title: human DR-GFP/U2OS cells that were transfected with pCBASce plasmid and collected at 20 h post-transfection

description: contains three biogical replicates

value: transfected with pCBASce plasmid and collected at 20 h post-transfection.


title: HCT116 medium MethylCap

status: Public on Mar 27 2012

type: SRA

city: Nijmegen

first: Arjen

last: Brinkman

address: NCMLS #274, Geert Grooteplein Zuid 30

department: Molecular Biology

country: Netherlands

institute: Radboud University, Nijmegen Center for Molecular Life Sciences

description: 1 to 30 ng was used for library preparation using the ChIP-seq DNA sample Prep Kit (Illumina, cat# IP-102–1001) using the recommended protocol. After ligation of adapters, a 300 bp band is excised using the E-Gel system (Invitrogen), which correspond to a 234 bp fragment of genomic DNA. PCR enrichment of adapter-ligated DNA was done using 14 cycles of PCR.

library_source: genomic

data_processing: Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human (hg18) reference genome using the Illumina Analysis Pipeline allowing, one mismatch. Only the tags uniquely aligning to the genome were considered for further analysis. Further analysis was performed using the 36 bp sequence reads. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All sequence analyses were conducted based on the Homo Sapiens hg18 genome assembly.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HCT116 cells were cultured in McCoy's 5A medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (all Gibco/Invitrogen) at 37C in 5% CO2 atmosphere.

extract_protocol: MethylCap (Capturing of methylated DNA) was done using in automated procedure using a SX-8G/IP-StarTM robot (Diagenode). 2 ug of His6-GST-MBD (Diagenode) was incubated with 1 ug of fragmented DNA in binding buffer (BB, 20 mM Tris-HCl pH 8.5, 0.1% Triton X-100) with 200 mM NaCl in a final volume of 200 ul. This solution is mixed at 4 C for 2 h. Magnetic GST-beads were prepared by washing 35 µl of a well-mixed beads suspension (Promega) with 200 µl of binding buffer + 200 mM NaCl at 4 C. The suspension was mixed and a magnet was used to collect the beads. After removal of the supernatant the procedure is repeated once. After the second wash the supernatant is removed, but the beads are not allowed to get dry. The GST-MBD solution is added to the washed beads and this suspension is mixed for another hour at 4C. After removal of the supernatant (the 'flow-through') the beads-GST-MBD-DNA complexes are washed/eluted. 200 µl of binding buffer with increasing concentrations of NaCl is added and the suspension is rotated for 10 min at 4 C. Beads are captured on the magnet, and the supernatant is collected. Three different eluates were collected (LOW, MEDIUM, HIGH), corresponding 500 mM, 600 mM and 800 mM NaCl. For MethylCap-BS-seq, only HIGH eluates were used.

tag: eluate

value: medium

tag: cell line

tag: sample type

value: human colon carcinoma cell line established from the primary colon carcinoma of an adult man

tag: technique

value: ChIP-sequencing

tag: binding/selection

value: Protein domain His6-GST-MBD (Diagenode)

tag: binding protein

tag: binding protein vendor

value: Diagenode


title: HCT116 high MethylCap

value: high


title: HCT116 H3K27me3-ChIP

extract_protocol: HCT116 cells were crosslinked with 1% formaldehyde for 30 min at room temperature, quenched with 0.125 M glycine and washed at 4C with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl in HEG buffer (1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6). Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, HEG) and sheared using a Biouptor (Diagenode). Sonicated chromatin was centrifuged for 5 min and then incubated overnight with 2 ug of antibody and protein A/G beads (Santa Cruz). Beads were washed six times with different buffers at 4C: twice with solution of composition 0.1% SDS, 0.1% DOC, 1% Triton, 150 mM NaCl, HEG, once with the solution same as before but with 500 mM NaCl, once with solution of composition 0.25 M LiCl, 0.5% DOC, 0.5% NP-40, HEG and twice with HEG. Precipitated chromatin was eluted with 400 µl of elution buffer (1% SDS, 0.1 M NaHCO3), incubated at 65C for 4 h in the presence of 200 mM NaCl, phenol extracted and precipitated with 20 ug of glycogen at -20C overnight.

value: Antibody  H3K27me3 (Millipore 07-449, DAM-1588246)

tag: antibody

tag: antibody vendor

value: Millipore

tag: antibody catalog #

tag: antibody lot #


title: HCT116 H3K27me3-ChIP-BS

description: 100 ng ChIP DNA or 10 ng MethylCap DNA was first subjected to end-repair in a 30 µl reaction containing 6 units T4 DNA polymerase, 2.5 units DNA Polymerase I (Large Klenow Fragment), 20 units T4 Polynucleotide Kinase (all New England Biolabs), dATP, dCTP, dGTP and dTTP (0.125 mM each), and 1x T4 Ligase buffer with ATP for 30 min at 20C. Illumina sequencing generates sequences corresponding to the 5'-ends of the input DNA fragments. Therefore, fill-in of 5'-overhangs did not alter sequenced DNA methylation patterns. Purification was performed using a standard phenol:chloroform:isoamyl alcohol (25:24:1) protocol and ethanol precipitation. DNA was then adenylated in a 20 µl reaction containing 10 units Klenow Fragment (3'->5' exo-) (New England Biolabs), 0.5 mM dATP and 1x NEB buffer 2 for 30 min at 37C. After phenol extraction and ethanol precipitation, Illumina genomic DNA adapters containing 5-methylcytosine instead of cytosine (atdbio, Southampton), preventing deamination during bisulfite conversion, were ligated. In a 20 µl reaction, DNA was incubated with 1.5 µM preannealed adapters, 2000 units T4 DNA Ligase (NEB) and 1x T4 Ligase buffer with ATP, for 16-20 h at 16C. Adapter-ligated DNA fragments were subsequently purified by phenol extraction and ethanol precipitation, and size-selected on gel. 50 ng sheared and dephosphorylated E-coli K12 genomic DNA was added to adapter-ligated DNA as carrier during size-selection and bisulfite conversion. DNA was run on 2.5% Nusieve 3:1 Agarose (Lonza) gels. Lanes containing marker (50 bp ladder New England Biolabs) were stained with SYBR Green (Invitrogen), and size regions to be excised were marked with toothpicks. To obtain 80-280 bp (low) and 280-430 bp (high) insert sizes, adapter-ligated DNA fragments from 200-400 and 400-550 bp, respectively, were excised. The Illumina adapters cause the fragments to run slower, presumably due to the forked structure. Note that after PCR, dsDNA libraries appear at 140-340 bp and 340-490 bp, in accordance with exact sizes. DNA was isolated from gel using the MinElute Gel Extraction kit (QIAGEN). The low and high libraries were kept separate in subsequent steps. Before proceeding to bisulfite conversion, analytical PCRs were performed to check the libraries. Amplifications were performed in 10 µl reactions containing 0.3 µl template DNA (from 20 µl eluted after size-selection), 0.5 units Pfu Turbo Cx Hotstart DNA Polymerase (Stratagene), Illumina primers LPX 1.1 and 2.1 (0.3 µM each), dNTPs (0.25 mM each), 1x Turbo Cx buffer, under the following thermocycler conditions: 94C for 5 min,  n x (94C for 30 s, 65C for 30 s, 72C for 1 min) and 72C for 7 min. We tested three different cycle numbers (n) - 10, 15 and 20 cycles - and analyzed PCR products on 4-20% TBE Criterion precast gels (BioRad) and subsequent SYBR Green staining. Adapter-ligated and size-selected DNA was subjected to two subsequent 5h bisulfite treatments using the EpiTect Bisulfite kit (QIAGEN) following the manufacturer's protocol for DNA isolated from FFPE tissue samples. After bisulfite conversion, analytical PCRs were performed as before to determine the minimum number of cycles required in the final amplification step for each sample. In this case, tested cycle numbers were several cycles higher as before bisulfite conversion, and 15, 19 and 22 PCR cycles were performed. The minimum cycle number for final large-scale amplification was determined as the lowest cycle number that generated enough PCR product of the desired size range to be visualized on analytical gels as above. Large-scale amplification was performed by 8 reactions of 25 µl, containing 3 µl DNA (from 40 µl eluted after bisulfite conversion, remains were stored at -80C as back-up), 1.25 units Pfu Turbo Cx Hotstart DNA Polymerase (Stratagene), primer LPX 1.1 and 2.1 (0.3 µM each), dNTPs (0.25 mM each), 1x Turbo Cx buffer and thermocycler conditions as above. Amplified libraries were purified with the MinElute PCR Purification kit (QIAGEN), and subsequently purified from gel essentially as described above; whole gels were stained with SYBR Green and no carrier DNA was added. Final libraries were analysed on analytical 4-20% TBE Criterion precast gels (BioRad), and measured by Quant-iT dsDNA HS Assays (Invitrogen). The protocol for preparation of captured DNA for bisulfite deep sequencing was adapted from 27-29. Sequence reads were generated on the Illumina Genome Analyzer IIx using a standard 36-base protocol. After sequencing low and high library reads were combined.

