired-end reads according to protocol

treatment_protocol: rRNA removal process using the Ribo-Zero™ rRNA Removal Kit


title: male brain RNA-Seq

source_name: adult brain

value: brain

value: male


title: CHCC5376


title: sRNA_adult

city: Cambridge

first: Jin-Wu

last: Nam

state: MA

address: Nine Cambridge Center

institute: Whitehead Institute

description: small RNAs with size fraction (18-30nt)

data_processing:
Sequenced reads were trimmed for adaptor sequence
All Solexa raw sequences (36nt) were preprocessed using a python script: removing adaptor sequences and counting read number for unique sequences. All small-RNA reads were mapped to genome (ce6), allowing no mismatches and discarding those mapping to the genome at more than 10 loci. If a read mapped to multiple loci, the read number assigned to each locus was divided by the number of loci.
Genome_build: ce6
Sample data table: unique sequence reads with counts

organism: Caenorhabditis elegans

source_name: small RNA_Young adult

extract_protocol: Gel fragment spanning both RNA 18nt and 30nt standards was excised to extract total RNAs from L4 and adult-stage animals (N2 strain). The gel-purified RNAs were incubated with 3’-adaptor oligonucleotide in ligation buffer at 22°C for 30 minutes. After the 3’-ligation reaction was purified on a gel, for the 5’-ligation, the 3’-ligation product was incubated with 5’ adaptor oligonucletide. The small-RNA libraries were constructed using a method that does not require a 5’ monophosphate (called 5’ monophosphate-independent method, Ambros et al., 2003). The ligated producted were purified and reverse transcribed using SuperScript II (Invitrogen) with the RT primer. PCR products generated for the samples were sequenced on a Solexa sequencing platform.

tag: developmental stage

value: Young adult


title: sRNA_L4

description: small RNAs with size fraction (18-30nt)

source_name: small RNA_L4


title: Combined immunoprecipitated DNA from Blood Donor No.1,2,3_non-stimulated PBMCs_Control IgG ChIP-Seq

status: Public on Jun 08 2012

city: Uppsala

first: Chuan

last: Wang

address: The University Hospital, Entrance 70, 3rd Floor, Research Department II

department: Medical Sciences

country: Sweden

institute: Uppsala University

description: Sample 1

data_processing:
Image analysis and base calling was carried out with the CASAVA Software v1.7 from Illumina.
The ChIP-Seq reads were aligned to the human reference genome (GRCh37, hg19) using Burrows-Wheeler Aligner (BWA) v0.5.8a. The reads that aligned to more than one position were filtered out by Samtools v0.1.8.
The aligned reads from the three stimulated PBMCs donors were combined into a single ChIP-Seq dataset for IRF5 and STAT4, respectively. The aligned reads from the three non-stimulated PBMCs donors were combined analogously.
Peaks of ChIP-Seq reads for IRF5 and STAT4 were called using Model-based Analysis of ChIP-Seq (MACS) v1.4.0beta using control IgG from non-stimulated PBMCs were used as control, and all default parameters were followed except that a read length of 36 bp was used, the range of high-confidence enrichment ratio against background (mfold) was set to 10-50, and PeakSplitter was invoked to refine the peaks.
Peaks of ChIP-Seq reads with a false discovery rate (FDR)>5% were filtered out. Peaks were annotated to the gene with the nearest TSS in the Ensembl database TSS.human.GRCh37. Peaks located in gene regulatory regions were retained for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genetic coordinates, enrichment p-values and annotated genes of the filtered ChIP-Seq peaks

source_name: Combined IP DNA_non-stimulated PBMCs_Control IgG ChIP-Seq

growth_protocol: PBMCs from healthy blood donors were prepared by Ficoll-Paque (GE Healthcare, Uppsala, Sweden) gradient centrifugation.

extract_protocol: Sequencing libraries were prepared using the Illumina ChIP-Seq DNA Sample Prep Kit (Illumina, San Diego, California, USA).

treatment_protocol: PBMCs were stimulated for 2.5 hours either with immune complexes consisting of small nuclear ribonucleoprotein (snRNP) particles and IgG from an SLE patient for IRF5, or with 500 U/ml of IFN-α2b for STAT4.

