title: MDA-MB-231 nuclear matrix biological replicate 2

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

institute: University of Vermont

data_processing:
Library strategy: MAR-Seq
Base calls and sequence reads were generated by Illumina CASAVA software (version 1.6; Illumina)
100bp paired-end reads were mapped to the hg19 build of the human genome using Bowtie2
peaks were called with MACS v1.4 -bw=400
bigwigs were generated using bedtools genomeCoverageBed and bedGraphToBigWig from UCSC
Genome_build: hg19
Supplementary_files_format_and_content: peak bed files indicate areas of enrichment identified by MACS.  bigwig values indicate reads per million.

source_name: mammary gland/breast epithelial cell

growth_protocol: MCF-10A cells, from a lab-maintained stock, were cultured in phenol-free DMEM/F12 media supplemented with EGF, insulin, cholera toxin and hydrocortisone and subcultured as described (Debnath et al., 2002). MDA-MB-231 cells, also from a lab-maintained stock, were grown and subcultured as previously described (Pratap et al., 2008)

extract_protocol:
DNA was isolated by extraction using phenol:chloroform:isoamyl alcohol (25:24:1) followed by chloroform:isoamyl alcohol (24:1) and RNA was digested by incubating with 200 μg/mL RNase A for 2h at 37°C. RNase was removed with a second phenol:chloroform:isoamyl alcohol/ chloroform:isoamyl alcohol extraction series and DNA was treated with 200 μg/mL Proteinase K for 2h at 55°C. Samples were then extracted a third time with phenol:chloroform:isoamyl alcohol, followed by chloroform:isoamyl alcohol, and precipitated overnight at –20°C in 100% ethanol
MAR-Seq DNA was quantified, fragmented by sonication, and converted into libraries for deep sequencing on the Illumina Hi-Seq 2000 platform, following the Illumina TruSeq DNA Sample Preparation v2 Guide.

treatment_protocol: Nuclear matrix bound DNA sequences were isolated using a modification of the method described previously (Nickerson et al., 1997). Confluent/nearly confluent cells were washed twice in incubated in CSK crosslinking buffer (100 mM NaCl, 1 mM EGTA, 10 mM PIPES pH 6.8, 3 mM MgCl2, 300 mM sucrose, 1% w/v formaldehyde) on ice for 10 min with gentle agitation. Glycine solution (2.5 M) was added to halt crosslinking, after 10 min, the glycine solution was removed and plates were washed twice in CSK wash buffer. Next, cells were incubated for 1h at 30°C in nuclear matrix digestion buffer containing a cocktail of restriction enzymes (50 mM NaCl, 1 mM EGTA, 10 mM PIPES pH 6.8, 3 mM MgCl2, 300 mM sucrose, 0.5% v/v Triton X-100, 600 U/mL MspI, 600 U/mL HaeIII, 600 U/mL RsaI, 600 U/mL AluI, 600 U/mL BamHI, 600 U/mL PvuII).  Plates were then placed on ice, washed twice with digestion wash buffer (50 mM NaCl, 11 mM EGTA, 10 mM PIPES pH 6.8, 3 mM MgCl2, 300 mM sucrose, 10 mM EDTA) and incubated on ice for 10 min in matrix extraction buffer (50 mM NaCl, 11 mM EGTA, 10 mM PIPES pH 6.8, 3 mM MgCl2, 300 mM sucrose, 10 mM EDTA, 250 mM ammonium sulfate) to further purify nuclear matrices and attached DNA. Matrix extraction buffer was aspirated off samples, they were washed twice more with digestion wash buffer, and then submerged in crosslink reversal buffer (100 mM NaHCO3, 0.5%w/v SDS, 10 mM EDTA, 10 mM EGTA). Cells and buffer were scraped into a 50 mL centrifugal concentrator with a 10,000 molecular weight cut-off (Amicon), 10 mL additional crosslink reversal buffer was added and samples were centrifuged to concentrate to ~400 μL; this was repeated a second time. The preparation was transferred to a microcentrifuge tube and digested with 200 μg/mL Proteinase K at 65°C for 16h.cold PBS and incubated for 10 min on ice in cytoskeletal (CSK) extraction buffer (100 mM NaCl, 1 mM EGTA, 10 mM PIPES pH 6.8, 3 mM MgCl2, 300 mM sucrose, 0.5% v/v Triton X-100). Cells were then washed twice with CSK wash buffer (100 mM NaCl, 1 mM EGTA, 10 mM PIPES pH 6.8, 3 mM MgCl2, 300 mM sucrose, 1 mM EDTA) and

value: breast

value: metastatic site derived

tag: atcc id

value: ATCC HTB-26


title: MDA-MB-231 nuclear matrix biological replicate 1

status: Public on Oct 06 2016

type: SRA

department: Biochemistry

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: tissue

tag: cell type


title: DMSO_NR_rep2

city: Göttingen

first: Ina

last: Klusmann

address: Justus-von-Liebig-Weg 11

country: Germany

institute: Institute of Molecular Oncology

library_source: transcriptomic

data_processing:
demultiplexed to fastq files with CASAVA (version 1.8.2)
Fastq files were mapped to the human reference transcriptome (UCSC hg19) using Tophat (Galaxy Version 0.9)
Read counts for each sample and each gene were aggregated using a htseq-count
DESeq2 (version 1.10.1) was used for measuring differential expression
Genome_build: hg19
Supplementary_files_format_and_content: CSV files

molecule: total RNA

source_name: osteosarcoma cell line

growth_protocol: Cells were cultured in DMEM (Gibco/Life Technologies) supplemented with 10 % fetal calf serum (FCS) and antibiotics

extract_protocol:
Total RNA was extracted from cells using TRIzol® (Invitrogen/Life Technologies).
For RNA-sequencing, the quality of total RNA was determined using the bioanalyzer 2100 from Agilent. All samples analyzed exhibited a RIN>8. Library preparation was conducted using the TruSeq RNA LT SamplePrep Kit (Illumina) starting from 1000 ng of total RNA. Barcodes used for sample preparation were used according to the indications given by the protocol. Accurate library quantitation of cDNA libraries was performed with the QuantiFluor™dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (290-310 bp). cDNA libraries were amplified and sequenced via cBot and HiSeq 2000 from Illumina (SR, 1×50 bp, 6 Gb/sample ca. 30 million reads per sample). Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA (version 1.8.2).

treatment_protocol: U2OS cells were incubated with thymidine at 2 mM in DMEM/10% FCS for 16 h, then washed and incubated in DMEM/10% FCS for 8 h, and then again incubated with 2 mM thymidine for 16 h (double-thymidine block). Four hours before release from the block (or maintaining the block), 10  M Nutlin (control: DMSO alone) was added. For release, thymidine was removed by washing and incubation with DMEM/10% FCS. When the block was removed, the previous concentration of Nutlin was maintained, followed by further incubation for 4 h before harvest.

value: non-released cells


title: MDA-MB-231 digested nuclei biological replicate 2


title: MDA-MB-231 digested nuclei biological replicate 1


title: DMSO_AS_rep1

value: asynchronous cells


title: DMSO_NR_rep1


title: DMSO_S_rep2

value: S-phase cells


title: MCF-10A nuclear matrix biological replicate 2

value: luminal ductal cells

value: ATCC CRL-10317


title: Nutlin_AS_rep3


title: MCF-10A nuclear matrix biological replicate 1


title: MCF-10A digested nuclei biological replicate 1


title: MCF-10A digested nuclei biological replicate 2


title: DMSO_S_rep3


title: MDA-MB-231 H3K9me2 ChIPseq biological replicate 1

data_processing:
Base calls and sequence reads were generated by Illumina CASAVA software (version 1.6; Illumina)
100bp paired-end reads were mapped to the hg19 build of the human genome using Bowtie2
peaks were called with MACS v1.4 -bw=400
bigwigs were generated using bedtools genomeCoverageBed and bedGraphToBigWig from UCSC
Genome_build: hg19
Supplementary_files_format_and_content: peak bed files indicate areas of enrichment identified by MACS.  bigwig values indicate reads per million.

growth_protocol: MCF-10A cells, from a lab-maintained stock, were cultured in phenol-free DMEM/F12 media supplemented with EGF, insulin, cholera toxin and hydrocortisone and subcultured as described (Debnath et al., 2002). MDAMB-231 cells, also from a lab-maintained stock, were grown and subcultured as previously described (Pratap et al., 2008). Cell lines are monitored for integrity by STR analysis and are routinely checked for mycoplasma contamination.

