title: H3K9me3_ab8898_ChIP_Seq_rep_1

status: Public on Nov 01 2009

first: Garrett

last: Frampton

address: 9 Cambridge Center

institute: Whitehead Instute - MIT

description: Chromatin IP against H3K9me3 using Ab8898 antibody

data_processing: Images acquired from the Illumina/Solexa sequencer were processed through the bundled Solexa image extraction pipeline which identified polony positions, performed base-calling and generated QC statistics. Sequences were aligned using ELAND software to NCBI Build 36 (UCSC mm8) of the mouse genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple reads mapped to the same genomic position, a maximum of two reads mapping to the same position were used. A summary of the total number of ChIP-Seq reads that were used in each experiment is provided (Supplemental Table S6). ChIP-Seq datasets profiling the genomic occupancy of H3K9me3 (Mikkelsen et al., 2007), H3K27me3 (Mikkelsen et al., 2007), H3K4me3 (Marson et al., 2008), H3K36me3 (Marson et al., 2008), H3K79me2 (Marson et al., 2008), Oct4 (Marson et al., 2008), Sox2 (Marson et al., 2008), Nanog (Marson et al., 2008),Tcf3 (Marson et al., 2008) and   9   Sequence reads from multiple flow cells for each IP target were combined. Each read was extended 100bp, towards the interior of the sequenced fragment, based on the strand of the alignment. Across the genome, in 25 bp bins, the number of ChIP-Seq reads within a 1kb window surrounding each bin (+/- 500bp) 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 1kb window can be modeled as a Poisson process in which the expectation can be estimated as the number of mapped reads multiplied by the number of bins (40) into which each read maps, divided by the total number of bins available (we estimated 70%). Enriched bins within 1kb of one another were combined into regions. The complete set of RefSeq genes was downloaded from the UCSC table browser (http://genome.ucsc.edu/cgi-bin/hgTables?command=start) on December 20, 2008. Gene with enriched regions within 5kb of their transcription start site were called bound.     The Poissonian background model assumes a random distribution of background reads, however 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 Solexa 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.

source_name: V6.5 mES cells

growth_protocol: V6.5 cells were grown under standard mES cell conditions as described previously (Boyer et al., 2005).  Briefly, cells were grown on 0.2% gelatinized tissue culture plates in ESC media; DMEM-KO supplemented with 15% fetal bovine serum, 1000 U/mL LIF, 100 uM nonessential amino acids, 2 mM L-glutamine, 100 U/mL penicillin, 100 ug/mL streptomycin and 8 nL/mL of 2-mercaptoethanol

extract_protocol: Embryonic stem cells were grown to a final count of 5-10 x 107 cells for each ChIP experiment. Cells were chemically crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 15 minutes at room temperature. Cells were rinsed twice with 1X PBS and harvested using a silicon scraper and flash frozen in liquid nitrogen. Cells were stored at –80oC prior to use. Cells were resuspended, lysed in lysis buffers and sonicated to solubilize and shear crosslinked DNA. Sonication conditions vary depending on cells, culture conditions, crosslinking and equipment. For H3K9me3, the sonication buffer was Tris-HCl pH8 20mM, 150mM NaCl, 2mM EDTA, 0.1% SDS, Triton X-100 1%. We used a Misonix Sonicator 3000 and sonicated at approximately 24 watts for 10 x 30 second pulses (60 second pause between pulses). Samples were kept on ice at all times.  The resulting whole cell extract was incubated overnight at 4°C with 100 μl of Dynal Protein G magnetic beads that had been pre-incubated with approximately 10 μg of the appropriate antibody. Beads were washed 4 times with: 1 time with the sonication buffer, 1 time with 20mM Tris-HCl pH8, 500mM NaCl, 2mM EDTA, 0.1% SDS, 1%Triton X-100, 1 time with 10mM Tris-HCl pH8, 250nM LiCl, 2mM EDTA, 1% NP40 and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65°C for 1 hour with occasional vortexing and crosslinking was reversed by overnight incubation at 65°C. Whole cell extract DNA reserved from the sonication step was also treated for crosslink reversal.    DNA was prepared for sequencing according to a modified version of the Illumina/Solexa Genomic DNA protocol. Fragmented DNA was prepared for ligation of Solexa linkers by repairing the ends and adding a single adenine nucleotide overhang to allow for directional ligation. A 1:100 dilution of the Adaptor Oligo Mix (Illumina) was used in the ligation step. A subsequent PCR step with limited (18) amplification cycles added additional linker sequence to the fragments to prepare them for annealing to the Genome Analyzer flow-cell. After amplification, a narrow range of fragment sizes was selected by separation on a 2% agarose gel and excision of a band between 150-300 bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence). The DNA was purified from the agarose and diluted to 10 nM for loading on the flow cell.    The DNA library (2-4 pM) was applied to the flow-cell (8 samples per flow-cell) using the Cluster Station device from Illumina. The concentration of library applied to the flow-cell was calibrated such that polonies generated in the bridge amplification step originate from single strands of DNA. Multiple rounds of amplification reagents were flowed across the cell in the bridge amplification step to generate polonies of approximately 1,000 strands in 1μm diameter spots. Double stranded polonies were visually checked for density and morphology by staining with a 1:5000 dilution of SYBR Green I (Invitrogen) and visualizing with a microscope under fluorescent illumination. Validated flow-cells were stored at 4 degrees C until sequencing.    Flow-cells were removed from storage and subjected to linearization and annealing of sequencing primer on the Cluster Station. Primed flow-cells were loaded into the Illumina Genome Analyzer 1G. After the first base was incorporated in the Sequencing-by-Synthesis reaction the process was paused for a key quality control checkpoint. A small section of each lane was imaged and the average intensity value for all four bases was compared to minimum thresholds. Flow-cells with low first base intensities were re-primed and if signal was not recovered the flow-cell was aborted. Flow-cells with signal intensities meeting the minimum thresholds were resumed and sequenced for 26 or 32 cycles.

treatment_protocol: Lentiviral Infections. For SetDB1 knockdown expression analysis, mES cells were split off MEFs, placed in a tissue culture dish for 45 minutes to selectively remove the MEFs and plated in gelatin treated 10 cm dishes. The following day cells were infected with lentiviral shRNAs targeting GFP  or SetDB1 shRNA (Open Biosystems, TRCN0000092975) in ESC media containing 8 ug/ml polybrene (Sigma, H9268-10G). After 24 hours the media was removed and replaced with ESC media containing 3.5 ug/mL puromycin (Sigma, P8833).  ESC media with puromycin was changed daily.  Cells were crosslinked 6-days post infection.