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: chip antibody

value: control IgG

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: female brain RNA-Seq


title: Blood Donor No.3_non-stimulated PBMCs_STAT4 ChIP-Seq

description: Sample 12

source_name: non-stimulated PBMCs_STAT4 ChIP-Seq

value: Santa Cruz Biotechnology


title: Blood Donor No.3_non-stimulated PBMCs_IRF5 ChIP-Seq

description: Sample 5

source_name: non-stimulated PBMCs_IRF5 ChIP-Seq


title: Arabidopsis nrpd1b-1 (Pol V) mutant inflorescence, barcoded with 5' "AG" - biological replicate 1

description:
Sample name: nrperep1
small RNA sequencing
*trimmed.txt files contain distinct small RNAs with their raw abundance after removing the adapter sequences.

data_processing:
The raw sequence reads were trimmed of adapters, matched to the genome (Arabidopsis TAIR9 genome) by custom Perl scripts developed in Blake Meyers' laboratory.
Genome Build:
nrpe_1_adapters_trimmed.txt: TAIR9


title: Blood Donor No.2_non-stimulated PBMCs_IRF5 ChIP-Seq

description: Sample 3


title: Blood Donor No.1_non-stimulated PBMCs_IRF5 ChIP-Seq

description: Sample 2


title: Blood Donor No.2_non-stimulated PBMCs_STAT4 ChIP-Seq

description: Sample 11


title: LU439_mRNA

city: Rochester

first: Krishna

middle: R

last: Kalari

state: MN

address: 200 1st ST SW

department: Department of Biomedical Statistics and Informatics

institute: Mayo Clinic

data_processing:
LU439_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm

source_name: Lung adenocarcinoma sample

growth_protocol: All cell lines were grown under conditions recommended by ATCC and RNA and DNA were extracted from mid log phase populations of low passage number cultures.

extract_protocol: Total RNA extraction was performed using Exiqon's miRCURY RNA Isolation Kit. Long-read mRNA-seq cDNA libraries were prepared from 1ug of total RNA using a modification of the Illumina mRNA-seq protocol.  Briefly, mRNA was resolved using poly-dT oligonucleotides attached to magnetic beads, fragmented using divalent cations under elevated temperatures, and converted to cDNA using random primers. After conversion of the cleaved fragments into cDNA, the cDNA underwent blunt end repair, addition of an 'A' base to the 3' blunt ends, and ligation of adapter molecules which will be used for PCR amplification, bridge amplification, and sequencing. The cDNA library was resolved by gel electrophoresis using conventional Illumina protocols except that we cut from the gel those cDNA fragments in the range of 300-400bp. The increased fragment length is necessary to accommodate paired end sequence analysis. The gel purified cDNA fragments were amplified by PCR and sequenced using the Illumina Cluster Station and Genome Analyzer. Paired-end sequence analysis (51 cycles/end) was carried out using sequencing primers that correspond to either end of the bridge-amplified cDNA fragments so as to obtain 50nt of sequence from either end of every cDNA fragment.

tag: kras status

value: KRAS wildtype

value: Lung adenocarcinoma

tag: passages

value: ATCC low passage


title: LU213_mRNA

data_processing:
LU213_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm

value: KRAS mutant ©


title: LU325_mRNA

data_processing:
LU325_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm


title: LU273_mRNA

data_processing:
LU273_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm


title: LU499_mRNA

data_processing:
LU499_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm


title: LU256_mRNA

data_processing:
LU256_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm


title: LU53_mRNA

data_processing:
LU53_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm


title: Blood Donor No.1_non-stimulated PBMCs_STAT4 ChIP-Seq

description: Sample 10


title: male liver RNA-Seq


title: LU350_mRNA

data_processing:
LU350_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm


title: LU528_mRNA

data_processing:
LU528_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm


title: LU330_mRNA

data_processing:
LU330_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm

value: KRAS mutant (v)