extract_protocol:
ChIP was performed on subconfluent cells as previously described (Lee et al., 2006) with the following modification: after sonication, buffer C was exchanged for FA buffer (50 mM HEPES-KOH, pH 7.5, 140 mM sodium chloride, 1 mM EDTA, 1% v/v Triton X-100, 0.1% w/v sodium deoxycholate, 0.1% w/v SDS, 1X Roche Complete EDTA-free protease inhibitor cocktail, 25 nM MG132 in nuclease-free water) prior to antibody pulldown using Amicon columns (10,000 kDa MWCO). The following antibodies were used for ChIP-Seq: H3K4me3 (mouse monoclonal, abcam ab1012),  H3K27me3 (rabbit polyclonal, Millipore 07-449), H3K9me2 (mouse monoclonal, abcam ab1220). Two  replicates were processed, normalized and the data combined for further analyses.
After genomic DNA was isolated for both specific IPs and input DNA, libraries were prepared for paired-end multiplexed tag Solexa/Illumina sequencing using the Illumina DNA Sample Prep Kit v2.0 according to manufacturer instructions.

tag: antibody


title: MDA-MB-231 input ChIPseq biological replicate 1


title: MDA-MB-231 input ChIPseq biological replicate 2


title: MDA-MB-231 H3K9me2 ChIPseq biological replicate 2


title: MDA-MB-231 H3K27me3 ChIPseq biological replicate 1


title: MDA-MB-231 H3K4me3 ChIPseq biological replicate 1


title: MDA-MB-231 H3K4me3 ChIPseq biological replicate 2


title: E12.5 RNA-seq Dup-L Rep2

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

institute: Berlin Institute of Health

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm9) using the STAR mapper (Dobin et al., 2013) (splice junctions based on RefSeq ;options: ‐‐alignIntronMin 20 ‐‐alignIntronMax 500000 --outFilterMultimapNmax 5 ‐‐outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.1).
The uniquely mapped read counts per gene (annotation based on RefSeq genes) were subsequently transformed to FPKM.
Differential Expression was calculated based on the raw read counts per gene via the DEseq2 package (Love et al 2014; default settings).
To create bigwig files coverage profiles were generated by creating a bedgraph file using bedtools genomecov (-ibam —bg split -scale (normalized per million reads)) (bedtools v2.17.0) and then transformed to bigwig files using the bedgraphtobigwig tool from UCSC (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v287/bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for normalized RNA-seq profiles

molecule: polyA RNA

organism: Mus musculus

source_name: E12.5 limb buds

extract_protocol:
RNA was extracted from snap-frozen tissue by lysis in Trizol and subsequent purification using the Qiagen RNAeasy Mini Kit
polyA enriched RNA-seq libraries were constructed using the Illumina TruSeq RNA V2 Kit according to manufacturer's instructions

tag: genotype

value: Dup-L

tag: age

value: limb buds


title: MCF-10A input ChIPseq biological replicate 1


title: MCF-10A H3K27me3 ChIPseq biological replicate 2


title: MCF-10A H3K4me3 ChIPseq biological replicate 1


title: MCF-10A H3K9me2 ChIPseq biological replicate 2


title: MCF-10A H3K4me3 ChIPseq biological replicate 2


title: MCF-10A H3K9me2 ChIPseq biological replicate 1


title: MCF-10A H3K27me3 ChIPseq biological replicate 1


title: MCF-10A input ChIPseq biological replicate 2


title: 1772122325_A11

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: ESMoleculeCounts.cef

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis. In some reads, one of the three Gs has been replaced by an A by the Illumina HiSeq software, representing failed base calling at that position. We rejected cells that had less than 2000 mRNA molecules, more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a separate cluster with no specific gene expression (putative damaged or dead cells). Genes that were detected at less than 4 molecules in the whole datasets were eliminated.
Genome_build: UCSC mm10 and UCSC hg19
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell identified by the "Title" field in Samples list. Mitochondrial genes and genes with less than 4 molecules have been omitted. The first two lines of each file are table metadata (see https://github.com/linnarsson-lab/ceftools)

source_name: stem cells

growth_protocol: Wild-type CD1 mice were mated overnight and noon of the day was considered E0.5. Mothers were killed and embryos were dissected out of the uterine horn between the time points E11.5 and E18.5. Adult CD1 animals were dissected at P19 to P27. Human tissue was collected at Addenbrooke’s Hospital (Cambridge, UK) and dissected in HIBERNATE medium (Gibco). Samples were shipped overnight on ice (in HIBERNATE solution) to Sweden. For the embryonic stem cells (hES DA),  iCell DopaNeurons from Cellular Dynamics International (DNC-301030001, lot #6003358) were differentiated following the manufacturer’s recommendations and harvested at day 5 and 21.

extract_protocol:
Human embryo ventral midbrain dissection was performed on ice in neuronal N2 culturing media. 10-17  tissue pieces were collected for each experiment. The tissue pieces were dissociated using the Papain dissociation system (Worthington) following manufacturers recommendations, adjusting incubation time based on tissue piece size to 25-45 mins. Using glass pipettes of increasingly smaller tip diameter, the cell suspension was then filtered with 20um filter (Partec) and cells kept in N2 media, and cells loaded into C1 chips for cell capture.
Fluidigm C1 Autoprep System  Cells medium (10-17 micrometer) microfluidic was used to capture the cells. 14 microlitre of cell suspension (approx. 800 cells/microlitre in N2 culturing medium with DNaseI) was mixed with 7 microlitre C1 Suspension Reagent after filtering. Single-cells were then captured for 30 min at 4°C using the “Cell Load (1772x/1773x)” script. The protocol for Lysis, RT and PCR was performed as previously described  (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). Amplified cDNA was harvested with 13 microlitre Harvest Reagent and cDNA library quality was measured on an Agilent BioAnalyzer. Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase as described previously. 1 microlitre Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in 20 microlitre Binding and Blocking buffer (10mM Tris, 250mM NaCl, 5mM EDTA, 0.5% SDS) and added to each well. After 15 min incubation at room temperature, all wells were pooled, the beads washed once with 100 microlitre Washing buffer (10mM Tris-150mM NaCl, 0.02% Tween), once in 100 microlitre Qiagen Qiaquick PB and then twice using 100 microlitre Washing buffer. Restriction was performed to cleave 3’ fragments: the beads were incubated in 100 microlitre restriction mix (1x NEB CutSmart, 0.4 U/microlitre PvuI-HF enzyme) for 1h at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in 30 μl ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 microlitre to remove short fragments.

