title: brain_ac_methylmaps_s4

description: Methyl-MAPS sequencing data

source_name: Brain auditory cortex


title: H3-HA (old) generation 6

status: Public on Oct 06 2011

type: SRA

city: Jerusalem

first: Assaf

last: Weiner

address: Givat Ram

department: Computer Science

country: Israel

institute: The Hebrew University of Jerusalem

library_source: genomic

data_processing: Mapped Reads: Unique reads were mapped to the yeast genome (S288C_reference_genome_R61-1-1_20080605; 05-Jun-2008) with minimal errors (as described in Yassour et al. PNAS, 2009 (PMID 19208812)).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: H3-HA, wt, generation 6

growth_protocol: For tag switch experiments, yeast cells were grown overnight in YPD in the presence of Hygromycin B (200 μg/mL, Invitrogen). The cells were then diluted 1:10 into fresh YPD and incubated for 30–36 h. Recombination was induced by the addition of 1 μM β-estradiol (E-8875, Sigma-Aldrich). Subsequently, cells were diluted 1:25 in fresh YPD media to release the cells back into the cell cycle and kept in log phase by 1:2 dilutions into fresh media after each population doubling. Samples were taken after 1, 3, and 6 cell divisions or after 5 hours of G2/M arrest. The number of population doublings was determined by microscopy and OD. G2/M arrest was induced by addition of 15 μg/ml Nocodazole (Sigma-Aldrich) and confirmed by FACS analysis.

extract_protocol: The majority of obtained fragments was around 150bp, as determined on a 2% TAE agarose gel stained with ethidium bromide. The isolated chromatin of the equivalent of 3x10^8 cells was immunoprecipitated overnight at 4°C using magnetic Dynabeads (Invitrogen), which were previously incubated with antibody O/N at 4°C.

treatment_protocol: ChIP was performed as described previously (PMID 20018668) with the following modifications. All steps were done at 4°C unless otherwise indicated. Following cell lysis by bead beating, the insoluble chromatin of 1x10^9 cells was washed, resuspended in 400 μl FA lysis buffer (50 mM HEPESKOH [pH 7.6], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), and sheared using a Bioruptor (Diagenode) for 6 minutes with 30 seconds intervals at high. The 16 soluble fraction was diluted three fold in buffer 15mM Tris-HCl pH 7.4, 50mM NaCl, 1.5mM CaCl2, 5mM β-meracptoethanol, 5mM MgCl2,  after which 25 units of micrococcal nuclease (MNase; Worthington) were added. The digestion reaction was incubated 20 minutes at 37°C and stopped by the addition of 10mM EDTA and 10mM EGTA, and tubes were placed on ice.

tag: genotype

value: wt

tag: epitope tag

value: HA

tag: histone h3

value: old

tag: sampling time

value: at 6 cell divisions


title: Glycine max Root

status: Public on Oct 24 2011

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

description:
GMA01
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

library_source: transcriptomic

data_processing: Adapter sequences were removed using a Perl script, generating small RNA sequences plus abundances . Twenty-one small RNA libraries were made the materials described above, representing four legume species, including eight libraries from M. truncatula, seven from Glycine max (soybean), two from Arachis hypogaea (peanut), and four from Phaseolus vulgaris (common bean); one PARE library was made from Medicago flower.These libraries were sequenced on an Illumina GAII, generating ~62 million small RNA sequences after removing adapters and low-quality reads, with trimmed lengths between 18 and 34 nucleotides. After excluding small RNAs matching structural RNAs (t/rRNA loci), 12.1 million and 12.6 million reads were mapped to the M. truncatula genome (Mt3.5) (http://www.medicago.org) and the Glycine max genome (Gmax101) (Schmutz et al., 2010), respectively.

molecule: total RNA

organism: Glycine max

source_name: Root

extract_protocol: Medicago small RNA libraries (except MTR01) were constructed and sequenced at Illumina; all other legume libraries plus MTR01 were constructed as previously described (Lu et al. 2007) and sequenced on an Illumina Genome Analyzer II instrument at the Delaware Biotechnology Institute. PARE library was constructed as previously described (German et al. 2008)

tag: accession/ecotype

value: Williams 82

tag: tissue

value: Root


title: brain_vpfc_methylmaps_s3

status: Public on Oct 05 2011

city: New York

first: Fatemeh

last: Haghighi

state: NY

address: 1051 Riverside Drive, Box 42

institute: Columbia University

description: Methyl-MAPS sequencing data

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (hg18, March, 2006) or mouse (mm9) genomes using the SOLiD mapping software. All reads mapping with two or fewer mismatches were retained.
Methyl-Analyzer: Mapped mate-pair reads were parsed to retore fragment information (i.e., start and end cooridinates), fragments were filtered based on enzyme recognition sites, and methylation probabilites were estimated using both methylated and unmethylated fragment information.

organism: Homo sapiens

source_name: Brain ventral prefrontal cortex

extract_protocol:
Genomic DNA was isolated using phenol-chloroform extraction and RNase A treatment followed by ethanol precipitation. Methylation-sensitive enzymes are HpaII, HhaI, AciI, BstUI and HpyCH4IV, and methylation-dependent enzyme is McrBC.
Follow Methyl-MAPS protocol: genomic DNA was digested by methylation-sensitive and -dependent enzymes, separately. Digested fragments were contructed into mate-pair libraries and sequenced on SOLiD platform.
Sequencing libraries were prepared by following an adaptation of Applied Biosystems  SOLiD System Mate-paired Library Preparation Protocol (http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_059675.pdf), and the corresponding adaptation for the library preparation can be found in: Xin Y, O'Donnell AH, Ge Y, et al. (2011). Role of CpG context and content in evolutionary signatures of brain DNA methylation. Epigenetics

value: Brain

tag: phenotype

value: Control


title: Wild-Type Lymphoma, biological replicate 2

status: Public on Nov 21 2011

city: Omaha

first: Ryan

last: Hlady

state: Nebraska

department: Eppley

institute: UNMC

description: Methyl-sensitive cut counting high-throughput sequencing data from Wild-Type Tumors

data_processing: The resulting 18 bp sequence tags were aligned with the mouse genome (mm9) using the short read sequence aligner Bowtie (40). The library was matched to all possible unique tags (courtesy of Madeleine Ball, Harvard University) and the appropriate gene using perl scripts developed by the UNO/UNMC Genetic Sequence Analysis Facility and Microsoft Access and Excel. Counts of each sequence tag that represented a unique unmethylated HpaII site were determined.

organism: Mus musculus

source_name: Tumor cells harvested from thymic lymphoma of Wild-Type Tumor mice

growth_protocol: Th-1, Th-2, Th-3, 3b24-1, 3b24-2, 3b24-3 were harvested at 24 days and sorted based on EGFP expression. All Final tumor mice were harvested when lymphoma tumor burden became apparent.

extract_protocol:
2 μg of genomic DNA was digested with 20 units of the restriction enzyme HpaII (NEB) and an adapter containing a recognition site for the restriction enzyme MmeI was ligated to digested DNA fragments using T4 DNA ligase (NEB). DNA was ethanol precipitated and nick repaired with eight units of Bst DNA polymerase (NEB). The DNA was digested with 2 units of MmeI to capture the 18 bases adjacent to HpaII sites and the fragments were subsequently ligated to a second adapter to allow PCR amplification and final high throughput sequencing.
After appropriate tag size purification using a 10% PAGE gel, DNA was PCR amplified using BioRad iProof high fidelity polymerase and quantitative PCR procedures to avoid over amplification and skewing the production of final tags. Final tags were checked for proper size and concentration using an Agilent, Bioanalyzer High Sensitivity DNA chip and Invitrogen, Qubit Fluorometer. High throughput sequencing of library tags was performed by Tufts University Core Facility and University of Nebraska Medical Center using an Illumina Genome Analyzer II.

value: Thymus

tag: tumor stage

value: Final Tumor


title: brain_ac_methylmaps_s3

description: Methyl-MAPS sequencing data


title: H3-HA (old) generation 3

source_name: H3-HA, wt, generation 3

value: at 3 cell divisions


title: Normal Thymocytes, biological replicate 3

description: Methyl-sensitive cut counting high-throughput sequencing data from normal thymocytes

source_name: Normal thymocytes from FVB control


title: brain_ac_methylmaps_s2

description: Methyl-MAPS sequencing data


title: brain_vpfc_methylmaps_s1

description: Methyl-MAPS sequencing data


title: 24 day pre-tumor Dnmt3b-deficient thymocytes, biological replicate 2

description: Methyl-sensitive cut counting high-throughput sequencing data from Dnmt3b-deficient pre-tumor thymocytes

source_name: Dnmt3b-deficient pre-tumor cells harvested from thymus of 24 day old Dnmt3b-deficient mice

value: 24 day pre-tumor


title: brain_vpfc_methylmaps_s2

description: Methyl-MAPS sequencing data


title: brain_ac_methylmaps_s1

description: Methyl-MAPS sequencing data


title: Medicago truncatula Dev.Seed

description:
MTR01
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Medicago truncatula


title: H3-T7 (new) generation 6

source_name: H3-T7, wt, generation 6

value: new


title: Dnmt3b-deficient Lymphoma, biological replicate 2

description: Methyl-sensitive cut counting high-throughput sequencing data from Dnmt3b-deficient tumors

source_name: Dnmt3b-deficient tumor cells harvested from thymic lymphoma of Dnmt3b-deficient tumor mice


title: HS2336

status: Public on Oct 01 2011

city: starkville

first: Ranjit

last: Kumar

state: MS

address: 240 Wise Center Drive,PO Box 6100

department: Dept of Basic Science

institute: MSU

data_processing: Perl script was written to convert Illumina reads into fastq format. Solexa fastq format was then converted to Sanger fastq format using the script 'fq_all2std.pl' from MAQ. All the reads in sanger fastq format were mapped to the Histophilus somni 2336 genome sequence (GenBank Accession number. CP000947) using the alignment tool Bowtie allowing for a maximum of two mismatches. The reads that map to more than one location were discarded. Samtools was used for data format conversion into SAM/BAM format and to generate alignment results in a pileup format. Subsequent analysis was performed using in house perl scripts.

organism: Histophilus somni

source_name: Cell culture

growth_protocol: H. somni 2336 was propagated on three TSA-blood plates for 16 hr till a fresh lawn of cells was visible. The plates were washed with brain heart infusion (BHI) broth and the culture was adjusted to an OD620nm=0.8, supplemented with RNAprotect reagent, and cells harvested by centrifugation and stored at -80°C.

extract_protocol: We used 100 ng enriched mRNA with Illumina mRNA-Seq sample preparation kit (Illumina,San Diego, CA) for library construction following manufacturer's protocols.

treatment_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's protocol. Total RNA preparations were treated with RNase-free DNAse (Invitrogen; Carlsbad, CA). We used the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) and determined the RIN of total RNA to be greater than 8. MICROBExpress Kit (Ambion) that specifically removes rRNAs was used for mRNA enrichment. Small RNAs (i.e., tRNA and 5S rRNA) are not removed with this enrichment step (confirmed by Bioanalyzer).