title: LU115_mRNA

data_processing:
LU115_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm


title: LU374_mRNA

data_processing:
LU374_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm


title: Blood Donor No.6_stimulated PBMCs_STAT4 ChIP-Seq

description: Sample 16

source_name: stimulated PBMCs_STAT4 ChIP-Seq

tag: stimulated with

value: 500 U/ml of IFN-α2b


title: Input1

city: Belfast

first: Simon

middle: S

last: McDade

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

data_processing: Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) to identify peaks (bed file) and generate wig files

source_name: Input

growth_protocol: Human neonatal foreskin keratinocytes were isolated and cultured in Epilife supplemented with human keratinocyte growth supplement (HKGS)

extract_protocol: p63 bound DNA was enriched for by chromatin immunoprecipitation. End repaired sequencing libraries were prepared from two independent p63 ChIPs and matched input control using NEBNext sample preparation kit (New England biolabs) according to manufacturer's instructions.  The resulting adapter ligated DNA was subjected to 16 cycles of adapter mediated pcr using Herculase II Fusion DNA Polymerase (Agilent). The resulting libraries were size fractionated in a 2% agarose gel and purified to obtain 2-400Bp fragments.  Each library was validated using an agilent 2100 bioanalyser and sequenced on the Illumina GAII sequencer according to manufacturer's instructions.

value: Human neonatal foreskin keratinocytes


title: Blood Donor No.4_stimulated PBMCs_STAT4 ChIP-Seq

description: Sample 13


title: LU242A_mRNA

data_processing:
LU242A_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm


title: LU99_mRNA

data_processing:
LU99_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm


title: p63_IP2


title: Blood Donor No.5_stimulated PBMCs_IRF5 ChIP-Seq

description: Sample 7

data_processing:
Image analysis and base calling was carried out with the CASAVA Software v1.7 from Illumina.
The ChIP-Seq reads were aligned to the human reference genome (GRCh37, hg19) using Burrows-Wheeler Aligner (BWA) v0.5.8a. The reads that aligned to more than one position were filtered out by Samtools v0.1.8.
The aligned reads from the three stimulated PBMCs donors were combined into a single ChIP-Seq dataset for IRF5 and STAT4, respectively. The aligned reads from the three non-stimulated PBMCs donors were combined analogously.
Peaks of ChIP-Seq reads for IRF5 and STAT4 were called using Model-based Analysis of ChIP-Seq (MACS) v1.4.0beta using control IgG from non-stimulated PBMCs were used as control, and all default parameters were followed except that a read length of 36 bp was used, the range of high-confidence enrichment ratio against background (mfold) was set to 10-50, and PeakSplitter was invoked to refine the peaks.
Peaks of ChIP-Seq reads with a false discovery rate (FDR)>5% were filtered out. Peaks were annotated to the gene with the nearest TSS in the Ensembl database TSS.human.GRCh37. Peaks located in gene regulatory regions were retained for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genetic coordinates, enrichment p-values and annotated genes of the filtered ChIP-Seq peaks

source_name: stimulated PBMCs_IRF5 ChIP-Seq

value: immune complexes


title: Blood Donor No.5_stimulated PBMCs_STAT4 ChIP-Seq

description: Sample 14


title: Blood Donor No.6_stimulated PBMCs_IRF5 ChIP-Seq

description: Sample 9


title: Blood Donor No.4_stimulated PBMCs_IRF5 ChIP-Seq

description: Sample 6


title: Input2


title: S2-DRSC-Input_DNA_replicate_2

city: Basel

first: Cem

last: Sievers

address: Mattenstrasse

country: Switzerland

institute: ETH Zurich

data_processing:
The Apr. 2006 D. melanogaster genome assembly (dm3, BDGP Release 5) provided by the Berkeley Drosophila Genome Project (BDGP, http://www.fruitfly.org/) was used as a basis for all analyses.  Alignments to the D. melanogaster genome were performed by the software bowtie (Langmead et al. 2009) with parameters '--best --chunkmbs 512 -M 100 -p 8 -k 1 -S'
Genome_build: dm3, BDGP Release 5

organism: Drosophila melanogaster

source_name: DRSC-S2 cell line

growth_protocol: Drosophila S2-DRSC cells were grown in Schneider’s Drosophila Medium (Invitrogen) supplemented with 10 % FBS (Hyclone) at 25°C.

