title: DNase_mES_Day3_Mesendoderm

source_name: Murine Mesendoderm Cells

value: mESC-derived Mesendoderm Cells


title: mdo ts M3 [batch1]

status: Public on Jan 19 2014

type: SRA

city: Lyon

first: Anamaria

last: Necsulea

address: 43 Bd. du 11 Novembre 1918

department: Laboratoire de Biométrie et Biologie Evolutive

country: France

institute: CNRS, Université Claude Bernard Lyon 1

library_source: transcriptomic

data_processing:
The basecalling was performed with the Illumina GAIIx pipeline, version 1.8  and with Ibis (Kircher et al, 2009). Ibis was used on non-strand specific samples and on hsa br M 2ss.. The quality values are given in the phred-33 format, for all samples.
Raw reads were aligned with TopHat version 1.4.0 and Bowtie version 0.12.5. Command line for TopHat: tophat -p 4 -o -a 8 -i 40 -m 1 -I 1000000 -F 0 --coverage-search --microexon-search.
Splice junctions were detected from TopHat unambiguous read alignments, requiring an anchor size of at least 8bp and at most 1 mismatch per alignment.
The genome-wide read coverage was determined using the "wiggles" utility in TopHat.
Expression levels for Ensembl-annotated genes were estimated with Cufflinks 2.0.0, using all reads, with the multi-read correction embedded in Cufflinks.Cufflinks command line: cufflinks -q  -G Transcripts_ProteinCoding.gtf -p 4 --library-type ${librarytype} --multi-read-correct. For strand-specific samples, the library-type was set at fr-secondstrand (batch 1) or fr-firststrand (batch 2), while for non-strand-specific samples the library-type was set at fr-unstranded. For expression level computation, GTF files were retrieved from Ensembl 62, and filtered to retain only transcripts annotated as "protein-coding" for protein-coding genes (all transcripts were kept for other gene biotypes).
Genome_build: hg19, gorGor3, MMUL_1, mm9, monDom5, ornAna1, galGal3, JGI 4.2
Supplementary_files_format_and_content: .FPKM files contain expression levels quantified with Cufflinks; the columns are tab-separated. .bedGraph files contain genome-wide read coverage statistics, in bedGraph format, obtained with the "wiggles" utility in TopHat.

molecule: polyA RNA

organism: Monodelphis domestica

source_name: Testis

extract_protocol:
Total RNA was extracted using the Trizol (Invitrogen) procedure or RNAeasy/RNAeasy Lipid/miRNeasy (Qiagen) column purification kits. RNA quality was assessed using an Agilent 2100 Bioanalyzer.
Non-strand-specific sequencing libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer's instructions. Briefly, polyadenylated RNA was isolated using a poly-dT bead procedure and then chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded cDNA were repaired. After 3'-end adenylation of these products, Illumina Paired-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were run on gels; 250-300 bp fragments were excised and then PCR-amplified (15 cycles). After column-purification, qualities of the resulting libraries were assessed using Agilent 2100 Bioanalyzers. Strand-specific libraries were prepared using an optimized version of the original Directional mRNA-seq Library Prep Pre-Release Protocol from Illumina. We used reagents from various companies instead of Illumina’s to decrease significantly the library cost and as a consequence adapted the reaction parameters for each step. In addition, we integrated a size selection step, right after fragmentation to optimize the insert size distribution and decrease the adapter contamination. This optimized protocol is available upon request.

tag: Sex

value: male

tag: strain

tag: age

value: adult

value: Illumina GAIIx, strand-specific

tag: library-type (for tophat and cufflinks)

value: fr-secondstrand


title: xtr lv M1 [batch1]

organism: Xenopus tropicalis

source_name: Liver

value: adult (4-6 months)


title: DNase_mES_Day0

city: Cambridge

first: David

middle: K.

last: Gifford

state: MA

address: 32 Vassar Street

department: Electrical Engineering and Computer Science

country: USA

institute: Massachusetts Institute of Technology

library_source: genomic

data_processing:
Illumina Casava 1.8 processing was used and reads were saved into FASTQ files using the standard 33 offset in ASCII Qscore encoding.
Sequenced reads were directly mapped to mm10 genome using BWA version 0.6.2 with default parameters.
Non-unique and low quality reads (MAPQ<20) were removed before normalization and analysis by the PIQ algorithm.
For each sample PIQ input mapped reads from a BAM file, a list of TF sequence PWMs, and produced a text file indicating putative TF binding sites per PWM. Only those PWMs found to exhibit a significant DNase I profile were included (significance threshold: >100 of the 399 bases within the profile passing 5% FDR).
Genome_build: mm10
Supplementary_files_format_and_content: PIQ output: one text file for each sample indicating putative TF binding sites. These files contain the following columns: Chromosome, TF motif center (beginning), TF motif center (end; equal to prior column if motif has odd length), TF identifier, PWM/Sequence match score, direction of PWM match, and PIQ TF binding score

molecule: genomic DNA

organism: Mus musculus

source_name: Murine Embryonic Stem Cells

growth_protocol: Mouse embryonic stem cell culture and endoderm differentiation was modified slightly from previously published protocols (Sherwood, et al., Mech. Dev. 2011). Undifferentiated 129P2/OlaHsd mESCs were maintained on gelatin-coated plates with mouse embryonic fibroblast (MEF) feeders in mESC medium composed of Knockout DMEM (Life Technologies) supplemented with 15% defined FBS (HyClone), 0.1 mM nonessential amino acids (Life Technologies), 1% Glutamax (Life Technologies), 0.55 mM 2-mercaptoethanol (Sigma) and 1x ESGRO LIF (Millipore). Before differentiation, ESCs were passaged onto gelatin-coated plates for 25 min to deplete MEFs. MEF-depleted ESCs were then seeded at 1x104 cells/cm2 onto gelatin-coated dishes in mESC medium. After 12–24 h, medium was changed to Advanced DMEM (Life Technologies) supplemented with N-2 (Life Technologies), B27 without vitamin A (Life Technologies) and 1% Glutamax. After 44–48 h, medium was changed to Advanced DMEM with 2% FBS, 1% Glutamax, 5 nM GSK-3 inhibitor XV and 50 ng/ml Escherichia coli–derived Activin A (Peprotech) for 24 h to produce mesendoderm. For endoderm differentiation, cells were then fed with Advanced DMEM with 2% FBS, 1% Glutamax, 50 ng/ml Activin A and 1 μM dorsomorphin (Sigma) for 48 h. For intestinal endoderm differentiation, cells at the endoderm stage were fed for 24 h with Advanced DMEM with B-27 supplement without vitamin A, 1% Glutamax and 100 nM GSK-3 inhibitor XV. For differentiation of prepancreatic endoderm, cells at the endoderm stage were fed for 24 h with Advanced DMEM with B-27 supplement without vitamin A, 1% Glutamax, 500 nM retinoic acid (Calbiochem), 50 nM A-83-01 (Calbiochem) and 8 ng/ml Bmp4 (Stemgent). For mesodermal differentiation, cells at the mesendoderm stage were treated for 48 h with 10 ng/ml Bmp4.

extract_protocol:
Samples prepared into Illumina libraries using the Beckman Coulter Genomics SPRI-works system using custom adapters. 6nt 3’ barcodes were added during PCR enrichment and the resulting fragments were evaluated using Agilent BioAnalyzer 2100.   Samples were sequenced one-per-lane using an Illumina HiSeq 2000.
Libraries were diluted to 10nM and then run on qPCR with p5 and p7 primers to determine final flow cell loading concentration, normalized to a PhiX control library. PhiX spike: Each lane was spiked with approximately 0.25-0.5% PhiX control library. Samples were run one-per-lane using Standard Illumina protocols using the following: TruSeq SR/PE Cluster kit V3 cBot, TruSeq SBS Reagent Kit V3, RTA version 1.12.4.2, and Control software version 1.4.8.

treatment_protocol:
DNase-Seq was performed using adaptations of previous protocols (Sekiya, et al., Genes Dev. 2009). 1-3 biological replicate DNase-Seq experiments were performed at six stages of mouse ES cell differentiation: mouse ES cells, mesendoderm, endoderm, lateral plate mesoderm, pre-pancreatic endoderm, and intestinal endoderm. A detailed protocol is as follows:
Mouse ES cells or differentiated cells of various stages (30-90 million cells) were harvested from 15 cm tissue culture plates, pelleted at 800g for 5 minutes at 4°C and the supernatant aspirated. Cells were washed twice with 2.5 ml/plate of ice-cold PBS and pelleted (800g, 5 minutes, 4°C). The supernatant was aspirated and cells were resuspended 2.5 mL/plate Buffer A containing 15 mM Tris HCl (pH 8), 15 mM NaCl, 60 mM KCl, 1 mM EDTA (Ambion, pH 8), 0.5 mM EGTA (pH 8) and 0.5 mM Spermidine (Sigma-Aldrich). An equal volume of 2X Igepal in Buffer A (earlier samples with a 0.05% Igepal final concentration, later samples with a 0.00165% Igepal final concentration) was added to the resuspended cells and the nuclei were pelleted (800g, 5 minutes, 4°C). The supernatant was aspirated promptly and the cells resuspended in 2.5 mL/plate Buffer A. An aliquot of the resuspended nuclei was taken and counted on a hematocytometer with 1:10 Trypan Blue. Nuclei were pelleted (800g, 5 minutes, 4°C) and either digested immediately as below, or stored in 20 mM Tris HCl (pH 8), 75 mM NaCl, 0.5 mM EDTA (Ambion) 50% glycerol, 0.85 mM DTT, and 0.125 mM PMSF, flash frozen in liquid nitrogen and stored at -80°C for a later digestion.
If frozen, nuclei were washed twice with 2.5 mL/plate Buffer A, pelleted (800g, 5 minutes, 4°C) and the supernatant discarded before proceeding to digestion. Digestion volumes are given for 107 nuclei.  Volumes should be scaled as per cell number. Digestion buffer (850 μl per 107 nuclei) was prepared by diluting 10X stock of CaCl2 and NaCl in Buffer A (above) for a final concentration of 6 mM CaCl2 and 75 mM NaCl. Stop buffer (950 μl  per 107 nuclei) was prepared with final concentrations as follows: 50 mM Tris HCl (pH 8), 100 mM Na Cl, 0.1 % SDS, 100 mM EDTA (Ambion, pH 8), 10 μg/ml RNase A (Invitrogen), 1 mM Spermidine (Sigma-Aldrich) and 0.5 M Spermine (Sigma-Aldrich). Both digestion and stop buffers were warmed at 37°C. DNase I enzyme was combined with warmed digestion buffer for a final volume of 100 μl per 107 nuclei. If multiple concentrations of DNase I were tested, nuclei were separated equally amongst each concentration. Prior to digestion, a small aliquot was reserved as an undigested control for quantitative PCR analysis. The DNaseI/ digestion buffer mix was warmed in a 37°C water bath for 2 minutes, and the nuclei were gently resuspended in digestion buffer. The warmed DNaseI/ digestion buffer mix was promptly added to the nuclei and digested for 2 minutes at 37°C. Pre-warmed stop buffer was added and the tube inverted multiple times to stop the digestion. Digested samples were transferred to a 55°C incubator for 15 minutes. Proteinase K (Ambion, 20 mg/mL) was added to each sample for a final concentration of 2μg/mL and samples were incubated overnight at 55°C.
DNA fragments were purified by adding an equal volume of phenol:chloroform:isoamyl alcohol to each sample and mixing. The suspension was transferred to a phase-lock tube and centrifuged for 5 minutes at 12-16,000g. The aqueous phase was isolated and combined with 0.1 volumes 3M sodium acetate, 2 volumes absolute ethanol and 1:600 Glycoblue. This mixture was incubated at -20°C for 5-6 hours or at -80°C for 30-45 minutes. DNA was pelleted by centrifugation at 12-16000g for 10-20 minutes and the supernatant aspirated. The DNA pellet was washed with 70% ethanol and re-pelleted by centrifugation at 4000 rpm for 5 minutes. The supernatant was carefully aspirated and the DNA pellet air-dried for 5-10 minutes before resuspending in TE buffer.
To enrich for hypersensitive regions, size selection was performed on the purified fragments by either 2% agarose gel band purification or the Invitrogen E-Gel Agarose System. Fragments were collected in the 175-400 bp region so as to avoid empirically-determined complications by the ~150 bp nucleosomal signal. Size selection enrichment was tested by quantitative PCR using primers (three positive control primers and three negative control primers) for constitutively DNase hypersensitive regions and insensitive regions as positive and negative controls respectively, on both the samples as well as the reserved undigested controls. Size selection enrichment was calculated as follows: Enrichment = 2^((Ct(negative control primer)-Ct(positive control primers))digested, size selected fragments-(Ct(negative control primer)-Ct(positive control primers))undigested control).