tag: strain


title: Wild-Type Lymphoma, biological replicate 3


title: 24 day pre-tumor Dnmt3b-deficient thymocytes, biological replicate 3


title: Phaseolus vulgaris Root

description:
PVU01
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Phaseolus vulgaris


title: Normal Thymocytes, biological replicate 2


title: Phaseolus vulgaris Flower

description:
PVU02
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

source_name: Flower

value: Flower


title: PBX1_ChiP_seq data

status: Public on Sep 30 2011

city: Lebanon

first: luca

last: magnani

state: NH

address: NCCC one medical drive

department: Genetics

institute: Dartmouth College

description: PBX1 ChIP

data_processing:
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Processed data file build: HG18

source_name: MCF7 cells

growth_protocol: MCF7 cells were cultered in standar DMEM (10% serum, penicilin/streptomycin) until 80% confluent

extract_protocol: Sonicated cells were incubated with PBX1 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 (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: MCF7 breast cancer cells

tag: era status

value: positive

tag: passage

tag: chip antibody

tag: chip antibody vendor

value: Abnova Corporation

tag: chip antibody lot#

tag: chip antibody catalog#


title: Wild-Type Lymphoma, biological replicate 4


title: Dnmt3b-deficient Lymphoma, biological replicate 3


title: Input DNA

description: PBX1 Input


title: Dnmt3b-deficient Lymphoma, biological replicate 1


title: Normal Thymocytes, biological replicate 1


title: SNU484-Smad3

status: Public on Sep 15 2011

city: incheon

first: DeokHoon

last: Kim

address: 7-45 songdo-dong yeonsu-ku

country: South Korea

institute: Lee Gil Ya cancer and diabets institute

description: SNU484-Smad3 small RNA.

data_processing: Small RNA was detected using the mirTools web program (http://centre.bioinformatics.zj.cn/mirtools/) using default parameters. Reads were aligned to the reference genome (hg18) using SOAP.

source_name: Gastric cancer cell line, SNU484-Smad3

growth_protocol: SNU484-LPCX cells, which do not express Smad3, and SNU484-Smad3 cells, which stably express flag-tagged Smad3, were maintained in RPMI 1640 media (Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Hyclone) and 1% streptomycin/penicillin (Invitrogen) in a 5% CO2 atmosphere at 37C as described in a previous report (Han et al., 2004).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen). A small RNA library was prepared with a small RNA preparation kit according to the manufacturer's instructions (Illumina). Briefly, 10 ug of total RNA was size-fractionated on a 15% TBE-Urea PAGE gel (Invitrogen), and an 18-30 base pair (bp) band of fractionated gel was excised and mashed. RNA was eluted from the mashed gel debris and filtered by a spin-x cellulose filter and precipitated. An SRA 5' adaptor (GUUCAGAGUUCUACAGUCCGACGAUC) was ligated to the small RNA with T4 RNA ligase, the ligated RNA was size-fractionated on a 15% TBE-Urea PAGE gel, and a 40-60 bp band was excised. The SRA 3' adaptors (UCGUAUGCCGUCUUCUGCUUGUidT) were ligated to small RNAs with T4 RNA ligase, the ligated 3' adaptor RNA was fractionated on a 10% TBE-Urea gel, and a 70-90 bp band was excised. The small RNA was converted to single-strand cDNA by Superscript II (Invitrogen) and SRA RT primer (CAAGCAGAAGACGGCATACGA). The cDNA was amplified using Illumina's PCR primer set (CAAGCAGAAGACGGCATACGA and AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA). PCR conditions were as follows: 30 sec at 98C; 18 cycles of 10 sec at 98C, 30 sec at 60C, and 15 sec at 72C; and a final extension at 72C for 10 min. The single-strand cDNA was fractionated on a 6% TBE gel. An approximately 92 bp band of size-fractionated gel was excised and the resulting slurry was filtered by a spin-X filter. The resulting cDNA was precipitated and resuspended to perform the sequencing. To validate the library, cDNA concentration and the 260/280 ratio was measured with a Nanodrop spectrophotometer (Thermo).

tag: cell type

value: gastric cancer

tag: smad3 expression

value: overexpressed


title: SNU484-LPCX

description: SNU484-LPCX small RNA.

source_name: Gastric cancer cell line, SNU484-LPCX


title: Glycine max Nodule

description:
GMA02
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

source_name: Nodule

value: Nodule


title: Glycine max Flower

description:
GMA03
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences


title: Simulated Condition 1, replicate 3

status: Public on Sep 10 2011

city: Cambridge

first: Cole

last: Trapnell

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing: TopHat and Cufflinks. Total sequencing yield for each replicate was chosen to match that of the real S2 data. Each replicate was mapped to the fly genome with TopHat v 1.3.1 seperately.  The replicates were assembled seperately with Cufflinks v 1.1.0. The replicate assemblies were merged with Cuffmerge.  This merged assembly was then analysed for differentially expressed and regulated genes with Cuffdiff.

organism: Drosophila melanogaster

source_name: C1 (simulated S2)

extract_protocol: Simulated unstranded Paired-end RNA-Seq .  Mean fragment length = 180bp, std. dev. = 20bp


title: Simulated Condition 1, replicate 2


title: Simulated Condition 1, replicate 1


title: chimp_4

status: Public on Sep 09 2011

city: Los Angeles

first: Dario

last: Boffelli

state: CA

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

description: HpaII digest

data_processing:
Raw sequencing data were quality-filtered using the Illumina Pipeline CHASTITY filter with default parameter (0.6).
Alignment ('_bwtout.txt' files): sequencing data were quality-filtered using the Illumina Pipeline CHASTITY filter with default parameter (0.6) and aligned using Bowtie v0.9.9.2 (bowtie-bio.sourceforge.net) to their respective reference genomes. Parameters used to run bowtie: --all -m 1. These parameters allow up to 2 mismatches in  the first 28nt. In v 0.9.9.2, hits are "stratified" by default: if a read has 1 zero mismatch hit, and 2 1-mismatch hits, the 1 zero mismatch hit is reported when-m 1 is specified.
Determination of metylation status ('_metmap.wig' files): reads that aligned to HpaII sites (CCGG) were analyzed with MetMap (http://www.cs.berkeley.edu/~meromit/MetMap) to infer methylation states. Results are reported for each CCGG site that can generate a sequenceable fragment (ie, the fragment is of a length that can pass the size selection step during library construction). Results are expressed as the probability p(U) that the site in unmethylated, and vary between 0 (methylated site) and 1 (unmethylated site).
Processed data file build: PanTro2

organism: Pan troglodytes

source_name: whole blood

growth_protocol: Whole-blod samples were obtained from healthy, young adult males.

extract_protocol: Neutrophils were isolated immediately after phlebotomy with CD-16 microbeads. An aliquot of each specimen was Wright-Giemsa stained and examined microscopically; all specimens contained >99% neutrophils. DNA was extracted by standard methods, and digested overnight with the methylation-sensitive enyzme HpaII (HpaII cuts CCGG sites when the central C is unmethylated). HpaII fragments of 50-300 bp in length were  isolated from an agarose gel, and used to construct single read sequencing libraries using the standard Illumina protocol.

value: neutrophil

tag: gender

value: male

tag: age

value: young adult


title: human_4

description: HpaII digest

data_processing:
Raw sequencing data were quality-filtered using the Illumina Pipeline CHASTITY filter with default parameter (0.6).
Alignment ('_bwtout.txt' files): sequencing data were quality-filtered using the Illumina Pipeline CHASTITY filter with default parameter (0.6) and aligned using Bowtie v0.9.9.2 (bowtie-bio.sourceforge.net) to their respective reference genomes. Parameters used to run bowtie: --all -m 1. These parameters allow up to 2 mismatches in  the first 28nt. In v 0.9.9.2, hits are "stratified" by default: if a read has 1 zero mismatch hit, and 2 1-mismatch hits, the 1 zero mismatch hit is reported when-m 1 is specified.
Determination of metylation status ('_metmap.wig' files): reads that aligned to HpaII sites (CCGG) were analyzed with MetMap (http://www.cs.berkeley.edu/~meromit/MetMap) to infer methylation states. Results are reported for each CCGG site that can generate a sequenceable fragment (ie, the fragment is of a length that can pass the size selection step during library construction). Results are expressed as the probability p(U) that the site in unmethylated, and vary between 0 (methylated site) and 1 (unmethylated site).
Processed data file build: hg18


title: Simulated Condition 2, replicate 3

source_name: C2 (simulated S2)


title: Simulated Condition 2, replicate 2


title: embryonic digit stage 31 LFa_Rep_mRNAseq

status: Public on Sep 08 2011

city: West Haven

first: Zhe

last: Wang

state: CT

address: 300 Heffernan Drive, B31-RA269

institute: Yale University

data_processing: txt: Reads from mRNA-seq data were aligned to Ensembl chicken genome (Gallus gallus WASHUC2) using GERALD module of Illumina CASAVA v1.6 software. After alignment, gene raw counts (gene expression levels) were counted by Illumina CASAVA v1.6 software, and then normalized using TMM method performed using the edgeR package.

organism: Gallus gallus

source_name: Embryonic chicken digit

growth_protocol: Fertilized chicken eggs were obtained from Charles River Laboratories International, Inc. and incubated between 37.5-39C at high relative humidity (>50%).

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Cat. No. 74106, Maryland, USA), and treated with DNase I using RNase-Free DNase Set (Qiagen, Cat. No. 79254, Hilden, Germany). Extracted total RNA of the samples was submitted to Yale Center for Genome Analysis for mRNA sequencing (mRNA-seq) using Illumina Genome Analyzer. mRNA-seq 8-Sample Prep Kit (Illumina, Cat. No. RS-100-0801, San Diego, USA), Standard Cluster Generation Kit (Illumina, Cat. No. GD-103-4001, San Diego, USA) and Illumina Sequencing Kit (Illumina, Cat. No. FC-104-1001, San Diego, USA) were used for constructing libraries for single-read sequencing, cluster amplification and final sequencing-by-synthesis.

tag: embryonic stage

value: Stage 31

value: embryonic digit


title: embryonic digit stage 31 LHb_Rep_mRNAseq


title: embryonic digit stage 31 LH4_mRNAseq

growth_protocol: Fertilized chicken eggs were obtained from Charles River Laboratories International, Inc. and incubated between 37.5-39C  at high relative humidity (>50%).

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Cat. No. 74106, Maryland, USA), and treated with DNase I using RNase-Free DNase Set (Qiagen, Cat. No. 79254, Hilden, Germany). Extracted total RNA of the 14 samples was submitted to Yale Center for Genome Analysis for mRNA sequencing (mRNA-seq) using Illumina Genome Analyzer. mRNA-seq 8-Sample Prep Kit (Illumina, Cat. No. RS-100-0801, San Diego, USA), Standard Cluster Generation Kit (Illumina, Cat. No. GD-103-4001, San Diego, USA) and Illumina Sequencing Kit (Illumina, Cat. No. FC-104-1001, San Diego, USA) were used for constructing libraries for single-read sequencing, cluster amplification and final sequencing-by-synthesis.


title: chimp_3

description: HpaII digest


title: embryonic digit stage 31 LF3_mRNAseq


title: Small RNAs from Vitis vinifera flowers

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

description:
VVI2
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

data_processing: Small RNA reads were analyzed after removal of 3' adapter (5' -TCGTATGCCGTCTTCTGCTTG) and filtering of 5' adapter (5'-GTTCAGAGTTCTACAGTCCGACGATC) or 3' adapter artefacts.

organism: Vitis vinifera

source_name: Flowers

extract_protocol: Total RNA was extracted  with the Plant RNA Purification Reagent (Invitrogen). Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000).

value: Flowers (a mixture of open flowers and flowers still encapsulated in the caliptra)


title: embryonic digit stage 31 LH2_mRNAseq


title: Simulated Condition 2, replicate 1


title: Small RNAs from Zostera marina roots and rhizoid

description:
ZMR3
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Zostera marina

source_name: Roots and rhizoid

value: Roots and rhizoids


title: embryonic digit stage 31 LH1_mRNAseq


title: Small RNAs from Silene latifolia flowers

description:
SLA2
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Silene latifolia

extract_protocol: Total RNA was extracted  with the TriReagent (Molecular Research Center). Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000).

value: Female


title: embryonic digit stage 31 LF1_mRNAseq


title: embryonic digit stage 28/29 EH3_mRNAseq

value: Stage 28/29


title: Small RNAs from Solanum tuberosum leaves

description:
STU1
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Solanum tuberosum

source_name: Leaves

tag: cultivar

value: Kennebec

value: Leaves (fully grown, middle or upper leaves)

tag: time

value: 72 days


title: embryonic digit stage 28/29 EH2_mRNAseq

tag: tissue


title: Small RNAs from Silene latifolia smutted flowers

description:
SLA3
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Roots

value: Flower smutted


title: Small RNAs from Vitis vinifera berries

description:
VVI3
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Fruit

value: Berries (intact berries collected soon after all asynchronous berries turned red over the bunches)


title: Small RNAs from Solanum tuberosum stolon

description:
STU3
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Stolon

value: Defender

value: Stolon (separated from tubers)


title: embryonic digit stage 28/29 EH1_mRNAseq


title: embryonic digit stage 28/29 EF3_mRNAseq


title: Small RNAs from Setaria italica roots

description:
SIT3
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Setaria italica

value: Roots


title: Small RNAs from Setaria italica leaves

description:
SIT1
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

growth_protocol: Growth conditions for seedlings:  -Seeds were surface disinfested in 3% bleach solution and rinsed in sterile water  -They were then planted in vermiculite and grown hydroponically. They were initially germinated in water amended with Erythromycin [100mg/L] and captan [1tbsp/gallon].  - After 2 weeks the germinated seedlings were moved to a nutrient solution.  - Seedlings were harvest 5-6 weeks after initial planting.

value: Leaves


title: Small RNAs from Triticum aestivum leaves

description:
TAE1
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Triticum aestivum

extract_protocol: Total RNA was extracted  with TriReagent (Molecular Research Center) or the Plant RNA Purification Reagent (Invitrogen). Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000).

value: Chinese Spring

value: 7-days old


title: Small RNAs from Solanum lycopersicum leaves

description:
SLY1
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Solanum lycopersicum

value: cv. Heinz 1706


title: hEB16d_27e_p44_RRBS

status: Public on Sep 01 2011

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

country: Germany

institute: Max Planck Institute of Psychiatry

description: reduced representation bisulfite sequencing

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using MAQ bisulfite alignment mode.
References: Smith, Z. D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput bisulfite sequencing in mammalian genomes. Methods 48, 226-232, doi:S1046-2023(09)00111-X
Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7, 133-136, doi:nmeth.1414

source_name: embryoid body from iPS 27e p44

growth_protocol: The pluripotent cell lines were grown in human ES media consisting of KO-DMEM (Invitrogen), 10% KOSR (Invitrogen), 10% plasmanate (Talecris), 1% glutamax or L-glutamin, nonessential amino acids, penicillin/streptomycin, 0.1% 2-mercaptoethanol and 10–20 ng/ml bFGF. All pluripotent cells were grown on a monolayer of irradiated CF1-MEFs (GlobalStem) and passaged using trypsin (0.05%) or dispase (Invitrogen). Before collection of DNA and RNA for analysis, ES and iPS cells were either isolated using trypsin (0.05%) or dispase, or plated on matrigel (BD Biosciences) for one passage and fed with human ES media conditioned in CF1-MEFs for 24 hr. The material from the rectal mucosa, rectal smooth muscle, skeletal muscle and stomach smooth muscle was obtained from MGH Pathology under the REMC project.  human blood CD19 and CD34 samples were obtained from Shelly Heimfeld’s lab. Pancreatic islet samples were retrieved from the islet donor network and supplied by Stuart Schreibers Group.

extract_protocol: RRBS was performed according to a previously published protocol (Smith et al., 2009) with some optimizations for small cell numbers (Gu et al., 2010)


title: hEB16d_15b_p54_RRBS

source_name: embryoid body from iPS 15b p54


title: Small RNAs from Solanum tuberosum flowers

description:
STU2
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: Kennebec, Katahdin, Pentland Ivory

value: Flower (mature)


title: Small RNAs from Sorghum bicolor stolon

description:
SBI3
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Sorghum bicolor

source_name: Panicle

value: Young panicle in early grain fill

tag: genotype/variation


title: Small RNAs from Solanum lycopersicum fruit

description:
SLY3
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: Fruit

tag: developmental stage

value: breaker stage


title: embryonic digit stage 31 LH3_mRNAseq

value: Stage 31

value: embryonic digit


title: hEB16d_HUES62_p18_RRBS

source_name: embryoid body from hES HUES62 p18


title: hEB16d_H9_p65_RRBS

source_name: embryoid body from hES H9 p65


title: hEB16d_HUES8_p40_RRBS

source_name: embryoid body from hES HUES8 p40


title: Small RNAs from Setaria italica flowers

description:
SIT2
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

growth_protocol: Growth conditions for flower spikes:  -Grown in 3:1 soil to sand mix under normal greenhouse conditions

value: Flower spikes (2 pre-anthesis stages)


title: Human_blood_replicate2_RRBS

source_name: Human whole blood replicate 2


title: Small RNAs from Zostera marina leaves

description:
ZMR1
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

tag: geographic location

value: All samples were harvested in the Indian River Bay, DE.


title: embryonic digit stage 28/29 EF2_mRNAseq

value: Stage 28/29


title: Human_blood_replicate1_RRBS

source_name: Human whole blood replicate 1


title: Human_blood_CD34_rep1_RRBS

source_name: Human blood CD34 positive replicate 1


title: Human_blood_CD34_rep2_RRBS

source_name: Human blood CD34 positive replicate 2


title: Small RNAs from Sorghum bicolor flowers

description:
SBI2
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: Flowers

value: ~9-week old plants


title: Small RNAs from Sorghum bicolor leaves

description:
SBI1
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: 3-week-old seedlings


title: Small RNAs from Triticum aestivum fusarium-infected spikelets

description:
TAE3
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Fusarium-infected spikelets

value: Spikelets

tag: infection

value: Fusarium

tag: harvest time

value: 24 hours after Fusarium inoculation


title: embryonic digit stage 28/29 EH4_mRNAseq

source_name: Embryonic chicken digit


title: Human_blood_CD19_RRBS

source_name: Human blood CD19 positive


title: Stomach_smooth_muscle_rep1_RRBS

source_name: Stomach smooth muscle replicate 1


title: Skeletal_muscle_rep2_RRBS

source_name: Skeletal muscle replicate 2


title: Small RNAs from Triticum aestivum control spikelets

description:
TAE2
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: control spikelets

value: control

value: 24 hours after water inoculation


title: hiPS_27e_p32_RRBS

source_name: hiPS 27e passage 32


title: hES_H9_p58_Rep2_RRBS

source_name: hES H9 passage 58 technical replicate


title: hiPS_27b_p31_RRBS

source_name: hiPS 27b passage 31


title: hiPS_29e_p32_RRBS

source_name: hiPS 29e passage 32


title: hiPS_17b_p35_RRBS

source_name: hiPS 17b passage 35


title: hES_H1_p37_RRBS

source_name: hES H1 passage 37


title: hES_H1_p34_RRBS

source_name: hES H1 passage 34


title: Small RNAs from Solanum lycopersicum flowers

description:
SLY2
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Flowers

value: cv. Heinz 1706

value: Flower

value: pre-anthesis


title: hES_H1_p32_RRBS

source_name: hES H1 passage 32


title: hES_H1_p30_RRBS

source_name: hES H1 passage 30


title: hES_H1_p25_RRBS

source_name: hES H1 passage 25


title: embryonic digit stage 31 LF2_mRNAseq


title: Skeletal_muscle_rep1_RRBS

source_name: Skeletal muscle replicate 1


title: hES_HUES1_p28_RRBS

source_name: hES HUES1 passage 28


title: hES_HUES1_p29_RRBS

source_name: hES HUES1 passage 29


title: WCEneg_ChIPSeq

status: Public on Aug 24 2011

first: Bill

last: Wong

address: 9 Cambridge Center

institute: Whitehead Institute

description: WCE control

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 (July 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection was performed using the Young Lab Analysis tool (described in PMID: 19884255)

source_name: fetal liver cells

growth_protocol: Primary fetal liver cells were isolated from E14.5 C57Bl6 pregnant mice and homogenized.  Using anti-Ter119 magnetic beads, the positive and negative fractions were separated for each samole (for each cell type listed above).  Fresh cells were fixed with 1% formaldehyde and then quenched with 2.5M glycine.

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 (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â 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: None, cells were isolated in-vivo and fixed immediately

tag: strain

value: fetal liver erythroid Ter119- cells

tag: passages

value: primary cells

value: female

tag: chip antibody


title: hES_HUES8_p29_RRBS

source_name: hES HUES8 passage 29


title: C2C12_ShA

status: Public on Aug 22 2011

city: Illkirch

first: Celine

last: Keime

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

description: C2C12 cells expressing a  shRNA to silence TEAD4 expression

data_processing:
Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6.
Alignment : Reads were mapped to reference genome mm9/NCBI37 using Tophat v1.0.12.
Quantification : Quantification of gene expression was done using Cufflinks v0.8.2 and annotations from Ensembl release 57. For each transcript the resulting FPKM were converted into raw read counts and these counts were added for each gene locus.
Normalization : Data normalization was performed with the DESeq Bioconductor package.

molecule: polyA RNA

source_name: C2C12 myoblasts

growth_protocol: C2C12 cells were cultured in DMEM with 10% FCS and differentiated by replacing growth medium with differentiation medium containing 2% horse serum

extract_protocol: The mRNA-seq libraries were prepared following the Illumina protocol with some modifications. Briefly, mRNA was purified from total RNA using oligo-dT magnetic beads and fragmented using divalent cations at 95C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers. This was followed by second strand cDNA synthesis using Polymerase I and RNase H. The double strand cDNA fragments were blunted, phosphorylated and ligated to single-end adapter dimers follwed by PCR amplification (30 sec at 98C; [10 sec at 98C, 30 sec at 65C, 30 sec at 72C] x 13 cycles; 5 min at 72C). After PCR amplification, surplus PCR primers and dimer adapters were removed by purification using AMPure beads (Agencourt Biosciences Corporation). Size selection was performed by electrophoresis on a 2% agarose gel and DNA fragments in the range of ~250-350bp were excised and purified using QIAquick Gel Extraction Kit (Qiagen). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 6pM concentration and clusters generated and sequenced on the Illumina Genome  Analyzer IIx as single-end 72 base reads

treatment_protocol: C2C12 cells were infected with lentiviral vectors and selected in the continuous presence of puromycin. Infected cell populations were then differentiated for 7 days in DMEM medium with 2% horse serum.