extract_protocol: Exponentially growing S2 cells were resuspended in the growth medium, and cross-linking buffer was added such that the final concentrations in the growth medium were : 5 mM HEPES, 5 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5% triton X-100 and 1% formaldehyde. The cells were incubated on end-over rotor at room temperature for 15 min, and the fixation was stopped by adding glycine at a final concentration of 100 mM. The fixed material was spun down and washed twice with cold buffer (50 mM Tris pH 8, 15 mM NaCl, 0.5 mM EGTA, 60 mM KCl). The pellet was resuspended thoroughly in cold sonnication buffer (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA). Sonnication was carried out in cold water in BioRuptor (Diagenode) according to manufacturer’s instructions until a DNA fragment size of 200 – 500 bp was reached. All through the experiments, protease inhibitors were added to cell suspension to avoid any degradation of material.Immunoprecipitation was carried out using anti-Hsp90 antibody (Tariq et al, 2009, PNAS, vol. 106 (4) pp. 1157-62). Libraries for sequencing were prepared with the ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina's instructions. After adapter ligation library fragments of ~250 bp were band isolated from an agarose gel. The DNA was PCR amplified with Illumina primers for 18 (ChIP-seq) cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II and Genome Analyzer IIx following the manufacturer's protocols.

tag: cell line

value: none (input)


title: Blood Donor No.5_stimulated PBMCs_STAT4 ChIP-Seq rep

description: Sample 15


title: S2-DRSC-Input_DNA_replicate_1

tag: antibody


title: USC_ChipSeq_MCF-7_Input_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: Input

tag: antibody description

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

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: labversion

value: remapped from hg18, MCF7 cells stably expressed a tagged HA-E2F1 were fragmented using Bioruptor, crosslinks were reversed at 67*C overnight and Input was Qiagen purified, PeakSeq 1.0 (fdr 0.001)

tag: replicate


title: Blood Donor No.5_stimulated PBMCs_IRF5 ChIP-Seq rep

description: Sample 8

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: stimulated with

value: immune complexes

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: LU242_mRNA

data_processing:
LU242_geneTable_start-count.txt; genome build: hg19
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: RefSeq gene read-counts are computed using an approach based on the UCSC genome binning algorithm

tag: kras status

value: KRAS wildtype

value: Lung adenocarcinoma

tag: passages

value: ATCC low passage


title: USC_ChipSeq_MCF-7_H3K9me3_UCDavis

value: immortalized cell line

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: line

tag: cell organism

value: human

tag: cell description

tag: cell karyotype

tag: cell lineage

tag: cell sex

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

tag: antibody targetdescription

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

tag: antibody vendorname

tag: antibody vendorid


title: USC_ChipSeq_HCT-116_H3K4me1_UCDavis

tag: cell

value: colorectal carcinoma (PMID:7214343)

value: cancer

value: endoderm

value: M

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: rabbit polyclonal. Antibody Target:H3K4me1

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

tag: control

value: UCDavis

tag: control description

tag: controlid

tag: replicate


title: debarshi_B61

city: Cleveland

first: Debarshi

last: Mustafi

state: OH

address: 2109 Aldelbert Rd

department: Pharmacology

institute: Case Western Reserve University

description: Isolated whole eye mRNA

data_processing:
Base-calling and alignment were performed using the Illumina pipeline software ELAND v1.7
Alignment was performed to the mouse genome assembly version mm9 and accompanying RefSeq annotation, downloaded from UCSC, and a splice-sites file downloaded from Illumina.
Alignment results from multiple lanes and/or runs were combined for analysis using the Illumina program CASAVA v1.7, which calculated FPKM (fragments per kilobase of exon model per million mapped reads) by gene, transcript, and exon.
The output from CASAVA was visualized with the GenomeStudio RNA Sequencing Module (Illumina)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each eye tissue sample