tag: cell type

value: mESC

tag: datatype

value: DNase-seq

tag: cell sex

value: F


title: mmu pl I 2 smallRNA [batch2]

description: small RNA

data_processing:
The basecalling was performed with the Illumina GAIIx pipeline, version 1.8, as well as with the Illumina HiSeq 2000 pipeline  and with Ibis (Kircher et al, 2009). Ibis was used on non-strand specific samples generated with Illumina GAII. The quality values are given in the phred-33 format, for all samples.
Raw reads were aligned with TopHat version 1.4.0 and Bowtie version 0.12.5. Command line for TopHat: tophat -p 4 -o -a 8 -i 40 -m 1 -I 1000000 -F 0 --coverage-search --microexon-search.
Splice junctions were detected from TopHat unambiguous read alignments, requiring an anchor size of at least 8bp and at most 1 mismatch per alignment.
The genome-wide read coverage was determined using the "wiggles" utility in TopHat.
Expression levels for Ensembl-annotated genes were estimated with Cufflinks 2.0.0, using all reads, with the multi-read correction embedded in Cufflinks.Cufflinks command line: cufflinks -q  -G Transcripts_ProteinCoding.gtf -p 4 --library-type ${librarytype} --multi-read-correct. For strand-specific samples, the library-type was set at fr-secondstrand, while for non-strand-specific samples the library-type was set at fr-unstranded. For expression level computation, GTF files were retrieved from Ensembl 62, and filtered to retain only transcripts annotated as "protein-coding" for protein-coding genes (all transcripts were kept for other gene biotypes).
Paired-end RNA-seq samples were treated as single-end for comparability, i.e. only the first read of the pair was used for expression analyses.
Small RNA-seq reads were trimmed to remove adapter sequences. We kept reads with trimmed sizes between 15 and 25 bp, which are compatible with mature miRNA sizes. The trimmed reads were mapped on the Ensembl 62 miRNA precursors, using Bowtie.  miRNA expression levels were computed as the number of reads that mapped uniquely to each Ensembl-annotated miRNA precursor.
Genome_build: hg19, mm9, monDom5, ornAna1, galGal3, JGI 4.2
Supplementary_files_format_and_content: The .FPKM files contain expression levels quantified with Cufflinks; the columns are tab-separated.
Supplementary_files_format_and_content: The .bedgraph files contain genome-wide read coverage statistics, obtained with the "wiggles" utility in TopHat.
Supplementary_files_format_and_content: For miRNA data, the .txt files contain the number of reads (unique and total) that could be assigned to a given miRNA precursor annotated in Ensembl. Reads that aligned to more than 1 Ensembl-annotated miRNA precursor were "divided" equally among the different precursors; thus, the "total" number of reads is not necessarily an integer.

molecule: total RNA

source_name: Placenta

extract_protocol:
Total RNA was extracted using the Trizol (Invitrogen) procedure or RNAeasy/RNAeasy Lipid/miRNeasy (Qiagen) column purification kits. RNA quality was assessed using an Agilent 2100 Bioanalyzer.
Non-strand-specific sequencing libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer's instructions. Briefly, polyadenylated RNA was isolated using a poly-dT bead procedure and then chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded cDNA were repaired. After 3'-end adenylation of these products, Illumina Paired-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were run on gels; 250-300 bp fragments were excised and then PCR-amplified (15 cycles). After column-purification, qualities of the resulting libraries were assessed using Agilent 2100 Bioanalyzers.
Strand-specific libraries were prepared using an optimized version of the original Directional mRNA-seq Library Prep Pre-Release Protocol from Illumina. We used reagents from various companies instead of Illumina’s to decrease significantly the library cost and as a consequence adapted the reaction parameters for each step. In addition, we integrated a size selection step, right after fragmentation to optimize the insert size distribution and decrease the adapter contamination. This optimized protocol is available upon request.

value: female

value: E 16.5 post-conception

value: Illumina HiSeq 2000,  strand-specific


title: hsa pl I 1 smallRNA [batch2]

description: small RNA

organism: Homo sapiens

value: 13 weeks post-conception


title: gga ov F 2 [batch2]

description: polyA RNA

data_processing:
The basecalling was performed with the Illumina GAIIx pipeline, version 1.8, as well as with the Illumina HiSeq 2000 pipeline  and with Ibis (Kircher et al, 2009). Ibis was used on non-strand specific samples generated with Illumina GAII. The quality values are given in the phred-33 format, for all samples.
Raw reads were aligned with TopHat version 1.4.0 and Bowtie version 0.12.5. Command line for TopHat: tophat -p 4 -o -a 8 -i 40 -m 1 -I 1000000 -F 0 --coverage-search --microexon-search.
Splice junctions were detected from TopHat unambiguous read alignments, requiring an anchor size of at least 8bp and at most 1 mismatch per alignment.
The genome-wide read coverage was determined using the "wiggles" utility in TopHat.
Expression levels for Ensembl-annotated genes were estimated with Cufflinks 2.0.0, using all reads, with the multi-read correction embedded in Cufflinks.Cufflinks command line: cufflinks -q  -G Transcripts_ProteinCoding.gtf -p 4 --library-type ${librarytype} --multi-read-correct. For strand-specific samples, the library-type was set at fr-secondstrand (batch 1) or fr-firststrand (batch 2), while for non-strand-specific samples the library-type was set at fr-unstranded. For expression level computation, GTF files were retrieved from Ensembl 62, and filtered to retain only transcripts annotated as "protein-coding" for protein-coding genes (all transcripts were kept for other gene biotypes).
Paired-end RNA-seq samples were treated as single-end for comparability, i.e. only the first read of the pair was used for expression analyses.
Small RNA-seq reads were trimmed to remove adapter sequences. We kept reads with trimmed sizes between 15 and 25 bp, which are compatible with mature miRNA sizes. The trimmed reads were mapped on the Ensembl 62 miRNA precursors, using Bowtie.  miRNA expression levels were computed as the number of reads that mapped uniquely to each Ensembl-annotated miRNA precursor.
Genome_build: hg19, mm9, monDom5, ornAna1, galGal3, JGI 4.2
Supplementary_files_format_and_content: The .FPKM files contain expression levels quantified with Cufflinks; the columns are tab-separated.
Supplementary_files_format_and_content: The .bedgraph files contain genome-wide read coverage statistics, obtained with the "wiggles" utility in TopHat.
Supplementary_files_format_and_content: For miRNA data, the .txt files contain the number of reads (unique and total) that could be assigned to a given miRNA precursor annotated in Ensembl. Reads that aligned to more than 1 Ensembl-annotated miRNA precursor were "divided" equally among the different precursors; thus, the "total" number of reads is not necessarily an integer.

organism: Gallus gallus

source_name: Ovary

value: fr-firststrand


title: mmu ts M4 [batch1]


title: gga ov F1 [batch1]


title: hsa ov F 3  [batch2]

description: polyA RNA

value: NA (pool of individuals)


title: gga br M2 [batch1]

source_name: Brain


title: xtr kd M1 [batch1]

source_name: Kidney


title: mmu pl M1 [batch1]

value: embryo, 10.5 days post-conception


title: mmu pl I 1 smallRNA [batch2]

description: small RNA

value: E 10.5 post-conception


title: ggo br F 2 [batch1]

description: Additional coverage for GSM752654.

organism: Gorilla gorilla

source_name: Brain, frontal cortex

value: Illumina GAIIx, non-strand-specific

tag: library-type (for tophat or cufflinks)

value: fr-unstranded


title: mmu pl I 4 [batch2]

description: polyA RNA

value: pooled male and female


title: hsa pl I 3 [batch2]

description: polyA RNA

value: male

value: 42 weeks post-conception


title: mdo pl I 3 [batch2]

description: polyA RNA

value: 12 days post-conception


title: xtr ts M 2 [batch2]

description: polyA RNA

value: adult


title: gga ts M3 [batch1]

value: Illumina GAIIx, strand-specific

value: fr-secondstrand


title: mdo pl I 2 [batch2]

description: polyA RNA

value: 14 days post-conception


title: hsa pl I 4 [batch2]

description: polyA RNA

value: female


title: oan ov F 3 [batch2]

description: polyA RNA

organism: Ornithorhynchus anatinus

value: Illumina HiSeq 2000,  strand-specific


title: mmu ov F 3 [batch2]

description: polyA RNA

value: adult (16 weeks)


title: mmu pl I 3 [batch2]

description: polyA RNA

data_processing:
The basecalling was performed with the Illumina GAIIx pipeline, version 1.8, as well as with the Illumina HiSeq 2000 pipeline  and with Ibis (Kircher et al, 2009). Ibis was used on non-strand specific samples generated with Illumina GAII. The quality values are given in the phred-33 format, for all samples.
Raw reads were aligned with TopHat version 1.4.0 and Bowtie version 0.12.5. Command line for TopHat: tophat -p 4 -o -a 8 -i 40 -m 1 -I 1000000 -F 0 --coverage-search --microexon-search.
Splice junctions were detected from TopHat unambiguous read alignments, requiring an anchor size of at least 8bp and at most 1 mismatch per alignment.
The genome-wide read coverage was determined using the "wiggles" utility in TopHat.
Expression levels for Ensembl-annotated genes were estimated with Cufflinks 2.0.0, using all reads, with the multi-read correction embedded in Cufflinks.Cufflinks command line: cufflinks -q  -G Transcripts_ProteinCoding.gtf -p 4 --library-type ${librarytype} --multi-read-correct. For strand-specific samples, the library-type was set at fr-secondstrand (batch 1) and fr-firststrand (batch 2), while for non-strand-specific samples the library-type was set at fr-unstranded. For expression level computation, GTF files were retrieved from Ensembl 62, and filtered to retain only transcripts annotated as "protein-coding" for protein-coding genes (all transcripts were kept for other gene biotypes).
Paired-end RNA-seq samples were treated as single-end for comparability, i.e. only the first read of the pair was used for expression analyses.
Small RNA-seq reads were trimmed to remove adapter sequences. We kept reads with trimmed sizes between 15 and 25 bp, which are compatible with mature miRNA sizes. The trimmed reads were mapped on the Ensembl 62 miRNA precursors, using Bowtie.  miRNA expression levels were computed as the number of reads that mapped uniquely to each Ensembl-annotated miRNA precursor.
Genome_build: hg19, mm9, monDom5, ornAna1, galGal3, JGI 4.2
Supplementary_files_format_and_content: The .FPKM files contain expression levels quantified with Cufflinks; the columns are tab-separated.
Supplementary_files_format_and_content: The .bedgraph files contain genome-wide read coverage statistics, obtained with the "wiggles" utility in TopHat.
Supplementary_files_format_and_content: For miRNA data, the .txt files contain the number of reads (unique and total) that could be assigned to a given miRNA precursor annotated in Ensembl. Reads that aligned to more than 1 Ensembl-annotated miRNA precursor were "divided" equally among the different precursors; thus, the "total" number of reads is not necessarily an integer.