data_processing: Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Mapping of bisulfite-converted sequence reads was done using a custom-made pipeline. To reduce PCR artifacts, a maximum of three identical sequence reads was allowed. To perform mapping independently of DNA methylation status, sequence reads were in silico bisulfite-converted (C to T), and subsequently mapped to two different in silico converted hg18 genome sequences; one C to T converted genome and one G to A converted genome. Reads mapping to both genomes were discarded, which typically represented a very minor fraction of all reads. Mapping was done using the Burrows-Wheeler Aligner (BWA), with default settings allowing a single mismatch. The obtained mapping positions were used to align unconverted sequence reads with their corresponding unconverted genomic sequence and to subsequently determine the methylation status of each sequenced cytosine within a CpG context, both on the forward strand as well as on the reverse strand.

value: ChIP-bisulfite sequencing


title: HCT116 low MethylCap

value: low


title: colon tumor high MethylCap-BS

source_name: tumor colon tissue

tag: tissue

value: tumor colon tissue

value: BioChain (lot# A704198). Both normal and tumor samples originate from the same donor, an 81-year-old male patient diagnosed with moderately differentiated adenocarcinoma

value: MethylCap-bisulfite sequencing


title: colon normal high MethylCap-BS

description: 100 ng ChIP DNA or 10 ng MethylCap DNA was first subjected to end-repair in a 30 µl reaction containing 6 units T4 DNA polymerase, 2.5 units DNA Polymerase I (Large Klenow Fragment), 20 units T4 Polynucleotide Kinase (all New England Biolabs), dATP, dCTP, dGTP and dTTP (0.125 mM each), and 1x T4 Ligase buffer with ATP for 30 min at 20C. Illumina sequencing generates sequences corresponding to the 5'-ends of the input DNA fragments. Therefore, fill-in of 5'-overhangs did not alter sequenced DNA methylation patterns. Purification was performed using a standard phenol:chloroform:isoamyl alcohol (25:24:1) protocol and ethanol precipitation. DNA was then adenylated in a 20 µl reaction containing 10 units Klenow Fragment (3' -> 5' exo-) (New England Biolabs), 0.5 mM dATP and 1x NEB buffer 2 for 30 min at 37C. After phenol extraction and ethanol precipitation, Illumina genomic DNA adapters containing 5-methylcytosine instead of cytosine (atdbio, Southampton), preventing deamination during bisulfite conversion, were ligated. In a 20 µl reaction, DNA was incubated with 1.5 µM preannealed adapters, 2000 units T4 DNA Ligase (NEB) and 1x T4 Ligase buffer with ATP, for 16-20 h at 16C. Adapter-ligated DNA fragments were subsequently purified by phenol extraction and ethanol precipitation, and size-selected on gel. 50 ng sheared and dephosphorylated E-coli K12 genomic DNA was added to adapter-ligated DNA as carrier during size-selection and bisulfite conversion. DNA was run on 2.5% Nusieve 3:1 Agarose (Lonza) gels. Lanes containing marker (50 bp ladder New England Biolabs) were stained with SYBR Green (Invitrogen), and size regions to be excised were marked with toothpicks. To obtain 80-280 bp (low) and 280-430 bp (high) insert sizes, adapter-ligated DNA fragments from 200-400 and 400-550 bp, respectively, were excised. The Illumina adapters cause the fragments to run slower, presumably due to the forked structure. Note that after PCR, dsDNA libraries appear at 140-340 bp and 340-490 bp, in accordance with exact sizes. DNA was isolated from gel using the MinElute Gel Extraction kit (QIAGEN). The low and high libraries were kept separate in subsequent steps. Before proceeding to bisulfite conversion, analytical PCRs were performed to check the libraries. Amplifications were performed in 10 µl reactions containing 0.3 µl template DNA (from 20 µl eluted after size-selection), 0.5 units Pfu Turbo Cx Hotstart DNA Polymerase (Stratagene), Illumina primers LPX 1.1 and 2.1 (0.3 µM each), dNTPs (0.25 mM each), 1x Turbo Cx buffer, under the following thermocycler conditions: 94C for 5 min,  n x (94C for 30 s, 65C for 30 s, 72C for 1 min) and 72C for 7 min. We tested three different cycle numbers (n) - 10, 15 and 20 cycles - and analyzed PCR products on 4-20% TBE Criterion precast gels (BioRad) and subsequent SYBR Green staining. Adapter-ligated and size-selected DNA was subjected to two subsequent 5h bisulfite treatments using the EpiTect Bisulfite kit (QIAGEN) following the manufacturer's protocol for DNA isolated from FFPE tissue samples. After bisulfite conversion, analytical PCRs were performed as before to determine the minimum number of cycles required in the final amplification step for each sample. In this case, tested cycle numbers were several cycles higher as before bisulfite conversion, and 15, 19 and 22 PCR cycles were performed. The minimum cycle number for final large-scale amplification was determined as the lowest cycle number that generated enough PCR product of the desired size range to be visualized on analytical gels as above. Large-scale amplification was performed by 8 reactions of 25 µl, containing 3 µl DNA (from 40 µl eluted after bisulfite conversion, remains were stored at -80C as back-up), 1.25 units Pfu Turbo Cx Hotstart DNA Polymerase (Stratagene), primer LPX 1.1 and 2.1 (0.3 µM each), dNTPs (0.25 mM each), 1x Turbo Cx buffer and thermocycler conditions as above. Amplified libraries were purified with the MinElute PCR Purification kit (QIAGEN), and subsequently purified from gel essentially as described above; whole gels were stained with SYBR Green and no carrier DNA was added. Final libraries were analysed on analytical 4-20% TBE Criterion precast gels (BioRad), and measured by Quant-iT dsDNA HS Assays (Invitrogen). The protocol for preparation of captured DNA for bisulfite deep sequencing was adapted from 27-29. Sequence reads were generated on the Illumina Genome Analyzer IIx using a standard 36-base protocol. After sequencing low and high library reads were combined.

source_name: normal colon tissue

value: normal colon tissue


title: RxT line in DCL2 corresponding wild-type background, 13-day seedlings

city: Beijing

first: Yijun

last: Qi

address: #7 Science Park Road, Zhongguancun Life Science Park

country: China

institute: National Institute of Biological Sciences

library_source: transcriptomic

data_processing: All reads obtained from Illumina GA IIx were sorted into respective libraries by parsing their barcodes. Then the adaptor sequences were removed using ‘vectorstrip’ in the EMBOSS package. Small RNA reads with length of 18-28nt were retained.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 13-day seedlings

growth_protocol: All plants were grown in Murashige and Skoog (MS) medium at 16-h-light/8-h-dark photoperiod. Human DR-GFP/U2OS cells [U2OS derivative cell line harboring an integrated HR reporter construct (DR-GFP)] were grown in Dulbecco's modified Eagle's medium with 10% fetal bovine serum.

extract_protocol: Small RNAs were extracted from whole plants or the purified AGO2 complex by Trizol reagent (Invitrogen), resolved on a 15% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-28 nt were excised, and the RNAs were eluted and purified for small RNA library construction. Cloning of small RNAs from Arabidopsis and human cells was carried out essentially as described in Mi et al., Cell, 2008.  The Illumina GA IIx was used for sequencing.

treatment_protocol: Columbia-0 plants were treated with 100 Gy γ-irradiation and placed in a growth chamber at 22℃ for 1.5 h. Seedlings without γ-irradiation treatment were used as controls.