value: stem cells

tag: Sex

tag: inferred cell type


title: 1772122326_C12

description: ESMoleculeCounts.cef


title: MDA-MB-231 H3K27me3 ChIPseq biological replicate 2


title: 1772122326_H12

description: ESMoleculeCounts.cef


title: 1772122325_C09

description: ESMoleculeCounts.cef


title: 1772122326_B02

description: ESMoleculeCounts.cef


title: 1772122325_A08

description: ESMoleculeCounts.cef


title: 1772122325_D02

description: ESMoleculeCounts.cef


title: 1772122325_F03

description: ESMoleculeCounts.cef

value: eRglf


title: 1772122325_E01

description: ESMoleculeCounts.cef


title: 1772122325_G01

description: ESMoleculeCounts.cef


title: 1772122324_E06

description: ESMoleculeCounts.cef


title: 1772122324_E02

description: ESMoleculeCounts.cef


title: 1772122324_B02

description: ESMoleculeCounts.cef


title: 1772122319_G05

description: EmbryoMoleculeCounts.cef

source_name: ventral midbrain

value: ventral midbrain

value: hProgFPM


title: 1772122325_G07

description: ESMoleculeCounts.cef


title: 1772122324_A12

description: ESMoleculeCounts.cef


title: 1772122324_C10

description: ESMoleculeCounts.cef


title: 1772122325_B12

description: ESMoleculeCounts.cef


title: 1772122319_F09

description: EmbryoMoleculeCounts.cef

value: hProgM


title: 1772122325_B10

description: ESMoleculeCounts.cef


title: 1772122319_D03

description: EmbryoMoleculeCounts.cef

value: Unk


title: 1772122319_F02

description: EmbryoMoleculeCounts.cef


title: 1772122319_E04

description: EmbryoMoleculeCounts.cef

value: hProgFPL


title: 1772122319_C02

description: EmbryoMoleculeCounts.cef


title: 1772122319_F06

description: EmbryoMoleculeCounts.cef


title: 1772122318_H11

description: EmbryoMoleculeCounts.cef


title: 1772122318_E06

description: EmbryoMoleculeCounts.cef


title: 1772122318_H12

description: EmbryoMoleculeCounts.cef

value: hNProg


title: 1772122325_A03

description: ESMoleculeCounts.cef


title: 1772122318_C06

description: EmbryoMoleculeCounts.cef


title: 1772122318_F08

description: EmbryoMoleculeCounts.cef


title: 1772122317_F03

description: EmbryoMoleculeCounts.cef


title: 1772122318_A09

description: EmbryoMoleculeCounts.cef


title: 1772122318_B05

description: EmbryoMoleculeCounts.cef


title: 1772122317_G09

description: EmbryoMoleculeCounts.cef


title: 1772122317_D12

description: EmbryoMoleculeCounts.cef

value: hOMTN


title: 1772122317_E10

description: EmbryoMoleculeCounts.cef


title: 1772122317_C05

description: EmbryoMoleculeCounts.cef


title: 1772122317_A09

description: EmbryoMoleculeCounts.cef

value: hProgBP


title: 1772122317_A05

description: EmbryoMoleculeCounts.cef


title: 1772122317_A04

description: EmbryoMoleculeCounts.cef


title: 1772122319_B05

description: EmbryoMoleculeCounts.cef


title: 1772122316_E06

description: EmbryoMoleculeCounts.cef


title: 1772122316_F04

description: EmbryoMoleculeCounts.cef


title: 1772122316_E02

description: EmbryoMoleculeCounts.cef


title: 1772122316_C05

description: EmbryoMoleculeCounts.cef


title: 1772122316_B05

description: EmbryoMoleculeCounts.cef


title: 1772122316_B10

description: EmbryoMoleculeCounts.cef


title: 1772122316_A09

description: EmbryoMoleculeCounts.cef


title: 1772122315_G10

description: ESMoleculeCounts.cef


title: 1772122315_G04

description: ESMoleculeCounts.cef


title: 1772122315_F04

description: ESMoleculeCounts.cef


title: 1772122317_D08

description: EmbryoMoleculeCounts.cef


title: 1772122315_E03

description: ESMoleculeCounts.cef


title: 1772122317_D06

description: EmbryoMoleculeCounts.cef


title: 1772122315_D05

description: ESMoleculeCounts.cef


title: 1772122315_C07

description: ESMoleculeCounts.cef


title: 1772122315_C03

description: ESMoleculeCounts.cef


title: 1772122315_A11

description: ESMoleculeCounts.cef


title: 1772122315_B08

description: ESMoleculeCounts.cef


title: 1772122315_D12

description: ESMoleculeCounts.cef


title: 1772122315_B09

description: ESMoleculeCounts.cef


title: 1772122314_G06

description: ESMoleculeCounts.cef

value: eSCa


title: 1772122315_F05

description: ESMoleculeCounts.cef


title: 1772122314_F02

description: ESMoleculeCounts.cef

value: eSCb


title: 1772122314_E06

description: ESMoleculeCounts.cef

value: eSCc


title: 1772122314_C08

description: ESMoleculeCounts.cef


title: 1772122314_B12

description: ESMoleculeCounts.cef


title: 1772122312_G09

description: ESMoleculeCounts.cef


title: 1772122312_H08

description: ESMoleculeCounts.cef


title: 1772122314_D03

description: ESMoleculeCounts.cef


title: 1772122312_H02

description: ESMoleculeCounts.cef


title: 1772122312_E09

description: ESMoleculeCounts.cef


title: 1772122315_D07

description: ESMoleculeCounts.cef


title: 1772122312_H10

description: ESMoleculeCounts.cef


title: 1772122312_E10

description: ESMoleculeCounts.cef


title: 1772122312_F02

description: ESMoleculeCounts.cef


title: 1772122312_C02

description: ESMoleculeCounts.cef


title: 1772122312_C01

description: ESMoleculeCounts.cef


title: 1772122314_H12

description: ESMoleculeCounts.cef


title: 1772122312_A09

description: ESMoleculeCounts.cef


title: 1772122311_G06

description: ESMoleculeCounts.cef


title: 1772122312_A03

description: ESMoleculeCounts.cef


title: 1772122311_H07

description: ESMoleculeCounts.cef


title: 1772122314_D08

description: ESMoleculeCounts.cef


title: 1772122311_F10

description: ESMoleculeCounts.cef


title: 1772122311_E10

description: ESMoleculeCounts.cef


title: 1772122314_A03

description: ESMoleculeCounts.cef


title: 1772122311_F02

description: ESMoleculeCounts.cef


title: 1772122311_E06

description: ESMoleculeCounts.cef


title: 1772122311_D11

description: ESMoleculeCounts.cef


title: 1772122311_C02

description: ESMoleculeCounts.cef


title: 1772122311_D07

description: ESMoleculeCounts.cef


title: 1772122311_C03

description: ESMoleculeCounts.cef


title: 1772122311_B06

description: ESMoleculeCounts.cef


title: 1772122312_B09

description: ESMoleculeCounts.cef


title: 1772122311_A05

description: ESMoleculeCounts.cef


title: 1772122310_H05

description: ESMoleculeCounts.cef


title: 1772122312_E05

description: ESMoleculeCounts.cef


title: 1772122310_E11

description: ESMoleculeCounts.cef


title: 1772122310_G10

description: ESMoleculeCounts.cef


title: 1772122311_A12

description: ESMoleculeCounts.cef


title: 1772122310_D08

description: ESMoleculeCounts.cef


title: 1772122310_C01

description: ESMoleculeCounts.cef


title: 1772122310_D02

description: ESMoleculeCounts.cef


title: 1772122311_E12

description: ESMoleculeCounts.cef


title: 1772122310_A09

description: ESMoleculeCounts.cef


title: 1772122306_H03

description: ESMoleculeCounts.cef


title: 1772122306_F09

description: ESMoleculeCounts.cef


title: 1772122306_F06

description: ESMoleculeCounts.cef


title: 1772122306_B12

description: ESMoleculeCounts.cef


title: 1772122306_A03

description: ESMoleculeCounts.cef


title: 1772122305_H05

description: ESMoleculeCounts.cef


title: 1772122310_F10

description: ESMoleculeCounts.cef


title: 1772122305_E09

description: ESMoleculeCounts.cef


title: 1772122305_D06

description: ESMoleculeCounts.cef


title: 1772122306_A07

description: ESMoleculeCounts.cef


title: 1772122305_C05

description: ESMoleculeCounts.cef


title: 1772122305_A12

description: ESMoleculeCounts.cef


title: 1772122306_C08

description: ESMoleculeCounts.cef


title: 1772122310_B02

description: ESMoleculeCounts.cef


title: 1772122305_C01

description: ESMoleculeCounts.cef


title: 1772122303_E09

description: ESMoleculeCounts.cef


title: 1772122302_G12

description: ESMoleculeCounts.cef

value: eRgla


title: 1772122303_E02

description: ESMoleculeCounts.cef


title: 1772122303_B01

description: ESMoleculeCounts.cef


title: 1772122303_G03