value: fr-firststrand


title: mmu ov F 2 [batch2]

description: polyA RNA


title: xtr ov F 2  [batch2]

description: polyA RNA


title: ggo ts M 1 [batch1]

description: Additional coverage for GSM752663.

value: adult, 51 years


title: MC

status: Public on Jan 18 2014

city: Chengdu

first: HAO

last: JIANG

address: RENMING ROAD SOUTH

country: China

institute: IMDE-CAS

description: plants were subjected to each treatment for 100 days

data_processing:
standard pepline of Illumina bioinfomatics analysis
3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 49nt long, raw sequences are with 3' adaptor sequences;
Empty reads removal (reads with only 3' adaptor sequences but no Tags);
Low quality Tags removal (Tags with unknown sequences 'N');
Removal of Tags which are too long or too short, leaving Tags of 21nt long;
Removal of Tags with a copy number of 1 (probably be sequencing error);
Generate Clean Tags
The data were normalised using the number of distinct clean tags for each gene and calculated, and then normalized to TPM (number of transcripts per million clean tags)
Genome_build: Populus trichocarpa v3.0
Supplementary_files_format_and_content: Populus_UVB.txt contains TPM value for each detected gene from each treatment and the corresponding annotation putatively.

organism: Populus cathayana

source_name: male plant_decreased UV-B

growth_protocol: The cuttings were planted in 10 liter plastic pots (one plant per pot) filled with 8 kg of homogenized soil and 8 g slow release fertilizer (13% N, 10% P and 14% K). After sprouting and growing for about two months (May, 2012), healthy plants with a similar crown size and equal height were chosen and kept in a greenhouse located in Wanglang National Nature Reserve (32°98′N and 104°08′E, Sichuan Province, China) for the experiments. The solar UV-B treatment was conducted for 100 days over one growing season.

extract_protocol:
Total RNA was extracted from four treatents and RNA samples from nine individuals from each treatment were pooled with equal proportions.
Digital gene expression (DGE) library construction and analysis followed the standard Illumina protocols. Briefly, total RNA was extracted from three biological replicates using E.Z.N.A.TM Plant RNA Kit (Omega, USA) according to the manufacturer’s instructions. Residual genomic DNA was removed with DNase I and the integrity of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). RNA samples from nine individuals from each treatment were pooled with equal proportions. Double-stranded cDNA was synthesized using oligo (dT) beads. The cDNA was then digested with an anchoring restriction enzyme Nla III, which recognizes and cuts 3’ ‘CATG’. The digested cDNA samples were ligated to the Illumina-specific adapter A, containing a recognition site for the enzyme Mme I. Following the Mme I digestion, the Illumina specific adapter B containing a 2-bp degenerated 3’ overhang was ligated. The adapter-ligated cDNA tag library was then enriched by PCR primers annealing to the adaptor ends. The PCR program was as follows: 30 s at 98 °C, followed by 15 cycles of 98 °C for 10 s, 60 °C for 30 s and 72 °C for 15 s, and then 72 °C for 5 min. After gel-purification, cDNA was used for cluster generation on a separated flow cell lane. Sequencing by synthesis was performed using the Illumina Genome Analyzer according to the manufacturer’s protocol. Image analysis, base calling, extraction of 17-bp tags and tag counting were performed using the Illumina pipeline.

treatment_protocol: 4 samples examined: (i) males exposure to decreased solar UV-B radiation; (ii) females exposure to decreased solar UV-B radiation; (iii) males exposure to ambient solar UV-B radiation; and (iv) females exposure to ambient solar UV-B radiation.The solar UV-B treatment was conducted for 100 days over one growing season.

tag: exposed to

value: decreased solar UV-B radiation for 100 days

tag: tissue

value: fourth full expanded leaves


title: FC

source_name: female plant_decreased UV-B


title: Betacat null Tcf4 chipseq

city: Villeurbanne

first: Philippe

last: Veber

address: 16 rue Raphael Dubois

institute: CNRS

description: TK

data_processing:
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/); mRNA sequencing was quantified using DESeq.
MACS peak (version 1.3.7.1)
DESeq .tsv output (version 1.1.13): mm9
Genome Build:
TK.bed: mm9

source_name: Transgenic Hepatocytes

growth_protocol: Hepatocytes freshly isolated from transgenic mice

extract_protocol: The chromatin from cross-linked hepatocytes was sonicated and immunoprecipitated with the appropriate antibody. It was then reverse crosslinked and 10 ng each of two treated mice were pooled per sequencing experiment. Illumina adapters were ligated to DNA fragments before size selection (Fasteris protocol)

treatment_protocol: Tamoxifen-inducible Cre-loxP strategy performed in vivo

value: Hepatocytes isolated from adult liver

tag: transgenic line

value: Bcatlox/lox;TTR-CreERT

tag: tamoxifen protocol

value: D21 after 3x1.5mg IP Tamoxifen

tag: ChIP

value: ChIP/ antibody against Tcf4


title: Betacat activated mRNAseq 1

data_processing:
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/); mRNA sequencing was quantified using DESeq.
MACS peak (version 1.3.7.1)
DESeq .tsv output (version 1.1.13): mm9

extract_protocol: Poly-A purified RNAs were obtained from five micrograms of total RNAs extracted using Trizol technique. They were then fragmented with Zinc, reverse-transcribed, end-repaired and adaptors were ligated before gel purification (Fasteris protocol)

value: Apclox/lox;TTR-CreERT

value: D6 after 1x1.5mg IP Tamoxifen


title: WT mRNAseq 2

value: Apclox/lox

value: no injection


title: Betacat null sonoseq

description: SK

data_processing:
Library strategy: Sono-Seq
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/); mRNA sequencing was quantified using DESeq.
MACS peak (version 1.3.7.1)
DESeq .tsv output (version 1.1.13): mm9
Genome Build:
SK.bed: mm9

extract_protocol: The chromatin from cross-linked hepatocytes was sonicated, reverse crosslinked and 10 ng each of two treated mice were pooled per sequencing experiment. Illumina adapters were ligated to DNA fragments before size selection (Fasteris protocol)

value: Cross-linked and sonicated chromatin


title: Betacat activated mRNAseq 2


title: Betacat null mRNAseq 1


title: Betacat control mRNAseq 2

value: Bcatlox/lox


title: WT mRNAseq 1


title: Betacat control mRNAseq 1


title: Betacat activated Betacat chipseq

description: BA

data_processing:
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/); mRNA sequencing was quantified using DESeq.
MACS peak (version 1.3.7.1)
DESeq .tsv output (version 1.1.13): mm9
Genome Build:
BA.bed: mm9

tag: chip antibody

value: beta-catenin (mouse monoclonal, clone 14)

tag: antibody manufacturer

value: BD Transduction Laboratories

tag: antibody catalog

tag: antibody lot


title: Betacat activated Tcf4 chipseq

description: TA

data_processing:
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/); mRNA sequencing was quantified using DESeq.
MACS peak (version 1.3.7.1)
DESeq .tsv output (version 1.1.13): mm9
Genome Build:
TA.bed: mm9

value: Tcf4 (mouse monoclonal, clone 6H5-3)

value: Millipore Upstate


title: Betacat null mRNAseq 2


title: 3_cornea_input

city: Madison

first: Sakae

last: Ikeda

state: WI

address: 425G Henry Mall

department: Medical Genetics

institute: University of Wisconsin - Madison

data_processing:
Fastq files contain Illumina chastity filtered reads with phred+33 quality scores
Sequences (50 nt reads, single end) were aligned to the mouse genome (mm10) using the BWA algorithm.
Aligns were extended in silico at their 3’-ends to a length of 150 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome.
The resulting histograms (genomic “signal maps”) were stored in BAR and bigWig files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1e-10.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: mm10
Supplementary_files_format_and_content: The resulting histograms (genomic “signal maps”) were stored in BAR and bigWig files. Excel files generated by Active Motif's proprietary software were generated and report, peaks, intervals, and genes

source_name: cornea

growth_protocol: Dstn-corn1 mutant mice were aged to ~8 weeks

extract_protocol:
Lysates were clarified from sonicated nuclei and SRF-DNA complexes were isolated with antibody.
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3’-ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200-300 bp) on an agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on HiSeq 2000.

treatment_protocol: No treatment was given to the mice

value: whole cornea

value: ~8 weeks

value: mixed background


title: Betacat activated sonoseq

description: SA

data_processing:
Library strategy: Sono-Seq
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/); mRNA sequencing was quantified using DESeq.
MACS peak (version 1.3.7.1)
DESeq .tsv output (version 1.1.13): mm9
Genome Build:
SA.bed: mm9

value: Hepatocytes isolated from adult liver


title: oan ov F 2 [batch2]

description: polyA RNA

tag: Sex

value: female

value: adult

value: Illumina HiSeq 2000,  strand-specific

value: fr-firststrand


title: FU

source_name: female plant_ambient UV-B

value: ambient solar UV-B radiation for 100 days

value: fourth full expanded leaves


title: 1_cornea_mutant

tag: strain

value: SRF (Santa Cruz Biotechnology, sc-335, Lot# I2712)


title: mdo ov F 2 [batch2]

description: polyA RNA

tag: age


title: miR397-wild type rep3

status: Public on Jan 17 2014

city: Raleigh

first: Sermsawat

last: Tunlaya-anukit

state: NC

address: 840 Main campus drive  room2500

department: Department of Forestry and Environmental Resources

institute: North Carolina State University

data_processing:
Illumina Casava1.7 software used for basecalling.
mapped to Populus trichocarpa v3 using TopHat v2.0.3 and bowtie b0.12.7 with command tophat -p 7 -G /genomes/ptrichocarpa/sequences/Ptrichocarpa_210_gene_exons.gff3 /genomes/ptrichocarpa/index/Ptrichocarpa_210.fa *.fq
convert mapped file to depth file by coverageBed v2.14.2 with parameter coverageBed -abam */accepted_hits.bam  -b genomes/ptrichocarpa/sequences/Ptrichocarpa_210_gene_exons.gff3 > *.rawcount
compile rawcount file from all libraries into tab-delimited text file using perl script
Genome_build: Populus trichocarpa version 3.0 (www.phytozyme.com)
Supplementary_files_format_and_content: tab-delimited text files raw count values of transcript for each sample

organism: Populus trichocarpa

source_name: developing xylem

growth_protocol: P. trichocarpa plants were grown in pots containing half Miracle- Gro Soil (Scotts Miracle-Gro, Maysville, OH) and half Metro-Mix 200 (Sun Gro, Bellevue, WA) in a greenhouse at 17–26 °C, 16 h light/8 h dark cycle (with supplemental light of ~300 μE/m2/s). Miracle-Gro Plant Food (Scotts Miracle-Gro) was applied once a week

extract_protocol:
Total RNA was isolted using the CTAB method (Chang et al. 1993. Plant Mol Biol Rep 11: 113-116).
TruSeq RNA Sample Prep v2 LS protocol (Illumina)

treatment_protocol: transgenic overexpression PtrMIR397a with CaMV 35s promoter

tag: genetic background

value: developing xylem

tag: genotype

value: wild type


title: wild type

city: Shanghai

first: Weiwei

last: Qi

address: 333 Nanchen Road

institute: Shanghai University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v2 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: B73 RefGen_v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: kernel