tag: strain

value: Columbia-0 DCL2 corresponding wild-type

tag: line

value: RxT

value: seedlings

tag: developmental stage

value: 13-day old

tag: rna

value: small RNA


title: patientB_input

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing: Peaks:  Peak finding analysis  was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/). There are two runs per patient; those have been combined before peak detection

source_name: patient B input

extract_protocol: Libraries of DNA fragments from chromatin immunoprecipitation or DNase I treatment  were prepared from approximately 10ng of DNA. Firstly, overhangs were repaired by treatment of sample material with T4 DNA polymerase, T4 PNK and Klenow DNA polymerase (all enzymes obtained from New England Biolabs UK) in a reaction also containing 50 mM Tris-HCl,10 mM MgCl2, 10 mM Dithiothreitol, 0.4 mM dNTPs and 1 mM ATP. Samples were purified after each step using Qiagen MinElute columns (according to the manufacturer’s guidelines). ‘A’ bases were added to 3’ ends of fragments using Klenow Fragment (3´- 5´ exo- ), allowing for subsequent ligation of adapter oligonucleotides (Illumina part #1000521) using Quick T4 DNA ligase. After a further column clean up to remove excess adaptors, fragments were amplified in an 18 cycle PCR reaction using adapter-specific primers The libraries were purified and adapter dimers removed by running PCR products on 2% agarose gels and excising gel slices corresponding to fragments approximately 200-300 bp in size, which were then extracted using the Qiagen gel extraction kit. Libraries from cells from patients A and B and their respective input DNA were preparing using a kit for paired end sequencing. Once prepared, DNA libraries were subject to massively parallel DNA sequencing on an Illumina Genome Analyzer.

tag: cell type

value: t(8;21) AML patient Blast cells


title: PatientB_ChIPSeq

data_processing:
patientB_ChIPSeq_peaks.txt; genome build: hg18
Peaks:  Peak finding analysis  was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/). There are two runs per patient; those have been combined before peak detection

source_name: Blast cells from human patient B with t(8;21) AML

value: ETO (E/S19)


title: RxT line in atr-2 mutant background, 13-day seedlings

value: Columbia-0 atr-2 mutant


title: RUNX1_siRE_ChIPSeq

data_processing:
RUNX1_siRE_ChIPSeq_peaks.txt; genome build: hg18
Peaks:  Peak finding analysis  was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/). There are two runs per patient; those have been combined before peak detection

source_name: Kasumi-1 transfection with RUNX1/ETO siRNA

growth_protocol: The Kasumi-1 cell line (acute myeloid leukemia FAB M2 with t(8;21)) was obtained from the DSMZ cell line repository (http://www.dsmz.de/ mutz/mutzhome.htm). The cells were grown in RPMI 1640 medium (Invitrogen, Heidelberg, Germany) supplemented 2 mM L-glutamine with 10% FCS and maintained in a humidified 37°C incubator with 5% CO.

treatment_protocol: Kasumi-1 cells were transfected with the 200 nM of siRNA using a Fischer EPI 3500 electroporator (Fischer, Heidelberg, Germany) as described previously (Martinez et al., 2004). The following siRNAs were used: RUNX1/ETO siRNAs (sense, 5'-CCU CGA AAU CGU ACU GAG AAG-3'; antisense, 5'-UCU CAG UAC GAU UUC GAG GUU-3')

tag: target

value: ETO(C20)sc ( lot number F1809)


title: PatientA_ChIPSeq

data_processing:
patientA_ChIPSeq_peaks.txt; genome build: hg18
Peaks:  Peak finding analysis  was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/). There are two runs per patient; those have been combined before peak detection

source_name: Blast cells from human patient A with t(8;21) AML


title: RUNX1_siMM_ChIPSeq

data_processing:
RUNX1_siMM_ChIPSeq_peaks.txt; genome build: hg18
Peaks:  Peak finding analysis  was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/). There are two runs per patient; those have been combined before peak detection

source_name: Kasumi-1 transfection with mismatch siRNA

treatment_protocol: Kasumi-1 cells  were transfected with the 200 nM of siRNA using a Fischer EPI 3500 electroporator (Fischer, Heidelberg, Germany) as described previously (Martinez et al., 2004). The following siRNAs were used: mismatch control (sense, 5'-CCU CGA AUU CGU UCU GAG AAG-3'; antisense, 5'-UCU CAG AAC GAA UUC GAG GUU-3')


title: mES_Dnmt-TKO_H3K27m3_ChIP

data_processing: Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina HiSeq2000 platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the mouse (mm9) reference genome using the Illumina Analysis Pipeline allowing, one mismatch. Only the tags uniquely aligning to the genome were considered for further analysis. Further analysis was performed using the 36 bp sequence reads. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All sequence analyses were conducted based on the Mus Musculus mm9 genome assembly.

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol:
HCT116 cells were cultured in McCoy's 5A medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (all Gibco/Invitrogen) at 37 °C in 5% CO2 atmosphere.
ES cells were cultured in normal cell culture containing ES-grade serum supplemented with LIF. These cells were grown on gelatin-coated plates

extract_protocol: ES cells were crosslinked with 1% formaldehyde for 30 min at room temperature, quenched with 0.125 M glycine and washed at 4C with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl in HEG buffer (1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6). Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, HEG) and sheared using a Biouptor (Diagenode). Sonicated chromatin was centrifuged for 5 min and then incubated overnight with 2 ug of antibody and protein A/G beads (Santa Cruz). Beads were washed six times with different buffers at 4C: twice with solution of composition 0.1% SDS, 0.1% DOC, 1% Triton, 150 mM NaCl, HEG, once with the solution same as before but with 500 mM NaCl, once with solution of composition 0.25 M LiCl, 0.5% DOC, 0.5% NP-40, HEG and twice with HEG. Precipitated chromatin was eluted with 400 µl of elution buffer (1% SDS, 0.1 M NaHCO3), incubated at 65C for 4 h in the presence of 200 mM NaCl, phenol extracted and precipitated with 20 ug of glycogen at -20C overnight.

tag: origin

value: Embryonic stem cells

value: ChIP-sequencing


title: HCT116 RNAseq

data_processing: Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human (hg18) reference genome using the Illumina Analysis Pipeline allowing, one mismatch. Only the tags uniquely aligning to the genome were considered for further analysis. For RNA-Seq, further analysis was performed using the 36 bp sequence reads. The 36 bp sequence reads were directionally extended to 300 bp, corresponding to the length of the original fragments used for sequencing, and tags mapping on exact the same genomic locus were discarded to obtain a non-redundant set. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All sequence analyses were conducted based on the Homo Sapiens hg18 genome assembly.

molecule: polyA RNA

extract_protocol: 100ug total RNA was subjected to two rounds of poly(A) selection (Oligotex mRNA Mini Kit, QIAGEN), followed by DNaseI treatment (QIAGEN). 100-200ng mRNA was fragmented by hydrolysis (5x fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94C for 90 s and purified (RNeasy MinElute Cleanup Kit, QIAGEN). cDNA was synthesized using 5ug random hexamers by Superscript III Reverse Transcriptase (Invitrogen). ds-cDNA synthesis was performed in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified (MinElute Reaction Cleanup Kit, QIAGEN).

tag: cell line

tag: sample type

value: human colon carcinoma cell line established from the primary colon carcinoma of an adult man

value: ds-cDNA-sequencing

value: Fragmentented & 2x Poly(A) selected ds-cDNA


title: Input

data_processing: Peaks: Peak finding analysis was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) using hg18

source_name: Kasumi-1 input

growth_protocol: The Kasumi-1 cell line (acute myeloid leukemia FAB M2 with t(8;21)) was obtained from the DSMZ cell line repository (http://www.dsmz.de/ mutz/mutzhome.htm). The cells were grown in RPMI 1640 medium (Invitrogen, Heidelberg, Germany) supplemented 2 mM L-glutamine with 10% FCS and maintained in a humidified 37C incubator with 5% CO.

extract_protocol: Libraries of DNA fragments from chromatin immunoprecipitation or DNase I treatment were prepared from approximately 10ng of DNA. Firstly, overhangs were repaired by treatment of sample material with T4 DNA polymerase, T4 PNK and Klenow DNA polymerase (all enzymes obtained from New England Biolabs UK) in a reaction also containing 50 mM Tris-HCl,10 mM MgCl2, 10 mM Dithiothreitol, 0.4 mM dNTPs and 1 mM ATP. Samples were purified after each step using Qiagen MinElute columns (according to the manufacturer's guidelines). "A" bases were added to 3' ends of fragments using Klenow Fragment (3' - 5' exo- ), allowing for subsequent ligation of adapter oligonucleotides (Illumina part #1000521) using Quick T4 DNA ligase. After a further column clean up to remove excess adaptors, fragments were amplified in an 18 cycle PCR reaction using adapter-specific primers The libraries were purified and adapter dimers removed by running PCR products on 2% agarose gels and excising gel slices corresponding to fragments approximately 200-300 bp in size, which were then extracted using the Qiagen gel extraction kit. Once prepared, DNA libraries were subject to massively parallel DNA sequencing on an Illumina Genome Analyzer.