source_name: Eye tissue-B6-1

extract_protocol: Mice were euthanized by cervical dislocation. Eyes were enucleated and immediately placed in RNAlater stabilization reagent (Qiagen, Valencia, CA, USA) to preserve RNA content and integrity for whole eye runs.  One mouse eye or two retinas were homogenized at once and passed through a QIAShredder column (Qiagen) as per manufacturer’s directions to further homogenize the eye tissues. Total RNA was then purified by using the RNeasy Mini Kit (Qiagen) with on column DNase treatment (Qiagen) as per manufacturer’s directions. Poly(A) RNA was isolated with the Oligotex kit (Qiagen) as per the manufacturer’s instructions. Pooled total RNA samples of 5 female mice 4 weeks of age were used for each whole eye library preparation.  For first strand cDNA synthesis, instructions from the SuperScript III kit protocol (Invitrogen) were followed. About 400-450 ng of isolated poly(A) RNA was mixed with 50 ng of random primers and 1 mM deoxyribonucleotide triphosphate (dNTP), incubated at 65°C for 5 min and then placed on ice for 5 min. A reaction mixture comprising 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT, and 200 U SuperScript III reverse transcriptase was added to the initial mix to achieve a total volume of 20 µL. The mixture was incubated at 25°C for 10 min, followed by 50 min at 50°C. The reaction was terminated at 85°C for 5 min and then chilled on ice for 10 min. At this point, 2 U RNase H was added and the mix was incubated at 37°C for 20 min. The first strand cDNA synthesis reaction was immediately used for second strand synthesis. To the first strand product, 300 µM dNTP, E. coli DNA polymerase I buffer, and water was added to obtain a total volume of 95 µL and allowed to incubate on ice for 10 min. Then, 0.05 U E. coli DNA polymerase I (New England Biolabs, Beverly, MA, USA) was added and the mixture was incubated at 16°C for 2.5 h. The resulting double stranded cDNA was purified with the Wizard SV Gel and PCR Clean-up System (Promega, Madison, WI, USA) and eluted in 100 µL nuclease-free water and then fragmented by the Covaris S2 instrument (Woburn, MA, USA) to generate ~200 bp fragments as follows: 10% duty cycle, intensity of 5, 100 cycles per burst, with a bath temperature of 7.7°C and an acoustic power of 24 W.   The Illumina library was prepared according to the manufacturer’s instructions and purified using the Wizard SV Gel and PCR Clean-up System (Promega). Overhangs were converted into blunt ends with T4 DNA polymerase and Klenow DNA polymerase by incubating the mixed sample at 20°C for 30 min. cDNA was purified and eluted in 32 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The purified sample was then mixed with Klenow fragment (3’ to 5’ exo minus) and incubated at 37°C for 30 min to add an ‘A’ base to the 3’ end of the blunt phosphorylated DNA fragments. The cDNA was then purified and eluted in 23 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). Eluted DNA was mixed with Illumina Adapter Oligo mix and T4 DNA ligase and incubated at room temperature for 15 min to ligate adapters to the ends of the DNA fragments to prepare them for hybridization to the flow cell. cDNA then was purified and eluted in 10 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). cDNAtemplates were purified by running samples on a 1% agarose gel at 120 V for 60 min and excising the region of the gel in the 200 bp range. The 200 bp cDNA enriched fragments were purified and eluted in 30 µL of nuclease free water with the Wizard PlusMinipreps DNA purification system (Promega). cDNA in the library was then amplified by a 15 cycle PCR with two primers that annealed to the ends of the adapters. The amplified cDNA was purified and eluted in 30 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The size, purity and concentration of the final library was checked with the Bio-Rad Experion DNA specific chip prior to sequencing by using the Illumina Genome Analyzer IIx.

tag: strain

tag: tissue

value: Whole Eye

tag: genotype

value: Wild Type

tag: gender

value: female

tag: age

value: 4 weeks


title: USC_ChipSeq_PANC-1_H3K4me3B_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell organism

tag: cell description

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

tag: cell karyotype

tag: cell lineage

tag: cell sex

tag: antibody

value: Rabbit monoclonal antibody. Antibody Target:H3K4me3

value: Histone H3 (tri-methyl K4) marks promoters in chromatin regions

value: Cell Signaling

value: Input library was prepared at UC Davis.