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

tag: developmental stage

value: 19 DAP

value: endosperm


title: 2_cornea_wildtype


title: miR397-line6

value: over expression miR397a


title: fl4 mutant

value: fl4 mutant


title: miR397-wild type rep2


title: miR397-line30


title: miR397-line5


title: miR397-line17


title: miR397-line26


title: miR397-line10


title: MDA-MB-435SmRNA

city: Guangzhou

first: Cuihua

last: Wang

state: Guangdong

address: 601 Huangpu Ave, Guangzhou

institute: Guangzhou Lab

description: High quality reads which passed Illumina filter were kept

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads were aligned to human mRNA reference sequence (RefSeq) for GRCh37/hg19 downloaded from UCSC Genome browser employing FANSe2 mapping algorithm ((http://bioinformatics.jnu.edu.cn/software/fanse2/intro.html)) along with the options –L80–S10 –E5.
Splice variants were summed. The mRNA abundance was calculated using rpkM (reads per kilobase per million reads).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values and raw fragment counts for each sample

source_name: breast cancer cells

growth_protocol: Human breast cancer cell lines MCF-7 and MDA-MB-435 were cultured in Dulbecco’s modified Eagle medium (DMEM, Gibco BRL, Grand island, NY) supplemented with 10 % fetal bovine serum (PAA Laboratories, Linz, Austria), 1% penicillin/streptomycin (Genom, China) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Standard Trizol protocol
Standard Illumina TruSeq mRNA library prep

tag: cell type

value: Breast cancer

tag: cell line


title: miR397-line1

tag: tissue


title: B73 3DAP

city: Tucson

first: Ramin

last: Yadegari

state: Arizona

address: 1140 E. South Campus Dr.

department: Plant Sciences

institute: University of Arizona

data_processing:
SOLiD™ System
Sequenced reads were mapped to maize reference genome using tophat1 with default parameters
Gene expression level was estimated as the sum of all reads mapped to the whole gene region using the intersectBed command implemented in the BEDTools package.
Genome_build: ZmB73_RefGen_v2.tar.gz; http://ftp.maizesequence.org/current/assembly/
Supplementary_files_format_and_content: tab-delimited text files include count-based values for each gene

growth_protocol: Plants of the reference maize genotype, B73, were grown under greenhouse conditions (16-hour day) at the University of Arizona during August-September 2009. All kernel and endosperm samples were collected from self-pollinated ovules. Self-pollinations were performed essentially as described by Poehlman (1977). The 0-, 2-, 3-, 4-, and 6-DAP kernels were collected by pushing down the glumes and pinching off the kernel at its base using a pair of forceps. The 8-, 10-, and 12-DAP endosperm samples were harvested by removing all tissues of the kernel from the pedicel up to the hilar region and cutting open the pericarp along the edge of the hilar region to expose and extract the endosperm free of the embryo and the pericarp using a surgical blade. In all cases, the staged kernels and endosperm samples were frozen immediately in liquid nitrogen and stored at -70°C before RNA extractions were carried out. Of the three individual biological replicates of each developmental stage collected for this work, one (bio-rep 1, except for 0 DAP where two technical replicates were sequenced) was used for RNA-Seq and all three were used for qRT-PCR analyses.

extract_protocol:
Total RNA was isolated using a SDS-Phenol method (Shirzadegan et al., 1991) except that 50-ml Phase-Lock-Gel Light Tubes (5Prime, Inc., Gaithersburg, MD, USA) were used to facilitate the phenol/chloroform extractions. Genomic DNA was removed using TURBO DNase I (Ambion) and RNA was further purified using RNeasy columns (Qiagen). For RNA-Seq analysis, two rounds of PolyA+ mRNA selection was carried out on 500 μg of total RNA using the Poly(A)PuristTM MAG kit (Ambion). RNA was quantified using a Nanodrop 1000 Spectrophotometer (Thermo Scientific, Inc., Wilmington, DE, USA), and RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA) found to be 9.3 to 10 in RNA integrity number (RIN).
RNA libraries were prepared for sequencing using standard protocols for SOLiD™ 4 System (Applied Biosystems)

tag: cultivar

value: 3 DAP


title: B73 12DAP

source_name: endosperm

value: 12 DAP


title: B73 10DAP

value: 10 DAP


title: B73 4DAP

value: 4 DAP


title: miR397-line9


title: MCF-7mRNA


title: B73 0bDAP

description: B73 0aDAP and B73 0bDAP are technical replicates

value: 0 DAP


title: B73 0aDAP


title: RNAseq_processed

city: Boston

first: Sinisa

last: Hrvatin

address: 220 Longwood ave, GB405

department: Neurobiology

institute: Harvard Medical School

data_processing:
Firecrest was performed in real time with the sequencing process on a dedicate IPARR server. Bustard was used for basecalling, and FASTQ files were output.
Reads were aligned to the human genome (GRCh37/hg19) using STAR (version 2.2.0c) guided by GENCODE gene annotations (version 14). RNA-seq FPKM values were generated using Cufflinks (version 2.0.2).
Genome_build: GRCh37
Supplementary_files_format_and_content: Cufflinks output (text) files indicating gene-level FPKM.

source_name: H1 human embryonic stem cells differentiated to insulin-expressing cells, processed

growth_protocol: Human embryonic stem cells were grown on matrigel using mTeSR media.

extract_protocol:
"Processed" sample was fixed with 4% paraformaldehyde, permabilized, antibody stained and mock sorted to collect all cells. RNA was extracted using a modified RecoverAll Total Nucleic Acid Isolation kit (Ambion). See "MARIS: Method for Analyzing RNA following Intracellular Sorting" manuscript for details.
Samples prepared into Illumina libraries using the Beckman Coulter Genomics SPRI-works system using custom adapters. 6nt 3' barcodes were added during PCR enrichment and the resulting fragments were evaluated using Agilent BioAnalyzer 2100. Samples were sequenced one-per-lane using an Illumina HiSeq 2000 with paired-end read lengths of 80nt.

treatment_protocol: Human embryonic stem cells were differentiated to insulin-expressing cells using a stepwise protocol described in the manuscript: "MARIS: Method for Analyzing RNA following Intracellular Sorting".

value: human embryonic stem cells differentiated to "stage 6" containing insulin-expressing cells

tag: sample type

value: processed (MARIS)


title: miR397-line3


title: ST cycle mice

status: Public on Jan 16 2014

city: Zurich

first: Steven

last: Brown

state: Switzerland

address: Winterthurerstrasse 190

department: Institute of Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich

data_processing:
Illumina Casava-1.8.2 software used for basecalling.
Sequence were mapped to mm9 whole genome using TopHat v1.2
Quantitative and differential gene expression was carried out using the Deseq using default parameters.  To identify the top differentially expressed genes, we used a twofold cutoff to the average change in gene expression (log2 ≥ 1) and 8 reads as cutoff for minimum number of reads per gene.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample and log2 fold change…..

source_name: SCN (Suprachiasmatic nucleus)

growth_protocol: First, 16 mice 5 to 6 weeks old were exposed to DD for 7 days in order to measure their FRP. Then, mice were separated into 2 groups of 8 and entrained to ST and NT cycle. After 4 weeks we recorded wheel-running behavior in constant darkness. After 5 days in DD, we used Clocklab software to predict time of activity onset for each mouse. Brains were isolated at CT4 and sliced with a microtome using a fresh HBSS medium (thickness 250 uM) and the SCN was cut out with the aid of a binocular microscope and stored immediately at –80°C.

extract_protocol:
Total RNA was extracted using the SurePrep™ Nuclear or Cytoplasmic RNA Purification Kit (Fisher Scientific) according to the manufacturer's protocol.  A total of 500 ng of RNA was used for subsequent steps. These steps included DNAase treatment, polyA selection, depletion of ribosomal RNA, overall quality check, and library preparation, and were performed by Fasteris (CH).
Libraries were prepared according to standard Illumina protocols.

value: SCN (Suprachiasmatic nucleus)

value: post natal day 68


title: RNA_seq_parental_rep1

city: Heidelberg

first: Lukas

last: Chavez

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
Paired-end sequencing data was mapped against mm9 using tophat (v. 2.0.0.) with the parameter setting: -g 1 -r 115 --mate-std-dev=70 --no-coverage-search --library-type=fr-secondstrand.
RNA-seq mapping results (sam files) were sorted (samtools v 0.1.18) and used as input for the python script dexseq_count.py which is part of Bioconductors DEXSeq package (version 1.2.1) in order to count the coverage at pre-computed exonic parts. Exonic parts were given in a GFF file which has been derived by applying the dexseq_prepare_annotation.py script, available in the DEXSeq package, to the Mus musculus Ensembl 67 GTF annotation file (provided at ftp://ftp.ensembl.org/pub/release-67/gtf/mus_musculus/Mus_musculus.NCBIM37.67.gtf.gz.). Exon count sets were created by importing the count files of all replicates per condition into R using the read.HTSeqCounts function. Subsequently, gene count tables were generated based on the exon count sets using the geneCountTable and newCountDataSet functions.
Genome_build: mm9
Supplementary_files_format_and_content: DESeq asn DEXSeq results table

source_name: V6.5 mES cells

growth_protocol: Mouse embryonic stem cells were cultured in Knockout D-MEM with 15% ES-qualified FBS (Gemini Bio-products), 2 mM L-glutamine with 0.1 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids, 50 units/ml penicillin/streptomycin and 1000 U/ml ESGRO® (LIF; Chemicon).

extract_protocol: Total RNA was isolated with an RNeasy kit (Qiagen, Chatsworth, CA). Around 400 ug total RNA were isolated and selected twice with Ambion® MicroPoly(A)Purist™ Kit. cDNA conversion and library preparation were performed using SOLiD RNA-seq library prep kit and EZ-beads prep kit.

treatment_protocol: Cells stably depleted of Tet1 and Tet2 were obtained by electroporating V6.5 mESC with pSUPER-puro-Tet1shRNA or pSUPER-puro-Tet2shRNA (320V, 250F). Cells were selected by 1.5 g/ml puromycin for 7-10 days on puromycin-resistant mitomycine C-inactivated SNL76/7-4 feeder cells.  Individual clones were picked and propagated in the absence of puromycin if the passage number was less than 10, or maintained in 1 g/ml puromycin if the passage number was longer than 10. Tet1 and Tet2 mRNA expression in individual clones was evaluated by qPCR.