title: DNasel_HS_Kasumi-1

value: DNasel HS


title: DNasel_HS_t(8;21)#2

source_name: CD34+ cells from human patient with t(8:21)

treatment_protocol: Mononuclear cells were prepared from samples by differential centrifugation using Lymphoprep (Axis-Shield UK, Cambridgeshire, UK), and CD34+ blast cells were then isolated using MACS Micro Beads staining and separation on magnetic columns according to the manufacturer's guidelines. Purity of CD34+ cells was >85%. DNase I digestions were carried out on permeabilised CD34+ cells suspended in nuclei digestion buffer (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 10 mM Tris (pH7.4), 300 mM glucose). Digestions were then performed in 2-6 ul DNase I (Worthington, DPPF grade) at 22C for 3 minutes, by adding the enzyme in an equal volume of digestion buffer containing 2mM CaCl2 and 0.4% Nonident P-40. Genomic DNA was extracted from DNase I-treated cells using phenol/chloroform extraction, and then run out on 0.8% agarose gels.

value: AML patient bone marrow CD34+


title: POLII_siMM_ChIPSeq

treatment_protocol: Kasumi-1 cells were transfected with the 200 nM of siRNA using a Fischer EPI 3500 electroporator (Fischer, Heidelberg, Germany) as described previously (Martinez et al., 2004). The following siRNAs were used: mismatch control (sense, 5'-CCU CGA AUU CGU UCU GAG AAG-3'; antisense, 5'-UCU CAG AAC GAA UUC GAG GUU-3')

value: RNA Polymerase II


title: POLII_siRE_ChIPSeq


title: H3K9Ac_siMM_ChIPSeq


title: H3K9Ac_siRE_ChIPSeq


title: DNasel_HS_t(8;21)#1


title: HCT116 H3K4me3-ChIP

tag: technique

tag: binding/selection

value: Antibody  H3K4me3 (Diagenode)

value: Diagenode


title: RUNX1_non-t(8;21)_ChIPSeq

source_name: Peripheral blood MNC CD34+ from non-t(8;21)AML patient

treatment_protocol: Mononuclear cells were prepared from samples by differential centrifugation using Lymphoprep (Axis-Shield UK, Cambridgeshire, UK), and CD34+ blast cells were then isolated using MACS Micro Beads staining and separation on magnetic columns according to the manufacturer's guidelines. Purity of CD34+ cells was >85%.

value: Peripheral blood MNC CD34+


title: DNasel_HS_non-t(8;21)

source_name: Peripheral blood MNC CD34+ from non-t(8;21) AML patient


title: patientA_input

source_name: patient A input


title: RUNX1ETO_control_ChIPSeq

source_name: Kasumi-1 control (without transfection)

value: ETO(C20)sc (lot number F1809)


title: RUNX1ETO_siMM_ChIPSeq


title: MM with NeuroD2

status: Public on Mar 26 2012

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

country: USA

institute: Fred Hutch Cancer Research Center

data_processing:
MM.ND2.1.map; genome build: mm9
MM.ND2.2.map; genome build: mm9
MM.ND2.bedGraph; genome build: mm9
Peaks are called using in-house developed R package peakSig.

growth_protocol: P19 cells were maintained in MEMα as previously described (Farah et al., 2000, PUBMED ID 10648228), and MEFs derived from Myod-/-/Myf5-/- mice were maintained in DMEM with 10% FBS.

extract_protocol:
Standard Illumina ChIP-Seq sample prep kit protocol with two modifications: (1) DNA fragments ranging from 150 to 300 bp were selected at the gel-selection step; (2) 21 cycles of PCR were performed at the PCR amplification step instead of 18.
For P19 and MM control PvuII seq sample, untranduced P19 or MEFs cells were trypsinized and washed once in reticulocyte suspension buffer (RSB: 10mM Tris pH 7.4, 10mM NaCl, 5mM MgCl2), followed by resuspension in lysis buffer (RSB + 0.1% NP-40) at a final concentration of 1.5x106 cells/mL and incubation on ice for 10 minutes. Nuclei were pelleted and washed in lysis buffer, followed by resuspension in 200μl of 1X NEB buffer 2, addition of 40 units of PvuII (NEB) per 106 nuclei, and incubation at 37C for 30 minutes. 200μl of STOP buffer (0.6M NaCl, 20mM Tris pH 7.4,10mM EDTA, 1% SDS, 2 mg/mL proteinase K) was added and the reaction was incubated at 37C overnight. Genomic DNA was isolated using Qiagen DNeasy spin columns. 5μg of DNA was used for labeling, beginning with addition of an 'A' tail to the blunt ends generated by PvuII digestion using Klenow 3-5' exo- (NEB). After purification through MinElute columns (Qiagen), custom designed biotinylated adapters with a 'T' overhang and an EcoRV site immediately upstream of the 'T' (purchased from IDT) were ligated onto the 'A'-tailed ends using Quick Ligase (NEB). After purification (Qiagen), DNA was fragmented to 150-350bp using a Diagenode Bioruptor (low amplitude, 30 seconds/cycle, 30 cycles). Biotinylated fragments were enriched with Streptavidin-conjugated Dynabeads (Invitrogen), and DNA was released from the beads by digestion with EcoRV for 1 hour at 37C. Fragments were subsequently purified and labeled for sequencing as above.

treatment_protocol: P19 cells and MEFs were infected with lentivirus in media containing polybrene (final concentration 8 µg /ml), after 24 hours the cells were switched into fresh media. MEFs transduced with MyoD were switched to differentiation media (1% heat inactivated horse serum, 10 μg/mL insulin, 10 μg/mL transferrin) 48 hours after infection.

value: mouse embryonic fibroblasts

tag: genotype/variation

value: transduced with NeuroD2 lentivirus

tag: chip antibody

value: two NEUROD2 antibodies raised in rabbits by our lab (1240J, 1168J)


title: P19 with MyoD

data_processing:
P19.MD.1.map; genome build: mm9
P19.MD.2.map; genome build: mm9
P19.MD.bedGraph; genome build: mm9
Peaks are called using in-house developed R package peakSig.

value: P19 cells

value: transduced with MyoD lentivirus

value: two MyoD antibody raised in rabbits by our lab (6196 and 6975) and previously described (Tapscott et al., 1988)


title: RUNX1ETO_siRE_ChIPSeq

tag: antibody


title: RUNX1_Kasumi-1_ChIPSeq

source_name: Kasumi-1 control


title: P19 control

data_processing:
P19.control.1.map; genome build: mm9
P19.control.2.map; genome build: mm9
Peaks are called using in-house developed R package peakSig.

source_name: P19_preimmune serum_ChIP-seq

value: untransduced control

value: preimmune serum


title: P19 with NeuroD2

data_processing:
P19.ND2.1.map; genome build: mm9
P19.ND2.2.map; genome build: mm9
P19.ND2.bedGraph; genome build: mm9
Peaks are called using in-house developed R package peakSig.


title: P19 with NeuroD2, AcH4

data_processing:
P19.ND2.AcH4.bam; genome build: mm9
Peaks are called using in-house developed R package peakSig.

value: acetyl-H4 antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat #

tag: chip antibody lot #


title: P19 control AcH4

data_processing:
P19.control.AcH4.bam; genome build: mm9
Peaks are called using in-house developed R package peakSig.


title: MM with MyoD

data_processing:
MM.MD.1.map; genome build: mm9
MM.MD.2.map; genome build: mm9
MM.MD.bedGraph; genome build: mm9
Peaks are called using in-house developed R package peakSig.


title: P19 control PvuII

description: chromatin accessibility using PvuII assay followed by high throughput sequencing

data_processing:
P19.control.P2.bam; genome build: mm9
Peaks are called using in-house developed R package peakSig.


title: MM control PvuII

data_processing:
MM.control.P2.bam; genome build: mm9
Peaks are called using in-house developed R package peakSig.


title: MCF-7 E2 DNaseI

status: Public on Mar 25 2012

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

country: Canada

institute: UNIVERSITY HEALTH NETWORK

description: DNase-seq

data_processing: bed: Sequence reads were obtained and mapped to the human (March, 2006) genomes

source_name: breast cancer cells

extract_protocol: H3K4me2 ChIPed DNA or the size selected DNase I digested DNA was used for library preparation. 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 18 cycles and library fragments of ~220 bp (for H3K4me2 ChIP-seq) or 200~300bp (for DNase-seq) (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 or HiSeq machine following the manufacturer's protocols.