title: p63_IP1

tag: chip antibody

tag: cell type

value: Human neonatal foreskin keratinocytes


title: USC_ChipSeq_HCT-116_Input_UCDavis (superseded by GSE86662)

description:
****************************
GSM945855 record metadata submitted on Jun 08 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE86662
****************************

value: Chromatin IP Sequencing

tag: cell

value: human

value: colorectal carcinoma (PMID:7214343)

value: cancer

value: endoderm

value: M

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: Input

tag: antibody description

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

tag: control

tag: control description

tag: controlid

tag: replicate


title: debarshi_Balb-C-3

description: Isolated whole eye mRNA

source_name: Eye tissue-BALB/c-3

tag: strain

value: BALB/c

tag: tissue

value: Whole Eye

tag: genotype

value: Wild Type

tag: gender

value: female

tag: age

value: 4 weeks


title: debarshi_B63

description: Isolated whole eye mRNA

source_name: Eye tissue-B6-3


title: debarshi_Balb-C-2

description: Isolated whole eye mRNA

source_name: Eye tissue-BALB/c-2


title: debarshi_B62

description: Isolated whole eye mRNA

source_name: Eye tissue-B6-2


title: Blood Donor No.2_non-stimulated PBMCs_IRF5 ChIP-Seq rep

description: Sample 4

value: peripheral blood mononuclear cells (PBMCs)

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: debarshi_AJ3

description: Isolated whole eye mRNA

source_name: Eye tissue-A/J-3

value: A/J


title: debarshi_Balb-C-1

description: Isolated whole eye mRNA

source_name: Eye tissue-BALB/c-1


title: UW_ChipSeq_WERI-Rb-1_Input

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

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell organism

tag: cell description

value: retinoblastoma (PMID:844036)

tag: cell karyotype

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: antibody

value: std

value: Standard input signal for most experiments.

tag: labexpid

tag: labversion

value: Bowtie 0.12.5


title: debarshi_AJ2

description: Isolated whole eye mRNA

source_name: Eye tissue-A/J-2

tag: strain

tag: tissue

value: Whole Eye

tag: genotype

tag: gender


title: UW_ChipSeq_GM12875_Input

tag: cell

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment:Epstein-Barr Virus transformed

value: normal

value: mesoderm

value: Input

tag: antibody description

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

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

tag: control description

tag: controlid

tag: replicate


title: USC_ChipSeq_HCT-116_H3K27ac_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

tag: datatype description

tag: cell organism

tag: cell description

value: colorectal carcinoma (PMID:7214343)

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

value: M

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody targetdescription

value: Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: UCDavis

value: Input library was prepared at UC Davis.


title: UW_ChipSeq_H7-hESC_H3K27me3_diffProtA_5d

status: Public on Jun 07 2012

value: UW

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: human

value: undifferentiated embryonic stem cells

value: inner cell mass

tag: cell sex

value: U

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K27me3

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

value: Millipore

tag: treatment

tag: treatment description

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage:mesoderm

value: std

value: Standard input signal for most experiments.

tag: labexpid

tag: labversion

value: Bowtie 0.12.7


title: UW_ChipSeq_H7-hESC_H3K27me3_diffProtA_2d

tag: lab

tag: lab description

tag: datatype

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage:mesoderm

tag: control

tag: control description

tag: controlid

tag: replicate


title: UW_ChipSeq_GM12864_Input

tag: datatype description

tag: cell organism

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment:Epstein-Barr Virus transformed

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

value: M

value: Input

tag: antibody description

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

value: No special treatment or protocol applies

value: Bowtie 0.12.5


title: UW_ChipSeq_H7-hESC_H3K36me3_diffProtA_14d

value: UW

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: human

value: undifferentiated embryonic stem cells

value: inner cell mass

tag: cell sex

value: U

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: treatment

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage:mesoderm


title: UW_ChipSeq_H7-hESC_H3K27me3_diffProtA_9d

tag: lab

tag: lab description

tag: datatype

value: rabbit polyclonal. Antibody Target:H3K27me3

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

value: Millipore

tag: treatment description

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage:mesoderm

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: labexpid

tag: labversion

value: Bowtie 0.12.7


title: debarshi_AJ1

description: Isolated whole eye mRNA

source_name: Eye tissue-A/J-1

tag: strain

value: A/J

tag: tissue

value: Whole Eye

tag: genotype

value: Wild Type

tag: gender

value: female

tag: age

value: 4 weeks