tag: knockdown

tag: biological replicate


title: miR397-wild type rep1


title: RNA_seq_Tet2kd_rep2

source_name: Tet2 kd mES cells

value: Tet2 kd


title: RNA_seq_Tet2kd_rep4


title: RNA_seq_parental_rep2


title: RNA_seq_Tet1kd_rep1

source_name: Tet1 kd mES cells

value: Tet1 kd


title: RNA_seq_Tet1kd_rep4


title: RNA_seq_Tet1kd_rep2


title: NT cycle mice

value: wild type


title: RNA_seq_Tet1kd_rep3


title: RNA_seq_Tet2kd_rep3


title: RNAseq_live

source_name: H1 human embryonic stem cells differentiated to insulin-expressing cells, live

extract_protocol:
RNA from "live" sample was extracted using the RNeasy protocol.
Samples prepared into Illumina libraries using the Beckman Coulter Genomics SPRI-works system using custom adapters. 6nt 3' barcodes were added during PCR enrichment and the resulting fragments were evaluated using Agilent BioAnalyzer 2100. Samples were sequenced one-per-lane using an Illumina HiSeq 2000 with paired-end read lengths of 80nt.

value: live


title: RNA_seq_parental_rep3


title: RNA_seq_Tet2kd_rep1


title: RNA_seq_parental_rep4


title: B73 6DAP

value: 6 DAP


title: B73 2DAP

value: 2 DAP


title: B73 8DAP

value: 8 DAP


title: (+)4SUTP_512cell_rep1

city: Dresden

first: Patricia

last: Heyn

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

description:
processed data file: GSE47709_comb_genes_2.tsv
processed data file: GSE47709_comb_genes_1.tsv
processed data file: GSE47709_comb_transcripts_1.tsv

data_processing:
Basecalling with Illumina Casava 1.7 software.
Overrepresented reads (adapter, SPIA-amplification primers) were identified from FastQ output and trimmed as described in Kircher M., Methods Mol Biol, 2012.
Reads were mapped to the zebrafish genome assembly Zv9/GCA_000002035.2 with TopHat 1.3.3 using the following parameters --butterfly-search --library-type=fr-unstranded --splice-mismatches=1 --max-multihits=100
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks 2.0.2 using the Ensembl release 64 with the following parameters: --multi-read-correct --max-bundle-frags=20000000 --library-type=fr-unstranded
Only transcripts or genes with a FPKM value larger than the width of the 95% confidence interval (FPKM > Δ95 FPKM) were considered to be expressed as described in Nagaraj et al., Mol Syst Biol., 2011.
Technical replicates of (+)4SUTP samples were pooled, mapped and sampled to the same number of reads per developmental time points, genes/transcripts had to be expressed in two of the 3 time points.
The sum of FPKM values for protein-coding mitochondrial transcripts/genes was assumed to be constant and used to normalize FPKM values for pooled (+)4SUTP samples between developmental time points.
For (-)4SUTP to (+)4SUTP comparison, reads from all samples were sampled to 8775274 before FPKM calculation.
Genome_build: Zv9
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl genes/transcripts and FPKM values for each sample.

organism: Danio rerio

source_name: embryo, 512-cell stage, 4-thio-UTP labeled

growth_protocol: Zebrafish WT AB strain was maintained and raised under standard conditions.

extract_protocol:
Total RNA from staged embryos was extracted with Trizol, biotinylated with EZ-Link HPDP-Biotin and subsequently purified with streptavidin-coated magnetic beads to isolate newly transcribed RNA. Labeled and unlabeled samples were treated in the same way.
Libraries were prepared for the HiSeq 2000 machine (Illumina). Briefly, RNA was amplified with the WT-Ovation™ One-Direct RNA Amplification System (NuGEN). The reaction was stopped after the SPIA amplification and double-stranded cDNA with random Hexamers created. Double-stranded cDNA was sheared to ~200-300bp fragment size, end-repaired with the NEBNext End Repair Module (NEB) and the resulting fragments were adenylated at the 3'-end with the NEBNext dA-Tailing Module (NEB).TruSeq adapters were ligated and the libraries were PCR amplified for 15 cycles. The concentration of molecules with adapters ligated in the final library was determined by qPCR with the KAPA Library Quant Kit (Kapa Biosystems).

treatment_protocol: Embryos were microinjected at the 1-cell stage with 1 nl of 50 mM 4-thio-UTP in 10 mM Tris-HCl pH 7.4 (Ambion).

value: AB

value: wild-type

value: embryo

tag: 4-thio utp labeling

value: labeled

tag: replicate

value: technical replicate 1


title: (+)4SUTP_128cell_rep2

source_name: embryo, 128-cell stage, 4-thio-UTP labeled

value: technical replicate 2


title: (-)4SUTP_128cell

description: processed data file: GSE47709_comb_genes_2.tsv

source_name: embryo, 128-cell stage, unlabeled

value: unlabeled

value: replicate 1


title: (+)4SUTP_512cell_rep2


title: (+)4SUTP_256cell_rep2

source_name: embryo, 256-cell stage, 4-thio-UTP labeled


title: (-)4SUTP_256cell

source_name: embryo, 256-cell stage, unlabeled


title: (+)4SUTP_128cell_rep1


title: (+)4SUTP_256cell_rep1


title: Anti-CMS_5hmC_Input_Tet2kd_rep1

data_processing:
Anti-CMS and Input reads derived from parental v6.5 mESC, Tet1 kd mESC, and Tet2 kd mESC input and CMS-IP were obtained and mapped against mm9 as previously described [Pastor et al. Nature 2011, PMID 21552279] by discarding all reads that map to multiple positions in the genome. Reads that map to the same genomic position were replaced by one representative. Mapping results from replicates were pooled.
In order to identify genome wide differentially hydroxymethylated regions (DHMRs) in parental v6.5 compared to Tet1, or Tet2 kd, respectively, we calculated library size normalized differential coverage of the CMS-IP data at genome wide 300 bp windows by employing a developmental version (v1.9.10) of the Bioconductor package MEDIPS (extend=200, uniq=F, window_size=300, BSgenome=BSgenome.Mmusculus.UCSC.mm9, diff.method = edgeR, p.vale = 1e-5), and adjacent significant windows with the same direction of 5hmC change were merged.
Genome_build: mm9
Supplementary_files_format_and_content: Result tables contain counts, rpkm, log2FC, and p-values at genome wide 300 bp windows as returned by the MEDIPS software for i) Tet1 kd mESC vs. v6.5mESC and ii) Tet2 kd mESC vs. V6.5mESC

source_name: Tet2kd mES cells

extract_protocol: Genomic DNA was sheared using Covaris Adaptive Focused Acoustic to the center at 150 bp. DNA fragments were size selected and ligated with methylated adaptors and treated with sodium bisulfite (invitrogen). The extra adapters were removed by AmpurXP (Beckman). The DNA was then denatured for 10 minutes at 95 °C (0.4 M NaOH, 10 mM EDTA), neutralized by the addition of cold 2M ammonium acetate (pH 7.0) for 10 min on ice. Then denatured DNA fragments were incubated with 1 μl anti-CMS antiserum in 1x IP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100) for 2 h at 4 °C, and then precipitated with protein G beads. Precipitated DNA was eluted with proteinase K, purified with phenol chloroform, amplified and enriched by 4-6 cycles PCR using Pfu TurboCx hotstart DNA polymerase (Stratagene).  DNA sequencing was carried out using Illumina Genome Analyzer 2 and HiSeq sequencing systems.

treatment_protocol: Cells stably depleted of Tet1 and Tet2 were obtained by electroporating V6.5 mESC with pSUPER-puro-Tet1shRNA or pSUPER-puro-Tet2shRNA (320V, 250F). Cells were selected by 1.5 g/ml puromycin for 7-10 days on puromycin-resistant mitomycine C-inactivated SNL76/7-4 feeder cells. Individual clones were picked and propagated in the absence of puromycin if the passage number was less than 10, or maintained in 1 g/ml puromycin if the passage number was longer than 10. Tet1 and Tet2 mRNA expression in individual clones was evaluated by qPCR.

tag: dna enrichment

value: none, input


title: Anti-CMS_5hmC_IP_Tet2kd_rep3

value: CMS antisera


title: Anti-CMS_5hmC_Input_parental_rep2

source_name: parental V6.5 mES cells

value: wt


title: (-)4SUTP_512cell

source_name: embryo, 512-cell stage, unlabeled


title: Anti-CMS_5hmC_IP_Tet2kd_rep2

value: Tet2 kd


title: Anti-CMS_5hmC_IP_parental_rep2


title: Anti-CMS_5hmC_IP_Tet1kd_rep2

source_name: Tet1kd mES cells

value: Tet1 kd


title: WCE_9_4_12

city: New York

first: Milan

middle: Girish

last: Chheda

state: NY

address: 408 E. 69th Street

department: Neurology

institute: Memorial Sloan-Kettering Cancer Center

description:
whole cell extract
Not applicable

data_processing:
ChIP-Seq reads were aligned using the software Bowtie (Langmead et al., 2009) to NCBI build 36 (hg18) of the human genome with default settings. Sequences uniquely mapping to the genome with zero or one mismatch were used in further analysis. When multiple reads mapped to the same genomic position, a maximum of two reads mapping to the same position were used.   Analysis methods were derived from previously published methods (Whyte et al., 2012). Sequence reads from multiple flow cells for each IP target and/or biological replicates were combined.  For all datasets, each read was extended 600bp towards the interior and 400bp towards the exterior of the sequenced fragment, based on the strand of the alignment. Across the genome, in 25 bp bins, the number of extended ChIP-Seq reads was tabulated.  The 25bp genomic bins that contained statistically significant ChIP-Seq enrichment were identified by comparison to a Poissonian background model.  Assuming background reads are spread randomly throughout the genome, the probability of observing a given number of reads in a genomic bin can be modeled as a Poissonian process in which the expectation can be estimated as the number of mapped reads multiplied by the number of bins (40 for all sequences datasets used here) into which each read maps, divided by the total number of bins available (we estimated 70% of the genome).  Enriched bins within 200bp of one another were combined into regions.    The Poissonian background model assumes a random distribution of background reads, but we have observed significant deviations from this expectation.  Some of these non-random events can be detected as sites of apparent enrichment in negative control DNA samples and can create many false positives in ChIP-Seq experiments. To remove these regions, we compared genomic bins and regions that meet the statistical threshold for enrichment to a set of reads obtained from Illumina sequencing of DNA from whole cell extract (WCE) in matched cell samples.  We required that enriched bins and enriched regions have five-fold greater ChIP-Seq density in the specific IP sample, compared with the control sample, normalized to the total number of reads in each dataset.  This served to filter out genomic regions that are biased to having a greater than expected background density of ChIP-Seq reads.
Assessing significance of co-binding: The total number of genomic regions available for occupancy by ZFHX4 or CHD4 was estimated by dividing the total Illumina sequence coverage of DNA from WCE (2,043,862,849bp) by the average sequence length of all ZFHX4-occupied and CHD4-occupied regions (622bp; Table S2 Sheets 4 and 5), yielding 3,284,154 regions. Based on the findings of 19,261 ZFHX4-occupied regions, 32,078 CHD4-occupied regions, and 5594 ZFHX4-occupied regions co-bound by CHD4 (Table S2 Sheets 4-6), enrichment of ZFHX4-bound regions for co-occupancy by CHD4 was calculated by dividing the fraction of ZFHX4-bound regions co-occupied by CHD4 (5594/19,261=0.29) by the fraction of all available regions bound by CHD4 (32,078/3,284,154=0.0098), and p-value was calculated using a two-tailed Fisher’s exact test.
The complete set of RefSeq genes was downloaded from the UCSC table browser (http://genome.ucsc.edu/cgi-bin/hgTables) on June 1, 2010. For all datasets, genes with enriched regions within the gene body or within 10kb of the start or stop of the gene were called bound. Co-bound genes were defined as containing, within the gene body or within 10kb of the start or stop, a ZFHX4-bound region co-bound by CHD4
Genome_build: NCBI build 36 (hg18) of the human genome
Supplementary_files_format_and_content: wig files; each ChIP sample was processed with the whole cell extract (WCE) input used for the chromatin immunoprecipitation, as indicated by the number tag in the titles,which represents date, in the Samples section.