description: ESMoleculeCounts.cef


title: 1772122302_H01

description: ESMoleculeCounts.cef


title: 1772122302_B07

description: ESMoleculeCounts.cef


title: 1772122302_D02

description: ESMoleculeCounts.cef


title: 1772122302_C08

description: ESMoleculeCounts.cef


title: 1772122303_C11

description: ESMoleculeCounts.cef


title: 1772122302_F09

description: ESMoleculeCounts.cef

value: eRglb


title: 1772122302_B02

description: ESMoleculeCounts.cef

value: eRgle


title: 1772122302_G08

description: ESMoleculeCounts.cef


title: 1772122301_F11

description: ESMoleculeCounts.cef


title: 1772122301_G04

description: ESMoleculeCounts.cef


title: 1772122301_H05

description: ESMoleculeCounts.cef


title: 1772122301_A03

description: ESMoleculeCounts.cef


title: 1772122301_C08

description: ESMoleculeCounts.cef


title: 1772122301_A09

description: ESMoleculeCounts.cef


title: 1772122301_A04

description: ESMoleculeCounts.cef


title: 1772122301_E07

description: ESMoleculeCounts.cef


title: 1772122300_H12

description: ESMoleculeCounts.cef


title: 1772122300_G03

description: ESMoleculeCounts.cef


title: 1772122300_G06

description: ESMoleculeCounts.cef


title: 1772122300_F06

description: ESMoleculeCounts.cef


title: 1772122300_F08

description: ESMoleculeCounts.cef


title: 1772122305_E01

description: ESMoleculeCounts.cef


title: 1772122300_F05

description: ESMoleculeCounts.cef


title: 1772122300_E09

description: ESMoleculeCounts.cef


title: 1772122300_D07

description: ESMoleculeCounts.cef


title: 1772122300_F01

description: ESMoleculeCounts.cef


title: 1772122300_C09

description: ESMoleculeCounts.cef


title: 1772122300_E07

description: ESMoleculeCounts.cef


title: 1772122299_F11

description: ESMoleculeCounts.cef


title: 1772122299_H07

description: ESMoleculeCounts.cef


title: 1772122300_C06

description: ESMoleculeCounts.cef


title: 1772122299_D11

description: ESMoleculeCounts.cef


title: 1772122301_B11

description: ESMoleculeCounts.cef


title: 1772122299_C01

description: ESMoleculeCounts.cef


title: 1772122298_H05

description: ESMoleculeCounts.cef


title: 1772122298_B05

description: ESMoleculeCounts.cef


title: 1772122299_A09

description: ESMoleculeCounts.cef

value: eRgld


title: 1772122298_D10

description: ESMoleculeCounts.cef

value: stem cells


title: 1772122264_H02

description: EmbryoMoleculeCounts.cef

value: hEndo


title: 1772122298_A10

description: ESMoleculeCounts.cef


title: 1772122264_F05

description: EmbryoMoleculeCounts.cef

value: ventral midbrain


title: 1772122298_G11

description: ESMoleculeCounts.cef


title: 1772122298_A02

description: ESMoleculeCounts.cef


title: 1772122264_G04

description: EmbryoMoleculeCounts.cef


title: 1772122264_F04

description: EmbryoMoleculeCounts.cef


title: 1772122264_D05

description: EmbryoMoleculeCounts.cef


title: 1772122264_D12

description: EmbryoMoleculeCounts.cef


title: 1772122264_D01

description: EmbryoMoleculeCounts.cef


title: 1772122263_C04

description: ESMoleculeCounts.cef


title: 1772122263_E03

description: ESMoleculeCounts.cef


title: 1772122299_E03

description: ESMoleculeCounts.cef


title: 1772122299_G09

description: ESMoleculeCounts.cef


title: 1772122262_E06

description: ESMoleculeCounts.cef


title: 1772122262_E10

description: ESMoleculeCounts.cef


title: 1772122262_F09

description: ESMoleculeCounts.cef


title: 1772122263_B03

description: ESMoleculeCounts.cef


title: 1772122262_G04

description: ESMoleculeCounts.cef


title: 1772122262_D01

description: ESMoleculeCounts.cef


title: 1772122262_E04

description: ESMoleculeCounts.cef


title: 1772122263_A11

description: ESMoleculeCounts.cef


title: 1772122236_F06

description: EmbryoMoleculeCounts.cef


title: 1772122262_A01

description: ESMoleculeCounts.cef


title: 1772122236_E11

description: EmbryoMoleculeCounts.cef


title: 1772122236_D08

description: EmbryoMoleculeCounts.cef

value: hPeric


title: 1772122226_H08

description: EmbryoMoleculeCounts.cef


title: 1772122226_H11

description: EmbryoMoleculeCounts.cef

value: hRN


title: 1772122236_A06

description: EmbryoMoleculeCounts.cef


title: 1772122264_A01

description: EmbryoMoleculeCounts.cef


title: 1772122226_F05

description: EmbryoMoleculeCounts.cef

value: Unk


title: 1772122236_B12

description: EmbryoMoleculeCounts.cef


title: 1772122224_H07

description: EmbryoMoleculeCounts.cef


title: 1772122226_G07

description: EmbryoMoleculeCounts.cef


title: 1772122226_E06

description: EmbryoMoleculeCounts.cef


title: 1772122236_A09

description: EmbryoMoleculeCounts.cef


title: 1772122224_H04

description: EmbryoMoleculeCounts.cef


title: 1772122262_B11

description: ESMoleculeCounts.cef


title: 1772122224_D10

description: EmbryoMoleculeCounts.cef

value: hNbM


title: 1772122224_C12

description: EmbryoMoleculeCounts.cef


title: 1772122224_B03

description: EmbryoMoleculeCounts.cef

value: hProgM


title: 1772122224_A02

description: EmbryoMoleculeCounts.cef

value: hProgFPM


title: 1772122224_A05

description: EmbryoMoleculeCounts.cef

value: hProgBP


title: 1772122224_A06

description: EmbryoMoleculeCounts.cef

value: hNProg


title: 1772122224_C06

description: EmbryoMoleculeCounts.cef


title: 1772122223_H08

description: EmbryoMoleculeCounts.cef

value: hOMTN


title: 1772122224_C08

description: EmbryoMoleculeCounts.cef


title: 1772122223_D06

description: EmbryoMoleculeCounts.cef


title: 1772122223_G02

description: EmbryoMoleculeCounts.cef


title: 1772122223_D04

description: EmbryoMoleculeCounts.cef


title: 1772122224_G12

description: EmbryoMoleculeCounts.cef


title: 1772122223_B08

description: EmbryoMoleculeCounts.cef


title: 4C SexRev SOX9TSS

data_processing:
4C-seq reads were cleaned of the primer sequence and mapped to a corresponding reference (GRCh37/hg19 or NCBI37/mm9) using BWA-MEM (v0.7.12-r1044) with default settings.
4C-seq contacts were analyzed in the murine region chr11:108500000-115000000 and the human region chr17:67000000-75000000.
To calculate read count profiles the viewpoint and adjacent fragments 1.5 kb up- and downstream were removed. A sliding window of 10 fragments was chosen to smooth the data and data was normalized to reads per million mapped reads (RPM).
To compare interaction profiles of different samples, we obtained the log2 fold change for each window of normalized reads.
Genome_build: mm9, hg19

Supplementary_files_format_and_content: bedgraph files of the coverage and the calculated ratios

source_name: human skin fibroblasts

extract_protocol:
4C-seq libraries were generated from microdissected tissues or cells as described previously (van de Werken et al., 2012). DpnII was used as primary, BfaI as secondary restriction enzymes (Csp6I and NlaIII for human samples). For each viewpoint, a total of 1.6 mg of each library was amplified in 8 or 16 PCR reactions, depending on PCR efficiencies. Samples were multiplexed and sequenced with Ilumina Hi-Seq technology. The following primers were used: Sox9-TSS_1 CCACGAAAGTGTGTTTATATTCT   Sox9-TSS_2 TGGCTATTGTTTGTAAATCTCTT  Kcnj2-TSS_1 CGGTGGTGGAGAGAAAGA   Kcnj2-TSS_2 TCACCAAACAACCTCTACAAA  LacZ_1 TCCGACTTCAACTGTAGGG  LacZ_2 GCAGAGCCATCTATTGCTTA  BOR-Sox9tel_1 TTTGACTCCAAGGACCAGA  BOR-Sox9tel_2 TGTGTAAAGGCGGACAGA  Sox9-TAD_1 AACTGGGTATAGTGTGGAGAGA  Sox9-TAD_2 GGACATCAATGGAACATAGC  BOR-Kcnj/Sox9_1 AATGCTGTGGACATCCTG  BOR-Kcnj/Sox9_2 TCCGTCAAGTTCCATGTG  Kcnj-TAD_1 TCTGTGCCAAATGAACTATTCT  Kcnj-TAD_2 AGCACCATCTGTCCTCCTAT  BOR-Kcnjcen_1 AAGAAGAGGGGCTCAAAAT  BOR-Kcnjcen_2 CTGATTGGCATGGGATAGT  SOX9-TSS_1 TCCAAGTGTGTAAGTTTGTCG  SOX9-TSS_2 AATCTCCTGGACCCCTTC  KCNJ2-TSS_1 TTCAGTGAACGTATTTGTTGAA  KCNJ2-TSS_2 GAGCGTTTGATGTTTTACCA
Samples were multiplexed and sequenced with Ilumina Hi-Seq technology using 100bp paired-end or single end reads according to the manufacturer´s protocol.