treatment_protocol: Cells were cultured in RPMI 1640 supplemented with 10%  charcoal-stripe FBS for 3 days, and then treated with DHT or Ethanol for 4 hours for prostate cancer cells, treated with E2 or Ethanal for 45mins for breast cancer cells

value: breast cancer cells

tag: passages

tag: treatment

value: DHT

value: DNase-seq


title: MCF-7 vehicle DNaseI

description: DNase-seq

value: ethanol


title: LNCaP DHT DNaseI

description: DNase-seq

source_name: prostate cancer cells

value: LNCaP

value: prostate cancer cells


title: LNCaP vehicle DNaseI

description: DNase-seq


title: MCF-7 E2 H3K4me2

description: Chromatin IP against H3K4me2

value: Chromatin IP against H3K4me2

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #


title: MCF-7 vehicle H3K4me2

description: Chromatin IP against H3K4me2

tag: cell type


title: HoxB4 ChIP_day 6

status: Public on Mar 23 2012

city: La Jolla

first: Kai

last: Tan

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

description: Sample 1

data_processing:
D6_HoxB4_IP.counts.wig; genome build: mm9
Counts: Sequence reads were obtained and mapped to the mouse (July, 2007) genomes using the Bowtie algorithm. Uniquely mapped reads with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows. Counts included.

source_name: day 6 embryoid body cells

growth_protocol: To differentiate ES cells into HSCs, a 2-stage culture strategy was adopted. Initially, ES cells were subjected to embryoid body (EB) formation over 6 days. At this stage, ES cells were plated to an ultra-low attachment Petri dish at a concentration of 2000 cells/mL in a methycellulose-based differentiation medium containing Iscove modified Dulbecco medium (Invitrogen), 15% FCS, 300 μg/mL transferrin, 2 mM L-glutamine, 100 U/mL penicillin, 100 μg/mL streptomycin, 5% protein-free hybridoma medium (Invitrogen), 4x10^-4 M monothioglycerol, and 50 μg/mL ascorbic acid. At second stage, EBs were dissociated into single-cell suspension using trypsin (2.75%), and 3.5x10^6 cells/mL cells were re-plated on another ultra-low attachment Petri dish in a serum-free hematopoietic differentiation medium that contained StemPro34 plus nutrient supplement (Invitrogen) and a cocktail of hematopoietic cytokines including murine stem cell factor (mSCF; 100 ng/mL; R&D Systems, Minneapolis, MN), mIL-3 (2 ng/mL), mIL-6 (5 ng/mL), Flt3-L (10 ng/mL), insulin-like growth factor-1 (IGF-1; 40 ng/mL; Promega, Madison, WI), and dexamethasone (1 μM; Sigma-Aldrich, St Louis, MO). Culture medium was changed every other day and cell density maintained below 4x106 cells/mL.

extract_protocol: Chromatin fragments with HoxB4 binding sites were enriched by immunoprecipitation with a rabbit monoclonal antibody against human HoxB4 immunogen (Epitomics, Burlingame, CA). After reversal of cross-linking, the enriched DNA fragments were precipitated and further purified using a PCR clean-up kit (Qiagen). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments 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.

value: day 6 embryoid body cells

value: Epitomics


title: HoxB4 ChIP_day 26

description: Sample 5

data_processing:
D26_HoxB4_IP.counts.wig; genome build: mm9
Counts: Sequence reads were obtained and mapped to the mouse (July, 2007) genomes using the Bowtie algorithm. Uniquely mapped reads with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows. Counts included.

source_name: EB cells cultured with a hematopietic cytokine cocktail for 20 days


title: Input_day 16

description: Sample 4

data_processing:
D16_Input.counts.wig; genome build: mm9
Counts: Sequence reads were obtained and mapped to the mouse (July, 2007) genomes using the Bowtie algorithm. Uniquely mapped reads with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows. Counts included.

source_name: EB cells cultured with a hematopietic cytokine cocktail for 10 days


title: HoxB4 ChIP_day 16

description: Sample 3

data_processing:
D16_HoxB4_IP.counts.wig; genome build: mm9
Counts: Sequence reads were obtained and mapped to the mouse (July, 2007) genomes using the Bowtie algorithm. Uniquely mapped reads with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows. Counts included.

value: EB cells cultured with a hematopietic cytokine cocktail for 10 days


title: Input_day 6

description: Sample 2

data_processing:
D6_Input.counts.wig; genome build: mm9
Counts: Sequence reads were obtained and mapped to the mouse (July, 2007) genomes using the Bowtie algorithm. Uniquely mapped reads with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows. Counts included.

source_name: day 6 embryoid body cels

value: day 6 embryoid body cels


title: Input_day 26

description: Sample 6

data_processing:
D26_Input.counts.wig; genome build: mm9
Counts: Sequence reads were obtained and mapped to the mouse (July, 2007) genomes using the Bowtie algorithm. Uniquely mapped reads with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows. Counts included.

value: EB cells cultured with a hematopietic cytokine cocktail for 20 days


title: rat vascular smooth muscle cells stimulated with Ang II for 3h

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

description: small RNA separated from total RNA

data_processing:
Raw data in FASTQ format generated from the Illumina pipeline was aligned against Rat Nov. 2004 (rn4) assembly using Novoalign software (http://www.novocraft.com). The 3’-adapter was trimmed by Novoalign before the alignment, and reads shorter than 16-base after adapter trimming were discarded. For reads aligned to multiple locations on the genome, one aligned region was randomly selected for counting the number of reads (Supplemental Table S1) as described (18). Genomic locus of each rat mature microRNA (miRNA) was generated by aligning rat mature miRNA sequences (miRBase v14) to rn4 assembly without allowing mismatches. For each sample, an aligned read was annotated to a specific genome feature in the order of mature miRNA, miRNA precursor, rRNA, tRNA, other ncRNA, Refseq gene and intergenic region if it completely falls in the specified region with 10 bp extension on both ends. Specifically, aligned reads were first annotated to rat mature miRNA (v14, www.miRbase.org) genomic loci. The reads that could not be annotated to mature miRNA regions were processed further to annotated pre-miRNA genomic regions (v14). Remaining reads were then annotated to non-coding RNAs (ncRNAs) other than miRNAs including rRNA and tRNA, using rat ncRNA annotation file downloaded from UCSC genome browser (http://genome.ucsc.edu/). Finally, the reads that were not annotated to any ncRNA regions were assigned to Refseq genes and the remaining reads were defined as intergenic regions. For each sample, the reads corresponding to the mature miRNA genomic loci (including 10-base extension on both ends) were counted to obtain expression levels of total miRNAs (Supplemental Table S2).The resulting miRNA expression dataset was further normalized by scaling the total mature miRNA counts in each sample to 8.5 million. Differentially expressed miRNAs induced by Ang II at indicated time points were selected using the criteria; a) reads in at least one sample were above 256, and b) showed at least 1.5 fold change between Ang II-treated samples versus untreated.
Genome Build:
AngII_3h_uniq_seq_count_filtered.txt: rn4

organism: Rattus norvegicus

source_name: vascular smooth muscle cells,  Ang II stimulation for 3h

growth_protocol: rat vascular smooth muscle cells were cultured in M199 medium supplemented with 10% FBS.

extract_protocol: Total RNA was used for the construction of small RNA libraries, cluster generation, and then deep sequencing (at the Beckman Research Institute Sequencing Core), using the Alternative v1.5 Protocol (Illumina Inc., San Diego, CA) with minor optimization. Briefly, 0.5 μg of total RNA was ligated to sRNA 3’adapter (AUCUCGUAUGCCGUCUUCUGCUUG) using T4 RNA Ligase 2, truncated (New England BioLabs, Ipswich, MA) at 22 °C for 1 h, and subsequently ligated to the SRA 5’adapter (GUUCAGAGUUCUACAGUCCGACGAUC) with T4 RNA ligase (New England BioLabs, Ipswich, MA) at 20 °C for 1 h. The adaptor-linked RNA was converted to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) and RT-Primer (5’-CAAGCAGAAGACGGCATACGA-3’), and then amplified with Phusion DNA Polymerase (Finnzymes Thermo Scientific, Pittsburgh, PA) for 12 cycles using primers (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA-3’). PAGE purification was carried out to select small RNAs of 17-52 nucleotides in length. The purified library was quantified using qPCR, used for cluster generation on cBot, and sequenced using Genome Analyzer IIx (Illumina Inc. San Diego, CA).