source_name: glioblastoma tumor intiating cells, 0308 line

growth_protocol: The previously established 0308 GBM TIC line (Lee et al., Cancer Cell 9, 391-403, 2006) was cultured in NBE medium (Neurobasal medium containing N-2 and B-27 supplements, EGF, bFGF, L-glutamine, and Penicillin-Streptomycin) as described (Lee et al., Cancer Cell 9, 391-403, 2006).

extract_protocol:
20-100 million target cells were cross-linked at room temperature for 10 min with fresh 11% formaldehyde, quenched with 2.5M glycine, and processed through the DNA elution steps following the Agilent Technologies Mammalian ChIP-on-chip protocol (version 10.2, March 2011, http://www.chem.agilent.com/Library/usermanuals/Public/G4481-90010_MammalianProtocol_10.2.pdf), with the following modifications: sonication buffer composition 20 mM Tris-HCl , 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100; sonication in 3 mL was performed on a Bioruptor Standard (Diagenode, Denville, NJ)  high setting at 4°C for 30 min total (cycles: 30 seconds on/30 seconds off); after sonication and centrifugation at 1400g, supernatant underwent immunoprecipitation with 10 ug antibody [anti-ZFXH4 (Abnova, H00079776-M11), mouse IgG2A (R&D Systems, AB003), anti-CHD4 (Abcam, ab72418), or rabbit polyclonal (Abcam, ab27478) antibodies] for four days for ZFHX4/mouse isotype control IP or overnight for CHD4/rabbit polyclonal control IP; protein G Dynabeads (Life Technologies, 1007D) were incubated with the IP lysates for 45 min and washed with sonication buffer x 2, buffer 1 (20 mM Tris HCl, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) x 2, buffer 2 (10 mM Tris HCl, 250 mM LiCl, 2 mM EDTA, 1% Igepal) x 2, and buffer 3 (10 mM Tris HCl, 1 mM EDTA, 50 mM NaCl) x 2.
Immunoprecipitated DNA was quantified by picogreen and size was evaluated on a HighSense BioAnalyzer chip. Fragments between 100 and 600 bp were collected using an automated system (Pippin Prep, Sage Science) then end repaired, ligated and amplified for 15 cycles using reagents included in the Truseq DNA Sample Preparation kit from Illumina. Experimental conditions followed strictly the instructions of the manufacturer, with the exception of the adaptors being diluted 1/10 for the input DNA and 1/50 for all other samples. 7 barcoded libraries were run on 2 lanes of a Hiseq 2000 in a 50bp/50bp paired end run, using the TruSeq SBS Kit v3 (Illumina). The average number of read pairs per sample was 48 million

tag: chip antibody

tag: number of replicates


title: WCE_8_20_12

description:
whole cell extract
Not applicable


title: ChIP_ZFHX4_9_4_12

description:
Chromatin IP
human_ZFHX4_merged_min10.wig

value: anti-ZFHX4,Abnova, H00079776-M11


title: ChIP_ZFHX4_7_17_12


title: ChIP_CHD4_8_20_12

description:
Chromatin IP
human_CHD4_merged_min10.wig

value: anti-CHD4, Abcam, ab72418


title: WTAP deficient 293T cells rep2

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description: WTAP deficient 293T cells rep2

data_processing:
Reads were aligned to the hg19 genome assembly using TopHat v2.0.9
For each sample, RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene.
Differentially expressed genes between control and  METTL3, WTAP deficient ES cells  samples were determined using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: hg19
Supplementary_files_format_and_content: Reads count and RPKM for each gene

source_name: Human 293T cells

extract_protocol:
RNA was isolated from control, METTL3 or WTAP deficient Human 293T cells cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100
Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 50 bp.

tag: treatment

value: WTAP deficient

tag: age

value: Embryo

value: Embryonic kidney


title: WCE_7_17_12

description:
whole cell extract
Not applicable


title: METTL3 deficient 293T cells rep2

description: METTL3 deficient 293T cells rep2

value: METTL3 deficient


title: WTAP deficient 293T cells rep1

description: WTAP deficient 293T cells rep1


title: METTL3 deficient 293T cells rep1

description: METTL3 deficient 293T cells rep1


title: normal Human 293T cells rep1

description: normal Human 293T cells rep1

value: normal


title: M3-ip

description: RNA got from Myc IP

data_processing:
Reads were aligned to the hg19 genome assembly using bowtie1
Clusters were got by PARalyzer (http://www.genome.duke.edu/labs/ohler/research/PARalyzer/).
cERMIT (Georgiev et al., 2010) was run on a list of the clusters to get the motif.
Genome_build: hg19
Supplementary_files_format_and_content: Mettl3_input_5deep_groups.csv including the group result and Mettl3_input_kde_plus3_5deep.csv including the cluster result for Mettl3_input data
Supplementary_files_format_and_content: WTAP_input_5deep_groups.csv including the group result and WTAP_input_kde_plus3_5deep.csv including the cluster result for WTAP_input data
Supplementary_files_format_and_content: Mettl3_IP_5deep_groups.csv including the group result and Mettl3_IP_kde_plus3_5deep.csv including the cluster result for Mettl3_IP data
Supplementary_files_format_and_content: WTAP_IP_5deep_groups.csv including the group result and WTAP_IP_kde_plus3_5deep.csv including the cluster result for WTAP_IPt data

source_name: Human 293T

extract_protocol:
label the cells overexpressed Myc tagged METTL3 and Flag tagged WTAP with 4-SU, the RNA bound by METT3,WTAP can be got by Myc or Flag IP followed by RNA isolation by using the TRIzol (Invitrogen) reagent by following the company manual.the RNA was then used for library preparation and sequencing.
the RNA got from IP was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 50 bp.

value: METTL3 overexpressed

tag: antibody

value: Myc METTL3 IP


title: W-ip

description: RNA got from Flag IP

value: WTAP overexpressed

value: Flag WTAP IP


title: female.rep1.NAG1_HF

city: RTP

first: ruifang

last: li

address: 111 T.W. Alexander Drive

institute: NIEHS

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw data was filtered to remove reads with average base quality score <20.
Reads were mapped against mm9 reference genome with Bowtie (v0.12.8) with the following parameters:  -m1 -v2
Replicate sequencing lanes from the same library were merged with MergeSamFiles.jar from the Picard suite (v1.62).
Duplicate mapped reads were removed with MarkDuplicates.jar from the Picard suite (v1.62).
Peak calls were performed with SICER (v1.03) with parameters  window size 200, gap size 200, fragment size 200, and FDR cutoff 0.001.  Input sequence was used for background.
Mapped reads were extended at their 3' end to a length of 200 bases and converted to aggregate coverage (bedGraph format).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph file per sample showing aggregate coverage of mapped extended reads; generated by BEDtools genomeCoverageBed.
Supplementary_files_format_and_content: Called peaks or H3K27ac enrichment in BED format; peaks identified by SICER with parameters window size 200, gap size 200, fragment size 200, and FDR cutoff 0.001.

extract_protocol:
Colonic epithelial cells were isolated as previously described (Roediger et al, 1979, Gut, 20: 484-488). Cells were treated with 1% formaldehyde in PBS for 10 min at room temperature. Cross-linking was terminated by addition of glycine. The cells were spun down and rinsed with ice-cold PBS two times. The cell lysates were sonicated using a Bioruptor (Diagenode) to generate 150–350 bp fragments for immunoprecipitation. h3k27ac antibody (Active Motif, cat no. 39133) was used for ChIP.
Libraries were prepared using TruSeq™ RNA Sample Preparation kit (Illumina) following the manufacturer’s instructions. Illumina TruSeq RNA Sample Preparation Kit v1 was used for library preparation.

treatment_protocol: Female h-NAG-1 transgenic mice and wild type C57BL/6J mice at 5 weeks of age were placed on either 10% fat diet (D12450B) or 60% fat diet (D12492, Research Diets, New Brunswick, NJ) for 20 weeks. Male C57BL/6J mice on either 10% fat diet (380056 DIO controls) or 60% fat diet (380050 DIO high fat diet) were purchased from Jackson Laboratories and acclimated for one more week after transfer. The male mice were used for experiments after 15 weeks on high-fat diet.

tag: strain background

value: colon epithelial cells

tag: genotype/variation

value: h-NAG-1 transgenic

value: high-fat diet

tag: gender

value: female

tag: chip antibody vendor

value: active motif

tag: chip antibody cat. #


title: female.rep1.input

tag: cell type

value: low-fat diet


title: female.rep1.WT_HF

value: wild type


title: male.WT_HF.input

extract_protocol:
Colonic epithelial cells were isolated as previously described (Roediger et al, 1979, Gut, 20: 484-488). Cells were treated with 1% formaldehyde in PBS for 10 min at room temperature. Cross-linking was terminated by addition of glycine. The cells were spun down and rinsed with ice-cold PBS two times. The cell lysates were sonicated using a Bioruptor (Diagenode) to generate 150–350 bp fragments for immunoprecipitation. h3k27ac antibody (Active Motif, cat no. 39133) was used for ChIP.
Libraries were prepared using TruSeq™ RNA Sample Preparation kit (Illumina) following the manufacturer’s instructions.
Illumina TruSeq RNA Sample Preparation Kit v1 was used for library preparation.

value: male


title: male.WT_LF.input


title: W-input

description: W-input

tag: cell line

tag: tissue

value: input


title: M3-input

value: Embryo


title: male.rep3.WT_LF


title: male.rep3.WT_HF


title: normal Human 293T cells rep2

description: normal Human 293T cells rep2

value: normal ES cells

value: Embryonic kidney


title: female.rep1.WT_LF


title: female.rep1.NAG1_LF


title: ChIP_CHD4_9_4_12

value: anti-CHD4, Abcam, ab72418


title: female.rep2.input


title: male.rep2.WT_LF


title: female.rep2.WT_LF


title: male.rep1.WT_LF


title: Anti-CMS_5hmC_Input_Tet1kd

tag: knockdown

value: Tet1 kd

value: none, input

tag: biological replicate


title: male.rep1.WT_HF


title: female.rep2.WT_HF


title: male.rep2.WT_HF


title: Anti-CMS_5hmC_Input_parental_rep3

value: wt


title: female.rep2.NAG1_LF


title: Anti-CMS_5hmC_IP_Tet2kd_rep1

value: Tet2 kd

value: CMS antisera


title: Anti-CMS_5hmC_IP_Tet1kd_rep1


title: Anti-CMS_5hmC_IP_Tet1kd_rep3


title: Anti-CMS_5hmC_Input_parental_rep1


title: Anti-CMS_5hmC_IP_parental_rep1


title: female.rep2.NAG1_HF

value: h-NAG-1 transgenic

value: colon epithelial cells


title: Anti-CMS_5hmC_Input_Tet2kd_rep3


title: M5W (experimental)