value: 46, XX Sex Reversal

tag: viewpoint

value: SOX9 TSS


title: 1772122221_D03

description: EmbryoMoleculeCounts.cef


title: 1772122221_D06

description: EmbryoMoleculeCounts.cef


title: 1772122221_H08

description: EmbryoMoleculeCounts.cef


title: 1772122221_H03

description: EmbryoMoleculeCounts.cef


title: 1772122223_A02

description: EmbryoMoleculeCounts.cef


title: 4C SexRev KCNJ2TSS

value: KCNJ2 TSS


title: E2F2 KO orthochromatic erythroblast replicate 1

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

description: E2F2 KO ortho-1

data_processing:
Ion Proton software used for basecalling
Adaptor sequences trimmed and low quality reads were removed from sequenced reads, and TMAP software was used to align reads to mm9 whole genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the Sailfish software package.
Genome_build: mm9
Supplementary_files_format_and_content: .txt file reports RPKMs for each sample and all well annotated genes.

source_name: E2F2 KO orthochromatic erythroblast

growth_protocol: Embryonic E14.5 fetal liver cells were harvested, lineage-depleted with a custom antibody cocktail (anti-CD5, CD19, CD45R, Gr1, Ter119, 7-4, CD8; STEMCELL Technologies).  Cells were cultured overnight in IMDM media, supplemented with 15% FBS, 10-4M β-mercaptoethanol, 100 U/ml penicillin/streptomycin, 2 mM L-glutamine, CHO-KL conditioned media (1:200), and, 10 ng/ml murine recombinant IL-3.  Cells were split into fibronectin (BD Biosciences)-coated plates and differentiated for 48 h in IMDM media supplemented with 15% FBS, 1% bovine serum albumin, 10 μg/ml insulin, 200 μg/ml holo-transferrin, 10-4 M β-mercaptoethanol, 100 U/ml penicillin/streptomycin, 2 mM glutamine, and 2 U/mL erythropoietin.

extract_protocol:
Sorted cells were saved in Trizol reagent and RNA was harvested using standard protocols.  Ion Proton library construction was performed with 200 ng of total RNA.
RNA libraries were prepared for sequencing using standard Ion Proton protocols.

treatment_protocol: Differentiated cells were stained with CD44 (APC) and Ter119 (PE) and orthochromatic erythroblasts were sorted using the Ter119/CD44/FSC sorting scheme.

tag: strain

value: fetal liver

value: orthochromatic erythroblast

tag: genotype/variation


title: E2F2 KO orthochromatic erythroblast replicate 2

description: E2F2 KO ortho-2


title: E2F2 KO undifferentiated replicate 1

description: E2F2 KO undiff-1

source_name: E2F2 KO undifferentiated hematopoietic cell

value: hematopoietic progenitor


title: 1772122224_B11

description: EmbryoMoleculeCounts.cef


title: 1772122221_A11

description: EmbryoMoleculeCounts.cef


title: WT orthochromatic erythroblast replicate 2

description: WT ortho-2

source_name: WT orthochromatic erythroblast

value: wildtype


title: 1772122236_A04

description: EmbryoMoleculeCounts.cef

value: ventral midbrain


title: E2F2 KO undifferentiated replicate 2

description: E2F2 KO undiff-2


title: RNA-seq rep2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: RNA-seq in 6 day seedlings (rep 2)

data_processing:
Adapter sequences were trimmed from the 3’ ends of all RNA-seq, GRO-seq, and 5’GRO-seq reads and the reads were then aligned to the TAIR10 arabidopsis genome using STAR. Only reads that aligned to the genome at a single unique location were considered for downstream analysis.
Transcript discovery and annotation were performed using routines in HOMER (v4.8). Transcription units were identified directly from GRO-seq data using the HOMER program findPeaks (-style groseq with default parameters). Transcription start sites (TSS) were found using findPeaks (-style tss) with the 5'GRO-seq data using using normal GRO-seq as a control. TSS discovered by 5’GRO-seq were then assigned to GRO-seq transcripts if they were found within 1 kb of the 5’ end of the GRO-seq transcript. In cases where multiple TSS could be assigned to the same transcript, the TSS with the highest read density was used. Only de novo identified transcripts that were assigned a valid 5’GRO-seq TSS were considered. Transcripts were annotated into different classes as follows: First, transcripts that strand-specifically overlap any known transcript (TAIR10) were assigned the accession number/annotation of the known transcript. Next transcripts that overlapped any known transcript on the opposite strand are assigned as ‘antisense transcripts’.  Next, transcripts found upstream of an annotated TSS in the opposite strand of the annotated genes were assigned as ‘promoter-antisense transcripts’. Transcripts failing to meet any of these critierion were assigned as ‘novel’ transcripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text

organism: Arabidopsis thaliana

source_name: 6 day seedlings

growth_protocol: A. thaliana accession Columbia (Col-0) was used as the wild type genetic background for experiments. All seeds were sterilized with chlorine gas by mixing 100 ml of bleach and 5 ml of concentrated HCl then grown on plates containing half Linsmaier and Skoog Medium (Caisson Laboratories). Plates were placed at 4C for 3 days for vernalization then placed in growth chambers with 24 hours light and 22¡C for 6 days before tissue collection.

extract_protocol:
For RNA-seq, total RNA was extracted from seedlings frozen in liquid nitrogen using RNeasy Plant Mini Kit (Qiagen). 10µg of total RNA was used for extraction of mRNA with the Poly(A)Purist MAG Kit (Ambion) according to manufacturer’s instructions. For GRO-seq/5'GRO-seq, approximately 20 grams of 6-day-old seedlings were homogenized with an OMNI International General Laboratory Homogenizer in ice cold grinding buffer (300 mM sucrose, 20 mM Tris, pH 8.0, 5 mM MgCl2, 5 mM KCl, 0.2% Triton X-100, 5 mM β-mercaptoethanol, 35% glycerol) at 4°C on low speed. Samples were filtered twice through a 250 micron nylon mesh and then miracloth before being split into 50ml conical tubes and spun for 10 minutes at 5000g. Supernatant was discarded, and the pellets were resuspended in grinding buffer using a Kimble loose dounce homogenizer (Fisher Scientific). Wash step was repeated twice. Nuclei were resuspended in freezing buffer (50 mM Tris, pH 8.0, 5 mM MgCl2, 20% glycerol, 5 mM β-mercaptoethanol) and frozen in liquid N2. Approximately 5x106 nuclei were used for run-ons at room temperature for 5’ and CTP concentration was limited to 20 nM. After run-on, samples were treated with RQ1 DNaseI (Promega) for 20 minutes at 37°C followed by Trizol LS (Fisher Scientific) extraction as described by the manufacturer. Samples were then treated with Terminator 5’-Phosphate-Dependent Exonuclease (Epicentre) for 1 hour at 30°C. RNA fragmentation was carried out with Fragmentation Reagents kit (Ambion) for 11’ at 70°C. Treatments were used to deplete ribosomal and chloroplast RNA. Nascent RNA was enriched by double pull down using BrdU antibody beads (Santa Cruz Biotechnology) for 80’ at 4C, washed three times with GRO-Binding buffer (0.25x SSPE, 0.05% Tween, 37.5 mM NaCl , 1 mM EDTA) then extracted with Trizol LS (Fisher Scientific).
Isolated mRNA was fragmented with Fragmentation Reagents (Ambion) for 14’. Fragmented RNA was incubated with T4 polynucleotide kinase (New England Biolabs) in low pH buffer (0.1 M MES, 10 mM MgCl2, 10 mM mercaptoethanol, 300 mM NaCl - pH 5.6) for 3’ repair, then T4PNK buffer for 5’ phosphorylation. For 5'GRO-seq, de-capping using TAP was replaced with RppH (New England Biolabs) and NEB Next Small RNA Library Prep Set (New England Biolabs) was used for library preparation. De-capping was performed in 3’ Ligation buffer at 37°C in the absence of 3’ adapter. 3’Adapter ligation was performed at 20°C instead of 25°C so RppH is inactive. The Small RNA Library Prep Set was (New England Biolabs) was used for final library preparation of short RNA fragments from each method.
Strand specific polyA RNA-seq, GRO-seq, and 5'GRO-seq