treatment_protocol: serum depleted for 48h and treated with or without Ang II (100nM) for 1h, 3h or 24h.

tag: strain

value: Sprague-Dawley

tag: tissue

value: aorta


title: rat vascular smooth muscle cells stimulated with Ang II for 24h

description: small RNA separated from total RNA

data_processing:
Raw data in FASTQ format generated from the Illumina pipeline was aligned against Rat Nov. 2004 (rn4) assembly using Novoalign software (http://www.novocraft.com). The 3’-adapter was trimmed by Novoalign before the alignment, and reads shorter than 16-base after adapter trimming were discarded. For reads aligned to multiple locations on the genome, one aligned region was randomly selected for counting the number of reads (Supplemental Table S1) as described (18). Genomic locus of each rat mature microRNA (miRNA) was generated by aligning rat mature miRNA sequences (miRBase v14) to rn4 assembly without allowing mismatches. For each sample, an aligned read was annotated to a specific genome feature in the order of mature miRNA, miRNA precursor, rRNA, tRNA, other ncRNA, Refseq gene and intergenic region if it completely falls in the specified region with 10 bp extension on both ends. Specifically, aligned reads were first annotated to rat mature miRNA (v14, www.miRbase.org) genomic loci. The reads that could not be annotated to mature miRNA regions were processed further to annotated pre-miRNA genomic regions (v14). Remaining reads were then annotated to non-coding RNAs (ncRNAs) other than miRNAs including rRNA and tRNA, using rat ncRNA annotation file downloaded from UCSC genome browser (http://genome.ucsc.edu/). Finally, the reads that were not annotated to any ncRNA regions were assigned to Refseq genes and the remaining reads were defined as intergenic regions. For each sample, the reads corresponding to the mature miRNA genomic loci (including 10-base extension on both ends) were counted to obtain expression levels of total miRNAs (Supplemental Table S2).The resulting miRNA expression dataset was further normalized by scaling the total mature miRNA counts in each sample to 8.5 million. Differentially expressed miRNAs induced by Ang II at indicated time points were selected using the criteria; a) reads in at least one sample were above 256, and b) showed at least 1.5 fold change between Ang II-treated samples versus untreated.
Genome Build:
AngII_24h_uniq_seq_count_filtered.txt: rn4

source_name: vascular smooth muscle cells,  Ang II stimulation for 24h


title: rat vascular smooth muscle cells stimulated with Ang II for 1h

description: small RNA separated from total RNA

data_processing:
Raw data in FASTQ format generated from the Illumina pipeline was aligned against Rat Nov. 2004 (rn4) assembly using Novoalign software (http://www.novocraft.com). The 3’-adapter was trimmed by Novoalign before the alignment, and reads shorter than 16-base after adapter trimming were discarded. For reads aligned to multiple locations on the genome, one aligned region was randomly selected for counting the number of reads (Supplemental Table S1) as described (18). Genomic locus of each rat mature microRNA (miRNA) was generated by aligning rat mature miRNA sequences (miRBase v14) to rn4 assembly without allowing mismatches. For each sample, an aligned read was annotated to a specific genome feature in the order of mature miRNA, miRNA precursor, rRNA, tRNA, other ncRNA, Refseq gene and intergenic region if it completely falls in the specified region with 10 bp extension on both ends. Specifically, aligned reads were first annotated to rat mature miRNA (v14, www.miRbase.org) genomic loci. The reads that could not be annotated to mature miRNA regions were processed further to annotated pre-miRNA genomic regions (v14). Remaining reads were then annotated to non-coding RNAs (ncRNAs) other than miRNAs including rRNA and tRNA, using rat ncRNA annotation file downloaded from UCSC genome browser (http://genome.ucsc.edu/). Finally, the reads that were not annotated to any ncRNA regions were assigned to Refseq genes and the remaining reads were defined as intergenic regions. For each sample, the reads corresponding to the mature miRNA genomic loci (including 10-base extension on both ends) were counted to obtain expression levels of total miRNAs (Supplemental Table S2).The resulting miRNA expression dataset was further normalized by scaling the total mature miRNA counts in each sample to 8.5 million. Differentially expressed miRNAs induced by Ang II at indicated time points were selected using the criteria; a) reads in at least one sample were above 256, and b) showed at least 1.5 fold change between Ang II-treated samples versus untreated.
Genome Build:
AngII_1h_uniq_seq_count_filtered.txt: rn4

source_name: vascular smooth muscle cells,  Ang II stimulation for 1h


title: rat vascular smooth muscle cells after 48h serum depletion

description: small RNA separated from total RNA

data_processing:
Raw data in FASTQ format generated from the Illumina pipeline was aligned against Rat Nov. 2004 (rn4) assembly using Novoalign software (http://www.novocraft.com). The 3’-adapter was trimmed by Novoalign before the alignment, and reads shorter than 16-base after adapter trimming were discarded. For reads aligned to multiple locations on the genome, one aligned region was randomly selected for counting the number of reads (Supplemental Table S1) as described (18). Genomic locus of each rat mature microRNA (miRNA) was generated by aligning rat mature miRNA sequences (miRBase v14) to rn4 assembly without allowing mismatches. For each sample, an aligned read was annotated to a specific genome feature in the order of mature miRNA, miRNA precursor, rRNA, tRNA, other ncRNA, Refseq gene and intergenic region if it completely falls in the specified region with 10 bp extension on both ends. Specifically, aligned reads were first annotated to rat mature miRNA (v14, www.miRbase.org) genomic loci. The reads that could not be annotated to mature miRNA regions were processed further to annotated pre-miRNA genomic regions (v14). Remaining reads were then annotated to non-coding RNAs (ncRNAs) other than miRNAs including rRNA and tRNA, using rat ncRNA annotation file downloaded from UCSC genome browser (http://genome.ucsc.edu/). Finally, the reads that were not annotated to any ncRNA regions were assigned to Refseq genes and the remaining reads were defined as intergenic regions. For each sample, the reads corresponding to the mature miRNA genomic loci (including 10-base extension on both ends) were counted to obtain expression levels of total miRNAs (Supplemental Table S2).The resulting miRNA expression dataset was further normalized by scaling the total mature miRNA counts in each sample to 8.5 million. Differentially expressed miRNAs induced by Ang II at indicated time points were selected using the criteria; a) reads in at least one sample were above 256, and b) showed at least 1.5 fold change between Ang II-treated samples versus untreated.
Genome Build:
no_treatment_uniq_seq_count_filtered.txt: rn4

source_name: vascular smooth muscle cells,  no Ang II stimulation


title: NCOR ChIP-seq (siGPS2)

city: Boston

first: Valentina

last: Perissi

state: MA

address: 72 E. Concord St

department: Department of Biochemistry

institute: Boston University School of Medicine

description: ChIP on NCOR

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline. The sequencing reads were aligned to the human genome UCSC build hg18 by using Bowtie (Langmead et al., 2009) or SOAP (Li et al, Bioinformatics, 2008). HOMER was used for peak finding (Heinz et al., 2010).
Genome Build:
NCOR_siGPS2.sample1.bowtie.alignments: hg18
NCOR_siGPS2.sample1.bowtie.bed: hg18
NCOR_siGPS2.sample2.soap.alignments: hg18
NCOR_siGPS2.sample2.soap.bed: hg18
NCOR_siGPS2.sample3.bowtie.alignments: hg18
NCOR_siGPS2.sample3.bowtie.bed: hg18
NCOR_siGPS2.sample3.soap.alignments: hg18
NCOR_siGPS2.sample3.soap.bed: hg18
NCOR_siGPS2.all-samples.bowtie.bed: hg18
NCOR_siGPS2.peaks: hg18

source_name: 293T cells

growth_protocol: 293T cells from ATCC were grown on poly-lysine coated culture dishes with DMEM medium supplemented with 10% FBS

extract_protocol: Anti-GPS2 antibody was generated in rabbit against a peptide representing aa 307-327. Guinea pig anti-TBL1 and rabbit anti-N-CoR were generated as described (Jepsen et al., 2000; Perissi et al., 2004). The libraries were constructed following Illumina's Chip-Seq sample preparation kit.

treatment_protocol: Transient siRNA transfection was performed with 10nM siCTL or siGPS2 following the protocol for Lipofectamine2000. The transfection mix was removed 4h after transfection and at this point cells were switched to DMEM with 1% FBS. Cells were harvested 2 days after transfection and subjected to ChIP.