value: C2C12 cell derived myotubes


title: C2C12_ShSC

description: C2C12 cells expressing a control shRNA sequence


title: Sleeping Beauty induced lymphoma13

status: Public on Aug 12 2011

city: Amsterdam

first: Jos

last: Jonkers

email: j.jonkers@nki.nl, m.koudijs@nki.nl

address: Plesmanlaan 121

department: Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: library strategy = barcode; library selection = LIGATION MEDIATED PCR

data_processing: Sequence reads are mapped to NCBI m37 using BLAT, sorted on barcode and processed using custom made algortihms as described in the associated manuscript. All scripts available on request. The export.txt files contain a summary of all unique integration sites. Per integration site 1 read ID is shown together with the cumulative number of sequence reads (depth), without specifying the individual read IDs per integrations site.

source_name: Lymphoma

extract_protocol: Isolation of gDNA and ligation-mediated amplification of regions flanking retroviral insertions after endonucelase digestion or acoustic shearing of gDNA. Subsequently, barcoded PCR products were pooled and sequenced on a 454 GS_FLX system according to the manufacturers protocol.

value: spleen

tag: transposon

value: Sleeping beauty

tag: 10bp barcode

value: ACTACTATGT


title: Sleeping Beauty induced lymphoma12

value: ACGTCTCATC


title: Sleeping Beauty induced lymphoma14

value: ACTAGCAGTA


title: Sleeping Beauty induced lymphoma15

value: ACTCACAGAG


title: Sleeping Beauty induced lymphoma11

value: ACGCGAGTAT


title: Sleeping Beauty induced lymphoma8

value: ACGAGTGCGT


title: hES_HUES8_p27_RRBS

source_name: hES HUES8 passage 27

tag: cell type


title: PiggyBac integrations in IB10 ES cells

description:
Cell line described in Bouwman et al, Nat. Struct. Mol Biol., June 2010
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: Mouse ES cell line

tag: cell line

value: IB10 ES cells

value: PiggyBac


title: Sleeping Beauty induced lymphoma7

value: ACGACTACAG


title: Sleeping Beauty induced lymphoma16

value: ACTCATCTAC


title: Sleeping Beauty induced lymphoma9

value: ACGCGATCGA


title: Sleeping Beauty induced lymphoma6

value: ACGACAGCTC


title: Sleeping Beauty induced lymphoma3

value: ACAGTCGTGC


title: C2C12_ShB


title: Sleeping Beauty induced lymphoma5

value: ACATGACGAC


title: Sleeping Beauty induced lymphoma4

value: ACATACGCGT


title: Tumor 15 Shearing BC15

description:
Associated SFF file contains 48 different barcodes in total, only the 16 indicated barcodes are decribed in the associated manuscript.
24-06-09-3.export.txt

data_processing:
> Mapping and processing of sequence reads <
Sequences from each sample were sorted on barcodes, filtered for the presence of the 5’ end of MMTV (not present in the oligonucleotides sequence) and the splinkerette sequence using Exonerate, mapped to the genome using BLAT (95% similarity) and aggregated by genomic coordinate of the transition of MMTV viral sequence to genomic DNA. A reference genome was generated using all unique BLAT hits in order to include short sequence reads that originally couldnot be mapped in a second round of mapping against this reference sequence. Unique LPs were determined by determining unique BLAT coordinates of reads per integration site. All reads were processed using Perl and all information was stored in an SQLite database.
> Read filtering and insertion determination <
All subsequent filtering and processing has been performed in R. To remove background and non-tumor related insertions we excluded all unique genomic coordinates that were supported by one read only (for the restriction enzyme experiments) or were supported by only one unique ligation point (for the shear- splink experiment). To determine insertion sites and to compensate for small (1- 10 bp) shifts in genomic coordinate at the MMTV-end we used hierarchical clustering to aggregate reads into insertions. Clustering was performed with absolute genomic distance in bp and single linkage. The resulting dendrogram was cut at a distance of 10 bp. This cutoff resulted in a mean within-cluster distance that was 7 orders of magnitude lower than the mean nearest between cluster distance, indicating a very tight clustering. The resulting clusters represent the unique insertions that we recovered in the analyses.
> Removal of contaminations <
In the process of library generation, cross contamination of DNA is possible. We eliminated all reads that reported a unique, identical genomic co-ordinate over more than 2 tumors. In the case where 2 tumors contained reads reporting the same unique genomic co-ordinate for insertion we kept the reads only if one of the two tumors had a 5-fold higher read-depth for that specific genomic co- ordinate. In all other cases the reads were discarded.
> Analysis of clonal cell lines <
We determined the clonal insertions for both cell lines from the 1:0 and 0:1 by selecting unique genomic co-ordinates for which we could determine at least 15 unique LPs. We determined the number of unique LPs for these selected insertions for all dilutions. R2 was determined using the stats package in the R software.
> Statistical analyses <
The Fisher-Exact test as implemented in the R software was used to compare the significance of the enrichment for known CIS genes between the restriction enzyme experiments and the shearing experiments. ROC curves were calculated and visualized using the ROCR package for R. The ranking required by the ROC analysis was based on the total number of reads per insertion for the restriction enzyme experiments and the total number of unique ligation points for the shearing experiments.
The export.txt files contain a summary of all unique integration sites. Per integration site 1 read ID is shown together with the cumulative number of sequence reads (depth), without specifying the individual read IDs per integrations site.

source_name: MMTV induced mammary tumor

extract_protocol: Isolation of gDNA and ligation-mediated amplification of regions flanking retroviral insertions after endonucelase digestion or acoustic shearing of gDNA. Subsequently,barcoded PCR products were pooled and sequenced on a 454 GS_FLX system according to the manufacturers protocol.

tag: library

value: Tumor 15 Shearing BC15

value: FVB

value: wildtype

tag: 9 bp spacer and 10 bp barcode

value: atgctgacgTGACGTATGT

tag: barcode

value: TGACGTATGT


title: Tumor 14 Shearing BC14

value: Tumor 14 Shearing BC14

value: atgctgacgTCGCACTAGT

value: TCGCACTAGT


title: Small RNAs from Vitis vinifera leaves

description:
VVI1
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Leaves

tag: cultivar

value: Merlot

value: Leaves (apical)


title: Tumor 1 Shearing BC1

value: Tumor 1 Shearing BC1

value: atgctgacgCGTGTCTCTA

value: CGTGTCTCTA


title: Tumor 5 Shearing BC5

value: Tumor 5 Shearing BC5

value: atgctgacgCGTCTAGTAC

value: CGTCTAGTAC


title: Cell lines 0:1 ratio BC41

source_name: Ratio of 2 cell lines derived from MMTV induced mammary tumor

value: Cell lines 0:1 ratio BC41

value: atgctgacgTAGTGTAGAT

value: TAGTGTAGAT


title: Tumor 2 Shearing BC2

value: Tumor 2 Shearing BC2

value: FVB

value: wildtype

value: atgctgacgTCTCTATGCG

value: TCTCTATGCG


title: Tumor 11 Shearing BC11

value: Tumor 11 Shearing BC11

value: atgctgacgTACACACACT

value: TACACACACT


title: Tumor 8 Shearing BC8

value: Tumor 8 Shearing BC8

value: atgctgacgCACGCTACGT

value: CACGCTACGT


title: Tumor 6 Shearing BC6

value: Tumor 6 Shearing BC6

value: atgctgacgTGTACTACTC

value: TGTACTACTC


title: Tumor 9 Shearing BC9

value: Tumor 9 Shearing BC9

value: atgctgacgCAGTAGACGT

value: CAGTAGACGT


title: Small RNAs from Silene latifolia leaves

description:
SLA1
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

tag: gender

value: Female

tag: tissue

value: Leaves


title: NPC_H9_derived_RRBS

description: reduced representation bisulfite sequencing

source_name: Nerual progenitors in vitro derived from hES H9


title: Tumor 3 Shearing BC3

value: Tumor 3 Shearing BC3

value: FVB

tag: genotype/variation

value: wildtype

value: atgctgacgTACTGAGCTA

value: TACTGAGCTA


title: Sleeping Beauty induced lymphoma1

value: spleen

value: Sleeping beauty

value: ACACATACGC


title: Tumor 13 Shearing BC13

value: Tumor 13 Shearing BC13

value: atgctgacgTACGCTGTCT

value: TACGCTGTCT


title: Tumor 7 Shearing BC7

value: Tumor 7 Shearing BC7

value: atgctgacgTACGAGTATG

value: TACGAGTATG


title: Tumor 4 Shearing BC4

value: Tumor 4 Shearing BC4

value: atgctgacgCGAGAGATAC

value: CGAGAGATAC


title: Tumor 12 Shearing BC12

value: Tumor 12 Shearing BC12

value: atgctgacgTACACGTGAT

value: TACACGTGAT


title: Tumor 10 Shearing BC10

value: Tumor 10 Shearing BC10

value: FVB

value: wildtype

value: atgctgacgCGACGTGACT

value: CGACGTGACT


title: Cell lines 1:9 ratio BC40

value: Cell lines 1:9 ratio BC40


title: Tumor 16 Shearing BC16

value: Tumor 16 Shearing BC16

value: atgctgacgTGTGAGTAGT

value: TGTGAGTAGT


title: Cell lines 1:3 ratio BC39

value: Cell lines 1:3 ratio BC39

value: atgctgacgTACAGATCGT

value: TACAGATCGT


title: Small RNAs from Zostera marina flowers

description:
ZMR2
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Flowers

value: Flowers

value: mix of male and female


title: Cell lines 1:2 ratio BC38

value: Cell lines 1:2 ratio BC38


title: Cell lines 1:1 ratio BC37

value: Cell lines 1:1 ratio BC37

value: atgctgacgTACACACACT

value: TACACACACT


title: Cell lines 1:0 ratio BC33

value: Cell lines 1:0 ratio BC33

value: FVB

value: atgctgacgATAGAGTACT

value: ATAGAGTACT


title: Cell lines 9:1 ratio BC34

value: Cell lines 9:1 ratio BC34

value: wildtype

value: atgctgacgCACGCTACGT

value: CACGCTACGT


title: Pancreatic_islet_normal_RRBS

source_name: Pancreatic islet


title: Tumor 16 X BfaI BC32

value: Tumor 16 X BfaI BC32

value: atgctgacgAGTACGCTAT

value: AGTACGCTAT


title: Cell lines 3:1 ratio BC35

value: Cell lines 3:1 ratio BC35

value: atgctgacgCAGTAGACGT

value: CAGTAGACGT


title: Tumor 14 X BfaI BC30

value: Tumor 14 X BfaI BC30

value: atgctgacgAGACTATACT

value: AGACTATACT


title: Tumor 11 X BfaI BC27

value: Tumor 11 X BfaI BC27

value: atgctgacgACGCGAGTAT

value: ACGCGAGTAT


title: Tumor 8 X BfaI BC24

value: Tumor 8 X BfaI BC24

value: FVB

value: atgctgacgTAGAGACGAG

value: TAGAGACGAG


title: Tumor 13 X BfaI BC29

value: Tumor 13 X BfaI BC29

value: wildtype

value: atgctgacgACTGTACAGT

value: ACTGTACAGT


title: Tumor 12 X BfaI BC28

value: Tumor 12 X BfaI BC28

value: atgctgacgACTACTATGT

value: ACTACTATGT


title: Cell lines 2:1 ratio BC36

value: Cell lines 2:1 ratio BC36

value: atgctgacgCGACGTGACT

value: CGACGTGACT


title: Tumor 7 X BfaI BC23

value: Tumor 7 X BfaI BC23

value: atgctgacgTACTCTCGTG

value: TACTCTCGTG


title: Tumor 9 X BfaI BC25

value: Tumor 9 X BfaI BC25

value: atgctgacgTCGTCGCTCG

value: TCGTCGCTCG


title: Tumor 10 X BfaI BC26

value: Tumor 10 X BfaI BC26

value: FVB

value: atgctgacgACATACGCGT

value: ACATACGCGT


title: Tumor 2 X BfaI BC18

value: Tumor 2 X BfaI BC18

value: wildtype

value: atgctgacgTCTACGTAGC

value: TCTACGTAGC


title: Tumor 15 X BfaI BC31

value: Tumor 15 X BfaI BC31

value: atgctgacgAGCGTCGTCT

value: AGCGTCGTCT


title: Tumor 1 X BfaI BC17

value: Tumor 1 X BfaI BC17

value: atgctgacgCGTCTAGTAC

value: CGTCTAGTAC


title: Tumor 6 X BfaI BC22

value: Tumor 6 X BfaI BC22

value: atgctgacgTACGAGTATG

value: TACGAGTATG


title: embryonic digit stage 28/29 EF1_mRNAseq

source_name: Embryonic chicken digit

tag: embryonic stage

value: Stage 28/29

value: embryonic digit


title: Tumor 4 X BfaI BC20

value: Tumor 4 X BfaI BC20

value: FVB

value: atgctgacgACGACTACAG

value: ACGACTACAG


title: Tumor 3 X BfaI BC19

value: Tumor 3 X BfaI BC19

value: wildtype

value: atgctgacgTGTACTACTC

value: TGTACTACTC


title: Tumor 15 X NlaIII BC15

value: Tumor 15 X NlaIII BC15

value: atgctgacgATACGACGTA

value: ATACGACGTA


title: Tumor 16 X NlaIII BC16

value: Tumor 16 X NlaIII BC16

value: atgctgacgTCACGTACTA

value: TCACGTACTA


title: Rectal_mucosa_rep1_RRBS

source_name: Rectal mucosa


title: Tumor 13 X NlaIII BC13

value: Tumor 13 X NlaIII BC13

value: atgctgacgCATAGTAGTG

value: CATAGTAGTG


title: Tumor 14 X NlaIII BC14

value: Tumor 14 X NlaIII BC14

value: atgctgacgCGAGAGATAC

value: CGAGAGATAC


title: Tumor 11 X NlaIII BC11

value: Tumor 11 X NlaIII BC11

value: FVB

value: atgctgacgTGATACGTCT

value: TGATACGTCT


title: Tumor 12 X NlaIII BC12

value: Tumor 12 X NlaIII BC12

value: wildtype

value: atgctgacgTACTGAGCTA

value: TACTGAGCTA


title: Tumor 9 X NlaIII BC9

value: Tumor 9 X NlaIII BC9

value: atgctgacgTAGTATCAGC

value: TAGTATCAGC


title: Tumor 8 X NlaIII BC8

value: Tumor 8 X NlaIII BC8

value: atgctgacgCTCGCGTGTC

value: CTCGCGTGTC


title: Tumor 10 X NlaIII BC10

value: Tumor 10 X NlaIII BC10

value: atgctgacgTCTCTATGCG

value: TCTCTATGCG


title: Tumor 6 X NlaIII BC6

value: Tumor 6 X NlaIII BC6

value: atgctgacgATATCGCGAG

value: ATATCGCGAG


title: Tumor 5 X NlaIII BC5

value: Tumor 5 X NlaIII BC5

value: FVB

value: atgctgacgATCAGACACG

value: ATCAGACACG


title: Tumor 7 X NlaIII BC7

value: Tumor 7 X NlaIII BC7

value: wildtype

value: atgctgacgCGTGTCTCTA

value: CGTGTCTCTA


title: Tumor 3 X NlaIII BC3

value: Tumor 3 X NlaIII BC3

value: atgctgacgAGACGCACTC

value: AGACGCACTC


title: Tumor 1 X NlaIII BC1

value: Tumor 1 X NlaIII BC1

value: atgctgacgACGAGTGCGT

value: ACGAGTGCGT


title: Tumor 2 X NlaIII BC2

value: Tumor 2 X NlaIII BC2

value: atgctgacgACGCTCGACA

value: ACGCTCGACA


title: Tumor 5 X BfaI BC21

value: Tumor 5 X BfaI BC21

value: atgctgacgCGTAGACTAG

value: CGTAGACTAG


title: FOXA1 input-seq, 4h DHT treatment

status: Public on Jul 11 2011

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

description:
FOXA1_MDA-MB-453_4hDHT-Input
Input-seq data
sequencing instrument: HeliScope Single Molecule Sequencer

data_processing:
Aligment: Sequence reads were obtained and mapped the human genome (hg18, March 2006) using Helicos Genetic Analysis System.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm, version 1.3.7.1 (http://liulab.dfci.harvard.edu/MACS/)

source_name: [input] MDA-MB-453 cells treated with 10nM DHT for 4h

growth_protocol: The MDA-MB-453 cells were maintained in DMEM supplemented with 10% fetal bovinw serum at 37C incubator.

extract_protocol: 6 ng ChIP DNA was used in the direct polyA tailing step according to Helicos HeliScope standard procedure.

treatment_protocol: The MDA-MB-453 cells were grown in the phenol red-free medium supplemented with 5% charcoal/dextran-treated fetal bovine serum for 3 days, followed by treatment of 10 nM DHT for 4h and 16h respectively for ChIP after crosslinking with 1% formadehyde.

value: MDA-MB-453 breast cancer cell line

tag: agent

value: DHT

tag: time

tag: antibody

value: none (input control)


title: AR 4h input-seq, 4h DHT treatment

description:
AR_MDA-MB-453_4hDHT-Input
Input-seq data
sequencing instrument: HeliScope Single Molecule Sequencer


title: AR 16h input-seq, 16h DHT treatment

description:
AR_MDA-MB-453_16hDHT-Input
Input-seq data
sequencing instrument: HeliScope Single Molecule Sequencer

source_name: [input] MDA-MB-453 cells treated with 10nM DHT for 16h


title: Tumor 4 X NlaIII BC4

value: Tumor 4 X NlaIII BC4

tag: strain

value: FVB

value: wildtype

value: atgctgacgAGCACTGTAG

value: AGCACTGTAG


title: Brg KO Input Seq

status: Public on Aug 01 2011

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

data_processing: Sequence reads were mapped to the mouse genome (mm8) using the Solexa Analysis Pipeline. The mapped reads were processed using the SISSRs peak-finder (Jothi et al, Nucl Acids Res 2008; PMID: 18684996) to identify STAT3 binding sites. H3K27me3 data was analyzed using custom scripts.

source_name: Brg f/f;Actin-Cre ER; Tamoxifen Treated (72hours) mouse ESCs

growth_protocol: We prepared the Brgcond ESC line from Brglox/lox;;Actin-CreER mice that allow conditional deletion of Brg upon addition of 4-hydroxytamoxifen (4OHT, Sigma). Cells were grown under the standard conditions for murine ESCs on irradiated mouse fibroblasts, and transferred to gelatin-coated plates 2 passages before harvesting for experimentation, in this case, for ChIP.

extract_protocol: Mouse ESCs  were crosslinked with formaldehyde and sonicated to generate chromatin fragments, which were immunoprecipitated with STAT3 (C20X, Santa Cruz) or H3K27me3 (07-449, Millipore) antibody. The DNA fragments were end-repaired and processed for sequencing on an Illumina Genome Analyzer using standard protocols.

treatment_protocol: To induce Brg deletion in these lines, we treated the cultures grown on MEFs with 1uM 4-hydroxytamoxifen (4-OHT Sigma, dissolved in ethanol) for 24 hours, then passaged them onto gelatinized plates for 48 more hours of 4-OHT treatment. As a control, 6-14 Brgcond cells were treated with ethanol, which does not induce Cre expression. Brg protein levels first decrease appreciably at 36 hours and are completely depleted by 48hours. Hence, cells treated for 72 hours have been Brg-deficient for 24-36 hours.

value: E14Tg2a embryonic stem cell line

value: BrgKO

tag: chip antibody


title: BrgWT H3K27me3 ChIP-Seq

source_name: Brg f/f;Actin-Cre ER; EtOH Treated  (72hours) mouse ESCs

value: BrgWT

tag: chip antibody vendor

value: Millipore

tag: chip antibody catalog#


title: FOXA1 ChIP-seq, 4h DHT treatment

description:
FOXA1_MDA-MB-453_4hDHT-ChIP
ChIP-seq data
sequencing instrument: HeliScope Single Molecule Sequencer

source_name: [ChIP] MDA-MB-453 cells treated with 10nM DHT for 4h

tag: antibody vendor

value: abcam

tag: antibody catalog#


title: BrgKO STAT3 ChIP-Seq

description: bsites file: ChIP-seq peaks as defined by SISSRs tool

tag: cell line

value: Santa Cruz


title: BrgKO H3K27me3 ChIP-Seq


title: Brg WT Input Seq


title: AR ChIP-seq, 16h DHT treatment

description:
AR_MDA-MB-453_16hDHT-ChIP
ChIP-seq data
sequencing instrument: HeliScope Single Molecule Sequencer

source_name: [ChIP] MDA-MB-453 cells treated with 10nM DHT for 16h

value: anti-AR (N-20)


title: AR ChIP-seq, 4h DHT treatment

description:
AR_MDA-MB-453_4hDHT-ChIP
ChIP-seq data
sequencing instrument: HeliScope Single Molecule Sequencer


title: Hippocampus rep2

status: Public on Jun 22 2011

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Modified Illumina small RNA sample prep kit v1.0
sequenced with Illumina index 7 (CAGAUC)

data_processing:
miRNA expression level: Sequence reads were trimmed by removing the index and the 3' adapter sequence, and filtered to remove sequences including adaptor dimers, mitochondrial or ribosomal sequences. Reads with homopolymers (1 nt appearing >80% of the sequence) or were <14 nt long were removed. Remaining reads were mapped against the miRBase v. 11 using Bowtie (allowing two mismatches).
Genomic alignment: Sequence reads were trimmed by removing the index and the 3' adapter sequence, and filtered to remove sequences including adaptor dimers, mitochondrial or ribosomal sequences. Reads with homopolymers (1 nt appearing >80% of the sequence) or were <14 nt long were removed. Remaining reads were mapped against the mouse genome (Mus_musculus.NCBIM37.59) using Bowtie (allowing two mismatches).

source_name: Hippocampus

extract_protocol: Total RNA was isolated using Trireagent. Modified Illumina Small RNA Sample Prep kit v.1.0 was used for library preparation.  5' adapter was modified by inserting a 6 nt tag before miRNA ligation site. Illumina indexes 3 (UUAGGC), 7 (CAGAUC), and 11 (GGCUAC) were used. Each replicate was sequenced with all 3 indexes, in separate lanes and in a lane which contained equal amounts of all 3 replicates with a different index.

treatment_protocol: Mice were orderd at 7 weeks of age and singly housed for 1 week. They were sacrificed by cervical dislocation at 9 am. Brains were quickly removed, rinsed with PBS, and placed on a filter paper on a petri dish filled with ice. Frontal cortex (cortical tissue dissected from a slice spanning Bregma -1.5 - -3.5) and the entire hippocampus were dissected and immediately frozen in liquid nitrogen, and stored at -80 Â°C until RNA extraction.

value: Hippocampus

tag: age

value: 8 weeks

tag: sample type

value: Small RNAs (15-35nt)


title: Input DNA

status: Public on Jul 01 2011

city: Columbus

first: Brian

middle: Alexander

last: Kennedy

state: Ohio

address: 278 Chittenden AVE

institute: The Ohio State University

description: Input DNA

data_processing: hg18, peak files produced using BELT

source_name: A2780 cells

growth_protocol: cells grown in RPMI 1640 supplemented with 10% FBS in 5% CO2 incubator at 37C. Cells were inspected daily and split at ~70% confluance.

extract_protocol: Lysates were clarified from sonicated nuclei and SMAD4-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the ChIP-seq DNA Sample prep Kit (Part# IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated from a 2% E-gel from invitrogen. 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: 80% confluant cells were stimulated with 10ng/ml recombinant TGFβ1 for 1 hour prior to formaldehyde crosslinking.

value: A2780 cells

tag: treatment


title: BrgWT STAT3 ChIP-Seq


title: Hippocampus rep2 pooled


title: Hippocampus rep3 pooled

description:
Modified Illumina small RNA sample prep kit v1.0
sequenced with Illumina index 11 (GGCUAC)


title: SMAD4 unstimulated cell ChIP-seq

description: Chromatin IP against SMAD4 in SMAD4 unstimulated cells

value: TGF-beta

value: SMAD4 (20% Cell Signaling Technology, 80% Santa Cruz Biotechnology)

tag: antibody manufacturer 1

value: Cell Signaling Technology

tag: antibody manufacturer 2

value: Santa Cruz Biotechnology

tag: antibody catalog number 1

tag: antibody catalog number 2

tag: antibody lot number 1

tag: antibody lot number 2

tag: antibody number 1 fraction

tag: antibody number 2 fraction


title: SMAD4 stimulated cell ChIP-seq

description: Chromatin IP against SMAD4 in SMAD4 stimulated cells

tag: chip antibody


title: Rectal_smooth_muscle_rep1_RRBS

source_name: Rectal smooth muscle

tag: tissue


title: Frontal Cortex rep1 pooled

description:
Modified Illumina small RNA sample prep kit v1.0
sequenced with Illumina index 3 (UUAGGC)

source_name: Frontal cortex

value: Frontal cortex

tag: strain


title: Frontal Cortex rep3


title: Frontal Cortex rep2 pooled


title: Hippocampus rep1 pooled


title: Frontal Cortex rep3 pooled


title: Frontal Cortex rep2


title: Frontal Cortex rep1


title: Hippocampus rep3


title: Hippocampus rep1


title: Sleeping Beauty induced lymphoma2

description: library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: Lymphoma

value: spleen

tag: transposon

value: Sleeping beauty

tag: 10bp barcode

value: ACAGTATATA


title: esc_18to24hr_INPUT_DNA

status: Public on Jun 15 2011

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

description: Chromatin

data_processing: Sequence reads were aligned to Release 4 of the Drosophila melanogaster genome using Illumina Genome Analyzer pipleine (ELAND) with default parameters. Only sequences with unique hits were included.

source_name: 18-24hr esc mutant

growth_protocol: The wild type and esc mutant Drosophila embryos were collected at different time points. For 0-2hr time point embryos were collected every two hours after discarding at least 3 pre-lays of one hour each. For the 8-12 hr time point embryos were collected for 4 hrs and aged for 8 hrs before harvesting for ChIP experiments. The 18-24hr old embryos were obtained by collecting embryos every 6 hrs and ageing then for 18 hrs.

extract_protocol: The chromatin obtained from fixed embryos was used for ChIP experiments. The DNA obtained after ChIP was subjected to end-filling, addition of 3'A nucleotide, adaptor ligation, size selection and LM-PCR according to Illumina library preperation protocol

treatment_protocol: The embryos were then dechorionated in 50% bleach and fixed in 5% Formaldehyde saturated Hexanes for 5 mins on a shaker. The embryos were subsequently washed with 1XPBS and 0.5% Triton X-100 and flash frozen in liquid Nitrogen and storage in -80 freezer.

value: yw

tag: genotype/variation

value: esc mutants

tag: developmental stage

value: 18-24hr esc mutant

tag: passages

value: Not applicable


title: yw_18to24hr_H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

source_name: 18-24hr Drosophila embryo

value: wildtype

value: 18-24hr Drosophila embryo

value: H3K4me3, Rabbit Polyclonal

tag: antibody vendor

value: Abcam

tag: antibody catalog #

tag: antibody lot #


title: esc_18to24hr_H3K27me3_ChIPSeq

description: Chromatin IP against H3K27me3

value: H3K27me3, Rabbit Polyclonal

value: Millipore


title: yw_8to12hr_PolII_ChIPSeq

description: Chromatin IP against Pol-II

source_name: 8-12hr Drosophila embryo

value: 8-12hr Drosophila embryo

value: RNA Polymerase II (Pol-II), Mouse Monoclonal,  a cocktail of antibodies Pol II 8WG16 and Pol II H14

value: Covance

value: MMS-126R (Pol II 8WG16)

value: MMS-134R (Pol II H14)


title: yw_18to24hr_H3K27me3_ChIPSeq

description: Chromatin IP against H3K27me3


title: esc_18to24hr_GROSeq

description: GRO-Seq, Genomic Run-on Assay (sequenced nascent transcripts)

data_processing: GRO-Seq reads were aligned with bowtie. Due to spurious nucleotides sequenced at the 5' end, the first 4nt were trimmed before alignment. The subsequent 26nt were aligned allowing one unique hit per sequence.

extract_protocol: For the GRO-seq protocol refer to (Core LJ, Waterfall JJ, Lis JT.Science. 2008 Dec 19;322(5909):1845-8. Epub 2008 Dec 4).


title: esc_18to24hr_PolII_ChIPSeq

description: Chromatin IP against Pol-II


title: esc_18to24hr_H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3


title: UAS>AbdB_18to24hr_PolII_ChIPSeq

description: Chromatin IP against Pol-II, with added Abd-B over-expression

source_name: 18-24hr Drosophila embryo with exogenous UAS>AbdB construct

value: exogenous UAS>AbdB construct


title: UAS>AbdBnoHS_18to24hr_PolII_ChIPSeq

description: Chromatin IP against Pol-II

value: 18-24hr Drosophila embryo with exogenous UAS>AbdB construct


title: yw_18to24hr_INPUT_DNA

description: Chromatin

value: yw


title: yw_0to2hr_PolII_ChIPSeq

description: Chromatin IP against Pol-II

source_name: 0-2hr Drosophila embryo

value: 0-2hr Drosophila embryo


title: Sleeping Beauty induced lymphoma10

value: spleen

value: Sleeping beauty

value: ACGCTCGACA


title: esc_8to12hr_PolII_ChIPSeq

description: Chromatin IP against Pol-II

source_name: 8-12hr esc mutant

value: esc mutants

value: 8-12hr esc mutant

value: Not applicable


title: yw_0to2hr_H3K27me3_ChIPSeq

description: Chromatin IP against H3K27me3

value: wildtype

value: H3K27me3, Rabbit Polyclonal


title: yw_0to2hr_H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

value: H3K4me3, Rabbit Polyclonal

value: Abcam


title: yw_18to24hr_PolII_ChIPSeq

description: Chromatin IP against Pol-II

value: 18-24hr Drosophila embryo

value: RNA Polymerase II (Pol-II), Mouse Monoclonal,  a cocktail of antibodies Pol II 8WG16 and Pol II H14

value: Covance


title: yw_0to2hr_IgG_ChIPSeq

description: Chromatin IP with IgG, non-specific

value: IgG non-specific


title: Prostate stromal cells (cell culture)

status: Public on Jun 13 2011

city: Seattle

first: Muneesh

last: Tewari

state: WA

address: 1100 Fairview Ave, N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: prostate primary cell culture stromal sample

data_processing: Once linkers were trimmed, reads were combined and counts tallied.

source_name: cell culture

extract_protocol: Linker ligation and amplification of prostate RNA samples were performed as described in (Mitchell et al. 2008).

tag: cell type

value: prostate stromal cells


title: Normal prostate

description: Size selected 18-24nt

source_name: normal prostate

value: prostate


title: Prostate epithelial cells (cell culture)

description: prostate primary cell culture epithelial sample

value: prostate epithelial cells


title: yw_0to2hr_INPUT_DNA

description: Chromatin

value: yw

value: 0-2hr Drosophila embryo


title: HepG2_no stimulation_HNF4A_ChIPSeq

status: Public on Jun 08 2011

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: Chromatin IP against HNF4A.

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006; hg18) genome using the Illumina Genome Analyzer Pipeline.
Peaks: Peaks were called using CisGenome v1.2 by one-sample analysis with window width of 100 bp.

HepG2_HN4a_TGFb-_Sc.wig: HNF4A binding sites in HepG2 cells without TGF-beta.
100809_S5_W100.bed: significant HNF4A binding positions in HepG2 cells without TGF-beta (FDR < 0.1%).

source_name: HepG2 cells, without TGF-beta3 stimulation

growth_protocol: HepG2 cells were maintained in MEM medium (GIBCO) supplemented with 10% FBS (Thermo Scientific, Rockford, IL), 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 100 U/ml of penicillin G, and 100 Âµg/ml of streptomycin. Cells were grown in a humidified incubator with 5% CO2 at 37Â°C.

extract_protocol: ChIP was performed as described (Koinuma et al., Mol Cell Biol 29: 172-186, 2009 [PMID 18955504]). HNF4A-DNA complexes were isolated by anti-HNF4A.  Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: Cells were stimulated with 3 ng/ml of TGF-beta for 1.5 h or left untreated.

tag: cell line

value: hepatoblastoma cells

tag: treatment

tag: treatment duration

value: 1.5 hrs

value: Santa Cruz

tag: antibody catalog number

tag: antibody lot number


title: HepG2_TGF-beta stimulation_HNF4A_ChIPSeq

description: Chromatin IP against HNF4A.

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006; hg18) genome using the Illumina Genome Analyzer Pipeline.
Peaks: Peaks were called using CisGenome v1.2 by one-sample analysis with window width of 100 bp.

HepG2_HN4a_TGFb+_Sc.wig: HNF4A binding sites in HepG2 cells treated with TGF-beta for 1.5 h.
100809_S6_W100.bed: significant HNF4A binding positions in HepG2 cells treated with TGF-beta for 1.5h (FDR < 0.1%).

source_name: HepG2 cells, stimulated with TGF-beta3 for 1.5 h

value: 3 ng/ml TGF-beta3

tag: chip antibody


title: H3K27me3_K562_ChIP-seq_rep1_2

status: Public on Jun 07 2011

city: Palo Alto

first: Philip

last: Cayting

address: 1501 S California Ave

institute: Stanford University

description: Chromatin IP against H3K27me3

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome assembly hg18 (March, 2006) or hg19 (February, 2009) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks were called with Sole-Search (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi)

source_name: chronic myeloid leukemia cell line

growth_protocol: All cells were grown according to ENCODE standards (http://genomewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines)

extract_protocol: Lysates were clarified from sonicated nuclei and protein-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 3â 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: ChIP assay was performed following the ChIP protocol provided at: http://farnham.genomecenter.ucdavis.edu/pdf/FarnhamLabChIP%20Protocol.pdf

tag: cell-type

value: K562 cell line

tag: harvest date

value: rabbit anti-H3K27me3 (Cell Signaling Technology, catalog#:9733S)


title: E2F6_K562_ChIP-seq_rep1 lane 1

description: Chromatin IP against E2F6

value: rabbit anti-E2F6 (Santa Cruz Biotechnology, catalog# sc-22823x)


title: 5 dpf DMSO_embryo_SC3_Cy5

status: Public on Jun 06 2011

type: RNA

city: Miami

first: Marjorie

middle: F.

last: Oleksiak

state: FL

address: 4600 Rickenbacker Causeway

department: Marine Biology and Fisheries

institute: University of Miami

hyb_protocol: Labeled aRNA samples (2 pmol dye/ul) were hybridized to slides in 10 ul of hybridization buffer [50% formamide buffer, 5x SSPE, 1% sodium dodecyl sulfate, 0.2 mg/ml bovine serum albumin, 1 mg/ml denatured salmon sperm DNA (Sigma), and 1 mg/ml RNAse free poly(A) RNA (Sigma)] for 44 hours at 42º C.

scan_protocol: Arrays were scanned using  a ScanArray Express 4000 (Perkin Elmer).  Resulting 16 bit Tiff Images were quantified using ImaGene® (Biodiscovery, Inc.) spotfinding software.

data_processing: Log2 measures of gene expression were normalized using a linear mixed model in JMP Genomics 3.2 (SAS, Cary, NC, USA) to remove the effects of dye (fixed effect) and array (random effect) following a joint regional and spatial Lowess transformation in MAANOVA version 0.98.8 for R to account for both intensity and spatial bias.  The model was of the form yij = μ  + Ai + Dj + (AxD)ij + εij where, yij is the signal from the ith array with dye j, μ is the sample mean, Ai and Dj are the overall variation in arrays (arrays 1-80) and dyes (Cy3 and Cy5), (AxD)ij is the array x dye interaction and εij is the stochastic error.  Because we were not interested in differences due to developmental stage, we analyzed residuals from the above model separately by time (e.g., separately for times 5, 10 and 15 dpf).  Thus, residuals from this model were used for gene-by-gene analyses by time of population and treatment effects, using population, treatment and dye as fixed effects, and array as a random effect.  The model was rijn = μ  + Ai + Dj + Pn + Tk + PnxTk + εijn where Pn is the nth population and Tk is the kth treatment (DMSO or PCB-126).  For all mixed model analyses, we used a false discovery rate (FDR) p-value of < 0.01 to control for multiple testing

organism: Fundulus heteroclitus

source_name: 5 dpf DMSO_embryo_SC3_Cy5

label_protocol: RNA for hybridization was prepared by one round of amplification (aRNA) using the Amino Allyl MessageAmp aRNA Kit (Ambion, Austin, TX, USA) to form copy template RNA by T7 amplification.  Amino-allyl UTP was incorporated into targets during T7 transcription, and resulting amino-allyl aRNA was coupled to Cy3 and Cy5 dyes (GE Healthcare, Piscataway, NJ, USA).

growth_protocol: F. heteroclitus adults were collected from New Bedford Harbor, MA USA and Scorton Creek, MA USA in May and June of 2007. For each site, eggs from 8 females (~1100 total) were fertilized using minced testes from 5 males. After non-fertile eggs were culled, embryos were exposed to vehicle (DMSO; 0.1%) or PCB-126 (50 nM) in filtered seawater (salinity 25 part per thousand, 65 embros per 20 ml in glass petri dish) for 4 hr at 20º C. After exposure, the embryos were washed in filtered seawater and incubated at 20º C under a 14-h light, 10-h dark cycle.  At 5-, 10-, and 15-dpf, embryos were collected as three pools of 20 embryos from each treatment group and flash frozen in liquid nitrogen and stored at -80º C until used for RNA isolation

extract_protocol: Total RNA was isolated from pools of embryos (20 embryos per pool) using STAT-60 (Tel-Test).

tag: population

value: Scorton Creek

tag: tissue

value: Whole embryo

value: vehicle control (DMSO)

tag: days post-fertilization


title: 15 DPF PCB-126_embryo_NBH32_Cy3

source_name: 15 DPF PCB-126_embryo_NBH32_Cy3

treatment_protocol: After non-fertile eggs were culled, embryos were exposed to vehicle (DMSO; 0.1%) or PCB-126 (50 nM) in filtered seawater (salinity 25 part per thousand, 65 embros per 20 ml in glass petri dish) for 4 hr at 20º C. After exposure, the embryos were washed in filtered seawater and incubated at 20º C under a 14-h light, 10-h dark cycle.  At 5-, 10-, and 15-dpf, embryos were collected as three pools of 20 embryos from each treatment group and flash frozen in liquid nitrogen and stored at -80º C until used for RNA isolation

value: New Bedford Harbor


title: 15 dpf DMSO_embryo_SC25_Cy5

source_name: 15 dpf DMSO_embryo_SC25_Cy5


title: 15 dpf DMSO_embryo_SC25_Cy3

source_name: 15 dpf DMSO_embryo_SC25_Cy3


title: 10 DPF PCB-126_embryo_NBH18_Cy3

source_name: 10 DPF PCB-126_embryo_NBH18_Cy3


title: 15 DPF PCB-126_embryo_SC30_Cy5

source_name: 15 DPF PCB-126_embryo_SC30_Cy5


title: 15 dpf DMSO_embryo_NBH30_Cy3

source_name: 15 dpf DMSO_embryo_NBH30_Cy3


title: 15 DPF PCB-126_embryo_NBH32_Cy5

source_name: 15 DPF PCB-126_embryo_NBH32_Cy5


title: 15 DPF PCB-126_embryo_SC30_Cy3

source_name: 15 DPF PCB-126_embryo_SC30_Cy3


title: 10 dpf DMSO_embryo_NBH15_Cy3

source_name: 10 dpf DMSO_embryo_NBH15_Cy3


title: 10 DPF PCB-126_embryo_NBH18_Cy5

source_name: 10 DPF PCB-126_embryo_NBH18_Cy5


title: 10 DPF PCB-126_embryo_SC16_Cy3

source_name: 10 DPF PCB-126_embryo_SC16_Cy3


title: 10 dpf DMSO_embryo_SC13_Cy3

source_name: 10 dpf DMSO_embryo_SC13_Cy3


title: 10 DPF PCB-126_embryo_SC16_Cy5

source_name: 10 DPF PCB-126_embryo_SC16_Cy5


title: 10 dpf DMSO_embryo_NBH15_Cy5

source_name: 10 dpf DMSO_embryo_NBH15_Cy5


title: 15 dpf DMSO_embryo_NBH30_Cy5

source_name: 15 dpf DMSO_embryo_NBH30_Cy5


title: 10 dpf DMSO_embryo_SC13_Cy5

source_name: 10 dpf DMSO_embryo_SC13_Cy5


title: 5 DPF PCB-126_embryo_SC6_Cy5

source_name: 5 DPF PCB-126_embryo_SC6_Cy5


title: Lateolabrax japonicus_DGE A

city: HangZhou

first: Ding

last: He

state: ZheJiang

address: YuHangTang road

department: College of Life Science

country: China

institute: ZheJiang University

data_processing: Raw sequences were transformed into clean tags by data-processing steps using bio-perl scripts, then about 0.33 and 0.27 million non-redundant tags with high qualities in both groups.

organism: Lateolabrax japonicus

source_name: head kidney and spleen tissues

growth_protocol: The fish were kept in running aerated seawater (salinity 30) at 25°C and fed with commercial pellet food at a daily ration of 0.7% of their body weight.

extract_protocol: The DGE analysis includes sample preparation and sequencing. Briefly, 6 µg of the total RNA was used for mRNA purification using oligo-dT magnetic beads adsorption, and then oligo-dT was used to guide reverse transcription to synthesize double-stranded cDNA. The generation of 5' ends of tags was recognized by endonuclease NlaIII, which recognizes and cuts off the CATG sites on cDNA. Then, cDNA fragments with 3' ends were purified by magnetic beads precipitation, and Illumina adapter 1 was added to their 5' ends. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which cuts at 17bp downstream of the CATG site, producing tags with adapter 1. After removing 3' fragments with magnetic beads precipitation, the 21 bp unique tags with adaptor 1 were purified and ligated to the adaptor 2 to form a cDNA tag library. These adapter-ligated cDNA tags were enriched after 15 cycles of linear PCR amplification. The resulting 85 bp fragments were purified by 6% TBE polyacrylamide gel electrophoresis. These fragments were then digested, and the single-chain molecules were fixed onto the Solexa Sequencing Chip (flowcell), and sequencing by synthesis was performed using the Illumina Genome Analyzer II system according to the manufacturer’s protocols. Image analysis, base calling, generation of millions of raw 17bp tags and tag counting were performed using the Illumina pipeline.  All tags were mapped to the reference transcriptome generated by RNA-seq. For monitoring the mapping events on both strands, both the sense and the complementary antisense sequences were included in this mapping process. Only perfect matches over the entire 21 bp length of the 17 bp tag plus the 4 bp NlaIII recognition site were allowed.

treatment_protocol: The fish in experimental groups were inoculated intraperitoneally with 0.2 ml of Vibrio harveyi at dosage of 1×108 CFU per fish. In parallel, the fish in control groups were administrated with 0.2 ml of mock PBS.