tag: library strategy

value: polyA+ RNA


title: WT orthochromatic erythroblast replicate 1

description: WT ortho-1


title: WT undifferentiated replicate 2

description: WT undiff-2

source_name: WT undifferentiated hematopoietic cell


title: WT undifferentiated replicate 1

description: WT undiff-1


title: RNA-seq rep1

description: RNA-seq in 6 day seedlings (rep 1)


title: GRO-seq rep1

description: GRO-seq in 6 day seedlings (rep 1)

data_processing:
Library strategy: GRO-Seq
Adapter sequences were trimmed from the 3’ ends of all RNA-seq, GRO-seq, and 5’GRO-seq reads and the reads were then aligned to the TAIR10 arabidopsis genome using STAR. Only reads that aligned to the genome at a single unique location were considered for downstream analysis.
Transcript discovery and annotation were performed using routines in HOMER (v4.8). Transcription units were identified directly from GRO-seq data using the HOMER program findPeaks (-style groseq with default parameters). Transcription start sites (TSS) were found using findPeaks (-style tss) with the 5'GRO-seq data using using normal GRO-seq as a control. TSS discovered by 5’GRO-seq were then assigned to GRO-seq transcripts if they were found within 1 kb of the 5’ end of the GRO-seq transcript. In cases where multiple TSS could be assigned to the same transcript, the TSS with the highest read density was used. Only de novo identified transcripts that were assigned a valid 5’GRO-seq TSS were considered. Transcripts were annotated into different classes as follows: First, transcripts that strand-specifically overlap any known transcript (TAIR10) were assigned the accession number/annotation of the known transcript. Next transcripts that overlapped any known transcript on the opposite strand are assigned as ‘antisense transcripts’.  Next, transcripts found upstream of an annotated TSS in the opposite strand of the annotated genes were assigned as ‘promoter-antisense transcripts’. Transcripts failing to meet any of these critierion were assigned as ‘novel’ transcripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text

value: nascent RNA


title: GRO-seq rep2

description: GRO-seq in 6 day seedlings (rep 2)


title: 1772122221_F11

description: EmbryoMoleculeCounts.cef


title: 5'GRO-seq

description: 5'GRO-seq in 6 day seedlings

value: 5' capped nascent RNA


title: TEAD1_WTpreBadh_ChIPseq

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

description: WTpreBadh

data_processing:
Basecalls were performed using  bcl2fastq v. 1.8.3
ChIP-seq reads were alligned to mm10 genome using BWA or STAR aligner with commands -alignIntronMax 1 --alignEndsType EndToEnd to discard  splicing events and enforce "end-to-end” read alignment
transcriptipn factor peaks or histone enrichment regions were called using findPeaks (HOMER) algorithm  with input chromatin as control
Peaks were identified with a threshold of false discovery rate of 0.001 for tag clustering, a 4-fold increase in tag density relative to input control in both local and average distributions (Poisson distribution p-value threshold of 0.0001) and for a 4-fold increase in tag density at peaks relative to a surrounding 10kb region (local Poisson distribution p-value threshold of 0.0001).
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: peak file format with annotation

source_name: stromal adherent  WT pre-B cell progenitors derived from WT mice

growth_protocol: Growth conditions were as described in Hu et al., G&D 2016

extract_protocol:
ChIP was performed according to previously described protocols (Zhang et al., NI 2011) and detailed in Hu et al., G&D 2016
Immunoprecipitated (ChIP) DNA and Input DNA were used to prepare sequencing libraries according to a modified version of the Illumina/Solexa Genomic DNA protocol and is detailed in Hu et al., G&D 2016.

value: stromal adherent pre-B cell progenitors

value: WT

tag: passages

value: 3 to 8

value: BD Transduction Laboratories/610923


title: RpIIS5_WTpreBadh_ChIPseq

description: WTpreBadh


title: 1772122223_H05

description: EmbryoMoleculeCounts.cef


title: TEAD1_IKDNpeBadh_ChIPseq

description: IKDNpreBadh

source_name: stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice

value: IKDN CD2 Cre


title: 1772122221_A12

description: EmbryoMoleculeCounts.cef

value: hProgFPM


title: MED1_WTpreBadh_ChIPseq

description: WTpreBadh

value: Bethyl Labs/A300-793A


title: PAX5_IKDNpreBadh_ChIPseq

description: IKDNpreBadh

value: Santa Cruz Biotech/sc-6059x


title: PAX5_WTpreBadh_ChIPseq

description: WTpreBadh


title: InputControl_WTpreBadh_ChIPseq

description: WTpreBadh

value: none (input)