value: anti-N-CoR


title: NCOR ChIP-seq (siCTL)

description: ChIP on NCOR

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline. The sequencing reads were aligned to the human genome UCSC build hg18 by using Bowtie (Langmead et al., 2009) or SOAP (Li et al, Bioinformatics, 2008). HOMER was used for peak finding (Heinz et al., 2010).
Genome Build:
NCOR_siCTL.sample1.bowtie.alignments: hg18
NCOR_siCTL.sample1.bowtie.bed: hg18
NCOR_siCTL.sample2.soap.alignments: hg18
NCOR_siCTL.sample2.soap.bed: hg18
NCOR_siCTL.sample3.bowtie.alignments: hg18
NCOR_siCTL.sample3.bowtie.bed: hg18
NCOR_siCTL.sample3.soap.alignments: hg18
NCOR_siCTL.sample3.soap.bed: hg18
NCOR_siCTL.all-samples.bowtie.bed: hg18
NCOR_siCTL.peaks: hg18


title: GPS2  ChIP-seq

description: ChIP on GPS2

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline. The sequencing reads were aligned to the human genome UCSC build hg18 by using Bowtie (Langmead et al., 2009) or SOAP (Li et al, Bioinformatics, 2008). HOMER was used for peak finding (Heinz et al., 2010).
Genome Build:
GPS2_minusTNFA.bowtie.alignments: hg18
GPS2_minusTNFA.bowtie.bed: hg18
GPS2_minusTNFA.peaks: hg18


title: H9 Small RNA, 76 cycles

status: Public on Mar 21 2012

city: San Francisco

first: Yun

last: Choi

address: 513 Parnassus Ave.

department: Diabetes Center

institute: UCSF

description:
Co-cultured on irradiated CF1 MEFs.
Collected cells were >99% free of MEFs.
RNA cloning selective for RNA with 5'-phosphate and 3'-OH.
Non-polyA-selected, non-fragmented small RNAs.

data_processing: Intensity files were processed by version SCS 2.5 to generate .fq files. Fastq files were aligned to the UCSC hg18 genome build with Novoalign (version 2.07). Reads aligned to unique loci were annotated using custom Python programs.

source_name: H9 hESC

growth_protocol: MEFs were plated on 0.1% gelatin-coated 6-well dishes in DMEM high glucose supplemented with 2 mM L-glutamine, 1X penicillin/streptomycin, and 10% fetal bovine serum. hESCs were grown on MEFs in KSR media: Knockout-DMEM medium containing 20% Knockout Serum Replacement, 2 mM Lglutamine, 0.1 mM (1X) non-essential amino acids, 4 ng/ml human basic fibroblast growth factor, and 0.1 mM beta-mercaptoethanol.

extract_protocol:
Small RNAs (<200 nt) were purified using the mirVana miRNA Isolation Kit.

DNA and RNA oligos for RNA sequencing were synthesized by IDT. The 3'-linker (5'-App-AGA TCG GAA GAG CGG TTC AGC AGG AAT GCC GAG/3InvdT/) was adenylated and purified as described in (Pfeffer et al. 2005). RNA linker ligation was done as previously described (Neilson et al. 2007) but briefly, pre-adenylated 3'-linker was ligated to small RNAs using T4 RNL2truc (NEB) without ATP in the reaction buffer. After ethanol precipitation, the reaction products were used for 5'-linker ligation (/5Cy3/rArCrA rCrUrC rUrUrU rCrCrC rUrArC rArCrG rArCrG rCrUrC rUrUrC rCrGrA rUrCrU) without gel purification with T4 RNL1 (NEB) with ATP. RNA was reverse transcribed (5'-GCT GAA CCG CTC TTC CGA TCT) with SuperScript III (Invitrogen) and amplified with 25 cycles of PCR with Platinum Taq polymerase (Invitrogen) and Illumina PE PCR primers (Illumina). PCR products greater than 140 bp were agarose gel purified (Qiagen QIAquick Gel Extraction Kit), ethanol precipitated and resuspended in elution buffer. Library fragment size and concentration were measured with the Bioanalyzer High Sensitivity DNA chip assay (Agilent). The average insert size was 153 bp with SD=54 (CV = 35.2%).

tag: cell line

value: embryonic stem cells


title: plusTNFa_siCTL

description: RNA-seq

data_processing: The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline. The RPKM values were computed by using rSeq (Jiang and Wong, 2009).

extract_protocol: Total RNA was extracted from 293T cells using the RNeasy Kit (QIAGEN) and reverse-transcribed with SuperScript III kit (Invitrogen).

treatment_protocol: Transient siRNA transfection was performed with 5nM siCTL or siGPS2 following the protocol for Lipofectamine2000. The transfection mix was removed 4h after transfection and at this point cells were switched to DMEM with 1% FBS. Cells were harvested 2 days after transfection and were treated with 10nM TNFa for 6h.

value: siRNA transfection with 5nM siCTL


title: plusTNFa_siGPS2

description: RNA-seq

value: siRNA transfection with 5nM siGPS2


title: minusTNFa_siGPS2

description: RNA-seq


title: TBL1  ChIP-seq

description: ChIP on TBL1

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline. The sequencing reads were aligned to the human genome UCSC build hg18 by using Bowtie (Langmead et al., 2009) or SOAP (Li et al, Bioinformatics, 2008). HOMER was used for peak finding (Heinz et al., 2010).
Genome Build:
TBL1_minusTNFA.bowtie.alignments: hg18
TBL1_minusTNFA.bowtie.bed: hg18
TBL1_minusTNFA.peaks: hg18


title: minusTNFa_siCTL

description: RNA-seq


title: Rag2.Pro-B.input [8149.8.30222AAXX]

status: Public on Mar 20 2012

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8149.8.30222AAXX.bed.gz: mm9

source_name: Pro-B

extract_protocol:
RNA-Seq: RNA was isolated from ex vivo sorted cells using the RNeasy Plus Mini Kit (Qiagen), and mRNA was obtained by two rounds of poly(A) selection using the Dynabeads mRNApurification kit (Invitrogen) followed by fragmentation by heating at 94oC for 3 min. The fragmented mRNA was used as template for first-strand cDNA synthesis with random hexamers using the SuperScript VILOTM cDNA Synthesis Kit (Invitrogen). dNTPs were removed on a Mini Quick Spin Column (Roche) prior the second-strand cDNA synthesis with 100 mM dATP, dCTP, dGTP and dUTP in the presence of RNase H, E. coli DNA polymerase I and DNA ligase (Invitrogen). The incorporation of dUTP allowed elimination of the second strand during library preparation.
ChIP-seq: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments 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: extraction method

value: 4-5 day culture (Cd19+ cells from Bone marrow)

value: Bone Marrow


title: WT.Mature_B.Input [8042.7.207JYAAXX]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8042.7.207JYAAXX.bed.gz: mm9

source_name: Mature B

value: WT

value: Ex vivo (MACS sort)

value: Lymph Node


title: WT.Mature_B.Input [8087]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8087.bed.gz: mm9


title: WT.Mature_B.Input [8042.8.208KDAAXX]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8042.8.208KDAAXX.bed.gz: mm9


title: WT.Mature_B.Input [8042.7.20CUYAAXX]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8042.7.20CUYAAXX.bed.gz: mm9


title: Rag2.Pro-B.input [8149.8.301DTAAXX]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8149.8.301DTAAXX.bed.gz: mm9


title: Rag2.Pro-B.input [8123.2]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8123.2.bed.gz: mm9


title: WT.Mature_B.Input [8094]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8094.bed.gz: mm9


title: Rag2.Pro-B.input [8123.3]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8123.3.bed.gz: mm9


title: Rag2.Pro-B.input [8112.6]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8112.6.bed.gz: mm9


title: Rag2.Pro-B.input [8112.1]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8112.1.bed.gz: mm9


title: Rag2.Pro-B.input [8091.5.]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8091.5.bed.gz: mm9


title: WT.Mature_B.Input [8096]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8096.bed.gz: mm9


title: Rag2.Pro-B.input [8091.6]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8091.6.bed.gz: mm9


title: RNA-seq mature B [10424]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
10424.30.counts.tab: mm9

source_name: FO B

value: Cd79a-Cre R26CA(Ebf1/+)

value: Ex vivo (FACS sort)

value: Spleen


title: RNA-seq mature B [10425]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
10425.30.counts.tab: mm9