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

data_processing:
Reads has been first filtered against pre-formated fasta file including, SOLiD P1 and P2 adaptors, SOLiD barcodes, polynucleotides (polyA,polyT,polyC and polyG), ribosomal RNAs.
Genome alignment was performs against mm9 release using Bowtie aligner allowing 2 mismatchs after discarding SOLiD adaptor.
Read count was performs using custom Java class based on the parsing of .bam alignment file and sequential annotation using .gff annotation files gathering genomic positions of microRNAs (mirbase release 18), UCSC tRNAs tracks table, Ensembl ncRNAs (release 69) and fRNAdb.
Differential expression analysis has been performed with the DESeq R (bionconductor) package. DESeq size factor normalization.
Genome_build: mm9
Supplementary_files_format_and_content: Not normalized table counts of features identified within all samples.

source_name: Testis

growth_protocol: Male mice (C57Bl/6) were continuously reared on diet with a high content of lipids (HFD, see Methods) starting at the age of 4 weeks. When 4-month old, they were mated to females grown on control diet. Males were removed after 1 day and control diet was exclusively provided during gestation, lactation, weaning and growth of the progeny.

extract_protocol:
Trizol procedure (Invitrogen)
SOLiD Total RNA-seq kit (STAR-cDNA-PCR)

tag: strain

tag: developmental stage

value: adult

value: Testis


title: Anti-CMS_5hmC_IP_parental_rep3

tag: dna enrichment


title: TN1 (control)


title: M1N (control)


title: M3W (experimental)


title: M1W (experimental)


title: M2N (control)


title: TN2 (control)


title: M2W (experimental)


title: Dsim_M_BR2_TR1

status: Public on Jan 15 2014

city: Gainesville

first: Lauren

last: McIntyre

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Primer and adapter sequences were trimmed using custom perl scripts.
Each sample was first evaluated with TopHat to create a set of read-supported junctions.
Reads were aligned to D. melanogaster genome FB (FlyBase v5.xx) using Bowtie (v0.1.X; --best, --tryhard, --paired end).  Reads aligning more than 10 times were removed from consideration.
Unaligned reads were were then unpaired and realigned using Bowtie
Remaining unaligned reads were mapped to the junctions frrom TopHat
Expression was then quantified for each exonic region using Reads Per Kilobase Per Million Mapped Reads (RPKM), Average Number of Reads Per Nucleotide (APN).
Genome_build: Flybase 5
Supplementary_files_format_and_content: Are in the CSV format. With the following columns: common contig id, number of reads in the common region, total mappable reads, length of the common region in bp, RPKM. See Series supplementary file for location of contig on the genome.

organism: Drosophila simulans

source_name: Adult Head Tissue

growth_protocol: Flies were raised on standard food medium at 25C on a 12 hour light dark cycle.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen).
Solexa/Illumina libraries were constructed according to manufacturer's instructions.

tag: technical replicate

tag: Sex

value: head


title: Dsim_M_BR2_TR2


title: Dsim_M_BR3_TR1


title: Dsim_M_BR3_TR2


title: Anti-CMS_5hmC_Input_Tet2kd_rep2


title: Dsim_M_BR1_TR2


title: SET5 Y402A rep2

city: Stanford

first: Gloria

last: Mas Martin

state: CA

address: 371 Serra Mall

institute: Stanford University

data_processing:
Basecalling was performed at the Stanford PAN facility after sequencing with an Illumina HiSeq2000 platform.
Raw read quality was assessed using FASTQC software.
Reads were mapped to an S.cerevisiae reference genome (Ensembl EF4) using TopHat (v.2.0.5) specifying --no-novel-juncs
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (v2.0.2) following the protocol from Trapnell et al, Nat Protoc. 2012.
Significant differential expression results from the Cuffdiff test were accessed in the R statistical computing environment (v2.15.1) using cummeRbund (v2.0.0)
Genome_build: S. cerevisiae (Ensembl EF4)
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM expression value calculated for each feature from indicated samples using 2 biological replicates per sample.

organism: Saccharomyces cerevisiae

source_name: whole-cell

growth_protocol: Cells were grown at 30C in YPD and harvested at mid-log phase.

extract_protocol:
Total RNA was extracted and purified with the MasterPure Yeast RNA purification kit.  Illumina TruSeq RNA Sample Preparation v2 Low-Throughput protocol (Catalog #: RS-122-2001) was used with 8 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: SET5 Y402A

tag: genotype


title: set1∆ set5∆ rep2

value: set1∆ set5∆

value: set1∆ set5∆ BY4741


title: set1∆ set5∆ rep1


title: set5∆ rep1

value: set5∆ BY4741


title: set5∆ rep2


title: MU

city: Chengdu

first: HAO

last: JIANG

address: RENMING ROAD SOUTH

institute: IMDE-CAS

data_processing:
standard pepline of Illumina bioinfomatics analysis
3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 49nt long, raw sequences are with 3' adaptor sequences;
Empty reads removal (reads with only 3' adaptor sequences but no Tags);
Low quality Tags removal (Tags with unknown sequences 'N');
Removal of Tags which are too long or too short, leaving Tags of 21nt long;
Removal of Tags with a copy number of 1 (probably be sequencing error);
Generate Clean Tags
The data were normalised using the number of distinct clean tags for each gene and calculated, and then normalized to TPM (number of transcripts per million clean tags)
Genome_build: Populus trichocarpa v3.0
Supplementary_files_format_and_content: Populus_UVB.txt contains TPM value for each detected gene from each treatment and the corresponding annotation putatively.

source_name: male plant_ambient UV-B

extract_protocol:
Total RNA was extracted from four treatents and RNA samples from nine individuals from each treatment were pooled with equal proportions.
Digital gene expression (DGE) library construction and analysis followed the standard Illumina protocols. Briefly, total RNA was extracted from three biological replicates using E.Z.N.A.TM Plant RNA Kit (Omega, USA) according to the manufacturer’s instructions. Residual genomic DNA was removed with DNase I and the integrity of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). RNA samples from nine individuals from each treatment were pooled with equal proportions. Double-stranded cDNA was synthesized using oligo (dT) beads. The cDNA was then digested with an anchoring restriction enzyme Nla III, which recognizes and cuts 3’ ‘CATG’. The digested cDNA samples were ligated to the Illumina-specific adapter A, containing a recognition site for the enzyme Mme I. Following the Mme I digestion, the Illumina specific adapter B containing a 2-bp degenerated 3’ overhang was ligated. The adapter-ligated cDNA tag library was then enriched by PCR primers annealing to the adaptor ends. The PCR program was as follows: 30 s at 98 °C, followed by 15 cycles of 98 °C for 10 s, 60 °C for 30 s and 72 °C for 15 s, and then 72 °C for 5 min. After gel-purification, cDNA was used for cluster generation on a separated flow cell lane. Sequencing by synthesis was performed using the Illumina Genome Analyzer according to the manufacturer’s protocol. Image analysis, base calling, extraction of 17-bp tags and tag counting were performed using the Illumina pipeline.

value: male

tag: exposed to

value: ambient solar UV-B radiation for 100 days

value: fourth full expanded leaves


title: WT rep1

value: WT

value: wildtype BY4741


title: set1∆ rep1

value: set1∆ BY4741


title: WT rep2


title: Meis2 P2 4C-seq

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: 4C-seq Meis2 promoter primer 2

data_processing:
library strategy: 4C-seq
Illumina Casava1.7 software used for basecalling.
Sequences retrieved using paired protocol were aligned to the mm9 genome assembly using bowtie version 2.1.0 with a parameter for paired-sequencing experiment.
Frequency of paired reads with target loci was calculated with in-house program.
Genome_build: mm9
Supplementary_files_format_and_content: Bed/wig files were generated using our in-house program and converted to TDF files using IGVTools version 2.2.1.

source_name: 11 dpc embryonic forebrain_4C-seq

extract_protocol:
Lysates were clarified from EcoRI digested nuclei and made 3C reaction.
Libraries were prepared by primer extention with biotinylated primer. Primer extention product was conjugated to streptoavidine beads and digested with NlaIII. After adaprtor ligation, 2 rounds of nesting PCR were carried out to adjust the library for highthroughput sequencing by Illumina MiSeq.

value: forebrain

tag: age

value: 11 dpc

tag: antibody

value: bait primer sequence:5’-biotin CCTCCAATTTGACCTGAGGTGGAG


title: set1∆ rep2


title: hfq mut 12hr Rep 3

city: East Lansing

first: Quan

last: Zeng

state: MI

address: 578 Wilson Rd. CIPS103

department: Plant, Soil, and Microbial Sciences

institute: Michigan State University

data_processing:
Basecalls were performed by Illumina Real Time Analysis software v 1.13.48. Demultiplexing and FASTQ conversion by Illumian BCL2Fastq v1.8.2
Reads were trimmed of Illumina adapter and low quality bases with Trimmomatic v0.22
Reads were mapped to the  Erwinia amylovora ATCC 49946 genome (Accession NC_013971) and Erwinia amylovora ATCC 49946 plasmid 1 (Accession NC_013972) using TopHat (v2.0.4) with parmeters --mate-inner-dist 110 --mate-std-dev 60 --coverage-search --microexon-search --library-type fr-secondstrand --segment-length 12 --segment-mismatches 1 --min-intron-length 10 --max-intron-length 100 --min-coverage-intron 10 --max-coverage-intron 100 --min-segment-intron 10 --max-segment-intron 100 --b2-very-sensitive --transcriptome-index /Users/kmcarr/Documents/PublicGenomeData/Erwinia_amylovora/ATCC_49946/gbrowse/tophat_trxIndex
Read aligned to previously annotated rRNAs or tRNAs were filtered out
From the remaining reads aligned to previously unannotated regions putative transcripts were defined (XLOCS) with cufflinks/cuffmerge (v2.0.2)
Expression from each sample for each XLOC was estimated (FPKM) with cuffdiff (v2.0.2) with parameters -p 8 -u -b /usr/local/PUBLIC_DATA/Erwinia_amylovora/ATCC_49946/gbrowse/Eam_ATCC49964_pEA29.fasta -L Q-6,Q-12,WT-6,WT-12 --library-type fr-secondstrand --emit-count-tables --max-bundle-frags 1000000 merged.gtf <BAM file List>
Genome_build: NC_013971.1,  NC_013972.1
Supplementary_files_format_and_content: merged.gtf file generated by cuffmerge is standard GTF with definitions of putative transcripts identified by cufflinks, genes.fpkm_tracking tab delimited text with expression estimates generated by cuffdiff; FPKM values are averaged across biological replicates for each condition

organism: Erwinia amylovora

source_name: bacteria cells cultured in hrp inducing minimal medium

growth_protocol: Bacterial strains were cultured in LB broth supplemented with appropriate antibiotics overnight.  Cells were harvested by centrifugation, washed by 0.5XPBS, and were resuspended in hrp-inducing minimal medium.  The cell concentration of each strain in hrp-inducing minimal medium was adjusted to 0.5 (OD600). Cells were cultured for 6 and 12 hours prior to RNA isolation.