tag: tag

value: V6.5 mES cells

tag: shrna

value: no


title: H3K9me3_ab8898_ChIP_Seq_rep_2

type: SRA

city: Cambridge

middle: M

state: MA

department: Biology

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: chip antibody


title: WCE_mES_ChIP_Seq_rep_1

description: Whole Cell Extract

value: WCE


title: H3K9me3_ab8898_ChIP_Seq_rep_3


title: ago2 knockdown

status: Public on Nov 15 2009

city: Cold Spring Harbor

first: Benjamin

last: Czech

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description: small RNA sequencing

library_source: transcriptomic

data_processing: The 36nt Illumina reads were stripped of the 3’ linker, collapsed, and the resulting small RNA sequences were matched without mismatches to the Drosophila release 5 genome, and to the genomes of Drosophila C virus, Flock house virus and Cricket paralysis virus with up to 3 mismatches. Only reads that met these conditions were subjected to further analyses. For annotations we used a combination of UCSC, miRBase, and Flybase tracks for protein coding genes, repeats/transposons, non-coding RNAs and microRNAs, as well as custom tracks (for synthetic markers, endo-siRNAs from structured loci, miR and miR* strands) with different priorities (annotation priority list available upon request). For comparison of small RNA counts between libraries, reads were normalized to the same total number after bioinformatic removal of those sequences that matched to synthetic cloning markers or assumed degradation products of abundant cellular RNAs (rRNAs, snoRNAs and tRNAs). SEQ = the sequence of the small RNA. LENGTH = the length of the small RNA. NAME = annotation name of the small RNA. READS = read count in respective library. All small RNAs were converted into DNA for sequencing, therefore U's are represented as T's.

molecule: total RNA

organism: Drosophila melanogaster

source_name: S2-NP cells

growth_protocol: 25°C in Schneider's medium (Invitrogen) supplemented with 10% FBS and 1% pen-strep (Invitrogen)

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen) and size-fractionated by PAGE.

treatment_protocol: ~3X10^6 S2-NP cells were soaked in 1.5 mL serum-free Schneider’s medium containing 10 µg dsRNAs in 6-well plates, and 3 mL serum-containing medium was added 45 minutes later. After 4 days of initial dsRNA treatment, cells were treated with dsRNAs for a second round and harvested another 4 days later. For IP libraries, cell extracts were prepared, evenly split and subjected to immunoprecipitation using antibodies against AGO1 (Abcam) or the FLAG epitope (Sigma), respectively, as described (Czech et al., 2008; Zhou et al., 2008). RNAs were recovered from the immunoprecipitated samples using Trizol (Invitrogen) and used for production of small RNA libraries.

tag: treatment

value: ago2 knockdown

tag: cell line

value: S2-NP cells


title: ago1 knockdown

description: small RNA sequencing

value: ago1 knockdown


title: H3K9me3_Up07222_ChIP_Seq_rep_1

description: Chromatin IP against H3K9me3 using Up 07-222 antibody


title: SetDB1_ChIP_Seq_rep_2

description: Chromatin IP against SetDB1


title: H3K9me3_mES_ChIP_Seq_rep_1

description: Chromatin IP against H3K9me3 using Ab8898 antibody in cells infected and selected with GFP shRNA

value: GFP


title: H3K9me3-Eset shRNA_ChIPseq

status: Public on Nov 04 2009

city: Singapore

first: Mikael

last: Huss

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description:
Anti-H3K9Me3 (ab8898; Abcam) antibody was used for ChIP of Eset shRNA knockdown sample.
A pool of 3 ChIP samples was used.

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches.
The control knockdown and Eset knockdown cells were directly compared for H3K9me3 enrichment, and the regions that were enriched in the control sample were identified.

The following supplementary files contain alignments:
GSM440258_CME037_R00087_lane1_s_1_sorted.txt
GSM440258_CME037_R00087_lane2_s_2_sorted.txt

source_name: embryonic stem cells, Eset shRNA

growth_protocol: E14 mouse ES cells, cultured under feeder-free conditions, were maintained in Dulbecco's Modified Eagle-Medium (DMEM, GIBCO), with 15 % heat-inactivated ES qualified fetal bovine serum (FBS, GIBCO), 0.055 mM beta-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1 mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon). Control shRNA and Eset shRNA knockdown samples were obtained by transfecting ES cells with the respective shRNAs using lipofectamine-2000(invitrogen). The transfected ES cells were maintained in the ES medium with 0.8ug/ml puromycin.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. ChIP-enriched DNA from multiple ChIP experiments was pooled and quantified using PicoGreen dsDNA quantitation kit (Invitrogen). The ChIP-enriched DNA was processed for Solexa sequencing using ChIP-Seq Sample Prep Kit (Illumina).

treatment_protocol: The ES cells were fixed in 1% formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 0.1 M glycine before harvest for extract preparation.

tag: cell type

value: embryonic stem cells

tag: knockdown

value: Eset

tag: antibody

value: anti-H3K9Me3 antibody


title: SetDB1_ChIP_Seq_rep_1

description: Chromatin IP against SetDB1


title: SetDB1_ChIP_Seq_rep_3

description: Chromatin IP against SetDB1


title: 2´-O-methylated small RNAs from r2d2 heterozygous flies

status: Public on Oct 31 2009

city: Worcester

first: Jia

last: Xu

address: 55 Lake Avenue North

department: Program in Bioinformatics and Integrative Biology

institute: UMASSMED

description: oxidized with periodate in presence of boric acid before library preparation

data_processing: For each sequence read, the first occurrence of the 6-mer perfectly matching the 5′ end of the 3′ linker was identified. Sequences without a match were discarded. Sequences  that mapped to let-7 without connonical 5'end have been removed because of contamination

source_name: fly heads

growth_protocol: Flies were grown according to standard protocols.

extract_protocol: 3´ adapter (described in Lau et al., 2001, Science 294:858) and 5´ adapter (sequence: 5´dAdTdC  dGdTrA rGrGrC rArCrC rUrGrA rArA3´) were ligated to the small RNAs, then the library was reverse-transcribed and amplified as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)).

treatment_protocol: Heads were dissected by vigorous shaking in liquid nitrogen in a metal sieve, as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)). Total RNA was extracted using the mirVana kit (Ambion), then short (18-29 nt) RNAs were gel-purified. 2S rRNA was depleted as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)). When applicable: small RNA preparations were oxidized with periodate in the presence of boric acid as described in Horwich et al. (2007) Curr. Biol. 17(14):1265-1272, except the final (alkaline) step was omitted.

tag: genotype

value: CyO-balanced r2d2^1 mutant strain (described in Liu et al., 2006, RNA 12:1514)

tag: tissue

value: head


title: Total small RNAs from r2d2 homozygous flies

description: untreated before library preparation

value: r2d2^1 mutant strain (described in Liu et al., 2006, RNA 12:1514)


title: 2´-O-methylated small RNAs from r2d2 homozygous flies


title: AGO2 IP dcr-2 knockdown

description: small RNA sequencing

value: AGO2 IP dcr-2 knockdown


title: Total small RNAs from r2d2 heterozygous flies

description: untreated before library preparation


title: 2´-O-methylated small RNAs from dcr-2 homozygous flies

value: dcr-2^L811fsX mutant strain (described in Lee et al., 2004, Cell 117:69)


title: Root_-Pi_sRNASeq

status: Public on Dec 01 2009

city: Taichung

first: Li-Ching

last: Hsieh

address: 145 Xingda Rd.

department: Graduate Institute of Genomics and Bioinformatics

country: Taiwan

institute: National Chung Hsing University

description: Treatment: 0uM KH2PO4 for 5 days

data_processing: Processed data files contain the perfectly mapped reads with 5' and 3' adapters removed (reads were mapped on the TAIR8 genome). Same reads are sorted together and the numbers of repetitivity are indicated

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Nine-day-old Arabidopsis seedlings grown on half-strength modified Hoagland nutrient solution containing 250 μM KH2PO4 (+Pi) and 1% sucrose were transferred to a hydroponic culture system with half-strength modified Hoagland nutrient solution containing 250 μM KH2PO4 for additional growth of 8 days. All plants were grown at 22oC under a 16-hr photoperiod with cool fluorescent light at 100 to 150 μE.

extract_protocol: Total RNA was isolated with the use of TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer's instructions.

treatment_protocol: Seventeen-day-old seedlings were subjected for phosphate starvation treatment by transferring them from 250 μM KH2PO4 (+Pi) into 0 μM KH2PO4 (-Pi) nutrient solution. Control samples were maintained under 250 μM KH2PO4 (+Pi) nutrient solution. Roots and shoots were collected separately after 5-day treatment.

tag: strain


title: 2´-O-methylated small RNAs from dcr-2 heterozygous flies

value: CyO-balanced dcr-2^L811fsX mutant strain (described in Lee et al., 2004, Cell 117:69)


title: Ago1-associated small RNAs from Oregon R

description: immunoprecipitated with anti-Ago1 antibody before library preparation

value: Oregon R strain


title: total small RNAs from heads (Drosophila pseudoobscura)

status: Public on Nov 24 2009

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description: Small RNA sequence data.

data_processing: 3' adapter sequences (CTGTAGG) were trimmed and inserts shorter than 18 nt were filtered out.

organism: Drosophila pseudoobscura

source_name: heads

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) from heads. 25 micrograms total RNA from each timepoint were pooled, and the ~18-26 nt fraction was isolated using PAGE and cloned using ligation to adapters requiring 5' monophosphate and 3' OH.

value: heads


title: Total small RNAs from dcr-2 homozygous flies

description: untreated before library preparation


title: H3K9me3_mES_ChIP_Seq_rep_2

description: Chromatin IP against H3K9me3 using Ab8898 antibody in cells infected and selected with SetDB1 shRNA

value: V6.5 mES cells


title: H3K9me3_Up07222_ChIP_Seq_rep_2

value: no


title: 2´-O-methylated small RNAs from Oregon R

description:
oxidized with periodate in presence of boric acid before library preparation
Quality scores for one of the 3 runs associated with this Sample were not provided. The raw sequence files for this run were not submitted to SRA, but linked as a supplementary file GSM466488_wt_oxidized.v3.tar.gz to the GEO record.


title: Total small RNAs from dcr-2 heterozygous flies

description: untreated before library preparation


title: Muscle_animal_4905

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

data_processing: The raw sequences were trimmed to 30 nucleotides, and it was set as a requirement that any sequence must appear at least three times and be present in at least two of the seven libraries. All identical reads within a library were grouped and converted into unique sequences. Reads containing Ns or long tracks (¡Ý8) of As were removed and the sequences were trimmed for adaptor-sequences. To annotate the unique sequences, a Decypher Tera-BLASTN Search was performed against a database of mature miRNAs obtained from miRBase (release 12.0). Hits with a match of 16 or more nucleotides to a miRNA from the database were gathered, and the count of each miRNA was normalized to the total number of sequence reads per lane.

organism: Sus scrofa

source_name: Longissimus dorsi muscle

extract_protocol: Total RNA was purified using the mirVanaTM miRNA isolation kit (Ambion) following the manufactures protocol and 10 µg total RNA from each sample was used for library constructions following the protocol supplied with the Small RNA Sample Prep Kit (Illumina, protocol version 1004239_RevA, March 2008) with minor modifications. Briefly, the 18-30 base pair fraction of total RNA was excised from 15 % Criterion Tris-Borate-EDTA (TBE)-Urea gels (Bio-Rad) stained with SYBR Safe DNA gel stain (Invitrogen) and visualised using a Dark Reader Transilluminator (Clare Chemical Research). Samples were electrophorised on individual gels throughout the library preparation to avoid cross-contamination. The small RNA was purified, ligated with the SRA 5´ and 3´ adaptors, reverse transcribed and amplified as recommended by the manufacturer. The 90 base pairs PCR products were purified on 4 % low range agarose gels (manufacturer) using the QIAquick Gel Extraction Kit (QIAGEN), eluted in 30 µL elution buffer and dried to a volume of 10 – 15 µL using a SC210A SpeedVac® Plus (ThermoSavant). The concentrations of the libraries were determined using a NanoDrop ND-1000 Spectrophotometer (manufacturer) and the size and purity were determined using an Agilent 2100 Bioanalyzer in combination with the Agilent DNA 1000 Kit. The seven libraries were diluted in buffer EB (QIAGEN) to 10 nM, denaturated with 2 N NaOH to a final DNA concentration of 0.5 nM, diluted to 2 pM with pre-chilled Hybridization buffer (Illumina) and loaded in individual lanes into a 1.0 mm flowcell together with a single lane of a 2 pM PhiX control library (Illumina). Clustering and 36 cycle sequencing were conducted on an Illumina Genome Analyzer (version I) using the Small RNA sequencing primer in combination with clustering and sequencing kits supplied by Illumina. The resulting images were transferred to the pipeline computer (DELL PowerEdge 2900, 8 cores (2 x 4 CPU, 2.6 GHz, 16 GB RAM, 4.7 TB hard drive) during the run using robocopy and analysed using the Genome Analyzer Pipeline Software (version 1.0, Illumina) generating the raw fastq files.

tag: longissimus dorsi muscle, animal

value: 4905, gender:male, age:1.5 years


title: Total small RNAs from Oregon R

description: untreated before library preparation


title: Ssolfataricus_cellulose_cDNA1

status: Public on Oct 21 2009

city: Rehovot

first: Omri

last: Wurtzel

address: Hertzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: cDNA sequencing not limited to 5' ends, not strand specific

data_processing:
Reads were aligned to the reference genome using blastn with e<0.0001, allowing maximum of 2 mismatches and minimal alignment length of 33. Every line in the coverage file represets the coverage of a specific position (line #100 represents the aligned read coverage in the 100th position).

Processed data files are formatted as follows:

coverage (_coverage.txt): <accession> <coverage over #position>

alignment (_aln.txt): <read_name> <accession> <from> <to> <strand>

Alignment files are not filtered for repeats. To filter ambiguously aligned reads, remove all lines with read names that appear more than once.

organism: Saccharolobus solfataricus P2

source_name: Sulfolobus solfataricus P2

growth_protocol: S. solfataricus (DSMZ 1617) was grown in defined modified Brock’s mineral medium containing (final concentrations) 0.25 g/liter CaCl2.2H2O, 0.25 g/liter KH2PO4, 1.3g/liter (NH4)2SO4, 0.28 g/liter MgSO4.7H2O, 0.02 g/l of FeCl3.6H2O and trace mineral solution (100x) containing 10 nM MnCl2, 120 nM Na2B4O7, 640 nM ZnSO4, 0.5 nM CuCl2, 0.1 nM NaMoO4, 0.1 nM VOSO4, 0.03 nM CoSO4, 0.09 nM NiSO4. The final pH of the solution was adjusted to pH 3.5 with H2SO4. Where mentioned, glucose, cellobiose and avicel (microcrystalline cellulose) were used as the sole carbon source at a final concentration of 0.4% (w/v).  The cells were grown to mid log phase at 80 oC at 170 rpm and growth was monitored using direct cell counts with a light microscope.

extract_protocol: For cDNA samples: 10ug of total RNA was treated with RQ1 RNase-free DNase in final volume of 50ul. Reaction was incubated for 30 mins in 37°C, and stopped by addition of RQ1 DNase stop solution and incubation in 65°C for 10 mins. Double strand cDNA was generated using the Double Stranded cDNA Synthesis kit (Invitrogen) as instructed, except that the oligo dT primers were replaced by random hexamers for first strand synthesis.

treatment_protocol: Total RNA was isolated from S. solfataricus using the Trizol method.

value: DSMZ 1617

tag: growth condition

value: Cellulose + Brock’s mineral medium

tag: library preparation

value: cDNA

tag: sequenced molecule

value: cDNA, strand-insensitive


title: Ssofataricus_cellobiose_cDNA2

value: Cellobiose + Brock’s mineral medium


title: Ssolfataricus_cellobiose_cDNA1


title: Ssolfataricus_glucose_cDNA1

value: Glucose + Brock’s mineral medium


title: Ssolfataricus_cellulose_RACE1

description: Sequencing products of 5' ends of RNA molecules, strand specific

extract_protocol: For RACE samples: 10ug of total RNA was incubated with 2U TAP (Epicentre) for 1.5 hours in 37°C to generate 5’ monophosphate RNAs. 3’ ends were blocked by incubating the TAP-treated RNA with 2.5ul of 100mM NaIO4 for 1.5 hours in 4°C in the dark. Excess NaIO4 was saturated by adding 1/10V of 1M lysine and incubating for 10 minutes in room temperature. Each reaction was then passed through NucAway spin columns (Ambion) to remove salts as instructed by the manufacturer. The 56 bp Illumina 5’ adapter (in an single-strand RNA form) was ligated to the resulting treated RNA by using T4 RNA ligase (Invitrogen) in the presence of RNase inhibitor (Invitrogen) in final volume of 50ul as instructed. The reaction was incubated at 16°C overnight. 5ul of 5M NH4OAc and 125ul of EtOH were then added, and the reaction was chilled for 20 mins in -20°C. Sample was spinned at max speed for 15 mins, and EtOH was removed. After a second wash with EtOH 70%, RNA was dissolved in 10ul of RNase-free water. For the first strand synthesis of cDNA, the SuperScriptTM First Strand Synthesis system (Invitrogen) was used according to the manufacturer’s instructions. The primers used were random hexamers attached to the Illumina 3’ adapter. RT products were cleaned using Montage Clear columns (Millipore) to remove primer dimers. The cleaned RT product was then amplified using primers matching the 5’ and 3’ Illumina adapters for 20 cycles of PCR. Resulting cDNA was ran on a 3% low melting agarose gel, and gel slice containing cDNA sized 150-500 bp was taken and cDNA was extracted.

value: RACE

value: 5' ends of cDNA, strand-sensitive


title: YRI NA19238 HapMap RNA Seq

status: Public on Oct 22 2009

city: Chicago

first: Jacob

middle: F

last: Degner

state: IL

department: Human Genetics

institute: University of Chicago

description:
RNA-Seq
1 lane of NA19238 mapped reads using MAQ to the SNP-MASKED version of hg18 (argonne_090312_HGAC_S100054_1_NA19238_3.5_2.35bp.aln.map)
1 lane of NA19238 mapped reads using MAQ to the unmodified version of hg18 (argonne_090312_HGAC_S100054_1_NA19238_3.5_2.35bpunmasked.aln.map)
1 lane of NA19238 mapped reads using MAQ to the SNP-MASKED version of hg18 (yale_090121_YOAV_FC310E0_5_NA19238_2.5.aln.map)
1 lane of NA19238 mapped reads using MAQ to the unmodified version of hg18 (yale_090121_YOAV_FC310E0_5_NA19238_2.5unmasked.aln.map)
RNA-Seq
RNA
Poly-A capture

data_processing: Mapped using MAQ v. 0.7.1

organism: Homo sapiens

source_name: lymphoblastoid cell line

growth_protocol: 37o in RPMI

extract_protocol: Total RNA from two HapMap Yoruba lymphoblastoid cell lines (GM19238 and GM19239) was extracted using an RNeasy Mini Kit (Qiagen) and assessed using an Agilent Bioanalyzer. mRNA was then isolated with Dyna1 oligo-dT beads (Invitrogen) from 10${\mu}g$ of total RNA. The mRNA was randomly fragmented using the RNA fragmentation kit from Ambion. First-strand cDNA synthesis was performed using random primers and SuperScriptII reverse-transcriptase (Invitrogen). This was followed by second-strand cDNA synthesis using DNA Polymerase I and RNaseH (Invitrogen).  The short cDNA fragments from each sample were prepared into a library for Illumina sequencing. Briefly, the Illumina adaptor was ligated to the ends of the double-stranded cDNA fragments and a 200 bp size-selection of the final product was performed by gel-excision, following the Illumina-recommended protocol. 200 bp cDNA template molecules with the adaptor attached were enriched by PCR to create the final library. Sequencing was performed on the Illumina Genome Analyzer II for 36 cycles (resulting in 35 bp reads after discarding the final base). The images taken during the sequencing reactions were processed using Illumina's standard analysis pipeline (v.1.3.2).  Two lanes of a flow-cell were used for each individual yielding 15,579,717 and 16,780,153 total sequence reads for GM19238 and GM19239, respectively.

tag: hapmap

value: YRI


title: Ssolfataricus_glucose_RACE1


title: Ssolfataricus_cellobiose_RACE1


title: Rice_degradome_seedling

status: Public on Nov 23 2009

city: Beijing

first: Yijun

last: Qi

address: No.7 Science Park Road,Zhongguancun Life Science Park

country: China

institute: National Institute of Biological Sciences, Beijing

description: mRNA fragments

data_processing: The adaptor sequences in Illumina 1G sequencing reads were removed by using ‘‘vectorstrip’’ in the EMBOSS package. The RNA reads with length of 20–21 nt were mapped to the cDNA using Blast. Only RNAs with perfect cDNA matches were retained. Unique sequences were counted.

organism: Oryza sativa

source_name: rice seedling

growth_protocol: Rice plants were grown in growth chambers with 12-h light/dark cycles, 28 oC during the day and 23 oC during the night.

extract_protocol: Degradome libraries were constructed as described (Nature Biotechnology, 2008, vol.26, 941-946)

treatment_protocol: Total RNAs were isolated using Trizol per manufacturer's instructions, and subsequent mRNA purification was performed using oligo dT agarose beads.

tag: developmental stage

value: 3-week-old seedling


title: Root_+Pi_sRNASeq

description: Treatment: 250uM KH2PO4 for 5 days


title: Ssolfataricus_glucose_cDNA2


title: total small RNAs from embryos (Drosophila simulans)

description: Small RNA sequence data.

organism: Drosophila simulans

source_name: embryos

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) from 0-12 hr embryos or 12-24 embryos. 25 micrograms total RNA from each timepoint were pooled, and the ~18-26 nt fraction was isolated using PAGE and cloned using ligation to adapters requiring 5' monophosphate and 3' OH.