source_name: B-1a B


title: RNA-seq mature B [10426]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
10426.30.counts.tab: mm9


title: RNA-seq mature B [9763]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
9763.30.counts.tab: mm9


title: WT.Mature_B.Input [8089]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8089.bed.gz: mm9


title: RNA-seq mature B [9764]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
9764.30.counts.tab: mm9


title: RNA-seq mature B [9765]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
9765.30.counts.tab: mm9


title: WT.Mature_B.Input [8042.5.208KBAAXX]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8042.5.208KBAAXX.bed.gz: mm9


title: RNA-seq mature B [9762]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
9762.30.counts.tab: mm9


title: RNA-seq mature B [9761]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
9761.30.counts.tab: mm9

value: Cd23-Cre Ebf1(fl/–)


title: EBF1 ChIP-seq mature B [9842]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
9842.bed.gz: mm9

value: anti EBF1 #0647 homemade


title: RNA-seq mature B [10423]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
10423.30.counts.tab: mm9


title: EBF1 ChIP-seq mature B [8271]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8271.bed.gz: mm9


title: EBF1 ChIP-seq [8246.2]

data_processing:
Illumina GA Pipeline RTA 1.8.7; ChIP-seq : Sequence reads that passed the Illumina quality filtering were considered for alignment against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al, 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard.
RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256 The RNA-seq samples were cut down to a common read length (30bp) and aligned to the mouse transcriptome (mm9) using TopHat version 1.3.1.(1). The number of reads per gene was counted using HTseq version 0.5.3 with the overlap resolution mode option set to "union".
Genome Build:
8246.2.bed.gz: mm9


title: 12042009_619VVAAXX_B3

status: Public on Mar 17 2012

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against Smad3 in BG03 cells undergoing endodermal differentiation

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Supplementary_files_format_and_content: Alignment (ylf) files: The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations determined by bowtie. The file contains the locations of the bowtie aligned reads with the following format:
#BWT1 (read category BWT1)
>1 (chromomsome 1)
-12345 (minus strand read)
-9876 (minus strand read)
54321 (plus strand read)
>2 (chromomsome 2)
-67890 (minus strand read)
98765 (plus strand read)
132323 (plus strand read)
#BWT2 (read category BWT2)
etc..

source_name: Endodermal Diff of BG03 cells, Activin A t=2h, Smad3

growth_protocol: hES cells were grown in mTESR media (Stem Cell Technologies) on plates coated with matrigel (BD Biosciences) in the absence of feeder cells.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. 1x10^8 cells were sonicated at 21 watts in 20 second pulses for 3 min of sonication time. Half of the cell lysate was used for immunoprecipitation. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: Once cells reached confluence they were rested for 24 hours in RPMI plus B27.  Cells were then treated with 50 ng/ml Activin at time 0.  Media was changed at 24 hours and fresh Activin was added at 50 ng/ml. At 46 hours fresh 50 ng/ml Activin was added and cells were cross-linked at 48 hours. Harvest times for treatment group were 0h, 2h, 48h.

tag: antibody catalog number

value: Abcam AB28379

value: BGO3 (feeder free)


title: 12042009_619VVAAXX_B2

source_name: Endodermal Diff of BG03 cells, Activin A t=0, Smad3


title: Seq for WM853.2 melanoma cells WCE

description: WM853.2 WCE

source_name: WM853.2 WCE

growth_protocol: Melanoma short-term cultures (STCs) were obtained from the Wistar Institute collection, and were derived from patients with metastatic disease. All lines were cultured in RPMI medium (cellgro) containing 10% FBS (cellgro) and penicillin/streptomycin (cellgro). In order to culture WM451-Lu cells, cell culture plates were pre-coated with 1% porcine gel solution (Sigma) to enhance cell adherence.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Melanoma

value: None WCE


title: 07212009_42F6FAAXX_B1

description: Chromatin IP against Pol2

source_name: ChipSeq for Pol2

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

value: RNA Pol II (8WG16)

value: Covance MMS-126R

value: embryonic stem cells


title: 12042009_619VVAAXX_B4

source_name: Endodermal Diff of BG03 cells, Activin A, t=48h Smad3


title: Seq for Wm451-lu WCE

description: Wm451-lu WCE

source_name: Wm451-lu WCE


title: 11182009_42YK9AAXX_B4

description: Chromatin IP against Smc1 in human ES cells

source_name: Smc1 ChipSeq in human ES cells

value: Bethyl A300-055A


title: ChIP-Seq for SetDB1 in WM853.2 melanoma cells

description: Chromatin IP against SetDB1

source_name: Chromatin IP against SetDB1

value: Santa Cruz SC-66884


title: 11132009_619PLAAXX_B6

description: Chromatin IP against Smc3 in human ES cells

source_name: Smc3 ChipSeq in human ES cells

value: Abcam AB9263


title: Mll1 -/- TNF

city: Wuhan

first: Min

last: Wu

state: Hubei

address: Room 5005, College of Life Sciences, Wuhan University

department: College of Life Science

institute: Wuhan University

data_processing:
We removed reads that contain either a base of N or overhalf qualities below 20. Then we got the clean reads.
TopHat was used for gene mapping. We mapped clean reads to the mRNA sequences of mouse, calculated the frequency of each mRNA being covered in four samples afterwards.
DESeq was used for differential expressed genes analysing. We compared every two samples each time, followed by Mll1+/+ TNFvsMll1-/- TNF, Mll1+/+vsMll1 -/--, Mll1+/+ TNFvsMll1+/+, Mll1 -/- TNFvsMll1 -/--. In the results, we picked genes only when its p value below 0.01. We defined these genes differentially expressed genes. We also calculated the RPKM values as the expression level of each gene in the four samples. We could get the fold change of genes through their RPKM values,  decide whether it is a up-regulated gene or a  down-regulated gene.
Genome_build: NCBI Build 37.2
Supplementary_files_format_and_content: Processed data (linked on Series record) includes RPKM values for each Sample.

source_name: Mll1-/- MEF cell with TNFa treatment

growth_protocol: Both Mll1+/+ and Mll1-/- cells were cultured in DMEM plus 10% FBS.

extract_protocol: Total RNA was extracted with Qiagen Rneasy mini kit. After testing the quality, mRNA was purified and fragmentated. The first and second strand cDNA was synthesized and End repair was performed.  After 3' Ends was adenylated, the adapters was ligated and cDNA was purified. After enrichment and validation, the cDNA templates was sent for sequencing.

treatment_protocol: Cells were treated with 10un/ml TNFa or control medium.  4hr later, cells were harvested and total RNA was isolated.

value: MEF

tag: agent

value: TNFa (10ng/ml)


title: Mll1 -/-

source_name: Mll1-/- MEF cell

tag: genotype/variation


title: Mll1+/+

source_name: Mll1+/+ MEF cell

value: wild type


title: 07212009_42F6FAAXX_B7

description: Brg1 ChIPseq in mES cells

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Supplementary_files_format_and_content: Alignment (ylf) files: The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations determined by bowtie. The file contains the locations of the bowtie aligned reads with the following format:
#BWT1 (read category BWT1)
>1 (chromomsome 1)
-12345 (minus strand read)
-9876 (minus strand read)
54321 (plus strand read)
>2 (chromomsome 2)
-67890 (minus strand read)
98765 (plus strand read)
132323 (plus strand read)
#BWT2 (read category BWT2)
etc..

source_name: Chromatin IP against Brg1

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

tag: chip antibody

value: Lab Generated (Crabtree) J1

value: V6.5 embryonic stem cells


title: 11102009_42YJEAXX_B3

description: ChIP-Seq for SA1 in mES cells

source_name: Chromatin IP against SA1

value: Bethyl A300-157A


title: 07012008_308MUAAXX_B8

description: H3K4me3 ChIPseq in mES cells

source_name: Chromatin IP against H3K4me3

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Abcam AB8550


title: 07012008_308MUAAXX_B7

description: H3K4me3 ChIPseq in mES cells

value: Abcam AB8580


title: 11102009_42YJEAXX_B4

description: ChIP-Seq for SA2 in mES cells

source_name: Chromatin IP against SA2

value: Bethyl A300-158A


title: 07282008_309NDAAXX_B1

description: H3K4me3 ChIPseq in mES cells


title: 05302008_205MGAAXX_B7

description: H2Bub ChIPseq in mES cells

source_name: Chromatin IP against H2Bub

value: Moshe Oren MOSHE OREN LABORATOR