extract_protocol:
Total bacterial RNA including the sRNAs was isolated by miRNeasy kit from Qiagen following the kit instruction.  DNA was removed from an on column digestion using an Rnase-free Dnase set (Qiagen).
Libraries were constructed using the Illumina TruSeq small RNA Library Prep Kit (direct ligation of adapters to RNA) with slight modification. The final library size selection included a much larger range of fragment sizes than the usual narrow range mean to capture only miRNAs

value: deletion mutant of hfq

tag: time

tag: sample type

value: small RNAs 50-350 nt


title: NRGFP-GFP

city: Nice

first: Alexander

last: Samuel

address: Parc Valrose

department: Institute of Biology Valrose

institute: CNRS, INSERM, Université de Nice Sophia-Antipolis

data_processing:
Quantity and quality of DNA was ensured before processing by Qubit dsDNA HS Kit (Invitrogen) and bioanalyzer 2100 (Agilent). For each sample, 10ng of DNA was used to generate ChIP-DNA library. Libraries were analyzed by bio-analyzer 2100 (Agilent), then, were massively sequenced by Illumina GAIIx sequencer.
Illumina Casava1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and aligned to the mm9 genome using bowtie v°.12.7
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited BED6 file in bed format

source_name: Neural Retina

extract_protocol:
RPE and neural retina were mechanically separated at the photoreceptor outer segment level, cross-linked in 1% formaldehyde, nuclei were then isolated with a dounce in cell lysis buffer.OTX2 (R&D systems, Minneapolis, MN, USA) and GFP (Abcam, Cambridge, UK) antibodies were used to precipitate chromatin–Otx2 complexes, Laminin B (Santa-Cruz, California) antibody was used as a control.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: retina

tag: chip antibody

value: GFP (Abcam, Cambridge, UK)


title: hfq mut 12hr Rep 2


title: NRLMNB-WT

value: Laminin B (Santa-Cruz, California)


title: hfq mut 12hr Rep 1


title: hfq mut 6hr Rep 1

value: 6 h


title: SET5 Y402A rep1

value: SET5 Y402A


title: hfq mut 6hr Rep 3


title: NRGFP-WT


title: RPEGFP-GFP

source_name: RPE


title: RPEOTX2-WT

value: OTX2 (R&D systems, Minneapolis, MN, USA)


title: ChIP-Seq analysis of H3K4me3 in human CD15 cells; Lib EpiLabSPL Row 1797

city: Cambridge

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: CL_0000775
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1797
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8043
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2562
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing: Various levels of processed data files will be made available as this project proceeds.

source_name: flow sorted CD15+ cells from cord blood; Lib EpiLabSPL Row 1797

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: CD15 Primary Cells

tag: molecule

value: genomic DNA

tag: disease

value: FHCRC

value: Primary Cell

tag: markers

value: Male

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: WT 12hr Rep 3

tag: strain

value: wild type

value: small RNAs 50-350 nt


title: Input DNA

city: Pittsburgh

first: Amir

last: Bahreini

state: PA

address: 204 Craft Ave A430

department: Human Genetics

institute: University of Pittsburgh

data_processing:
Alignment performed using BWA version 0.7.3a-r367
Calling the peaks was done by MACS version 1.4.2 using the default criteria with a p-value cutoff of 10-5
Genome_build: hg18
Supplementary_files_format_and_content: Bed files were generated by MACS

source_name: Mammary epithelial cells

growth_protocol: cells were hormone deprived in phenol red-free IMEM (#A10488, Life Technologies) supplemented with 10% CSS

extract_protocol:
Input DNA was purified from cell lysate and ER-DNA complexes were isolated by the corresponding antibody.
DNA samples were sent to Genome Quebec Innovation Center (McGill University, Montreal, Quebec, Canada) for next generation sequencing. Libraries were prepared according to Illumina TruSeq ChIP Sample Prep Kit (#IP-202-1012).

treatment_protocol: The cells were treated with 1 nM E2 or 0.01% EtOH for 45 minutes.

tag: cell type

value: invasive lobular carcinoma cells

tag: cell line

tag: cell passage


title: WT 12hr Rep 2


title: Dsim_M_BR1_TR1

tag: biological replicate

tag: technical replicate

tag: Sex

value: male

tag: developmental stage

value: adult

tag: tissue

value: head


title: V-ER ChIP-seq

value: ERα (Santa Cruz, HC-20)


title: WT 12hr Rep 1

tag: genotype

tag: time


title: WT 6hr Rep 3

value: 6 h

tag: sample type


title: E-ER ChIP-seq

tag: chip antibody


title: E-IgG ChIP-seq

value: IgG (Santa Cruz, sc2027)


title: RPELMNB-WT

value: retina

value: WT

value: Laminin B (Santa-Cruz, California)


title: NROTX2-WT

value: OTX2 (R&D systems, Minneapolis, MN, USA)


title: Whole Genome Sequencing analysis of  derived from human H9 ES cells; WGS_Lib 5

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000124
nucleic_acid_term_id: SO_0000352
Design description: WGS REMC Sequencing on Illumina
Library name: WGS_Lib 5
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.18845
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.18852
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Human Embryonic Stem Cell 9 ; WGS_Lib 5

extract_protocol: Library construction protocol: Genomic DNA (0.5~1.5µg) was fragmented to 100-1,000 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with paired-end adapters. Adapter-attached DNA fragments of 470-570 bp, which contain 350-450 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were utilized as templates for PCR enrichment (5-6 cycles) by using Phusion HF polymerase (NEB). The PCR amplified DNA fragments were purified using 1.5X of Agencourt AMPure XP beads (Beckman Coulter) to remove PCR primers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit (Invitrogen). Library sequencing was performed using 101 BP PE Illumina

tag: sample alias

value: BioSam 1819

tag: sample common name

value: H9 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: HUES general media - KO DMEM, 20% KSR, bFGF (10ng/mL)

value: presumed normal

tag: passage

tag: line

value: H9 ES cells

value: adherence

tag: batch

value: BioSAli 2828

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard

value: Covaris shearing conditions:four cycles of two consecutive treatments (T1-Duty cycle 5%, Intensity  5, cycle per burst 200, duration 30 sec; T2-Duty cycle 1%, Intensity  5, cycle per burst 200, duration 5 sec).

value: Whole Genome Sequencing

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: Covaris S2 (TM)


title: hfq mut 6hr Rep 2

tag: strain

value: deletion mutant of hfq

value: 6 h

value: small RNAs 50-350 nt


title: WT 6hr Rep 2

value: wild type


title: Bisulfite-Seq analysis of WGBS_Lib 71 derived from human fStomach cells; WGBS_Lib 71

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 71
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.17369
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.17380
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Primary fetal stomach tissue; WGBS_Lib 71

extract_protocol: Library construction protocol: Genomic DNA (1.5~5µg) was fragmented to 100-500 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with methylated paired-end adapters. Adapter-attached DNA fragments of 300-400 bp, which contain 150-250 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were subjected to two cycles of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen). Adapter-attached, bisulfite-converted DNA molecules were enriched by PCR using PfuTurboCx Hotstart DNA polymerase (Stratagene). The PCR amplified DNA fragments were subjected to a second gel size selection to remove PCR primers and adapter dimers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit. Library sequencing was performed using 101 BP PE Illumina technology.

value: BioSam 1242

value: Fetal Stomach

value: Post-Mortem

tag: disease

value: Female

value: Primary Tissue

value: Stomach

value: University of Washington

value: 98.0 Days

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start


title: Endogenous small RNAs from rice, elicitor-treated ROOTS (30')

city: Bellaterra (Cerdanyola del Vallés)

first: Sonia

last: Campo

state: Barcelona

address: Parc de Recerca UAB Edifici CRAG, Campus UAB

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

description:
Total Endogenous small RNAs from rice, elicitor leaves (30')
library strategy: Barcode

data_processing: Small RNA sequences were parsed from FASTA formatted files containing reads from 454 sequencing and assigned to each one of the 8 specific libraries (leaf and root tissues, treated or not with elicitors for 30 min or 2h) through identification of the small RNA/adapter boundaries and barcode analysis. The adapter sequences in the 454 sequencing reads were removed and the remaining sequences were collected and mapped to the rice genome (Oryza sativa, version 5.0 - http://www.tigr.org/tdb/e2k1/osa1/pseudomolecules/info.shtml) using BLASTn. The unique RNA sequences that perfectly matched the genome were subjected to subsequent analysis.

organism: Oryza sativa Japonica Group

source_name: Elicitor Roots

growth_protocol:
Leaf tissues were collected from 15 day-old Nipponbare rice plants that had been grown at 28ÂºÂ±2ÂºC using a 16-h/8-h light/dark cycle
Root tissues were collected from rice seedings that had been grown in square-plates (24cmx24cm) containing Â½ MS agar medium for 8 days, grown at 28ÂºÂ±2ÂºC using a 16-h/8-h light/dark cycle. During this period, rice roots were allowed to grow over a piece of sterile paper placed over the agar medium.
Elicitors from the Magnaporthe oryzae strain 18.1 were prepared as previously described (Casacuberta JM, Raventos D, Puigdomenech P and Segundo BS. (1992). Expression of the Gene Encoding the PR-Like Protein PRms in Germinating Maize Embryos. Mol Gen Genet 234(1): 97-104.)

extract_protocol: Total RNA was extracted from tissues using TRIzol reagent according to manufacturerâs instructions (Invitrogen). 300 Âµg of total RNA were used for construction of small RNA libraries as described (Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. 2007. Genome-Wide Profiling and Analysis of Arabidopsis siRNAs. PLoS Biol 5(3): e57.; Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer KF, Aranda MA, Llave C. 2009. Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. Virology 392(2): 203-214.)

treatment_protocol:
Elicitor treatment of rice leaves was performed by spraying the rice plants with 100 mL of a Magnaporthe oryzae 18.1 suspension (300 Âµg elicitor/mL) of sterile water containing 0.02% Tween-20 (v/v)
Elicitor treatment of rice roots was performed by covering the roots covered 30mL of a Magnaporthe oryzae 18.1 suspension (300 Âµg elicitor/mL) of sterile water containing 0.02% Tween-20 (v/v) and another piece of sterile paper

tag: age

value: 15-days old plants

tag: cultivar

value: Nipponbare


title: Bisulfite-Seq analysis of WGBS_Lib 69 derived from human fSpinal Cord cells; WGBS_Lib 69

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 69
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.17368
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.17378
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Primary fetal spinal cord tissue; WGBS_Lib 69

value: BioSam 1240

value: Fetal Spinal Cord

value: Post-Mortem

value: presumed normal

value: Unknown

value: Spinal Cord

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: Covaris S2 (TM)


title: Bisulfite-Seq analysis of WGBS_Lib 64 derived from human adult CD56 cells; WGBS_Lib 64

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 64
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.17365
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.17375
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Adult Primary CD56+ cells; WGBS_Lib 64

value: BioSam 1237

value: CD56 Primary Cells

tag: markers

value: adult CD56

value: Male

value: Primary Cell

value: UW

value: 37.0 Years

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes