title: NCCIT-siRNF20_mRNA_seq

description: polyA RNA

data_processing: For mRNA-seq, the sequence tags were mapped to the human genome (UCSC hg18) by using TopHat40 with default parameters. The mapped sequence reads were extended to the average size of fragment length (200bp).

source_name: siRNF20-transfected NCCIT cells, mRNA

extract_protocol: RNA extraction and preparation: The sequencing library of mRNA was generated by using the mRNA-seq sample prep kit (Illumina, San Diego, CA). Polyadenylated mRNA was purified from 10g of total RNA by Sera-mag oligo(dT) beads (Illumina). The mRNA was fragmented by incubating with fragmentation buffer (Illumina) at 94oC for 5 min. First strand cDNA was synthesized by SuperScript II (Invitrogen) and random primers (Illumina). Second strand cDNA was synthesized by RNaseH and DNA ol I (Illumina). cDNA fragments were ligated to a pair of adaptors for sequencing on the Illumina Genome Analyzer. The ligation products were size-fractioned to obtain 200 bp fragments on a 2% agarose gel and subjected to 15 cycles of PCR amplification. Cluster generation and 72 cycles of single-read sequencing were done.

value: siRNF20-transfected NCCIT


title: MEFs_H3K9me2_Bix

status: Public on Mar 07 2012

type: SRA

city: New York

first: Terry

last: Fang

state: NY

address: 1230 York Ave

country: USA

institute: Rockefeller University

description: chromatin IP against H3K9me2 in WT MEFs treated with BIX01294

library_source: genomic

data_processing: Raw data processed using onboard SCS/RTA, alignments performed using Bowtie keeping only unique reads with 2 or fewer mismatches in 36bp. Alignments summed in 100bp windows for wig files

molecule: genomic DNA

organism: Mus musculus

source_name: MEF

growth_protocol: MEFs were grown in 10 cm plates with DMEM medium containing 15% FBS, Pen/Strep, Glutamine, NEAA and 2-mercaptoethanol. After immortalization with SV40-LTA, MEFs were grown in 15 cm plates with the same medium except FBS was 10%. DC were isolated from WT C57Bl/6, G9af/f, G9a;Vav-cre or IFNaR1 -/- mice that subcutaneously injected with B16-Flt3L cells. 2 weeks later splenic DCs were enriched for the CD11c+ population using CD11c MACS beads.  ChIP was carried out directly on ex vivo isolated cells.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Primary MEFs were immortalized at passage 2. At passage 5,  MEFs were treated witheither EtOH as a vehicle control or Tamoxifen to induce deletion of G9a.  MEFs were either left untreated, treated with Lipofectamine 200, the tranfection reagent or tranfected with PolyIC.

tag: strain

tag: cell type

value: Fibroblasts from day 13.5 embryos immortalized with SV40-LTA

tag: genotype

value: Wild-type

tag: passages

value: Passaged 12-15 times

tag: chip antibody

tag: vendor

value: Abcam (ab1220)

tag: lot


title: NCCIT_mRNA_seq

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description: polyA RNA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

source_name: NCCIT, mRNA

growth_protocol: NCCIT embryonic carcinoma cell lines on a 10cm dish were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS, Hyclone) and 1% antibiotic-antimycotic solution (Hyclone) at 37ºC in a humidified atmosphere composed of 5% CO2.

tag: cell line

value: NCCIT

value: embryonic carcinoma cells


title: islet preparation 4 under control condition

status: Public on Mar 09 2012

city: Brussels

first: Guy

last: Bottu

address: U.L.B. CP618, Route de Lennik 808

department: Faculty of Medecine

country: Belgium

institute: Free University of Brussels

description: Sample 7

data_processing:
BED files: Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program gem-mapper from the GEM suite (http://gemlibrary.sourceforge.net). The GEM mapper reports exhaustively all mappings and split-mappings up to a user-defined amount of mismatches (default 2 mismatches), disregarding presumptive base-calling errors as identified by low associated quality values.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome Build:
ID4_ctl.bed: GRCh37/hg19
ID4_ctl.gtf: GRCh37/hg19

molecule: total RNA

source_name: islet preparation_control condition

growth_protocol: Human islet preparations were obtained from heart-beating organ donors with no medical history of diabetes or metabolic disorders. The islets were isolated using collagenase digestion and density gradient purification. They were cultured in M199 culture medium containing 5.5 mM glucose and shipped within 1-5 days following isolation. Upon arrival, the human islet cells were cultured in Ham's F-10 medium containing 6.1 mM glucose, 10% fetal bovine serum (FBS), 2 mM GlutaMAX, 50 μM 3-isobutyl-1-methylxanthine, 1% BSA, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands), which favors purification of all RNA molecules longer than 200 nucleotides and sample preparation was done as described by the manufacturer (Illumina, Eindhoven, The Netherlands). Briefly, mRNA was purified from two μg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 3’-monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel. Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bioanalyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 μL cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on one sequencing lane of an Illumina Genome Analyzer II system (GAII, Illumina).

treatment_protocol: The islets were exposed or not to cytokines in the same medium as used for preparation but without FBS for 2 days. The following cytokine concentrations were used: recombinant human IL-1β (specific activity 1.8x107 U/mg; a kind gift from C.W. Reinolds, National Cancer Institute, Bethesda, MD, USA) at 50 U/ml; recombinant human IFN-γ (specific activity 2x107 U/mg; R&D Systems, Abingdon, UK) at 1000 U/ml. The evaluation of islet cell purity, i.e. the percentage of beta cells present in the preparations, was done by immunocytochemistry with an anti-insulin antibody (1/1000; Sigma, Bornem, Belgium) and donkey anti-mouse IgG rhodamine (1/200; Lucron Bioproducts, De Pinte, Belgium). Only preparations with more than 40% beta cells were used for the RNA-seq analyses; on average they contained 58% beta cells.

tag: tissue

value: islets of Langerhans


title: H3K79me1_ChIP_seq

data_processing: The sequence tags were mapped to the human genome (UCSC hg18) by using the Genome Analyzer data analysis pipeline. The mapped sequence reads were extended to the average size of fragment length (200bp).

source_name: NCCIT, H3K79me1 ChIP

extract_protocol:
Genomic DNA extraction: Cross-linking was performed by incubating cells in 1% formaldehyde (Sigma) for 20 min at 25°C. Cells were quenched with 125 mM Glycine. PBS-washed cells were lysed in 400 μl of SDS Lysis Buffer, and DNA was sonicated to create fragments of 400-500 nucleotides in length using a Sonic Dismembrator (Model 500, Fisher).

Chromatin immunoprecipitation: Chromatin cleared by centrifugation for 15 minutes at 13,000 rpm, 4°C were subjected to immunoprecipitation using antibodies of interest with a mixture of protein A and G agarose (GE Healthcare) for 2 hr at 4°C. Protein A and G agarose/antibody/chromatin complexes then were washed for 10 minutes with each of the following solutions: Low Salt Wash Buffer (150 mM NaCl lysis buffer without 0.2% SDS), High Salt Wash Buffer (500 mM NaCl lysis buffer without 0.2% SDS), LiCl buffer (10 mM Tris-Cl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Sodium deoxycholate), and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). The chromatin complexes were then eluted twice in 250 μl elution buffer (1% SDS, 0.1M NaHCO3) by incubation at 25°C for 15min with rotation and were reverse-crosslinked by heating at 68ºC for O/N with 400mM NaCl.
Antibodies: Antibodies recognizing H3ac, H3K4me3, H3K36me3, H3K79me1, H3K79me2, H3K79me3 were polyclonal rabbit antibodies purchased from Abcam or produced in-house. H2Bub antibody was obtained from Millipore (17-650).

The purified ChIP DNA fragments were ligated to a pair of adaptors for sequencing on the Illumina Genome Analyzer. The ligation products were size-fractioned to obtain 200- to 300-bp fragments on an agarose gel and subjected to 18 cycles of PCR amplification. Cluster generation and 72 cycles of single-read sequencing were done.

tag: antibody vendor

value: Abcam mixed with in-house antibody

tag: antibody catalog number

tag: antibody lot#


title: H3K36me3_ChIP-seq

source_name: NCCIT, H3K36me3 ChIP

value: Abcam


title: H3K4me3_ChIP-seq

source_name: NCCIT, H3K4me3 ChIP


title: H2BUb1_ChIP-seq

source_name: NCCIT, H2BUb1 ChIP

value: Millipore


title: H2Bub_MT_replicate3

status: Public on Mar 06 2012

first: Brian

last: Dynlacht

address: 550 1st avenue

institute: NYU Langone Medical Center

data_processing:
Sequence reads within each individual replicate were filtered to remove identical sequence tags since those were likely generated by the LM-PCR amplification process while identical sequences present after the merging of replicates were retained. The sequence reads were aligned against the mouse mm9 genome build using the Illumina Pipeline and only tags locating to a single unique position were retained.
Peaks were identified using Qeseq, an algorithm developed in collaboration with Dr Klugers bioinformatics group. Setting for all MNAse libraries: sigma=50 and cut-off=15. For sonicated libraries the settings used were: sigma=100 and cut-off=12.

source_name: C1C12 myotubes differentiated for 96h

growth_protocol: C1C12 myoblasts were grown in DMEM containing 10% FBS and harvested at ~40% confluency for MB chromatin. For myotube differentiation, cells were allowed to grow to complete confluence at which point differentiation was induced by changing the media to DMEM containing 2% horse serum. Induced cells were incubated for 4 days with one change of media (DMEM/2% horse serum) after two days and myotubes were harvested after 4 days of differentiation.

extract_protocol: Libraries were generated from input chromatin or ChIP enriched chromatin according to Illumina's standard protocol but using reagents from other companies: DNA end-repair was performed using the End-It DNA repair kit, Epicentre (cat:ER81050). A-overhang generation was performed uising Klenow from NED (cat: M0212). Adapter ligation was performede using the LigaFast kit from Promega (cat:M8225). LM-PCR was performed using Phusion DNA pol master mix from NEB (cat:F-531S). Very stringent quality controls were applied to the libraries: 1. Enrichment of a given site had to be preserved in the libraries in a manner comparable to the original ChIP. 10-12 positive and negative sites were tested for library preparation. 2. The total yield of the LM-PCR had to be ~500 ng. 3. The size distribution had to be centred around 250 bp for libraries generated from MNAse chromatin and around 350 bp for sonicated with a variation no larger than +/- 75 bp. Libraries that did not pass these criteria were considered substandard and were not used for sequencing.

treatment_protocol: Isolated chromatin was either sonicated to an average size of 250 bp or digested with MNAse to yield ~85% mono nucleososomal fragments.

tag: chromatin preparation method

value: MNAse digestion

value: H2Bub, Millipore:05-1312, clone 56

tag: antibody lot number


title: Input DNA

source_name: NCCIT, input

value: IgG


title: MNase-seq

source_name: NCCIT, MNase

extract_protocol: MNase digestion: For the purification of mononucleosomes, PBS-washed cells were lysed in 400 μl of Lysis Buffer (18% Ficoll-400 (Sigma F2637), 10 mM KH2PO4, 10 mM K2PO4, 1 mM MgCl2, 0.25 mM EGTA, 0.1 mM PMSF) and centrifuged for 15 minutes at 13,000 rpm, 4°C. The nuclei pellets were resuspended with 1 ml of A Buffer (10 mM Tris-Cl pH 7.4, 150 mM NaCl, 5mM KCl, 1 mM EDTA, 0.1 mM PMSF) and then 5 μl of CaCl2 (final 5mM) and 1.5 μl of MNase (500unit/ 2.5μl, NEB) were added. After incubation at 37°C for 5 min, the reactions were stopped by adding 100 μl of 1% SDS and 50 μl of 0.5mM EDTA. MNase-digested nuclei were reverse-crosslinked by heating at 68ºC for O/N with 350mM NaCl. Finally, the reverse-crosslinked samples were treated with RNase A and proteinase K (Sigma), isolated by phenol/chloroform extraction, and precipitated using 3 M sodium acetate (pH 5.2) with absolute ethanol.


title: H2Bub_MB_replicate3

source_name: Growing C1C12 myoblasts


title: H2Bub_MT_replicate2


title: H2Bub_MB_replicate2


title: H2Bub_MT_replicate1


title: G1ME_ETS1

status: Public on Mar 05 2012

city: Chicago

first: Louis

middle: C

last: Dore

state: IL

address: 303 E Superior St., Lurie Bldg 5-250D

department: Feinberg School of Medicine

institute: Northwestern University

description:
Chromatin IP against ETS1
Cells were derived from J1 ES cells [Fujiwara, PNAS, 1996; Stachura, Blood, 2006].

data_processing: Eland or eland_extended output from Illumina Pipeline was converted to BED format and analyzed with either MACS v1.3.7.1 (for transcription factors) using default p-value and mfold of 10 (ETS1), 15 (GATA1), or 32 (GATA2) or SICER (for histone marks) using default parameters. Datasets were analyzed 3 times against randomly selected size-matched subsets of a large INPUT dataset; the results of these analyses are the BED files labeled A, B, and C. The intersection of these 3 peak calls (BED files labeled ABC) were used for further analysis.

source_name: Megakaryocyte Progenitor Cell Line (G1ME)

growth_protocol: Cells were grown in alpha-MEM with 20% serum, 1% pen/strep and 1% TPO-conditioned medium, as described [Stachura et al., Blood 2006].

extract_protocol: G1ME cells were crosslinked in 1% formaldehyde at room temperature and the crosslinking reaction was quenched with 125mM glycine. Cells were then lysed and isolated nuclei were lysed and sonicated to shear the chromatin. After centrifugation to remove debris, chromatin was pre-cleared with pre-immune IgG and protein G agarose beads. Pre-cleared chromatin was immunoprecipitated overnight, then RNase and proteinase treated, followed by organic extraction. Purified immunoprecipitated chromatin was subjected to end repair, dA addition, and linker ligation followed by 25 rounds of PCR amplification, gel purification, and an additional 15 rounds of PCR amplification and purification. Purified, amplified DNA was subjected to NanoDrop analysis and loaded on the flow cell of an Illumina GAII or GAIIx.

treatment_protocol: GATA1 ChIPs are from G1ME cells 48 hours after transduction with GATA1 retrovirus. All other ChIPs are from proliferating, untreated G1ME cells.

tag: Stage

value: Progenitor, GATA1-null

tag: antibody

value: Santa Cruz


title: G1ME_H3K4me3

description:
Chromatin IP against H3K4me3
Cells were derived from J1 ES cells [Fujiwara, PNAS, 1996; Stachura, Blood, 2006].


title: G1ME_GATA1

description:
Chromatin IP against GATA1
Cells were derived from J1 ES cells [Fujiwara, PNAS, 1996; Stachura, Blood, 2006].

value: Mature, HA-GATA1-restored

value: anti-HA


title: G1ME_INPUT (GAII)

description:
Input DNA
Cells were derived from J1 ES cells [Fujiwara, PNAS, 1996; Stachura, Blood, 2006].


title: G1ME_INPUT (GAIIx)


title: G1ME_H3K27me3

description:
Chromatin IP against H3K27me3
Cells were derived from J1 ES cells [Fujiwara, PNAS, 1996; Stachura, Blood, 2006].


title: p53S18P_ChIP_seq_Adr8h

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

description: Treated with adriamycin, chromatin IP against p53S18P.

data_processing: Short reads were mapped to build mm9 using Illumina's pipeline. Only reads that passed the quality filtering and are unique are retained.

source_name: embryonic stem cells, treated, p53S18P ChIP

growth_protocol: Cells were grown in mESC growth medium, Knockout DMEM (KO-DMEM), 15% Fetal Bovine Serum, 100mM MEM non-essential amino acids, 0.1mM 2-mercaptoethanol, 2mM L-glutamine and 1X penicillin-streptomycin (All from Invitrogen) plus 1000 units/ml leukemia inhibitory factor (Lif, Millipore).

extract_protocol: DNA was extracted with the phenol/chloroform approach. ChIP assays were performed according to the Agilent mammalian ChIP-chip protocol (version 10, May 2008). Library construction was performed as per Illumina's ChIP-seq library construction protocol.

treatment_protocol: Cells were either untreated or treated with 0.5 micromolar adriamycin for 8 hours in growth medium.

tag: background/strain

value: embryonic stem (ES) cells

value: less than 15

tag: agent

value: adriamycin

value: Cell Signaling

tag: antibody catalog #

tag: antibody lot #


title: p53S18P_ChIP_seq_untreated

description: Untreated, chromatin IP against p53S18P.

source_name: embryonic stem cells, untreated, p53S18P ChIP

tag: cell type

tag: passages

value: untreated


title: input genomic DNA for HTR5

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

description: Sample 3

data_processing:
Alignment: Sequence reads were obtained and mapped to the TAIR8 Arabidospis genome using Bowtie (Langmead et al., 2009 Genome Biol). Uniquely mapping with two or fewer mismatches were retained. Reads mapping to identical positions were collapsed into one read.
input_for_HTR5_ChIP_mapped.txt; genome build: TAIR8

organism: Arabidopsis thaliana

source_name: input genomic DNA for HTR5

extract_protocol: ChIP-seq were generated and sequenced on HiSeq 2000 as per the manufacturer instructions (Illumina).

tag: ecotype

value: 10 day seedlings


title: input genomic DNA for HTR13

description: Sample 4

data_processing:
Alignment: Sequence reads were obtained and mapped to the TAIR8 Arabidospis genome using Bowtie (Langmead et al., 2009 Genome Biol). Uniquely mapping with two or fewer mismatches were retained. Reads mapping to identical positions were collapsed into one read.
input_for_HTR13_ChIP_mapped.txt; genome build: TAIR8

source_name: input genomic DNA for HTR13


title: HTR5 Myc ChIP-seq

description: Sample 1

data_processing:
Alignment: Sequence reads were obtained and mapped to the TAIR8 Arabidospis genome using Bowtie (Langmead et al., 2009 Genome Biol). Uniquely mapping with two or fewer mismatches were retained. Reads mapping to identical positions were collapsed into one read.
HTR5_ChIP_mapped.txt; genome build: TAIR8

source_name: HTR5 Myc ChIP-seq

tag: chip antibody

value: anti Myc antibody, clone 4A6

tag: chip antibody vendor

tag: chip antibody cat. number


title: p53_ChIP_seq_untreated

description: Untreated, chromatin IP against p53.

source_name: embryonic stem cells, untreated, p53 ChIP

tag: antibody vendor


title: Input_seq_untreated

description: Untreated, input DNA.

source_name: embryonic stem cells, untreated, input


title: Input_seq_Adr8h

description: Treated with adriamycin, input DNA.

source_name: embryonic stem cells, treated, input


title: 09-01-0257

status: Public on Mar 03 2012

city: Gaithersburg

first: Justin

middle: M

last: Zook

state: Maryland

address: 100 Bureau Dr., MS8313

department: Biochemical Science Division

institute: National Institute of Standards and Technology

data_processing:
The raw data was mapped using Bioscope v.1.3 (for SOLiD data) or bwa v.0.5.9 (for Illumina data) to hg18 with the ERCC spike-in sequences appended, using default mapping parameters. The BAM files were split into reads mapping to hg18 or to the spike-ins, and base quality score recalibration was done separately on these two files.  To generate base quality score recalibration tables, GATK v.1.2-62 was used with the dbSNP v.132 vcf file for genome recalibration or ercclowpur99skip50basepolyA.vcf for spike-in standard recalibration.
Genome Build:
111014_09-01-0257_nopair_bwa_hg18_ERCConly_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
111014_09-01-0257_nopair_bwa_hg18_hg18only_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18

source_name: RNA extracted from B Lymphoblastoid cell lines established by Epstein-Barr Virus, with equimolar concentrations of ERCC spike-in standards at 5 % of total RNA

extract_protocol: Total RNA was extracted using the Rneasy Mini kit (Qiagen, MD).  Fragmentation was performed using the Covaris S2AFA platform, and size selection of adapter-ligated cDNA was done using the Pippin Prep instrument.


title: 08-01-0277

data_processing:
The raw data was mapped using Bioscope v.1.3 (for SOLiD data) or bwa v.0.5.9 (for Illumina data) to hg18 with the ERCC spike-in sequences appended, using default mapping parameters. The BAM files were split into reads mapping to hg18 or to the spike-ins, and base quality score recalibration was done separately on these two files.  To generate base quality score recalibration tables, GATK v.1.2-62 was used with the dbSNP v.132 vcf file for genome recalibration or ercclowpur99skip50basepolyA.vcf for spike-in standard recalibration.
Genome Build:
111014_08-01-0277_nopair_bwa_hg18_ERCConly_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
111014_08-01-0277_nopair_bwa_hg18_hg18only_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18

value: RNA extracted from B Lymphoblastoid cell lines established by Epstein-Barr Virus, with equimolar concentrations of ERCC spike-in standards at 5 % of total RNA


title: 08-01-0417

data_processing:
The raw data was mapped using Bioscope v.1.3 (for SOLiD data) or bwa v.0.5.9 (for Illumina data) to hg18 with the ERCC spike-in sequences appended, using default mapping parameters. The BAM files were split into reads mapping to hg18 or to the spike-ins, and base quality score recalibration was done separately on these two files.  To generate base quality score recalibration tables, GATK v.1.2-62 was used with the dbSNP v.132 vcf file for genome recalibration or ercclowpur99skip50basepolyA.vcf for spike-in standard recalibration.
Genome Build:
111014_08-01-0417_nopair_bwa_hg18_ERCConly_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
111014_08-01-0417_nopair_bwa_hg18_hg18only_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18


title: 08-01-0462

data_processing:
The raw data was mapped using Bioscope v.1.3 (for SOLiD data) or bwa v.0.5.9 (for Illumina data) to hg18 with the ERCC spike-in sequences appended, using default mapping parameters. The BAM files were split into reads mapping to hg18 or to the spike-ins, and base quality score recalibration was done separately on these two files.  To generate base quality score recalibration tables, GATK v.1.2-62 was used with the dbSNP v.132 vcf file for genome recalibration or ercclowpur99skip50basepolyA.vcf for spike-in standard recalibration.
Genome Build:
111014_08-01-0462_nopair_bwa_hg18_ERCConly_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
111014_08-01-0462_nopair_bwa_hg18_hg18only_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18


title: BLM1Plus

data_processing:
The raw data was mapped using Bioscope v.1.3 (for SOLiD data) or bwa v.0.5.9 (for Illumina data) to hg18 with the ERCC spike-in sequences appended, using default mapping parameters. The BAM files were split into reads mapping to hg18 or to the spike-ins, and base quality score recalibration was done separately on these two files.  To generate base quality score recalibration tables, GATK v.1.2-62 was used with the dbSNP v.132 vcf file for genome recalibration or ercclowpur99skip50basepolyA.vcf for spike-in standard recalibration.
Genome Build:
101214_WT1_FC1_PE_Quad_1_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC1_PE_Quad_1_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC1_PE_Quad_4_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC1_PE_Quad_4_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_1_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_1_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_4_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_4_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18

source_name: 45:30:25 mixture of brain, liver, and muscle RNA, respectively, with large dynamic concentration range of ERCC spike-in standards at 5 % of total RNA

extract_protocol: Five micrograms of each total RNA plus spike sample was ribodepleted using the RiboMinus™ Human/Mouse Transcriptome Isolation Kit, Catalog Number K1550-01 (Invitrogen, Carlsbad, CA).  Approximately 400 ng of ribodepleted RNA in solution was converted to cDNA libraries with SOLiD™ adaptors and barcodes, using the SOLiD™ Total RNA-Seq Kit, PN 4445374, and protocol PN4452437 Rev. A (Life Technologies, Carlsbad, CA).  Ribodepleted RNA was enzymatically fragmented with RNase III using the stated protocol methods and assessed on a  2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) with the RNA 6000 Pico Kit (Agilent Technologies, Santa Clara,  CA).  Fragment distributions were found to have a median size of approximately 125 base pairs.  SOLiD™ adaptors were then ligated onto the RNA and the RNA reverse transcribed.  cDNA products were then amplified and uniquely barcoded using the SOLiD™ RNA Barcoding Kit, Modules 17-32 (Life Technologies, Carlsbad, CA).  Following barcoding and amplification, completed cDNA libraries were assessed for size distribution and yield on the 2100 Bioanalyzer with the DNA 1000 Kit (Agilent Technologies, Santa Clara, CA).


title: G1ME_GATA2

description:
Chromatin IP against GATA2
Cells were derived from J1 ES cells [Fujiwara, PNAS, 1996; Stachura, Blood, 2006].

tag: cell line

tag: antibody catalog number


title: H2Bub_MB_replicate1

tag: chromatin preparation method


title: U2OS_H3K27Me3_ChIP-seq

status: Public on Mar 02 2012

city: BALTIMORE

first: hari

last: easwaran

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

institute: Johns Hopkins University

description:
U2OS-H3K27Me3
The anti-H3K27Me3 antibody was a kind gift from Thomas Jenuwein/Nicholas Shukeir.

data_processing:
Sequencing reads were aligned to genome build hg18 (NCBI 36) using Bioscope 1.2.1. The software guarantees finding all alignments between the first 25 base pairs of the read (seed) and the reference sequence with up to 2 mismatches. Each match is extended to the full length of the read, scoring 1 point for matching and -2 points for mismatching bases. The read is trimmed to the length with the highest score. If there is only one alignment or if an alignment scores significantly higher than the others for the same read, it is considered unique and reported. Aligned reads were analyzed using Model-based Analysis of ChIP-Seq (MACS) to detect regions enriched for the histone marks (called peaks) with default settings. Input was used as background for peak identification.
Genome Build:
U2_hg18.gff3: hg18
U2vUinput_extend_peaks.bed: hg18

source_name: U2OS cell line, H3K27Me3 ChIP

growth_protocol: MSCs derived from adult  bone marrow were cultured and differentiated to osteoblasts as described by Jaiswal et al., 1997 (J Cell Biochem 64, 295-312 (PMID 9027589)). U2OS cells were cultured in McCoy's 5A medium supplemented with 10% FBS.

extract_protocol:
Cells were crosslinked in 3.7% formaldehyde, lysed and sonicated to obtain chromatin fragments in the range of 200 to 600 base pairs. Sonicated chromatin was incubated with primary antibody, H3K4Me3 (Millipore, 07-473) or H3K27Me3 (kind gift from Thomas Jenuwein/ Nicholas Shukeir), overnight at 4°C, followed by capturing primary antibodies by adding ProteinA/G magnetic beads (DynaBeads) and incubating at room temperature for 3-4 hrs. Captured chromatin was washed in low- and high-salt buffers, as well as TE. Chromatin fragments were subjected to simultaneous elution, de-crosslinking and Proteinase-K treatment at 65°C in elution buffer followed by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
Following elution, the immunoprecipitated DNA was end repaired and then purified with Agencourt AMPure magnetic beads. Fragments were then ligated with SOLiD System's P1 and P2 adaptors, followed by another purification step using Agencourt's AMPure magnetic beads, followed by nick translation and amplification using the SOLiD library PCR primers 1 and 2.  After amplification, the samples were purified with the Agencourt AMPure magnetic beads once again and the final library was quantitated by performing qPCR and run through the Agilent Bioanalyzer for QC analysis. New England BioLabs NEBNext DNA Sample Prep Master Mix 3 was used for library construction.

treatment_protocol: No treatment.

tag: cell identity

value: osteosarcoma cancer cells

value: osteosarcoma cell line


title: p53_ChIP_seq_Adr8h

description: Treated with adriamycin, chromatin IP against p53.

source_name: embryonic stem cells, treated, p53 ChIP


title: U2OS_H3K4Me3_ChIP-seq

data_processing:
Sequencing reads were aligned to genome build hg18 (NCBI 36) using Bioscope 1.2.1. The software guarantees finding all alignments between the first 25 base pairs of the read (seed) and the reference sequence with up to 2 mismatches. Each match is extended to the full length of the read, scoring 1 point for matching and -2 points for mismatching bases. The read is trimmed to the length with the highest score. If there is only one alignment or if an alignment scores significantly higher than the others for the same read, it is considered unique and reported. Aligned reads were analyzed using Model-based Analysis of ChIP-Seq (MACS) to detect regions enriched for the histone marks (called peaks) with default settings. Input was used as background for peak identification.
Genome Build:
U1_hg18.gff3: hg18
U1vUinput_extend_peaks.bed: hg18

source_name: U2OS cell line, H3K4Me3 ChIP

value: Millipore


title: Osteoblasts_H3K4Me3_ChIP-seq

data_processing:
Sequencing reads were aligned to genome build hg18 (NCBI 36) using Bioscope 1.2.1. The software guarantees finding all alignments between the first 25 base pairs of the read (seed) and the reference sequence with up to 2 mismatches. Each match is extended to the full length of the read, scoring 1 point for matching and -2 points for mismatching bases. The read is trimmed to the length with the highest score. If there is only one alignment or if an alignment scores significantly higher than the others for the same read, it is considered unique and reported. Aligned reads were analyzed using Model-based Analysis of ChIP-Seq (MACS) to detect regions enriched for the histone marks (called peaks) with default settings. Input was used as background for peak identification.
Genome Build:
O1_hg18.gff3: hg18
O1vOinput_extend_peaks.bed: hg18

source_name: Osteoblasts derived from MSCs, H3K4Me3 ChIP

value: osteoblasts

value: differentiated cell


title: U2OS_input_ChIP-seq

data_processing:
Sequencing reads were aligned to genome build hg18 (NCBI 36) using Bioscope 1.2.1. The software guarantees finding all alignments between the first 25 base pairs of the read (seed) and the reference sequence with up to 2 mismatches. Each match is extended to the full length of the read, scoring 1 point for matching and -2 points for mismatching bases. The read is trimmed to the length with the highest score. If there is only one alignment or if an alignment scores significantly higher than the others for the same read, it is considered unique and reported. Aligned reads were analyzed using Model-based Analysis of ChIP-Seq (MACS) to detect regions enriched for the histone marks (called peaks) with default settings. Input was used as background for peak identification.
Genome Build:
U2OS_input_hg18.gff3: hg18

source_name: U2OS cell line, input


title: Osteoblasts_input_ChIP-seq

description: Osteoblasts-input

data_processing:
Sequencing reads were aligned to genome build hg18 (NCBI 36) using Bioscope 1.2.1. The software guarantees finding all alignments between the first 25 base pairs of the read (seed) and the reference sequence with up to 2 mismatches. Each match is extended to the full length of the read, scoring 1 point for matching and -2 points for mismatching bases. The read is trimmed to the length with the highest score. If there is only one alignment or if an alignment scores significantly higher than the others for the same read, it is considered unique and reported. Aligned reads were analyzed using Model-based Analysis of ChIP-Seq (MACS) to detect regions enriched for the histone marks (called peaks) with default settings. Input was used as background for peak identification.
Genome Build:
Osteo_input_hg18.gff3: hg18

source_name: Osteoblasts derived from MSCs, input


title: MSC_H3K27Me3_ChIP-seq

description:
MSC-H3K27Me3
The anti-H3K27Me3 antibody was a kind gift from Thomas Jenuwein/Nicholas Shukeir.

data_processing:
Sequencing reads were aligned to genome build hg18 (NCBI 36) using Bioscope 1.2.1. The software guarantees finding all alignments between the first 25 base pairs of the read (seed) and the reference sequence with up to 2 mismatches. Each match is extended to the full length of the read, scoring 1 point for matching and -2 points for mismatching bases. The read is trimmed to the length with the highest score. If there is only one alignment or if an alignment scores significantly higher than the others for the same read, it is considered unique and reported. Aligned reads were analyzed using Model-based Analysis of ChIP-Seq (MACS) to detect regions enriched for the histone marks (called peaks) with default settings. Input was used as background for peak identification.
Genome Build:
M2_hg18.gff3: hg18
M2vMinput_extend_peaks.bed: hg18

source_name: Adult bone marrow MSCs, H3K27Me3 ChIP

tag: tissue

value: bone marrow

value: mesenchymal stem cells (MSCs)

value: adult stem cell


title: MSC_input_ChIP-seq

description: MSC-input

data_processing:
Sequencing reads were aligned to genome build hg18 (NCBI 36) using Bioscope 1.2.1. The software guarantees finding all alignments between the first 25 base pairs of the read (seed) and the reference sequence with up to 2 mismatches. Each match is extended to the full length of the read, scoring 1 point for matching and -2 points for mismatching bases. The read is trimmed to the length with the highest score. If there is only one alignment or if an alignment scores significantly higher than the others for the same read, it is considered unique and reported. Aligned reads were analyzed using Model-based Analysis of ChIP-Seq (MACS) to detect regions enriched for the histone marks (called peaks) with default settings. Input was used as background for peak identification.
Genome Build:
MSCinput_hg18.gff3: hg18

source_name: Adult bone marrow MSCs, input


title: Osteoblasts_H3K27Me3_ChIP-seq

description:
Osteoblasts-H3K27Me3
The anti-H3K27Me3 antibody was a kind gift from Thomas Jenuwein/Nicholas Shukeir.