tag: pooled 0-12 and 12-24 hour embryos


title: hESC-NANOG-1b

status: Public on Oct 14 2009

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Base calling performed with Illumina Genome Analyzer Pipeline Software version 1.0
eland_multi
- Generated using ELAND
- ELAND parameters:
1.  Mapping length:  25 bases
2.  Maximum number of matches (0 mismatches, 1 mismatch, 2 mismatches): 250,250,250

bed (hg18)
- Generated using a custom perl script
- Input was the eland_multi file.
- Only reads mapping uniquely were retained.
- Read length is 36
- The score field contains the number of copies of the read

source_name: embryonic stem cells

value: NANOG


title: hESC-NANOG-1a


title: BY 10uL Mnase

status: Public on Oct 15 2009

city: Jerusalem

first: Assaf

last: Weiner

address: Givat Ram

department: Computer Science

institute: The Hebrew University of Jerusalem

description: Typical digested Mnase-seq genomic DNA (~80% mononucleosomes)

data_processing: Mapped Reads: Unique reads mapped to the yeast genome with minimal errors (as described in Yassour et al. PNAS, 2008)

organism: Saccharomyces cerevisiae

growth_protocol: For rpb1-1 temperature shifts, cells were grown to an OD of 0.6 in YPD at 25 C, then culture aliquots were immediately shifted to 37 C by addition of an equal volume of YPD at 49 C.

extract_protocol: After recovery of digested DNA, mononucleosomes were gel-purified and subjected to Solexa sequencing as described in Shivwaswamy et al

treatment_protocol: Yeast culture, fixation, and MNase titrations were carried out as previously described (Yuan et al. 2005)


title: BY 15uL Mnase

description: Over digested Mnase-seq genomic DNA (~100% mononucleosomes)


title: hESC-SOX2-1a


title: RPO21 20 min

description: MNase-seq at 20 minutes after shifting the RPO21 yeast strain from 25 C to 37 C


title: YRI NA19239 HapMap RNA Seq

description:
RNA-Seq
1 lane of NA19239 mapped reads using MAQ to the SNP-MASKED version of hg18 (argonne_090312_HGAC_S100054_2_NA19239_3.5_2.35bp.aln.map)
1 lane of NA19239 mapped reads using MAQ to the unmodified version of hg18 (argonne_090312_HGAC_S100054_2_NA19239_3.5_2.35bpunmasked.aln.map)
1 lane of NA19239 mapped reads using MAQ to the SNP-MASKED version of hg18 (yale_090121_YOAV_FC310E0_3_NA19239_2.5_2.aln.map)
1 lane of NA19239 mapped reads using MAQ to the unmodified version of hg18 (yale_090121_YOAV_FC310E0_3_NA19239_2.5_2unmasked.aln.map)
RNA-Seq
RNA
Poly-A capture


title: hESC-TAFII-1b

status: Public on Oct 13 2009

value: TAFII


title: hESC-TAFII-1a

data_processing:
Base calling performed with Illumina Genome Analyzer Pipeline Software version 0.3
eland_multi
- Generated using ELAND
- ELAND parameters:
1.  Mapping length:  25 bases
2.  Maximum number of matches (0 mismatches, 1 mismatch, 2 mismatches): 250,250,250

bed (hg18)
- Generated using a custom perl script
- Input was the eland_multi file.
- Only reads mapping uniquely were retained.
- Read length is 36
- The score field contains the number of copies of the read


title: hESC-MYC-1a

value: MYC


title: hESC-P300-1a


title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; methylC-seq_imr90_r1c

first: UCSD AND

last: SALK

address: Health Sciences Drive

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Library name: methylC-seq_imr90_r1c
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1114

****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM432689_UCSD.IMR90.Bisulfite-Seq.methylC-seq_imr90_r1c.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r1c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line, Library methylC-seq_imr90_r1c were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5118
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS 1c
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Library methylC-seq_imr90_r1c EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.47
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 88

**********************************************************************

ANALYSIS FILE NAME: GSM432689_UCSD.IMR90.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r1a-methylC-seq_imr90_r1b-methylC-seq_imr90_r1c-methylC-seq_imr90_r2a-methylC-seq_imr90_r2b-methylC-seq_imr90_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5128
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Combined Libraries methylC-seq_imr90_r1a EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.4
SPECIAL NOTE: generated from combined data in GSM432687, GSM432688, GSM432689, GSM432690, GSM432691, GSM432692 (thus .wig files on these records are identical)

**********************************************************************

extract_protocol: Library construction protocol: Genomic DNA was purified from IMR90 human embryonic stem cells, sheared by sonication to 50-500 bp, ligated to methylated single-end Illumina adaptors, fragments of 140-210 bp isolated after agarose gel electrophoresis, bisulfite converted, amplified by PCR and sequenced using the Illumina Genome Analyzer II according to manufacturer's instructions

value: IMR90 cells

tag: molecule

value: genomic DNA

tag: disease

value: ATCC

value: Cell Line

tag: line

tag: lineage

tag: batch

value: Replicate 1

value: Fetal lung fibroblast

tag: passage

tag: medium

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

tag: Sex

value: Female

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions'

value: Diagenode Bioruptor

value: 20 cycles of:30 seconds on high power, 2 minutes off

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina

value: Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments

value: Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol

value: 99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM

value: Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments.


title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; methylC-seq_imr90_r1b

description:
Library name: methylC-seq_imr90_r1b
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1113

****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM432688_UCSD.IMR90.Bisulfite-Seq.methylC-seq_imr90_r1b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r1b.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line, Library methylC-seq_imr90_r1b were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5117
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS 1b
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Library methylC-seq_imr90_r1b EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.49
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 94

**********************************************************************

ANALYSIS FILE NAME: GSM432688_UCSD.IMR90.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r1a-methylC-seq_imr90_r1b-methylC-seq_imr90_r1c-methylC-seq_imr90_r2a-methylC-seq_imr90_r2b-methylC-seq_imr90_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5128
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Combined Libraries methylC-seq_imr90_r1a EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.4
SPECIAL NOTE: generated from combined data in GSM432687, GSM432688, GSM432689, GSM432690, GSM432691, GSM432692 (thus .wig files on these records are identical)

**********************************************************************

value: genomic DNA

value: ATCC

value: Cell Line

value: Replicate 1

value: Fetal lung fibroblast

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

value: Female


title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; methylC-seq_imr90_r2c

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Library name: methylC-seq_imr90_r2c
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1122
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1117

****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM432692_UCSD.IMR90.Bisulfite-Seq.methylC-seq_imr90_r2c.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line, Library methylC-seq_imr90_r2c were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5116
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS 2c
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Library methylC-seq_imr90_r2c EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.43
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 76

**********************************************************************

ANALYSIS FILE NAME: GSM432692_UCSD.IMR90.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r1a-methylC-seq_imr90_r1b-methylC-seq_imr90_r1c-methylC-seq_imr90_r2a-methylC-seq_imr90_r2b-methylC-seq_imr90_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5128
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Combined Libraries methylC-seq_imr90_r1a EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.4
SPECIAL NOTE: generated from combined data in GSM432687, GSM432688, GSM432689, GSM432690, GSM432691, GSM432692 (thus .wig files on these records are identical)

**********************************************************************

value: IMR90 cells

value: Replicate 2

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions'

value: Diagenode Bioruptor

value: 20 cycles of:30 seconds on high power, 2 minutes off

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina


title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; methylC-seq_imr90_r2b

description:
Library name: methylC-seq_imr90_r2b
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1122
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1116