title: IRF4_IKDNpreBAdh_ChIPseq

description: IKDNpreBadh


title: MED1_IKDNpreBadh_ChIPseq

description: IKDNpreBadh


title: LMO2_IKDNpreBadh_ChIPseq

description: IKDNpreBadh

value: Novus Biologicals/NB110-78626


title: IKAROS_WTpreBadh_ChIPseq

description: WTpreBadh

value: EMD Millipore/MABE912 & MABE913


title: IRF4_WTpreBAdh_ChIPseq

description: WTpreBadh


title: H3K36me3_WTpreBAdh_ChIPseq

description: WTpreBadh


title: H3K27me3_WTpreBadh_ChIPseq

description: WTpreBadh

value: EMD Millipore/07-449


title: InputControl_IKDNpreBadh_ChIPseq

description: IKDNpreBadh


title: LHX2_IKDNpreBadh_ChIPseq

description: IKDNpreBadh

value: Santa Cruz Biotech/sc-349x


title: H3K36me3_IKDNpreBAdh_ChIPseq

description: IKDNpreBadh


title: 1772122220_G06

description: EmbryoMoleculeCounts.cef

value: ventral midbrain

value: hProgFPL


title: H3K27Ac_WTpreBadh_ChIPseqz

description: WTpreBadh


title: H3K4me3_WTpreBadh_ChIPseq

description: WTpreBadh

value: Active Motif/AM39155


title: H3K4me2_WTPreBadh_ChIPseq

description: WTpreBadh

value: EMD Millipore/07-030


title: H3K27ac_IkDNpreBadh_ChIPseq

description: IKDNpreBadh

value: stromal adherent pre-B cell progenitors


title: H3K4me3_IKDNpreBadh_ChIPseq

description: IKDNpreBadh

value: Active Motif/AM39297


title: H3K4me2_IKDNpreBadh_ChIPseq

description: IKDNpreBadh

value: 3 to 8


title: H3K4me1_WTpreBadh_ChIPseq

description: WTpreBadh

value: WT


title: H3K4me1_IKDNpreBadh_ChIPseq

description: IKDNpreBadh

value: IKDN CD2 Cre


title: ETS1_WTpreBadh_ChIPseq

description: WTpreBadh

value: Santa Cruz Biotech/sc-350x


title: RpIIS5_IKDNpreBadh_ChIPseq

description: IKDNpreBadh


title: ETS1_IKDNpreBadh_ChIPseq

description: IKDNpreBadh


title: AIO_IKDNpreBadh_ChIPseq

description: IKDNpreBadh

value: EMD Millipore/MABE911


title: EBF1_WTpreBadh_ChIPseq

description: WTpreBadh


title: EBF1_IKDNpreBadh_ChIPseq

description: IKDNpreBadh


title: 1772122220_G10

description: EmbryoMoleculeCounts.cef

value: hProgM


title: E2A_WTpreBAdh_ChIPseq

description: WTpreBadh


title: H3K27me3_IKDNpreBadh_ChIPseq

description: IKDNpreBadh


title: E2A_IKDNpreBad_ChIPseq

description: IKDNpreBadh

value: Santa Cruz Biotech/sc-6059x


title: 1772122220_E06

description: EmbryoMoleculeCounts.cef

value: hProgBP


title: AIO_WTpreBad_ChIPseq

description: WTpreBadh


title: 1772122208_H12

description: EmbryoMoleculeCounts.cef

value: hEndo


title: 1772099011_G07

description: MouseAdultDAMoleculeCounts.cef

source_name: substantia nigra-ventral tegmental area

value: substantia nigra-ventral tegmental area

value: pooled male and female


title: 1772122220_B11

description: EmbryoMoleculeCounts.cef

value: ventral midbrain


title: 1772096115_G06

description: MouseEmbryoMoleculeCounts.cef

value: mNbDA


title: 1772096146_D07

description: MouseAdultDAMoleculeCounts.cef

value: DA-SNC


title: 1772096118_F09

description: MouseAdultDAMoleculeCounts.cef


title: 1772122220_C10

description: EmbryoMoleculeCounts.cef

value: hNProg


title: 1772122208_G03

description: EmbryoMoleculeCounts.cef


title: 1772122208_F02

description: EmbryoMoleculeCounts.cef


title: 1772122208_E10

description: EmbryoMoleculeCounts.cef

value: hNbM


title: 1772096115_F11

description: MouseEmbryoMoleculeCounts.cef


title: 1772122208_D01

description: EmbryoMoleculeCounts.cef

value: Unk


title: 1772096115_D01

description: MouseEmbryoMoleculeCounts.cef

value: mUnclassified


title: 1772096115_C09

description: MouseEmbryoMoleculeCounts.cef

value: mOMTN


title: 1772096115_B10

description: MouseEmbryoMoleculeCounts.cef


title: 1772099002_G09

description: MouseAdultDAMoleculeCounts.cef


title: 1772122207_G09

description: EmbryoMoleculeCounts.cef


title: 1772096115_A09

description: MouseEmbryoMoleculeCounts.cef


title: 1772122208_B10

description: EmbryoMoleculeCounts.cef


title: 1772122208_A11

description: EmbryoMoleculeCounts.cef


title: 1772096114_G07

description: MouseEmbryoMoleculeCounts.cef


title: 1772122207_F12

description: EmbryoMoleculeCounts.cef

value: hPeric


title: 1772096114_E08

description: MouseEmbryoMoleculeCounts.cef


title: 1772096114_E01

description: MouseEmbryoMoleculeCounts.cef

value: mNProg


title: 1772096114_E03

description: MouseEmbryoMoleculeCounts.cef


title: 1772096114_D05

description: MouseEmbryoMoleculeCounts.cef

value: mSert


title: 1772096114_C09

description: MouseEmbryoMoleculeCounts.cef


title: 1772122207_C09

description: EmbryoMoleculeCounts.cef


title: 1772122207_E05

description: EmbryoMoleculeCounts.cef


title: 1772122207_C03

description: EmbryoMoleculeCounts.cef


title: 1772122207_E01

description: EmbryoMoleculeCounts.cef


title: 1772096114_C10

description: MouseEmbryoMoleculeCounts.cef


title: 1772122207_D01

description: EmbryoMoleculeCounts.cef

value: hGaba


title: 1772096112_H06

description: MouseEmbryoMoleculeCounts.cef


title: 1772122208_C01

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title: VCaP_GROseq_DHT_4h_rep2

city: Kuopio

first: Sari

last: Toropainen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description:
nascent RNA
GRO-seq
processed data file: VCaP_DHT_gene_expression.xlsx

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.7) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
The ChIP-seq peak detection was done by using HOMER software (V 4.7.2; http://homer.salk.edu/homer/). Binding sites were determined with findPeaks command (using -factor mode and IgG sample as a background). BedGraph file was done by combining two replicates and normalizing total number of reads to 10 million. GRO-seq analysis were done by using HOMER software (V 4.7.2) to determine the gene expression with analyzeRepeats command.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks (found in both replicates). BedGraph file show signal intensities. Exel file of GRO-seq data show gene expression values.

source_name: VCaP cells

growth_protocol: The cells were grown in DMEM containing 10% (v/v) defined FBS, 25 U/ml penicillin and 25 mg/ml streptomycin in a 5% CO2 atmosphere at 37 C incubator.

extract_protocol:
Nuclei were extracted from 10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and Br-UTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. Br-UTP-labeled run-on RNA was immunopurified with anti-BrdU-coated agarose beads and precipitated overnight.
Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified with 11-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000.

treatment_protocol: Steroid-depleted medium (DMEM containing 2.5% charcoal-stripped FBS) was changed to the cells 3 days before exposing the cells to vehicle (EtOH) or R1881 (10 nM) for both GRO-seq samples and ChIP-seq samples.

value: Vertebral Cancer of Prostate (VCaP)

tag: origin

value: bone metastasis of prostate cancer

tag: treatment

value: 100nM DHT

tag: time


title: 1771013118_H04

description: MouseEmbryoMoleculeCounts.cef


title: VCaP_GROseq_EtOH_for_DHT_rep2

value: Ethanol


title: VCaP_GROseq_DHT_4h_rep1


title: VCaP_H3K9me3_R1881

description:
genomic DNA
ChIP-seq
processed data file: VCaP_H3K9me3_R1881_ucsc.bedGraph.gz

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.7) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
The ChIP-seq peak detection was done by using HOMER software (V 4.7.2; http://homer.salk.edu/homer/)). Binding sites were determined with findPeaks command (using -factor mode and IgG sample as a background). BedGraph file was done by combining two replicates and normalizing total number of reads to 10 million. GRO-seq analysis were done by using HOMER software (V 4.7.2) to determine the gene expression with analyzeRepeats command.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks (found in both replicates). BedGraph file show signal intensities. Excel file of GRO-seq data show gene expression values.

extract_protocol:
Lysates were derived from sonicated (Bioruptor, Diagenode) nuclei and AR-, CTCF- and H3K9me3-DNA complexes were isolated with 1 microgram of antibody and protein-A magnetic beads.
DNA fragments were purified and libraries were prepared for sequencing using standard Illumina protocol. Samples were deep-sequenced with HiSeq2000 at the GeneCore in EMBL (Heidelberg, Germany).

value: H3K9me3 (Abcam 8898)


title: VCaP_CTCF_R1881_rep2

description:
genomic DNA
ChIP-seq
processed data file: VCaP_CTCF_R1881_rep1+rep2_peaks.bed

value: CTCF (Millipore 07-729)


title: VCaP_CTCF_EtOH_rep1

description:
genomic DNA
ChIP-seq
processed data file: VCaP_CTCF_EtOH_rep1+rep2_peaks.bed


title: VCaP_CTCF_R1881_rep1


title: VCaP_CTCF_EtOH_rep2


title: VCaP_AR_R1881_4h_rep1

description:
genomic DNA
ChIP-seq
processed data file: VCaP_AR_R1881_4h_rep1+2_peaks.bed

value: rabbit antiserum against AR


title: VCaP_AR_R1881_4h_rep2


title: VCaP_GROseq_R1881_30min_rep2

description:
nascent RNA
GRO-seq
processed data file: VCaP_gene_expression.xlsx


title: VCaP_GROseq_R1881_2h_rep1


title: VCaP_AR_R1881_30min_rep2

description:
genomic DNA
ChIP-seq
processed data file: VCaP_AR_R1881_30min_rep1+2_peaks.bed


title: VCaP_AR_R1881_30min_rep1


title: VCaP_IgG_EtOH_R1881

description:
genomic DNA
ChIP-seq

value: EtOH and 10nM R1881


title: cell line K36M #2 K36M ChIP-Seq repeat 2

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

description: sample name: hj144

data_processing:
For the H3K36me2 and H3K36me3 ChIP, there are all with yeast chromatin as spike-in references. All these spike-in samples were aligned to a combined hg19/sacCer3 genome and reads were separated into each organism post-alignment. For the H3.3M36 ChIP, paired-end reads were aligned to the human genome (hg19) using the Bowtie2 software. For the further analysis, the consistent pair reads were used. Sequence reads from RNA-seq samples were aligned to the human genome hg19 and to gene annotations from Refseq gene using TopHat v2.05.
The genome-wide read coverage was calculated by BEDTools and in-house Perl programs.
To identify the genes showing differential occupancy of H3K36me2 and H3K36me3 marks between H3F3B WT or H3F3B K36M mutant cells or tissues, the number of reads in gene body was counted by BEDTools, the corresponding yeast chromation reads were used to do normalization, then DESeq differential read count analysis was performed. For the RNA-seq, Cufflinks v2.0.2 was used to calculate FPKM values of genes. Differential gene expression was analyzed by Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated, scores represent the normalization reads density. For spike-in samples, the scores is the reference-adjusted reads per million (RRPM). For H3.3M36 ChIP, the scores means standard Reads Per Million.

source_name: whole cell

growth_protocol: The immortalized human juvenile costal chondrocyte cell line, T/C 28a2, was cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic solution. T/C 28a2 cells were differentiated in the DMEM medium supplemented with 5% FBS, 1% antibiotic solution, 50 μg/ml ascorbic acid, 10 mM β-glycerol-phosphate, and 1X Insulin-Transferrin-Selenium (ITS) (Invitrogen, Carlsbad, CA) as previously described (3).  Human primary bone cells were generated from surgical waste of bone tissues collected from the patients undergoing elective orthopedic procedures at Mayo Clinic (Rochester, MN) under IRB approved protocol (IRB# 13-005619). Bone tissues were trypsinized overnight, washed thoroughly with PBS, and minced using a scalpel. The minced tissues were incubated in Advanced MEM supplemented with 10% FBS and 1% antibiotic solutionat 37°C and 5% CO2. The primary osteoblasts and osteocytes were plated into new culture dishes and were cultured for 3 passages at which time they become references/control cells for primary human chondroblastomas in ChIP-seq and RNA-seq assays.

extract_protocol:
The frozen tissues were cut and divided into 50 mg aliquots and stored in tubes at -80°C. The frozen tissues were homogenized on ice for 15–30 seconds in 500 μL 1X PBS using a tissue grinder (ACTGene, Piscataway, NJ). Tissue homogenates or cultured cells were cross-linked to final 1% formaldehyde for 10 min and quenched with 125 mM glycine for 5 min at room temperature and washed once with TBS. The pellets were resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. The lysates were divided into two aliquots and washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After resuspending in 500 μL MNase digestion buffer containing a proteinase inhibitor cocktails (Sigma, St. Louis, MO), the lysates were incubated in the presence of 1,000 units of MNase (NEB, Ipswich, MA, Cat.# M0247S) at 37 °C for 20 min with continuous mixing in thermal mixer (Fisher Scientific, Pittsburgh, PA). After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysates were sonicated for 15 min (30 sec on / 30 sec off) using Bioruptor Twin (UCD-400) (Diagenode, Inc., Denville, NJ) and centrifuged at 21,130 x g for 10 min. The cleared supernatant equivalent to 10–20 mg of tissue or 1–2x106 cells was incubated with 2 ug of rabbit polyclonal anti-H3K36me3 antibody (Active Motif, Carlsbad, CA, Cat.# 61101) or 1.5 ug of rabbit monoclonal anti-H3K36me2 antibody (Cell Signaling Technology, Danvers, MA, Cat.#2901) on rocker overnight. After adding 30 μL protein G-magnetic beads (Life technologies, Carlsbad, CA), the reactions were incubated for 3 hours. The beads were extensively washed with ChIP buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl2 buffer (10 mM Tris-HCl, pH8.0,0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatins were eluted and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen, Valencia, CA) after the treatment of RNase A and proteinase K.For RNA-seq, total RNA was extracted using the miRNeasy Mini kit (Qiagen, Valencia, CA).
ChIP-seq libraries were prepared from 10 ng ChIP and input DNA using the Ovation ultralow DR Multiplex kit (NuGEN, San Carlos, CA). The ChIP-seq libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 2000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.RNA-seq libraries were prepared with ovation RNA-seq system v2 kit (NuGEN) according to the manufacture’s instruction, and were sequenced on an Illumina HiSeq 2000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

value: immortalized juvenile costal chondrocyte cell line T/C 28a2

tag: mutation

tag: media

value: DMEM

tag: cell cycle stage

value: asynchronization

tag: chip antibody

value: H3.3M36 (RevMAb Biosciences, catalog# 31-1085-00, lot# O-08-00294)


title: VCaP_GROseq_EtOH_for_DHT_rep1

tag: cell line


title: VCaP_GROseq_R1881_2h_rep2


title: cell line K36M #1 K36M ChIP-Seq repeat 1

description: sample name: hj127


title: VCaP_GROseq_R1881_30min_rep1


title: VCaP_GROseq_EtOH_rep2


title: VCaP_GROseq_EtOH_rep1


title: cell line K36M #1 input repeat 1

description: sample name: hj126


title: cell line WT input repeat 1

description: sample name: hj124

value: WT


title: tissue RNA-Seq K36M #3

description:
ref_fpkm.txt
sample name: hjR25

source_name: tissue

tag: tissue

value: chondroblastoma

value: frozen tissues


title: cell line K36M #2 K36M ChIP-Seq repeat 1

description: sample name: hj129


title: tissue RNA-Seq K36M #2

description:
ref_fpkm.txt
sample name: hjR10


title: tissue RNA-Seq WT control #2

description:
ref_fpkm.txt
sample name: hjR22

tag: cell type

value: primary bone cells (generated from surgical waste of bone tissues)


title: cell line K36M #2 input repeat 1

description: sample name: hj128


title: tissue RNA-Seq K36M #1

description:
ref_fpkm.txt
sample name: hjR9


title: 1771013118_A08

description: MouseEmbryoMoleculeCounts.cef

value: ventral midbrain

tag: Sex

value: pooled male and female

tag: age


title: cell line RNA-Seq K36M #1

description:
ref_fpkm.txt
sample name: hjR18


title: cell line K36M #1 K36M ChIP-Seq repeat 2

description: sample name: hj142


title: cell line WT K36M ChIP-Seq repeat 2

description: sample name: hj140


title: cell line WT K36M ChIP-Seq repeat 1

description: sample name: hj125


title: cell line K36M #2 input repeat 2

description: sample name: hj143


title: 1771013117_C07

description: MouseEmbryoMoleculeCounts.cef

tag: inferred cell type


title: cell line K36M #1 input repeat 2

description: sample name: hj141


title: tissue WT k36me3 ChIP-Seq WT repeat 2

description: sample name: hj46

value: H3K36me3 (Active Motif, catalog# 61101 lot # 32412003)

tag: spike-in

value: yeast reference chromatin


title: cell line RNA-Seq WT

description:
ref_fpkm.txt
sample name: hjR20


title: tissue WT k36me3 ChIP-Seq WT repeat 1

description: sample name: hj147


title: tissue RNA-Seq WT control #1

description:
ref_fpkm.txt
sample name: hjR21


title: 1771013118_B02

description: MouseEmbryoMoleculeCounts.cef

tag: strain


title: cell line RNA-Seq K36M #2

description:
ref_fpkm.txt
sample name: hjR19


title: tissue K36M #1 k36me2 ChIP-Seq

description: sample name: hj152

value: H3K36me2 (Cell Signaling Technonelogy, catalog# 2901, lot# 5)


title: tissue WT k36me2 ChIP-Seq repeat 1

description: sample name: hj146


title: tissue K36M #2 k36me3 ChIP-Seq

description: sample name: hj30


title: tissue K36M #2 k36me2 ChIP-Seq

description: sample name: hj149


title: tissue K36M #1 k36me3 ChIP-Seq

description: sample name: hj150


title: cell line WT input repeat 2

description: sample name: hj139


title: cell line K36M #2 k36me3 ChIP-Seq repeat 1

description: sample name: hj69


title: cell line K36M #2 k36me3 ChIP-Seq repeat 2

description: sample name: hj138


title: cell line K36M #1 k36me3 ChIP-Seq repeat 2

description: sample name: hj135


title: tissue K36M #1 input

description: sample name: hj151


title: tissue WT input repeat 1

description: sample name: hj145


title: cell line WT k36me3 ChIP-Seq repeat 2

description: sample name: hj132


title: 1771013111_A09

description: MouseEmbryoMoleculeCounts.cef


title: cell line WT k36me3 ChIP-Seq repeat 1

description: sample name: hj67


title: cell line K36M #1 k36me2 ChIP-Seq repeat 2

description: sample name: hj134


title: cell line K36M #2 k36me2 ChIP-Seq repeat 2

description: sample name: hj137


title: cell line K36M #2 k36me2 ChIP-Seq repeat 1

description: sample name: hj87


title: cell line K36M #1 k36me2 ChIP-Seq repeat 1

description: sample name: hj85


title: 1771013118_C03

description: MouseEmbryoMoleculeCounts.cef


title: cell line WT k36me2 ChIP-Seq repeat 1

description: sample name: hj83


title: cell line WT k36me2 ChIP-Seq repeat 2

description: sample name: hj131


title: tissue K36M #2 input

description: sample name: hj10


title: cell line K36M #2 spike-in input repeat 1

description: sample name: hj86


title: cell line K36M #1 spike-in input repeat 2

description: sample name: hj133


title: cell line K36M #2 spike-in input repeat 2

description: sample name: hj136