data_processing:
Sequencing reads were aligned to genome build hg18 (NCBI 36) using Bioscope 1.2.1. The software guarantees finding all alignments between the first 25 base pairs of the read (seed) and the reference sequence with up to 2 mismatches. Each match is extended to the full length of the read, scoring 1 point for matching and -2 points for mismatching bases. The read is trimmed to the length with the highest score. If there is only one alignment or if an alignment scores significantly higher than the others for the same read, it is considered unique and reported. Aligned reads were analyzed using Model-based Analysis of ChIP-Seq (MACS) to detect regions enriched for the histone marks (called peaks) with default settings. Input was used as background for peak identification.
Genome Build:
O2_hg18.gff3: hg18
O2vOinput_extend_peaks.bed: hg18

source_name: Osteoblasts derived from MSCs, H3K27Me3 ChIP


title: MSC_H3K4Me3_ChIP-seq

data_processing:
Sequencing reads were aligned to genome build hg18 (NCBI 36) using Bioscope 1.2.1. The software guarantees finding all alignments between the first 25 base pairs of the read (seed) and the reference sequence with up to 2 mismatches. Each match is extended to the full length of the read, scoring 1 point for matching and -2 points for mismatching bases. The read is trimmed to the length with the highest score. If there is only one alignment or if an alignment scores significantly higher than the others for the same read, it is considered unique and reported. Aligned reads were analyzed using Model-based Analysis of ChIP-Seq (MACS) to detect regions enriched for the histone marks (called peaks) with default settings. Input was used as background for peak identification.
Genome Build:
M1_hg18.gff3: hg18
M1vMinput_extend_peaks.bed: hg18

source_name: Adult bone marrow MSCs, H3K4Me3 ChIP


title: BLM2Plus

data_processing:
The raw data was mapped using Bioscope v.1.3 (for SOLiD data) or bwa v.0.5.9 (for Illumina data) to hg18 with the ERCC spike-in sequences appended, using default mapping parameters. The BAM files were split into reads mapping to hg18 or to the spike-ins, and base quality score recalibration was done separately on these two files.  To generate base quality score recalibration tables, GATK v.1.2-62 was used with the dbSNP v.132 vcf file for genome recalibration or ercclowpur99skip50basepolyA.vcf for spike-in standard recalibration.
Genome Build:
101214_WT1_FC1_PE_Quad_1_BLM2_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC1_PE_Quad_1_BLM2_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC1_PE_Quad_4_BLM2_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC1_PE_Quad_4_BLM2_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_1_BLM2_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_1_BLM2_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_4_BLM2_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_4_BLM2_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18

source_name: 30:45:25 mixture of brain, liver, and muscle RNA, respectively, with large dynamic concentration range of ERCC spike-in standards at 5 % of total RNA


title: Uwe_H3K9me2_IFNaR_KO_unstDCs_4

description: chromatin IP against H3K9me2 in IFNaR1 -/- splenic DCs

data_processing: Raw data processed using onboard SCS/RTA 2.6, alignments performed using Bowtie keeping only unique reads with 2 or fewer mismatches in 36bp. Alignments summed in 100bp windows for wig files and integrated profiles.

source_name: DC

growth_protocol: MEFs were grown in 10 cm plates with DMEM medium containing 15% FBS, Pen/Strep, Glutamine, NEAA and 2-mercaptoethanol. After immortalization with SV40-LTA, MEFs were grown in 15 cm plates with the same medium except FBS was 10%. DC were isolated from WT C57Bl/6 or IFNaR1 -/- mice that subcutaneously injected with B16-Flt3L cells. 2 weeks later splenic DCs were enriched for the CD11c+ population using CD11c MACS beads.  ChIP was carried out directly on ex vivo isolated cells.

treatment_protocol: Primary MEFs were immortalized at passage 2. At passage 5,  MEFs were treated with either EtOH as a vehicle control or Tamoxifen to induce deletion of G9a.  MEFs were either left untreated, treated with Lipofectamine 200, the tranfection reagent or tranfected with PolyIC.

tag: strain

value: Splenic dendritic cells

tag: genotype

value: Ex vivo isolated

tag: vendor

value: Abcam (ab1220)

tag: lot


title: Uwe_H3K9me2_IFNaR_KO_unstDCs_3


title: Uwe_H3K9me2_IFNaR_KO_unstDCs_2


title: Uwe_H3K4me3_WT

description: chromatin IP against H3K4me3 in WT splenic DCs

value: WT

value: Millipore (17614)


title: Uwe_H3K9me2_WT_unstDCs_4

description: chromatin IP against H3K9me2 in WT splenic DCs


title: H3K9me2_IFNaR_KO_unstDCs


title: HTR13 Myc ChIP-seq

description: Sample 2

data_processing:
Alignment: Sequence reads were obtained and mapped to the TAIR8 Arabidospis genome using Bowtie (Langmead et al., 2009 Genome Biol). Uniquely mapping with two or fewer mismatches were retained. Reads mapping to identical positions were collapsed into one read.
HTR13_ChIP_mapped.txt; genome build: TAIR8

source_name: HTR13 Myc ChIP-seq


title: Uwe_H3K9me2_WT_unstDCs_3


title: Uwe_H3K9me2_WT_unstDCs_2


title: G9a_minus_minus_L2K_PolII_total

description: chromatin IP against Pol II in G9a -/- MEFs treated with transfection reagent only

source_name: MEF

value: Fibroblasts from day 13.5 embryos immortalized with SV40-LTA

value: G9a -/-, ERT2-Cre

value: Passaged 12-15 times

value: Pol II

value: Abcam (ab5408)

tag: treatment

value: treated with transfection reagent only


title: G9a_minus_minus_L2K_H3K9me2

description: chromatin IP against H3K9me2 in G9a -/- MEFs treated with transfection reagent only

tag: cell type


title: G9a_minus_minus_L2K_H3K9Ac

description: chromatin IP against H3K9Ac in G9a -/- MEFs treated with transfection reagent only

tag: passages


title: G9a_minus_minus_4h_pIC_H3K9Ac

description: chromatin IP against H3K9Ac in G9a -/- MEFs transfected with polyIC

value: transfected with polyIC


title: G9a_minus_minus_L2K_H3K4me3

description: chromatin IP against H3K4me3 in G9a -/- MEFs treated with transfection reagent only

value: Abcam (ab4441)


title: G9a_minus_minus_4h_pIC_H3K9me2_redo

description: chromatin IP against H3K9me2 in G9a -/- MEFs transfected with polyIC


title: G9a_f_f_L2K_H3K9me2

description: chromatin IP against H3K9me2 in G9a f/f MEFs treated with transfection reagent only

value: G9a f/f, ERT2-Cre


title: G9a_minus_minus_4h_pIC_PolII_total

description: chromatin IP against Pol II in G9a -/- MEFs transfected with polyIC


title: G9a_minus_minus_4h_pIC_H3K4me3

description: chromatin IP against H3K4me3 in G9a -/- MEFs transfected with polyIC


title: G9a_minus_minus_L2K_H3K9me2_redo


title: G9a_f_f_L2K_PolII_total

description: chromatin IP against Pol II in G9a f/f MEFs treated with transfection reagent only


title: G9a_minus_minus_4h_pIC_H3K36me3

description: chromatin IP against H3K36me3 in G9a -/- MEFs transfected with polyIC

value: Abcam (ab9050)


title: G9a_minus_minus_4h_pIC_H3K9me2


title: G9a_f_f_L2K_H3K9me2_redo


title: G9a_minus_minus_L2K_H3K36me3

description: chromatin IP against H3K36me3 in G9a -/- MEFs treated with transfection reagent only


title: Uwe_H3K9me2_WT_unstDCs_1


title: G9a_f_f_L2K_H3K4me3

description: chromatin IP against H3K4me3 in G9a f/f MEFs treated with transfection reagent only


title: G9a_f_f_L2K_H3K9Ac

description: chromatin IP against H3K9Ac in G9a f/f MEFs treated with transfection reagent only


title: G9a_f_f_4h_pIC_H3K4me3

description: chromatin IP against H3K4me3 in G9a f/f cells transfected with polyIC


title: G9a_f_f_4h_pIC_H3K9me2

description: chromatin IP against H3K9me2 in G9a f/f cells transfected with polyIC


title: G9a_f_f_L2K_H3K36me3

description: chromatin IP against H3K36me3 in G9a f/f MEFs treated with transfection reagent only


title: G9a_f_f_4h_pIC_PolII_total

description: chromatin IP against Pol II in G9a f/f MEFs transfected with polyIC


title: H3K9me2 WT 5

description: chromatin IP against H3K9me2 in G9a f/f cells

growth_protocol: MEFs were grown in 10 cm plates with DMEM medium containing 15% FBS, Pen/Strep, Glutamine, NEAA and 2-mercaptoethanol. After immortalization with SV40-LTA, MEFs were grown in 15 cm plates with the same medium except FBS was 10%.

treatment_protocol: Primary MEFs were immortalized at passage 2. At passage 5,  MEFs were treated witheither EtOH as a vehicle control or Tamoxifen to induce deletion of G9a.


title: H3K9me2 G9a KO 3

description: chromatin IP against H3K9me2 in G9a -/- cells


title: H3K9me2 G9a KO 4


title: G9a_f_f_4h_pIC_H3K9me2_redo

description: chromatin IP against H3K9me2 in G9a f/f MEFs transfected with polyIC


title: G9a_f_f_4h_pIC_H3K9Ac

description: chromatin IP against H3K9Ac in G9a f/f cells transfected with polyIC


title: H3K9me2 WT 2


title: G9a_f_f_4h_pIC_H3K36me3

description: chromatin IP against H3K36me3 in G9a f/f cells transfected with polyIC


title: H3K9me2 WT 4


title: H3K9me2 G9a KO 5


title: H3K9me2 G9a KO 2


title: H3K9me2 WT 3


title: H3K9me2 WT 1


title: H3K9me2 G9a KO 1


title: Small RNA population (drb4)

status: Public on Mar 01 2012

city: Perpignan

first: Jean-Marc

last: Deragon

address: 58 avenue Paul Alduy

department: Biology

country: France

institute: Université de Perpignan, CNRS

description: 21 to 24-nt

data_processing: Small read counts were normalized by taking highly expressed conserved miRNAs that were shown by northern hybridization to be invariant in Col0, and calculating normalization factors for each condition. The normalized data was cross-confirmed by calculating the normalization factor for all significantly expressed 36-nt (that represent general breakdown RNA products), which yielded similar values. Only small RNAs having 10 or more read counts in at least one condition were considered

source_name: immature flowers

growth_protocol: Plant seeds were stratified for two days at 4°C before growth in chambers on soil at 23°C under a 16h-light/8h-dark cycle.

extract_protocol: Total RNA was extracted as described in Pelissier et al. (2004) NAR 32:3957-3966) using immature floral inflorescences (stages 1-12). 12 to 18ug of total RNA samples were heat-treated in 1.5 volume of standard formamide buffer and loaded on 15% polyacrylamide (19 :1 acrylamide :bis-acrylamide) – 8.3M urea - 0.5X TBE gel and separated by electrophoresis. Small RNAs (18 to 36 nucleotides) were cut out of the gels, used to construct libraries according to the manufacturer protocol (Illumina Small RNA Sample Prep Kits) and sequenced on a HiSeq 2000 system (Illumina) at the MGX platform (http://www.mgx.cnrs.fr/)

tag: ecotype

tag: developmental stage

value: inflorescences stages 1-12

tag: genotype/variation

value: drb4-1 mutant


title: Small RNA population (drb2)

description: 21 to 24-nt

value: drb2-1 mutant


title: embryo_sphere_rep2

city: Boston

first: Chunyao

last: Wei

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Mass General Hospital

data_processing:
fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm, which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a "_x" and the reads counts. e.g. unique ID_x counts.
alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm, which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome (Zv8) from Ensembl (http://www.ensembl.org) were retrieved using megaBLAST (http://www.ncbi.nlm.nih.gov/blast/megablast.shtml) and Bowtie (http://bowtie-bio.sourceforge.net/tutorial.shtml). To identify piRNAs, consensus sequences from zebrafish repetitive elements were retrieved from Repbase (http://www.girinst.org/repbase/index.html) and Repeat Maskers using the UCSC genome browser (http://genome.ucsc.edu).  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence.
fasta files description: small RNA 15-30 nt
alignment file description: piRNA map to repetitive elements

organism: Danio rerio

source_name: the whole embryo

growth_protocol: Embryos were raised at 28Â°C in egg water (0.03% Instant Ocean marine salt mix) for the initial several hours of development

extract_protocol: Zebrafish embryos were collected at the 256-cell stage, sphere stage, shield stage, and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15-30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR, as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.

value: AB*WT

value: sphere

value: the whole embryos


title: embryo_1dpf_rep1


title: embryo_Shield_rep1

value: Shield


title: LB

city: Baltimore

first: Jason

last: Sahl

address: 801 West Baltimore St.

department: School of Medicine

institute: University of Maryland

data_processing: Reads were mapped to the chromosome and six plasmids with bwa.  GenomeCoverageBed was then used to map the coverage across the genome.

organism: Escherichia coli O139:H28 str. E24377A

source_name: Bacterial culture

growth_protocol: Single colony was grown in 5ml LB overnight.  Culture was diluted 1:100 in 25ml LB.  Growth conditions consisted of 37C at 225 rpm until an OD600=0.5 was reached.

extract_protocol: Paired end libraries were generated for each sample: insert size=300bp, insert size stdev:150bp

treatment_protocol: RNA was extracted using an acid phenol/lithium chloride method.  rRNA was depleted with the RiboZero kit from Ambion.

value: LB


title: LB + bile

value: LB + bile


title: embryo_sphere_rep1


title: embryo_256-cell_rep1

value: AB* WT


title: Af_replicate1

city: Guangzhou

first: Zhumei

last: He

address: 135 Xingangxi Street

country: China

institute: Sun Yat-sen University

description: sample for paired-end library with insert size of 200 bp

data_processing: After removal of the adaptor sequences, the 49 bp reads from each of the biological replicates were aligned to the A. flavus genome. Because of the strand specificity of DNA methylation, two rounds of alignments were carried out. All cytosines of the bisulfite-converted reads were transformed to thymine and aligned to the genome sequences termed the "T genome", whose cytosines had been converted to thymine. Also, all guanine of the bisulfite converted reads were transformed to adenosine and aligned to the genome sequences termed the "A genome" whose guanines had been converted to adenosine. The alignments were carried out with BGI SOAPaligner verison 2.01, allowing up to two mismatches for successful mapping. And then, we transformed each aligned read and the two strands of the A. flavus genome back to their original forms to build an alignment between the original forms. Cytosines in the BS-seq reads that are also matched to the corresponding cytosines in the plus (Watson) strand, or otherwise guanines in the MethylC-seq reads, that are also matched to the corresponding guanines in the minus (Crick) strand will be regarded as potential 5mCs. We emphasized this here for easier comprehension of the further analysis. We carried out several filtrations of the data to ensure the accuracy for methylation calls. First, we filtered out all cytosines with an Illumina Q score smaller than 20, which guaranteed that a base was correctly called at more than 99% probability. Second, multiple reads mapped to the same start positions as well as the same end positions were defined as clonal duplicates because these events seldom occur with the sonicated pair-end reads. We filtered these reads to avoid inaccuracy that might be caused by the bias during the PCR amplification. Third, we filtered out the reads that were mapped to multiple sites within the genome. Finally, all the+B7 non-clonal reads with sufficient Q scores and unambiguously mapped to the genome were applied for further analysis.

organism: Aspergillus flavus

source_name: fungal mycelium DNA

growth_protocol: using fresh mycelium of aspergillus flavus

extract_protocol: Genomic DNA was extracted from A. flavus mycelia using a modified method as described on the web site of Integrated Fungal Research Center (http://www.aspergillusflavus.org/protocols/). A total of 2 g of mycelia, obtained through filtered culture, was grinded to a fine powder in liquid nitrogen. The powder was promptly scooped into a 10 ml tube containing 2 ml phenol and 4 ml H buffer (10 mM Tris-HCl, pH 7.5; 100 mM LiCl; 10 mM EDTA; 0.5% SDS), and vortexed thoroughly. The suspension was incubated at 60°C for 5 min and cooled on ice before 2 ml chloroform: isoamyl alcohol (24:1, v/v) was added. After centrifugation at 11 000 rpm in 4°C for 10 min, the aqueous layer was transferred into a fresh tube. A total volume of 4 ml phenol and 4 ml chloroform: isoamyl alcohol (24:1, v/v) were used successively to purify DNA. The aqueous layer was transferred into a fresh tube. NaAc and isopropanol were added to a final concentration of 0.3 M and 50% (v/v), respectively, mixed gently, and placed in a -20°C freezer for at least 45 min for precipitation. After centrifugation at 11 000 rpm in 4°C for 10 min, the precipitate was resuspended in 2 ml TE buffer containing 10 ug/ml protease K and incubated in 37°C for over 60 min. Another 2 ml TE was add before 4 ml phenol and 4 ml chloroform: isoamyl alcohol (24:1, v/v) were used successively to purify DNA. RNase I was added into the aqueous layer collection with a final concentration of 10 ug/ml and then incubated at 37°C for at least 60 min. A volume of 4 ml chloroform: isoamyl alcohol (24:1, v/v) were used several times to remove the impurities completely. NaAc and isopropanol were added into the aqueous layer collection to a final concentration of 0.3 M and 50% (v/v) respectively, mixed gently, and placed in -20°C freezer for at least 1 h for precipitation. The mixture was then centrifuged for 10 min at 11 000 rpm in 4°C. After washing with 70% ethanol twice, the precipitated DNA was resuspended in 100 ul TE buffer. The concentration and purity of DNA was determined by the measurement of A260 and A280 using a NanoVue spectrophotometer (GE Healthcare).

treatment_protocol: bisulphite treated

value: mycelium cells


title: ES_XX_Solexa_i_IDT

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

description: Small RNA-Seq

data_processing:
The remaining part of the adapter sequences were removed from the reads. The trimmed reads were mapped on the mm9 genome using Bowtie. Respectively, two mismatches in nucleotide space or colour space were allowed for the mapping of the 454 and the SOLiD data, while for Solexa the sum of qualities of mismatching bases was required to not exceed 50. Only the best alignments are reported for each reads. The reads with up to 5,000 repeated alignments on the genome were used for the repeats analysis.

Mature miRNAs profiling: The genomic positions of mature miRNAs and miR* were obtained from the database miRBase (release 16). Aligned reads of length 19-26nt were considered to correspond to a mature miRNA (or miR*) only if: 1) the aligned position did not differ from the annotated position of the mature miRNA by more than 2 bp and 2) the reads had at most as many genomic match positions as the number of genomic copies of the respective mature miRNA. The miRNA profiling data are in the supplementary *miRNA.bed files.

Repeats profiling: The repeats profiles contain the coverage of raw reads mapped on the genome (without pre-miRNAs) and intersected with the RepeatMasker annotation. Strands are separated. These profiles are not normalized. The repeats profiling data are in the supplementary *rmsk.bed files.

Genome Build:
ES_XX_Solexa_i_IDT_minus_rmsk.bed: mm9
ES_XX_Solexa_i_IDT_plus_rmsk.bed: mm9
ES_XX_Solexa_i_IDT_miRNA.bed: mm9

source_name: ES PGK female cells

growth_protocol: Female PGK and male E14 embryonic stem (ES) cell lines (from the Dr. E. Heard laboratory) were cultured in Dulbecco’s Modified Eagle Media (DMEM) (Invitrogen) containing 15% FCS (Bio West), 1000 U/ml LIF (Chemicon), 0.1 mM beta-mercaptoethanol (Invitrogen), 0.05 mg/ml of streptomycin (Invitrogen) and 50 U/ml of penicillin (Invitrogen) on a gelatin-coated support in the absence of feeder cells. The culture medium was changed daily. All cells were grown at 37°C in 8% CO2.

extract_protocol: Total cellular RNA samples (5-10 μg), prepared using Trizol reagent (MRC Molecular Research Center), were processed into sequencing libraries using: 1) a homemade protocol (Pfeffer, 2007) for the 454 technology and sequenced at Genoscope (Evry, France), 2) adapted Illumina protocols for Solexa technology and sequenced by Fasteris ((http://www.fasteris.com, Switzerland), and 3) the Small RNA Expression Kit (SREK, Life Technology, version C)  and the SOLiD Total RNA kit (STaR-Seq, Life Technology) for the SOLiD technology and sequenced at Institut Curie (Paris, France) or Life Technology (USA).

value: PGK

value: embryonic stem cells

tag: technology

value: Solexa

tag: barcode/index

value: index

tag: comment

value: Illumina 3' adapter


title: ES_XY_SOLID_v3

description: Small RNA-Seq

data_processing:
The remaining part of the adapter sequences were removed from the reads. The trimmed reads were mapped on the mm9 genome using Bowtie. Respectively, two mismatches in nucleotide space or colour space were allowed for the mapping of the 454 and the SOLiD data, while for Solexa the sum of qualities of mismatching bases was required to not exceed 50. Only the best alignments are reported for each reads. The reads with up to 5,000 repeated alignments on the genome were used for the repeats analysis.

Mature miRNAs profiling: The genomic positions of mature miRNAs and miR* were obtained from the database miRBase (release 16). Aligned reads of length 19-26nt were considered to correspond to a mature miRNA (or miR*) only if: 1) the aligned position did not differ from the annotated position of the mature miRNA by more than 2 bp and 2) the reads had at most as many genomic match positions as the number of genomic copies of the respective mature miRNA. The miRNA profiling data are in the supplementary *miRNA.bed files.

Repeats profiling: The repeats profiles contain the coverage of raw reads mapped on the genome (without pre-miRNAs) and intersected with the RepeatMasker annotation. Strands are separated. These profiles are not normalized. The repeats profiling data are in the supplementary *rmsk.bed files.

Genome Build:
ES_XY_SOLID_v3_minus_rmsk.bed: mm9
ES_XY_SOLID_v3_plus_rmsk.bed: mm9
ES_XY_SOLID_v3_miRNA.bed: mm9

source_name: ES E14 male cells

tag: cell line

value: SOLiD

value: SREK kit v.B


title: ES_XX_SOLID_v3

description: Small RNA-Seq

data_processing:
The remaining part of the adapter sequences were removed from the reads. The trimmed reads were mapped on the mm9 genome using Bowtie. Respectively, two mismatches in nucleotide space or colour space were allowed for the mapping of the 454 and the SOLiD data, while for Solexa the sum of qualities of mismatching bases was required to not exceed 50. Only the best alignments are reported for each reads. The reads with up to 5,000 repeated alignments on the genome were used for the repeats analysis.

Mature miRNAs profiling: The genomic positions of mature miRNAs and miR* were obtained from the database miRBase (release 16). Aligned reads of length 19-26nt were considered to correspond to a mature miRNA (or miR*) only if: 1) the aligned position did not differ from the annotated position of the mature miRNA by more than 2 bp and 2) the reads had at most as many genomic match positions as the number of genomic copies of the respective mature miRNA. The miRNA profiling data are in the supplementary *miRNA.bed files.

Repeats profiling: The repeats profiles contain the coverage of raw reads mapped on the genome (without pre-miRNAs) and intersected with the RepeatMasker annotation. Strands are separated. These profiles are not normalized. The repeats profiling data are in the supplementary *rmsk.bed files.

Genome Build:
ES_XX_SOLID_v3_minus_rmsk.bed: mm9
ES_XX_SOLID_v3_plus_rmsk.bed: mm9
ES_XX_SOLID_v3_miRNA.bed: mm9


title: ES_XY_Solexa_Illu

description: Small RNA-Seq

data_processing:
The remaining part of the adapter sequences were removed from the reads. The trimmed reads were mapped on the mm9 genome using Bowtie. Respectively, two mismatches in nucleotide space or colour space were allowed for the mapping of the 454 and the SOLiD data, while for Solexa the sum of qualities of mismatching bases was required to not exceed 50. Only the best alignments are reported for each reads. The reads with up to 5,000 repeated alignments on the genome were used for the repeats analysis.

Mature miRNAs profiling: The genomic positions of mature miRNAs and miR* were obtained from the database miRBase (release 16). Aligned reads of length 19-26nt were considered to correspond to a mature miRNA (or miR*) only if: 1) the aligned position did not differ from the annotated position of the mature miRNA by more than 2 bp and 2) the reads had at most as many genomic match positions as the number of genomic copies of the respective mature miRNA. The miRNA profiling data are in the supplementary *miRNA.bed files.

Repeats profiling: The repeats profiles contain the coverage of raw reads mapped on the genome (without pre-miRNAs) and intersected with the RepeatMasker annotation. Strands are separated. These profiles are not normalized. The repeats profiling data are in the supplementary *rmsk.bed files.

Genome Build:
ES_XY_Solexa_Illu_minus_rmsk.bed: mm9
ES_XY_Solexa_Illu_plus_rmsk.bed: mm9
ES_XY_Solexa_Illu_miRNA.bed: mm9


title: ES_XY_Solexa_IDT

description: Small RNA-Seq

data_processing:
The remaining part of the adapter sequences were removed from the reads. The trimmed reads were mapped on the mm9 genome using Bowtie. Respectively, two mismatches in nucleotide space or colour space were allowed for the mapping of the 454 and the SOLiD data, while for Solexa the sum of qualities of mismatching bases was required to not exceed 50. Only the best alignments are reported for each reads. The reads with up to 5,000 repeated alignments on the genome were used for the repeats analysis.

Mature miRNAs profiling: The genomic positions of mature miRNAs and miR* were obtained from the database miRBase (release 16). Aligned reads of length 19-26nt were considered to correspond to a mature miRNA (or miR*) only if: 1) the aligned position did not differ from the annotated position of the mature miRNA by more than 2 bp and 2) the reads had at most as many genomic match positions as the number of genomic copies of the respective mature miRNA. The miRNA profiling data are in the supplementary *miRNA.bed files.

Repeats profiling: The repeats profiles contain the coverage of raw reads mapped on the genome (without pre-miRNAs) and intersected with the RepeatMasker annotation. Strands are separated. These profiles are not normalized. The repeats profiling data are in the supplementary *rmsk.bed files.

Genome Build:
ES_XY_Solexa_IDT_minus_rmsk.bed: mm9
ES_XY_Solexa_IDT_plus_rmsk.bed: mm9
ES_XY_Solexa_IDT_miRNA.bed: mm9

value: IDT 3' adapter


title: ES_XX_SOLID_v4

description: Small RNA-Seq

data_processing:
The remaining part of the adapter sequences were removed from the reads. The trimmed reads were mapped on the mm9 genome using Bowtie. Respectively, two mismatches in nucleotide space or colour space were allowed for the mapping of the 454 and the SOLiD data, while for Solexa the sum of qualities of mismatching bases was required to not exceed 50. Only the best alignments are reported for each reads. The reads with up to 5,000 repeated alignments on the genome were used for the repeats analysis.

Mature miRNAs profiling: The genomic positions of mature miRNAs and miR* were obtained from the database miRBase (release 16). Aligned reads of length 19-26nt were considered to correspond to a mature miRNA (or miR*) only if: 1) the aligned position did not differ from the annotated position of the mature miRNA by more than 2 bp and 2) the reads had at most as many genomic match positions as the number of genomic copies of the respective mature miRNA. The miRNA profiling data are in the supplementary *miRNA.bed files.

Repeats profiling: The repeats profiles contain the coverage of raw reads mapped on the genome (without pre-miRNAs) and intersected with the RepeatMasker annotation. Strands are separated. These profiles are not normalized. The repeats profiling data are in the supplementary *rmsk.bed files.

Genome Build:
ES_XX_SOLID_v4_minus_rmsk.bed: mm9
ES_XX_SOLID_v4_plus_rmsk.bed: mm9
ES_XX_SOLID_v4_miRNA.bed: mm9

value: barcode

value: STaR-Seq kit


title: Af_replicate2

description: sample for paired-end library with insert size of 250 bp


title: ES_XY_SOLID_v4

description: Small RNA-Seq

data_processing:
The remaining part of the adapter sequences were removed from the reads. The trimmed reads were mapped on the mm9 genome using Bowtie. Respectively, two mismatches in nucleotide space or colour space were allowed for the mapping of the 454 and the SOLiD data, while for Solexa the sum of qualities of mismatching bases was required to not exceed 50. Only the best alignments are reported for each reads. The reads with up to 5,000 repeated alignments on the genome were used for the repeats analysis.

Mature miRNAs profiling: The genomic positions of mature miRNAs and miR* were obtained from the database miRBase (release 16). Aligned reads of length 19-26nt were considered to correspond to a mature miRNA (or miR*) only if: 1) the aligned position did not differ from the annotated position of the mature miRNA by more than 2 bp and 2) the reads had at most as many genomic match positions as the number of genomic copies of the respective mature miRNA. The miRNA profiling data are in the supplementary *miRNA.bed files.

Repeats profiling: The repeats profiles contain the coverage of raw reads mapped on the genome (without pre-miRNAs) and intersected with the RepeatMasker annotation. Strands are separated. These profiles are not normalized. The repeats profiling data are in the supplementary *rmsk.bed files.

Genome Build:
ES_XY_SOLID_v4_minus_rmsk.bed: mm9
ES_XY_SOLID_v4_plus_rmsk.bed: mm9
ES_XY_SOLID_v4_miRNA.bed: mm9


title: E14_Day0_MRE-seq

status: Public on Feb 28 2012

city: La Jolla

first: Pengfei

last: Yu

state: CA

address: 9500 Gilman Drive MC 0419

department: Bioengineering

institute: University of California San Diego

data_processing:
Sequence reads were obtained and mapped to reference genomes (mm9, hg19, susScr2) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.
Genome Build:
E14_MRE.bed.gz: mm9
The processed data for MRE-seq is BedGraph format. Each row is a CpG site and the value in fourth column is the MRE signal at that CpG site.

source_name: mouse embryonic stem cells (E14)

growth_protocol: E14(mESC) were plated onto gelatin-coated dishes in Dulbecco's modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM -mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Millipore ESG1107) in incubator set at 37 ºC in 5% CO2.

extract_protocol:
The RNA extraction method is Trizol reagent (15596-026, Invitrogen).  The antibodies used in the experiment are listed below:  Histone H2A.Z antibody - ChIP Grade (ab4174), ab4174 Histone H3 (mono methyl K4) antibody - ChIP Grade , ab8895 Histone H3 (di methyl K4) antibody [Y47] - ChIP Grade (ab32356), ab32356 Histone H3 (tri methyl K4) antibody [mAbcam1012] - ChIP Grade (ab1012), ab1012 Histone H3 (tri methyl K4) antibody - ChIP Grade, ab8580 Histone H3 (tri methyl K9) antibody - ChIP Grade, ab8898 Histone H3 (tri methyl K36) antibody - ChIP Grade , ab9050 Histone H3 (acetyl K27) antibody - ChIP Grade, ab4729 antibody for TAF II p250 (6B3), sc735 Nanog antibody-ChIP Grade, ab21624 Oct4 antibody-ChIP Grade, ab19857 antibody for p300 (C-20), sc-585 KAT3B / p300 antibody [NM11] , ab3164 monoclonal antibody against 5-methylcytindine (catalog number: bi-mecy-0100)
DNA products for ChIP-seq are immuno-precipitated by antibodies of H3K27me3(Millipore, 07-449),H2AZ(Abcam, ab4174). MRE-seq was performed as described (NATURE| Vol 466|8 July 2010). DNA product for 5-hmC_ChIP-seq is generated by a selctive chemical labeling method (Nat. Methods 2011, 9, 75-77). Four parallel digests were performed (HpaII, Hin6I and SsiI are from Fermentas; HpyCH4IV is from NEB), each with 1 ug of DNA. Five units of enzyme per microgram DNA were added and incubated at 37˚C for 3 hrs. A second dose of five units-enzyme was added and the DNA was incubated for an additional 3 hrs. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube.  Combined DNA was size-selected by electrophoresis on a 1% agarose gel. A 100-500 bp gel slice was excised and gel-purified using Qiagen Qiaquick columns, eluting in 30 ul of Qiagen EB buffer. Library construction was performed using the Illumina Genomic DNA Sample kit with paired-end adapters, following the manufacturer’s instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the klenow DNA polymerase was diluted 1:5 in water and 1 ul used per reaction. For paired-end oligo adapter ligation, adapters were diluted 1:10 in water and 1 ul used per reaction. After the second size selection, DNA was eluted in 36 ul EB buffer using Qiagen Qiaquick columns, and 12 ul used as template for PCR, using Illumina reagents and cycling conditions with 15 cycles. After cleanup with Qiagen MinElute columns, each library is examined by Quant-iT™ dsDNA HS Assay Kit (Qubit, Invitrogen, USA) and Agilent DNA Biaanalyzer (Agilent, USA). The libraries were sequenced with an Illunima Hi-seq Sequencing Systems. MeDIP-seq was performed as described (NATURE| Vol 466|8 July 2010). 3 ug DNA isolated as described above was sonicated to ,100–500 bp with a Bioruptor sonicator (Diagenode). Sonicated DNA was end-repaired, A-tailed, and ligated to paired-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 1 ug of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody (1 mg/ml, Eurogentec). For this, DNA was heat-denatured at 95 ˚C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 ul primary antibody per microgram of DNA overnight at 4 ˚C with rocking agitation in 500 ml immunoprecipitation buffer (10mMsodium phosphate buffer, pH 7.0, 140mMNaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 2ul of rabbit anti-mouse IgG secondary antibody (2.5 mg/ml, Jackson Immunoresearch) and 100 ml Protein A/G beads (Pierce Biotechnology) were added and incubated for an additional 2 h at 4 ˚C with agitation. After immunoprecipitation a total of six to ten immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. A nonspecific mouse IgG immunoprecipitation (Jackson Immunoresearch) was performed in parallel to methyl DNA immunoprecipitation as a negative control. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg/ml proteinase K for 2 h at 55 ˚C and then allowed to cool to room temperature. MeDIP and supernatant DNA were purified using Qiagen Qiaquic columns and eluted in 30 ul EB (Qiagen). Twelve cycles of PCR were performed on 10 ul of the immunoprecipitated DNA using the paired-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (192–592 bp) was performed by electrophoresis in 2% agarose. Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis. An aliquot of each library was diluted in EB to 5 ng/ul and 1 ul used as template in four independent PCR reactions to confirm enrichment for methylated and de-enrichment for unmethylated sequences, compared to 5 ng of input (sonicated DNA). Two positive controls (SNRPN and MAGEA1 promoters) and two negative controls (a CpG-less sequence on chromosome 15 and GAPDH promoter) were amplified (Supplementary). Cycling was 95 ˚C for 30 s, 58 ˚C for 30 s, 72 ˚C for 30 s with 30 cycles. PCR products were visualized by 1.5% agarose gel electrophoresis.

value: mouse embryonic stem cells (E14)


title: ES_XY_454

description: Small RNA-Seq

data_processing:
The remaining part of the adapter sequences were removed from the reads. The trimmed reads were mapped on the mm9 genome using Bowtie. Respectively, two mismatches in nucleotide space or colour space were allowed for the mapping of the 454 and the SOLiD data, while for Solexa the sum of qualities of mismatching bases was required to not exceed 50. Only the best alignments are reported for each reads. The reads with up to 5,000 repeated alignments on the genome were used for the repeats analysis.

Mature miRNAs profiling: The genomic positions of mature miRNAs and miR* were obtained from the database miRBase (release 16). Aligned reads of length 19-26nt were considered to correspond to a mature miRNA (or miR*) only if: 1) the aligned position did not differ from the annotated position of the mature miRNA by more than 2 bp and 2) the reads had at most as many genomic match positions as the number of genomic copies of the respective mature miRNA. The miRNA profiling data are in the supplementary *miRNA.bed files.

Repeats profiling: The repeats profiles contain the coverage of raw reads mapped on the genome (without pre-miRNAs) and intersected with the RepeatMasker annotation. Strands are separated. These profiles are not normalized. The repeats profiling data are in the supplementary *rmsk.bed files.

Genome Build:
ES_XY_454_minus_rmsk.bed: mm9
ES_XY_454_plus_rmsk.bed: mm9
ES_XY_454_miRNA.bed: mm9

value: 454 adapter


title: Small RNA population (wt)

description: 21 to 24-nt

value: inflorescences stages 1-12

value: WT


title: piPSC_MRE-seq

data_processing:
Sequence reads were obtained and mapped to reference genomes (mm9, hg19, susScr2) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.
Genome Build:
piPS_MRE.bed.gz: susScr2
The processed data for MRE-seq is BedGraph format. Each row is a CpG site and the value in fourth column is the MRE signal at that CpG site.

organism: Sus scrofa

source_name: pig induced pluripotent stem cells

value: pig induced pluripotent stem cells


title: ES_XX_454

description: Small RNA-Seq

data_processing:
The remaining part of the adapter sequences were removed from the reads. The trimmed reads were mapped on the mm9 genome using Bowtie. Respectively, two mismatches in nucleotide space or colour space were allowed for the mapping of the 454 and the SOLiD data, while for Solexa the sum of qualities of mismatching bases was required to not exceed 50. Only the best alignments are reported for each reads. The reads with up to 5,000 repeated alignments on the genome were used for the repeats analysis.

Mature miRNAs profiling: The genomic positions of mature miRNAs and miR* were obtained from the database miRBase (release 16). Aligned reads of length 19-26nt were considered to correspond to a mature miRNA (or miR*) only if: 1) the aligned position did not differ from the annotated position of the mature miRNA by more than 2 bp and 2) the reads had at most as many genomic match positions as the number of genomic copies of the respective mature miRNA. The miRNA profiling data are in the supplementary *miRNA.bed files.

Repeats profiling: The repeats profiles contain the coverage of raw reads mapped on the genome (without pre-miRNAs) and intersected with the RepeatMasker annotation. Strands are separated. These profiles are not normalized. The repeats profiling data are in the supplementary *rmsk.bed files.

Genome Build:
ES_XX_454_minus_rmsk.bed: mm9
ES_XX_454_plus_rmsk.bed: mm9
ES_XX_454_miRNA.bed: mm9


title: ES_XY_Solexa_i_IDT

description: Small RNA-Seq

data_processing:
The remaining part of the adapter sequences were removed from the reads. The trimmed reads were mapped on the mm9 genome using Bowtie. Respectively, two mismatches in nucleotide space or colour space were allowed for the mapping of the 454 and the SOLiD data, while for Solexa the sum of qualities of mismatching bases was required to not exceed 50. Only the best alignments are reported for each reads. The reads with up to 5,000 repeated alignments on the genome were used for the repeats analysis.

Mature miRNAs profiling: The genomic positions of mature miRNAs and miR* were obtained from the database miRBase (release 16). Aligned reads of length 19-26nt were considered to correspond to a mature miRNA (or miR*) only if: 1) the aligned position did not differ from the annotated position of the mature miRNA by more than 2 bp and 2) the reads had at most as many genomic match positions as the number of genomic copies of the respective mature miRNA. The miRNA profiling data are in the supplementary *miRNA.bed files.

Repeats profiling: The repeats profiles contain the coverage of raw reads mapped on the genome (without pre-miRNAs) and intersected with the RepeatMasker annotation. Strands are separated. These profiles are not normalized. The repeats profiling data are in the supplementary *rmsk.bed files.

Genome Build:
ES_XY_Solexa_i_IDT_minus_rmsk.bed: mm9
ES_XY_Solexa_i_IDT_plus_rmsk.bed: mm9
ES_XY_Solexa_i_IDT_miRNA.bed: mm9


title: piPSC_MeDIP-seq

data_processing:
Sequence reads were obtained and mapped to reference genomes (mm9, hg19, susScr2) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.
Genome Build:
piPS_MeDIP.bed.gz: susScr2


title: mRNA-seq for PP242 treated PC3 cells, replicate #2.

city: San Francisco

first: Andrew

middle: Caleb

last: Hsieh

address: 1450 3rd Street, HD Rm 319

department: Urology

institute: UCSF

description: 3hr PP242 treated human PC3 prostate cancer cells.

data_processing:
Each sequencing run resulted in approximately 20-25 million raw reads per sample, of which 5-12 million unique reads were used for subsequent analysis. Ribosome footprint and RNA-Seq sequencing reads were aligned against a library of transcripts from the UCSC Known Genes database GRCh37/hg19. The first 25 nucleotides of each read were aligned using Bowtie and this initial alignment was then extended to encompass the full fragment-derived portion of the sequencing read while excluding the linker sequence. Read density profiles were then constructed for the canonical transcript of each gene, using only reads with 0 or 1 total mismatches between the read sequence and the reference sequence, comprised of the transcript fragment followed by the linker sequence. Footprint reads were assigned to an A site nucleotide at position +15 to +17 of the alignment, based on the total fragment length; mRNA reads were assigned to the first nucleotide of the alignment. The average read density per codon was then computed for the coding sequence of each transcript, excluding the first 15 and last 5 codons, which can display atypical ribosome accumulation.
Average read density was used as a measure of mRNA abundance (RNA-Seq reads) and of protein synthesis (ribosome profiling reads). For most analyses, genes were filtered to require at least 256 reads in the relevant RNA-Seq samples. Translational efficiency was computed as the ratio of ribosome footprint read density to RNA-Seq read density, scaled to normalize the translational efficiency of the median gene to 1.0 after excluding regulated genes (log2 fold-change +/- 1.5 after normalizing for the all-gene median). Changes in protein synthesis, mRNA abundance, and translational efficiency were similarly computed as the ratio of read densities between different samples, normalized to give the median gene a ratio of 1.0. This normalization corrects for differences in the absolute number of sequencing reads obtained for different libraries. 5333 (replicate #1) and 3977 (replicate #2) unique mRNAs passed a preset read threshold of 256 reads for single-gene quantification for all treatment conditions.
processed data file contains per gene read count, columns: 1) UCSC ID, 2) Length of trimmed CDS, 3) Read count in trimmed CDS
Genome Build:
mrna_pp242_b_qexpr.txt: UCSC GRCh37/hg19

source_name: PC3 human prostate cancer cells

extract_protocol: PC3 cells were treated with rapamycin (50 nM - Calbiochem) or PP242 (2.5 µM - Intellikine) for 3 hours. Cells were subsequently treated with cycloheximide (100 µg/mL - Sigma) and detergent lysis was performed in the dish. The lysate was treated with DNase and clarified, and a sample was taken for RNA-Seq analysis. Lysates were subjected to ribosome footprinting by nuclease treatment. Ribosome-protected fragments were purified, and deep sequencing libraries were generated from these fragments, as well as from poly(A) mRNA purified from non-nuclease treated lysates. These libraries were analyzed by sequencing on the Illumina GAII.

tag: sample type

value: polyA RNA


title: Footprint for PP242 treated PC3 cells, replicate #2.

data_processing:
Each sequencing run resulted in approximately 20-25 million raw reads per sample, of which 5-12 million unique reads were used for subsequent analysis. Ribosome footprint and RNA-Seq sequencing reads were aligned against a library of transcripts from the UCSC Known Genes database GRCh37/hg19. The first 25 nucleotides of each read were aligned using Bowtie and this initial alignment was then extended to encompass the full fragment-derived portion of the sequencing read while excluding the linker sequence. Read density profiles were then constructed for the canonical transcript of each gene, using only reads with 0 or 1 total mismatches between the read sequence and the reference sequence, comprised of the transcript fragment followed by the linker sequence. Footprint reads were assigned to an A site nucleotide at position +15 to +17 of the alignment, based on the total fragment length; mRNA reads were assigned to the first nucleotide of the alignment. The average read density per codon was then computed for the coding sequence of each transcript, excluding the first 15 and last 5 codons, which can display atypical ribosome accumulation.
Average read density was used as a measure of mRNA abundance (RNA-Seq reads) and of protein synthesis (ribosome profiling reads). For most analyses, genes were filtered to require at least 256 reads in the relevant RNA-Seq samples. Translational efficiency was computed as the ratio of ribosome footprint read density to RNA-Seq read density, scaled to normalize the translational efficiency of the median gene to 1.0 after excluding regulated genes (log2 fold-change +/- 1.5 after normalizing for the all-gene median). Changes in protein synthesis, mRNA abundance, and translational efficiency were similarly computed as the ratio of read densities between different samples, normalized to give the median gene a ratio of 1.0. This normalization corrects for differences in the absolute number of sequencing reads obtained for different libraries. 5333 (replicate #1) and 3977 (replicate #2) unique mRNAs passed a preset read threshold of 256 reads for single-gene quantification for all treatment conditions.
processed data file contains per gene read count, columns: 1) UCSC ID, 2) Length of trimmed CDS, 3) Read count in trimmed CDS
Genome Build:
fp_pp242_b_qexpr.txt: UCSC GRCh37/hg19

value: ribosome protected RNA


title: H1_H2AZ_ChIP-seq

data_processing:
Sequence reads were obtained and mapped to reference genomes (mm9, hg19, susScr2) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.
Genome Build:
H1_H2AZ.bed.gz: hg19

source_name: human embryonic stem cell (H1)

value: human embryonic stem cell (H1)

tag: ChIP


title: E14_Day0_MeDIP-seq

data_processing:
Sequence reads were obtained and mapped to reference genomes (mm9, hg19, susScr2) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.
Genome Build:
E14_MeDIP.bed.gz: mm9


title: Footprint for PP242 treated PC3 cells, replicate #1.

data_processing:
Each sequencing run resulted in approximately 20-25 million raw reads per sample, of which 5-12 million unique reads were used for subsequent analysis. Ribosome footprint and RNA-Seq sequencing reads were aligned against a library of transcripts from the UCSC Known Genes database GRCh37/hg19. The first 25 nucleotides of each read were aligned using Bowtie and this initial alignment was then extended to encompass the full fragment-derived portion of the sequencing read while excluding the linker sequence. Read density profiles were then constructed for the canonical transcript of each gene, using only reads with 0 or 1 total mismatches between the read sequence and the reference sequence, comprised of the transcript fragment followed by the linker sequence. Footprint reads were assigned to an A site nucleotide at position +15 to +17 of the alignment, based on the total fragment length; mRNA reads were assigned to the first nucleotide of the alignment. The average read density per codon was then computed for the coding sequence of each transcript, excluding the first 15 and last 5 codons, which can display atypical ribosome accumulation.
Average read density was used as a measure of mRNA abundance (RNA-Seq reads) and of protein synthesis (ribosome profiling reads). For most analyses, genes were filtered to require at least 256 reads in the relevant RNA-Seq samples. Translational efficiency was computed as the ratio of ribosome footprint read density to RNA-Seq read density, scaled to normalize the translational efficiency of the median gene to 1.0 after excluding regulated genes (log2 fold-change +/- 1.5 after normalizing for the all-gene median). Changes in protein synthesis, mRNA abundance, and translational efficiency were similarly computed as the ratio of read densities between different samples, normalized to give the median gene a ratio of 1.0. This normalization corrects for differences in the absolute number of sequencing reads obtained for different libraries. 5333 (replicate #1) and 3977 (replicate #2) unique mRNAs passed a preset read threshold of 256 reads for single-gene quantification for all treatment conditions.
processed data file contains per gene read count, columns: 1) UCSC ID, 2) Length of trimmed CDS, 3) Read count in trimmed CDS
Genome Build:
fp_pp242_a_qexpr.txt: UCSC GRCh37/hg19


title: mRNA-seq for rapamycin treated PC3 cells, replicate #2.

description: 3hr rapamycin treated human PC3 prostate cancer cells.

data_processing:
Each sequencing run resulted in approximately 20-25 million raw reads per sample, of which 5-12 million unique reads were used for subsequent analysis. Ribosome footprint and RNA-Seq sequencing reads were aligned against a library of transcripts from the UCSC Known Genes database GRCh37/hg19. The first 25 nucleotides of each read were aligned using Bowtie and this initial alignment was then extended to encompass the full fragment-derived portion of the sequencing read while excluding the linker sequence. Read density profiles were then constructed for the canonical transcript of each gene, using only reads with 0 or 1 total mismatches between the read sequence and the reference sequence, comprised of the transcript fragment followed by the linker sequence. Footprint reads were assigned to an A site nucleotide at position +15 to +17 of the alignment, based on the total fragment length; mRNA reads were assigned to the first nucleotide of the alignment. The average read density per codon was then computed for the coding sequence of each transcript, excluding the first 15 and last 5 codons, which can display atypical ribosome accumulation.
Average read density was used as a measure of mRNA abundance (RNA-Seq reads) and of protein synthesis (ribosome profiling reads). For most analyses, genes were filtered to require at least 256 reads in the relevant RNA-Seq samples. Translational efficiency was computed as the ratio of ribosome footprint read density to RNA-Seq read density, scaled to normalize the translational efficiency of the median gene to 1.0 after excluding regulated genes (log2 fold-change +/- 1.5 after normalizing for the all-gene median). Changes in protein synthesis, mRNA abundance, and translational efficiency were similarly computed as the ratio of read densities between different samples, normalized to give the median gene a ratio of 1.0. This normalization corrects for differences in the absolute number of sequencing reads obtained for different libraries. 5333 (replicate #1) and 3977 (replicate #2) unique mRNAs passed a preset read threshold of 256 reads for single-gene quantification for all treatment conditions.
processed data file contains per gene read count, columns: 1) UCSC ID, 2) Length of trimmed CDS, 3) Read count in trimmed CDS
Genome Build:
mrna_rapa_b_qexpr.txt: UCSC GRCh37/hg19

value: rapamycin


title: Footprint for vehicle treated PC3 cells, replicate #2.

description: 3hr vehicle treated human PC3 prostate cancer cells.

data_processing:
Each sequencing run resulted in approximately 20-25 million raw reads per sample, of which 5-12 million unique reads were used for subsequent analysis. Ribosome footprint and RNA-Seq sequencing reads were aligned against a library of transcripts from the UCSC Known Genes database GRCh37/hg19. The first 25 nucleotides of each read were aligned using Bowtie and this initial alignment was then extended to encompass the full fragment-derived portion of the sequencing read while excluding the linker sequence. Read density profiles were then constructed for the canonical transcript of each gene, using only reads with 0 or 1 total mismatches between the read sequence and the reference sequence, comprised of the transcript fragment followed by the linker sequence. Footprint reads were assigned to an A site nucleotide at position +15 to +17 of the alignment, based on the total fragment length; mRNA reads were assigned to the first nucleotide of the alignment. The average read density per codon was then computed for the coding sequence of each transcript, excluding the first 15 and last 5 codons, which can display atypical ribosome accumulation.
Average read density was used as a measure of mRNA abundance (RNA-Seq reads) and of protein synthesis (ribosome profiling reads). For most analyses, genes were filtered to require at least 256 reads in the relevant RNA-Seq samples. Translational efficiency was computed as the ratio of ribosome footprint read density to RNA-Seq read density, scaled to normalize the translational efficiency of the median gene to 1.0 after excluding regulated genes (log2 fold-change +/- 1.5 after normalizing for the all-gene median). Changes in protein synthesis, mRNA abundance, and translational efficiency were similarly computed as the ratio of read densities between different samples, normalized to give the median gene a ratio of 1.0. This normalization corrects for differences in the absolute number of sequencing reads obtained for different libraries. 5333 (replicate #1) and 3977 (replicate #2) unique mRNAs passed a preset read threshold of 256 reads for single-gene quantification for all treatment conditions.
processed data file contains per gene read count, columns: 1) UCSC ID, 2) Length of trimmed CDS, 3) Read count in trimmed CDS
Genome Build:
fp_dmso_b_qexpr.txt: UCSC GRCh37/hg19

value: vehicle


title: mRNA-seq for vehicle treated PC3 cells, replicate #2.

data_processing:
Each sequencing run resulted in approximately 20-25 million raw reads per sample, of which 5-12 million unique reads were used for subsequent analysis. Ribosome footprint and RNA-Seq sequencing reads were aligned against a library of transcripts from the UCSC Known Genes database GRCh37/hg19. The first 25 nucleotides of each read were aligned using Bowtie and this initial alignment was then extended to encompass the full fragment-derived portion of the sequencing read while excluding the linker sequence. Read density profiles were then constructed for the canonical transcript of each gene, using only reads with 0 or 1 total mismatches between the read sequence and the reference sequence, comprised of the transcript fragment followed by the linker sequence. Footprint reads were assigned to an A site nucleotide at position +15 to +17 of the alignment, based on the total fragment length; mRNA reads were assigned to the first nucleotide of the alignment. The average read density per codon was then computed for the coding sequence of each transcript, excluding the first 15 and last 5 codons, which can display atypical ribosome accumulation.
Average read density was used as a measure of mRNA abundance (RNA-Seq reads) and of protein synthesis (ribosome profiling reads). For most analyses, genes were filtered to require at least 256 reads in the relevant RNA-Seq samples. Translational efficiency was computed as the ratio of ribosome footprint read density to RNA-Seq read density, scaled to normalize the translational efficiency of the median gene to 1.0 after excluding regulated genes (log2 fold-change +/- 1.5 after normalizing for the all-gene median). Changes in protein synthesis, mRNA abundance, and translational efficiency were similarly computed as the ratio of read densities between different samples, normalized to give the median gene a ratio of 1.0. This normalization corrects for differences in the absolute number of sequencing reads obtained for different libraries. 5333 (replicate #1) and 3977 (replicate #2) unique mRNAs passed a preset read threshold of 256 reads for single-gene quantification for all treatment conditions.
processed data file contains per gene read count, columns: 1) UCSC ID, 2) Length of trimmed CDS, 3) Read count in trimmed CDS
Genome Build:
mrna_dmso_b_qexpr.txt: UCSC GRCh37/hg19


title: E14_Day6_H3K9me3_ChIP-seq

data_processing:
Sequence reads were obtained and mapped to reference genomes (mm9, hg19, susScr2) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.
Genome Build:
E14_H3K9me3_d6.bed.gz: mm9

source_name: mESC E14 under Activin A differentiation, day 6


title: E14_Day6_H3K4me3_ChIP-seq

data_processing:
Sequence reads were obtained and mapped to reference genomes (mm9, hg19, susScr2) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.
Genome Build:
E14_H3K4me3_d6.bed.gz: mm9

value: mESC E14 under Activin A differentiation, day 6