****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM432691_UCSD.IMR90.Bisulfite-Seq.methylC-seq_imr90_r2b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r2b.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line, Library methylC-seq_imr90_r2b were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5114
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS 2b
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Library methylC-seq_imr90_r2b EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.43
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 76

**********************************************************************

ANALYSIS FILE NAME: GSM432691_UCSD.IMR90.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r1a-methylC-seq_imr90_r1b-methylC-seq_imr90_r1c-methylC-seq_imr90_r2a-methylC-seq_imr90_r2b-methylC-seq_imr90_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5128
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Combined Libraries methylC-seq_imr90_r1a EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.4
SPECIAL NOTE: generated from combined data in GSM432687, GSM432688, GSM432689, GSM432690, GSM432691, GSM432692 (thus .wig files on these records are identical)

**********************************************************************

value: Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments

value: Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol

value: 99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM

value: Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments.


title: Whole genome shotgun bisulfite sequencing of the H1 cell line; methylC-seq_h1_r1b

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Library name: methylC-seq_h1_r1b
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1105
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1108

****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM432686_UCSD.H1.Bisulfite-Seq.methylC-seq_h1_r1b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1_r1b.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 Cell Line, Library methylC-seq_h1_r1b were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5124
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 BS 1b
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Bisulfite-Seq Library methylC-seq_h1_r1b EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.24
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 12

**********************************************************************

ANALYSIS FILE NAME: GSM432686_UCSD.H1.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1_r1a-methylC-seq_h1_r1b-methylC-seq_h1_r2a-methylC-seq_h1_r2b-methylC-seq_h1_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 Cell Line combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5127
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Bisulfite-Seq Combined Libraries EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.1
SPECIAL NOTE: generated from combined data in GSM432685, GSM432686, GSM429321, GSM429322, GSM429323 (thus .wig files on these records are identical)

**********************************************************************

extract_protocol: Library construction protocol: Genomic DNA was purified from H1 human embryonic stem cells, sheared by sonication to 50-500 bp, ligated to methylated single-end Illumina adaptors, fragments of 140-210 bp isolated after agarose gel electrophoresis, bisulfite converted, amplified by PCR and sequenced using the Illumina Genome Analyzer II according to manufacturer's instructions

value: genomic DNA

value: Thomson Laboratory

value: Cell Line

value: Replicate 1

value: embryonic stem cell

value: TeSR

value: Male


title: Whole genome shotgun bisulfite sequencing of the H1 cell line; methylC-seq_h1_r1a

description:
Library name: methylC-seq_h1_r1a
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1105
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1107

****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM432685_UCSD.H1.Bisulfite-Seq.methylC-seq_h1_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1_r1a.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 Cell Line, Library methylC-seq_h1_r1a were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5121
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 BS 1a
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Bisulfite-Seq Library methylC-seq_h1_r1a EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 96.96
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 6

**********************************************************************

ANALYSIS FILE NAME: GSM432685_UCSD.H1.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1_r1a-methylC-seq_h1_r1b-methylC-seq_h1_r2a-methylC-seq_h1_r2b-methylC-seq_h1_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 Cell Line combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5127
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Bisulfite-Seq Combined Libraries EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.1
SPECIAL NOTE: generated from combined data in GSM432685, GSM432686, GSM429321, GSM429322, GSM429323 (thus .wig files on these records are identical)

**********************************************************************

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions'

value: Diagenode Bioruptor

value: 20 cycles of:30 seconds on high power, 2 minutes off

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina


title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; methylC-seq_imr90_r2a

description:
Library name: methylC-seq_imr90_r2a
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1122
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1115

****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM432690_UCSD.IMR90.Bisulfite-Seq.methylC-seq_imr90_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r2a.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line, Library methylC-seq_imr90_r2a were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5113
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS 2a
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Library methylC-seq_imr90_r2a EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.44
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 82

**********************************************************************

ANALYSIS FILE NAME: GSM432690_UCSD.IMR90.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r1a-methylC-seq_imr90_r1b-methylC-seq_imr90_r1c-methylC-seq_imr90_r2a-methylC-seq_imr90_r2b-methylC-seq_imr90_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5128
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Combined Libraries methylC-seq_imr90_r1a EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.4
SPECIAL NOTE: generated from combined data in GSM432687, GSM432688, GSM432689, GSM432690, GSM432691, GSM432692 (thus .wig files on these records are identical)

**********************************************************************

value: ATCC

value: Replicate 2

value: Fetal lung fibroblast

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

value: Female

value: Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments

value: Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol

value: 99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT


title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; methylC-seq_imr90_r1a

description:
Library name: methylC-seq_imr90_r1a
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1112

****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM432687_UCSD.IMR90.Bisulfite-Seq.methylC-seq_imr90_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r1a.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line, Library methylC-seq_imr90_r1a were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5115
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS 1a
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Library methylC-seq_imr90_r1a EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.51
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 100

**********************************************************************

ANALYSIS FILE NAME: GSM432687_UCSD.IMR90.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r1a-methylC-seq_imr90_r1b-methylC-seq_imr90_r1c-methylC-seq_imr90_r2a-methylC-seq_imr90_r2b-methylC-seq_imr90_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5128
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: IMR90 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Combined Libraries methylC-seq_imr90_r1a EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.4
SPECIAL NOTE: generated from combined data in GSM432687, GSM432688, GSM432689, GSM432690, GSM432691, GSM432692 (thus .wig files on these records are identical)

**********************************************************************

value: genomic DNA

value: Cell Line

value: Replicate 1

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions'

value: Diagenode Bioruptor

value: 25 µM

value: Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments.


title: Strand-specific, shotgun sequencing of mRNA from the H1 cell line; mRNA-seq_h1_r1

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Library name: mRNA-seq_h1_r1
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1105
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1437

****************
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.

extract_protocol: Library construction protocol: Total RNA was isolated from H1 cells and mRNA isolated by RiboMinus depletion of rRNA. mRNA was fragmented, dephosphorylated, 5' phosphorylated, then sequentially ligated to the adenylated 3' RNA adapter then to the 5' RNA adapter. Following reverse transcription of the adapter ligated RNA, the library was enriched by 15 cycles of PCR.

value: Thomson Laboratory

value: embryonic stem cell

value: TeSR

value: Male

value: mRNA-Seq

value: mirVana miRNA isolation kit (Applied Biosystems), performed as per manufacturer's instructions to isolate total RNA, followed by treatment with DNaseI (Qiagen) for 30 min at room temperature

value: 2 x RiboMinus (Life Technologies) rRNA depletion (5S, 5.8S, 12S, 18S, 28S)

value: 15 min at 70 ˚C with RNA Fragmentation kit (Ambion/Applied Biosystems) as per manufacturer's instructions

value: 5' GUUCAGAGUUCUACAGUCCGACGAUC

value: 5' UCGUAUGCCGUCUUCUGCUUGidT, 5' adenylated (Illumina)

value: 5' CAAGCAGAAGACGGCATACGA

value: Fragmented RNA was treated with 5 U Antarctic phosphatase (New England Biolabs) for 40 min at 37˚C in the presence of 40 U RNaseOut followed by phosphatase heat inactivation at 65˚C for 5 min. The RNA was purified using 66 µl SPRI beads (Agencourt) and eluted in 11 µl 10 mM Tris buffer pH 8.0.

value: Phosphorylation was performed by addition of 10 U PNK (New England Biolabs), 1 mM ATP, and 20 U RNaseOut  (Life Technologies) and incubation at 37˚C for 1 h.

value: 1 µl of 1:10 diluted adenylated 3’ RNA adapter oligonucleotide was added to the phosphorylated RNA and incubated at 70˚C for 2 min followed by placement on ice. The 3’ RNA adapter ligation reaction was performed by addition of 2 µl 10x T4 RNA ligase 2 truncated ligation buffer, 1.6 µl 100 mM MgCl2, 20 U RNaseOut and 300 U T4 RNA ligase 2 truncated (New England Biolabs) and incubation at 22˚C for 1 h.

value: Ligation of the 5’ RNA adapter was performed by addition to the 3’ adapter ligated reaction of 1 µl 1:1 diluted, heat denatured (70˚C 2 min) 5’ RNA adapter oligonucleotide, 1 µl 10 mM ATP, and 10 U T4 RNA ligase (Promega), and incubation at 20˚C for 1 h. RNA was purified using 66 µl SPRI beads and eluted in 10 µl 10 mM Tris buffer pH 8.0.

value: To the RNA ligation products, 2 µl 1:5 diluted RT primer was added and heat denatured (70˚C 2 min), followed by incubation on ice. Added to the denatured RNA/primer solution was 4 µl 5x first strand buffer, 1 µl 12.5 mM dNTPs, 2 µl 100 mM DTT, and 40 U RNaseOut, followed by incubation at 48˚C for 1 min. To this, 200 U Superscript II reverse transcriptase (Life Technologies) was added, followed by incubation at 44˚C for 1 h.

value: The entire reverse transcription reaction was used in the PCR enrichment of the library.

value: Phusion hot-start high fidelity DNA polymerase (New England Biolabs). 1x Phusion polymerase buffer and 4 U Phusion hot-start high fidelity DNA polymerase was used in a 100 µl reaction.

value: 98˚C 30 sec; 98˚C 10 sec, 60˚C 30 sec, 72˚C 15 sec; 72˚C 10 min

value: PCR products were purified in two steps, first by purification using 180 µl SPRI beads and elution in 30 µl 10 mM Tris buffer pH 8.0, followed by purification with 39 µl SPRI beads and elution in 10 µl 10 mM Tris buffer pH 8.0.


title: Whole genome shotgun bisulfite sequencing of the H1 cell line; methylC-seq_h1_r2c

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Library name: methylC-seq_h1_r2c
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1106
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.995

****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM429323_UCSD.H1.Bisulfite-Seq.methylC-seq_h1_r2c.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 Cell Line, Library methylC-seq_h1_r2c were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5123
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 BS 2c
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Bisulfite-Seq Library methylC-seq_h1_r2c EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.37
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 29

**********************************************************************

ANALYSIS FILE NAME: GSM429323_UCSD.H1.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1_r1a-methylC-seq_h1_r1b-methylC-seq_h1_r2a-methylC-seq_h1_r2b-methylC-seq_h1_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 Cell Line combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5127
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Bisulfite-Seq Combined Libraries EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.1
SPECIAL NOTE: generated from combined data in GSM432685, GSM432686, GSM429321, GSM429322, GSM429323 (thus .wig files on these records are identical)

**********************************************************************

value: genomic DNA

value: Thomson Laboratory

value: Cell Line

value: Replicate 1

value: embryonic stem cell

value: TeSR

value: Male

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions'

value: Diagenode Bioruptor

value: 20 cycles of:30 seconds on high power, 2 minutes off

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina

value: Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments

value: Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol

value: 99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM

value: Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments.


title: Sequencing of small RNA from the H1 cell line; smRNA-seq_h1_r1

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000276
Library name: smRNA-seq_h1_r1
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1105
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1438

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

extract_protocol: Library construction protocol: The small RNA fraction was isolated from H1 cells then sequentially ligated to the adenylated 3' RNA adapter then to the 5' RNA adapter. Following reverse transcription of the adapter ligated small RNAs, the library was enriched by 12 cycles of PCR.

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell

value: TeSR

value: Male

value: smRNA-Seq

value: mirVana miRNA isolation kit (Applied Biosystems), performed as per manufacturer's instructions to isolate small RNAs, followed by treatment with DNaseI (Qiagen) for 30 min at room temperature.

value: The small RNA fraction were separated by electrophoresis on a 15% TBE-urea gel and RNA molecules between approximately 10 and 50 nt were excised and eluted from the gel fragments then ethanol precipitated, resuspending in 6 µl.

value: Equivalent to the quantity of smRNAs isolated from 5 µg of total RNA.

value: 5' GUUCAGAGUUCUACAGUCCGACGAUC

value: 5' UCGUAUGCCGUCUUCUGCUUGidT, 5' adenylated (Illumina)

value: 5' CAAGCAGAAGACGGCATACGA

value: 1 µl of 1:10 diluted adenylated 3’ RNA adapter oligonucleotide was added to the 6 µl of smRNA and incubated at 70˚C for 2 min followed by placement on ice. The 3’ RNA adapter ligation reaction was performed by addition of 2 µl 5x T4 RNA ligase 2 truncated ligation buffer, 20 U RNaseOut and 300 U T4 RNA ligase 2 truncated (New England Biolabs) and incubation at 22˚C for 1 h.

value: Ligation of the 5’ RNA adapter was performed by addition to the 3’ adapter ligated reaction of 0.5 µl heat denatured (70˚C 2 min) 5’ RNA adapter oligonucleotide, 1 µl 10 mM ATP, and 10 U T4 RNA ligase (Promega), and incubation at 20˚C for 6 h.

value: To 4 µl of the RNA ligation products, 1 µl 1:5 diluted RT primer was added and heat denatured (70˚C 2 min), followed by incubation on ice. Added to the denatured RNA/primer solution was 2 µl 5x first strand buffer, 0.5 µl 12.5 mM dNTPs, 1 µl 100 mM DTT, and 20 U RNaseOut, followed by incubation at 48˚C for 3 min. To this, 100 U Superscript II reverse transcriptase (Life Technologies) was added, followed by incubation at 44˚C for 1 h.

value: The entire reverse transcription reaction was used in the PCR enrichment of the library.

value: Phusion hot-start high fidelity DNA polymerase (New England Biolabs). 1x Phusion polymerase buffer and 2 U Phusion hot-start high fidelity DNA polymerase was used in a 50 µl total reaction.

value: 98˚C 30 sec; 98˚C 10 sec, 60˚C 30 sec, 72˚C 15 sec; 72˚C 10 min

value: PCR products were separated by electrophoresis on a 6% polyacrylamide gel and the PCR products (~90-125 bp) were excised, eluted from the crushed gel by rotation in 100 µl 1x gel elution buffer for 2 h, then ethanol precipitation of the DNA within the supernatant.


title: hESC-Oct4-2a

tag: cell line

tag: chip antibody


title: RPO21 0 min

description: MNase-seq at 0 minutes after shifting the RPO21 yeast strain from 25 C to 37 C

tag: strain


title: Shoot_+Pi_sRNASeq

description: Treatment: 250uM KH2PO4 for 5 days

data_processing: Processed data files contain the perfectly mapped reads with 5' and 3' adapters removed (reads were mapped on the TAIR8 genome). Same reads are sorted together and the numbers of repetitivity are indicated

source_name: shoot


title: Sequencing of small RNA from the IMR90 cell line; smRNA-seq_imr90_r1

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000276
Library name: smRNA-seq_imr90_r1
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1439

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

extract_protocol: Library construction protocol: The small RNA fraction was isolated from IMR90 cells then sequentially ligated to the adenylated 3' RNA adapter then to the 5' RNA adapter. Following reverse transcription of the adapter ligated small RNAs, the library was enriched by 12 cycles of PCR.

value: ATCC

value: Cell Line

value: Fetal lung fibroblast

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

value: Female


title: Hi-C (HindIII,GM,2) 3

status: Public on Oct 09 2009

first: Erez

last: Lieberman-Aiden

address: 7 Cambridge Circle

institute: Harvard/MIT/Broad

description: contains both read ends

data_processing: Independent alignment of both ends of each read using Maq (http://maq.sourceforge.net/)

growth_protocol: Human cell line GM06990, an EBV-transformed lymphoblastoid cell line (Coriell, Camden, NJ), was cultured in RPMI1640, 15% fetal calf serum, 1% penicillin-streptomycin, and 2mM L-glutamine. Human erythroleukemia cell line K562 (ATCC, Manassas, VA) was cultured in DMEM, 10% fetal calf serum, 1% penicillinstreptomycin, and 2mM L-glutamine.

extract_protocol: Hi-C approach as described in the paper

tag: restriction enzyme

value: HindIII

tag: biological sample #

tag: pcr # from biological sample

tag: lane

tag: read end


title: Rice_Total

description: small RNA

data_processing: The adaptor sequences in Illumina 1G sequencing reads were removed by using ‘‘vectorstrip’’ in the EMBOSS package. The small RNA reads with length of 19–27 nt were mapped to the genome using Blast. Only small RNAs with perfect genomic matches were retained.

source_name: Seedling

extract_protocol: Small RNAs were ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified using a pair of Illumina cloning primers and then provided for Illumina sequencing.

treatment_protocol: RNAs were extracted from total extract and immunopurified AGO1 complexes by Trizol reagents. Bigger RNAs were removed by PEG precipitation, and enriched small RNAs were seperated on 15% PAGE/7M Urea gel, and small RNA within the range of 18-28 nt were purified from the gel.

tag: protein complex

value: total extract


title: hESC-Oct4-1a


title: Hi-C (HindIII,GM,2) 2

description: contains both read ends


title: Hi-C (HindIII,GM,Biological Repeat)

description: contains both read ends


title: Hi-C (HindIII,K562,1) 8

description: contains both read ends


title: Hi-C (NcoI,GM,1) 1

description: contains both read ends

value: NcoI


title: Hi-C (HindIII,K562,1) 7

description: contains both read ends


title: Shoot_-Pi_sRNASeq

description: Treatment: 0uM KH2PO4 for 5 days


title: Hi-C (NcoI,GM,1) 2

description: contains both read ends


title: S2_DRSC_CG7878_RNAi-2

city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

description:
dsRNA treatment: CG7878
read length: 75
read length: 76
library_source: RNA
library_selection: RT and size selection

data_processing: Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

growth_protocol: Schneider's medium + 10% heat-inactivated FCS

extract_protocol:
Oligo-dT selected, double stranded cDNA, Single Read Sequencing
TRIzol Dnase Rneasy

treatment_protocol: Cells were treated with dsRNA to the indicated gene


title: S2_DRSC_CG3249_RNAi-2

description:
dsRNA treatment: CG3249
read length: 75
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG5821_RNAi-1

description:
dsRNA treatment: CG5821
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG5836_RNAi-1

description:
dsRNA treatment: CG5836
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG3249_RNAi-1

description:
dsRNA treatment: CG3249
read length: 75
read length: 75
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG31000_RNAi-1

description:
dsRNA treatment: CG31000
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: Rice_degradome_inflorescence

description: mRNA fragments

data_processing: The adaptor sequences in Illumina 1G sequencing reads were removed by using ‘‘vectorstrip’’ in the EMBOSS package. The RNA reads with length of 20–21 nt were mapped to the cDNA using Blast. Only RNAs with perfect cDNA matches were retained. Unique sequences were counted.

source_name: rice young panicle

tag: developmental stage

value: young panicle


title: Hi-C (HindIII,GM,1)

description: contains both read ends


title: S2_DRSC_CG10128_RNAi-1

description:
dsRNA treatment: CG10128
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG18426_RNAi-1

description:
dsRNA treatment: CG18426
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG7437_RNAi-1

description:
dsRNA treatment: CG7437
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG7971_RNAi-1

description:
dsRNA treatment: CG7971
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG10851_RNAi-1

description:
dsRNA treatment: CG10851
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG1559_RNAi-1

description:
dsRNA treatment: CG1559
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG4602_RNAi-1

description:
dsRNA treatment: CG4602
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG10203_RNAi-1

description:
dsRNA treatment: CG10203
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG5655_RNAi-1

description:
dsRNA treatment: CG5655
read length: 75
read length: 75
read length: 76
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG16901_RNAi-1

description:
dsRNA treatment: CG16901
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG5099_RNAi-1

description:
dsRNA treatment: CG5099
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG17838_RNAi-1

description:
dsRNA treatment: CG17838
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG13425_RNAi-1

description:
dsRNA treatment: CG13425
read length: 75
read length: 76
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG9983_RNAi-1

description:
dsRNA treatment: CG9983
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG8144_RNAi-4

description:
dsRNA treatment: CG8144 dsRNA
read length: 37
library_source: RNA
library_selection: RT and size selection

data_processing: Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to GFF files and .bedgraph files which indicate the number of reads that map to each base in the genome.

extract_protocol:
Oligo-dT selected, double stranded cDNA, Paired-end sequencing
TRIzol Dnase Rneasy


title: S2_DRSC_CG5442_RNAi-1

description:
dsRNA treatment: CG5422
read length: 78
read length: 80
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG17136_RNAi-1

description:
dsRNA treatment: CG17136
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG8144_RNAi-1

description:
dsRNA treatment: CG8144 dsRNA
read length: 45
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG8144_RNAi-3


title: S2_DRSC_Untreated-3

description:
dsRNA treatment: Untreated
read length: 37
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG30122_RNAi-1

description:
dsRNA treatment: CG30122
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_Untreated-1

description:
dsRNA treatment: Untreated
read length: 45
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_Untreated-4


title: total small RNAs from embryos (Drosophila pseudoobscura)

description: Small RNA sequence data.

data_processing: 3' adapter sequences (CTGTAGG) were trimmed and inserts shorter than 18 nt were filtered out.

tag: pooled 0-12 and 12-24 hour embryos


title: S2_DRSC_CG12749_RNAi-1

description:
dsRNA treatment: CG12749
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG9373_RNAi-1

description:
dsRNA treatment: CG9373
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_CG6946_RNAi-1

description:
dsRNA treatment: CG6946
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection


title: S2_DRSC_Untreated-6

description:
dsRNA treatment: Untreated
read length: 75
read length: 75
library_source: RNA
library_selection: RT and size selection