value: 0.2 ml of mock PBS


title: 5 dpf DMSO_embryo_NBH3_Cy3

source_name: 5 dpf DMSO_embryo_NBH3_Cy3


title: 5 DPF PCB-126_embryo_NBH4_Cy5

source_name: 5 DPF PCB-126_embryo_NBH4_Cy5


title: 5 DPF PCB-126_embryo_NBH4_Cy3

source_name: 5 DPF PCB-126_embryo_NBH4_Cy3


title: 5 DPF PCB-126_embryo_SC6_Cy3

source_name: 5 DPF PCB-126_embryo_SC6_Cy3


title: Lateolabrax japonicus_DGE B

value: 0.2 ml of Vibrio harveyi


title: 5 dpf DMSO_embryo_SC3_Cy3

source_name: 5 dpf DMSO_embryo_SC3_Cy3


title: 15 DPF PCB-126_embryo_NBH33_Cy3

source_name: 15 DPF PCB-126_embryo_NBH33_Cy3


title: 5 dpf DMSO_embryo_SC2_Cy5

source_name: 5 dpf DMSO_embryo_SC2_Cy5


title: 15 dpf DMSO_embryo_SC26_Cy5

source_name: 15 dpf DMSO_embryo_SC26_Cy5


title: 15 dpf DMSO_embryo_SC26_Cy3

source_name: 15 dpf DMSO_embryo_SC26_Cy3


title: 5 dpf DMSO_embryo_NBH3_Cy5

source_name: 5 dpf DMSO_embryo_NBH3_Cy5


title: 15 DPF PCB-126_embryo_SC29_Cy5

source_name: 15 DPF PCB-126_embryo_SC29_Cy5


title: 15 dpf DMSO_embryo_NBH29_Cy3

source_name: 15 dpf DMSO_embryo_NBH29_Cy3


title: 10 dpf DMSO_embryo_NBH17_Cy5

source_name: 10 dpf DMSO_embryo_NBH17_Cy5


title: 10 dpf DMSO_embryo_NBH17_Cy3

source_name: 10 dpf DMSO_embryo_NBH17_Cy3


title: 15 dpf DMSO_embryo_NBH29_Cy5

source_name: 15 dpf DMSO_embryo_NBH29_Cy5


title: 10 DPF PCB-126_embryo_NBH20_Cy3

source_name: 10 DPF PCB-126_embryo_NBH20_Cy3


title: 10 DPF PCB-126_embryo_NBH20_Cy5

source_name: 10 DPF PCB-126_embryo_NBH20_Cy5


title: 10 DPF PCB-126_embryo_SC17_Cy3

source_name: 10 DPF PCB-126_embryo_SC17_Cy3


title: 10 DPF PCB-126_embryo_SC17_Cy5

source_name: 10 DPF PCB-126_embryo_SC17_Cy5


title: 10 dpf DMSO_embryo_SC15_Cy5

source_name: 10 dpf DMSO_embryo_SC15_Cy5


title: 5 DPF PCB-126_embryo_NBH5_Cy3

source_name: 5 DPF PCB-126_embryo_NBH5_Cy3


title: 10 dpf DMSO_embryo_SC15_Cy3

source_name: 10 dpf DMSO_embryo_SC15_Cy3


title: 5 dpf DMSO_embryo_NBH2_Cy3

source_name: 5 dpf DMSO_embryo_NBH2_Cy3


title: 5 dpf DMSO_embryo_NBH2_Cy5

source_name: 5 dpf DMSO_embryo_NBH2_Cy5


title: 5 DPF PCB-126_embryo_SC5_Cy3

source_name: 5 DPF PCB-126_embryo_SC5_Cy3


title: 5 DPF PCB-126_embryo_NBH5_Cy5

source_name: 5 DPF PCB-126_embryo_NBH5_Cy5


title: 15 DPF PCB-126_embryo_NBH34_Cy3

source_name: 15 DPF PCB-126_embryo_NBH34_Cy3


title: wt_rep1

status: Public on Jul 13 2011

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

data_processing: All small RNA sequences except low-quality reads are provided with the number of reads for each unique sequence. Illumina SRA v1.5 3' adapter sequences are trimmed using half-open Smith-Waterman algorithm (score parameters: 2 for match, -2 for mismatch, -3 for linear gap penalty). Software used in the data processing is provided in the paper (Park et al. 2011).

organism: Mus musculus

source_name: Dicer-null mES rescued with wild-type Dicer

growth_protocol: Dicer null mES (a gift from G. Hannon) was grown on a feeder layer of mouse CF-1 cells or on gelatin coated dishes with knockout DMEM (Gibco, Invitrogen) supplemented with 15% fetal bovine serum (Gibco, Invitrogen), nonessential amino acids (Gibco, Invitrogen), 2mM L-Glutamine (Sigma), 0.1mM 2-mercaptoethanol (Sigma), and 1000unit/ml leukemia inhibitory factor (Chemicon). Another mES cell line R1 was grown on a feeder layer of mouse CF-1 cells or on gelatin coated dishes with GlutaMAX DMEM (Gibco, Invitrogen) supplemented with 10% fetal bovine serum (Hyclone), 100 unit/mL penicillin, 100 µg/mL streptomycin (WelGENE), nonessential amino acids (Gibco, Invitrogen), 100 µM 2-mercaptoethanol (Amresco), and 10ng/mL leukemia inhibitory factor (Sigma).

extract_protocol: To prepare small RNA cDNA libraries, total RNAs were separated on 15% urea-PAGE and 17~26nt RNAs were gel-purified. Size fractionized RNAs were ligated with 3' adapter using T4 RNA ligase2 trucated form (NEB). After gel purification, 3' adapter-ligated RNAs were ligated with 5' adapter using T4 RNA ligase1 (NEB). The gel-purified ligation products were reverse transcribed using superscript II (Invitrogen) and the cDNA was PCR-amplified with Phusion DNA polymerase (NEB).

treatment_protocol: To prepare Dicer null ES cells for transfection, feeder cells were removed and 1,500,000 ES cells were seeded on gelatin-coated 6 well plate 1day before transfection. The 10ug plasmids (either wild-type Dicer-pCK or 5' pocket mutant Dicer-pCK) and 10ul Lipofectamine 2000 (Invitrogen) were used for transfection. RNA was extracted at 48hr after transfection and used for preparation of small RNA cDNA libraries. In the case of R1 cells, feeder cells were also removed and 300,000 R1 cells were seeded onto gelatin-coated 60mm-dish. The 30 nM siRNA against GFP and Lipofectamine 2000 (Invitrogen) were used for the transfection. RNA was extracted at 48hr after transfection and used for preparation of small RNA cDNA libraries.

value: mouse embryonic stem cell

tag: genotype/variation

value: wt


title: 5 dpf DMSO_embryo_SC2_Cy3

source_name: 5 dpf DMSO_embryo_SC2_Cy3


title: 5 dpf DMSO_embryo_SC1_Cy5

source_name: 5 dpf DMSO_embryo_SC1_Cy5


title: 15 dpf DMSO_embryo_NBH31_Cy3

source_name: 15 dpf DMSO_embryo_NBH31_Cy3


title: 15 DPF PCB-126_embryo_NBH34_Cy5

source_name: 15 DPF PCB-126_embryo_NBH34_Cy5


title: 15 DPF PCB-126_embryo_SC28_Cy3

source_name: 15 DPF PCB-126_embryo_SC28_Cy3


title: 15 dpf DMSO_embryo_NBH31_Cy5

source_name: 15 dpf DMSO_embryo_NBH31_Cy5


title: 5 DPF PCB-126_embryo_SC5_Cy5

source_name: 5 DPF PCB-126_embryo_SC5_Cy5


title: 15 DPF PCB-126_embryo_SC28_Cy5

source_name: 15 DPF PCB-126_embryo_SC28_Cy5


title: 15 dpf DMSO_embryo_SC27_Cy5

source_name: 15 dpf DMSO_embryo_SC27_Cy5


title: 15 dpf DMSO_embryo_SC27_Cy3

source_name: 15 dpf DMSO_embryo_SC27_Cy3


title: 5pmut_rep1

source_name: Dicer-null mES rescued with 5' pocket mutant Dicer


title: R1

source_name: R1 embryonic stem cell line treated with siGFP


title: 5pmut_rep2


title: 10 DPF PCB-126_embryo_NBH19_Cy5

source_name: 10 DPF PCB-126_embryo_NBH19_Cy5


title: 10 dpf DMSO_embryo_NBH16_Cy3

source_name: 10 dpf DMSO_embryo_NBH16_Cy3


title: 10 DPF PCB-126_embryo_NBH19_Cy3

source_name: 10 DPF PCB-126_embryo_NBH19_Cy3


title: wt_rep2


title: 10 dpf DMSO_embryo_SC14_Cy5

source_name: 10 dpf DMSO_embryo_SC14_Cy5


title: 10 dpf DMSO_embryo_NBH16_Cy5

source_name: 10 dpf DMSO_embryo_NBH16_Cy5


title: 5 DPF PCB-126_embryo_N6_Cy3

source_name: 5 DPF PCB-126_embryo_N6_Cy3


title: 10 DPF PCB-126_embryo_SC18_Cy3

source_name: 10 DPF PCB-126_embryo_SC18_Cy3


title: 10 DPF PCB-126_embryo_SC18_Cy5

source_name: 10 DPF PCB-126_embryo_SC18_Cy5


title: 5 DPF PCB-126_embryo_N6_Cy5

source_name: 5 DPF PCB-126_embryo_N6_Cy5


title: 5 dpf DMSO_embryo_NBH1_Cy3

source_name: 5 dpf DMSO_embryo_NBH1_Cy3


title: 10 dpf DMSO_embryo_SC14_Cy3

source_name: 10 dpf DMSO_embryo_SC14_Cy3


title: 5 dpf DMSO_embryo_NBH1_Cy5

source_name: 5 dpf DMSO_embryo_NBH1_Cy5


title: 15 DPF PCB-126_embryo_SC29_Cy3

source_name: 15 DPF PCB-126_embryo_SC29_Cy3


title: EMSA-Seq of RELAp50

status: Public on May 24 2011

city: Oxford

first: Jiannis

last: Ragoussis

address: Roosevelt Drive

department: Wellcome Trust Centre for Human Genetics

country: United Kingdom

institute: University of Oxford

description: EMSA-Seq selection of ligands that bind a transcription factor

data_processing: Raw data in the form of reads (FASTQ format) obtained after deep sequencing has been subsequently processed using both UNIX and perl scripts. Briefly, only sequenced reads that contained matches to at least 4 bp-sequences flanking the degenerate region were considered acceptable for   further processing. In addition, for reads to be acceptable the three regions on the DNA ligand (two flanks and degenerate) must not contain bases annotated as 'N' and furthermore, bases must have a Phred quality score of at least 20. For ligands with 10-mer degnerate regions, a 10-mer sequence was extracted. For ligands with 20-mer degenerate region, 20-mer sequences corresponding to the degenerate segment of DNA ligands were then extracted and 'lower' order 11-mer sequences were derived from these. 11-mer or 10-mer sequence counts obtained from these processed reads have been normalized against the dataset with the lowest number of acceptable reads for that sequence. A binomial distribution model has been used to determine enrichment (z-score) of 11-mer or 10-mer for all datasets.

organism: Homo sapiens

extract_protocol:
Purified protein was  mixed with 60  base pair long double-stranded DNA molecules in a 20 ul-reaction, in the presence of 125 ug/ul poly dI-dC buffered in 12 mM HEPES pH7.8, 75 mM KCl, 1 mM EDTA, 4 mM GTP and 12.5 % glycerol.The mixture was incubated at room temperature for 1 h. A DNA: protein of 8:1 molecules was maintained in all the experiments. TF-DNA mixtures were subsequently loaded onto a 6 % DNA Retardation Gel (Invitrogen #EC6365BOX) alongside 'no protein' and 'no DNA' controls, and migrated in Novex 0.5 X TBE Running Buffer (Invitrogen #LC6675) for 1.5 h. Gels were stained using Invitrogen's EMSA-Kit (#E33075) following manufacturer's procedures. Visualization of gels was performed using either a DR46B Transilluminator (Clare Chemical Research, USA) or LAS-4000 system (Fujifilm, Japan). Bands containing TF-DNA complexes were excised from gels, elution of DNA carried out overnight at room temperature using a diffusion buffer (0.5 M ammonium acetate; 10 mM magnesium acetate; 1 mM EDTA pH 8.0; 0.1 % SDS) and the DNA purified using QIAGEN's Polyacrylamide Gel Extraction Protocol (QIAGEN #20021). This was then processed for deep sequencing. The libraries were created using standard 'Paired-End' adaptor-molecules  as described in Illumina's ChIP-protocol and the NEBNext DNA Sample Prep kit (NEB#E6000S). 10 ng of DNA was used for each library-preparation.
For experiments in which several rounds of SELEX were carried out the following procedure was adopted. DNA obtained after the first round of TF-DNA binding followed by EMSA, elution and purification was amplified using a high-fidelity PCR procedure . Briefly, multiple 100 ul reactions each comprised of 0.2 mM dNTPs, 1uM of Primers 1 and 2, together with 2 units of KOD Hot Start Polymerase (Merck #71086-3) buffered in accompanying 1X PCR Buffer were incubated for 15 s at 95°C, then subjected to 25 PCR cycles (5 s 95°C, 5 s 60°C, 5 s 70°C). DNA was pooled, purified using phenol-chloroform and concentrated via ethanol precipitation. This was subsequently used as starting material for TF-DNA binding in the second round of SELEX.

tag: 4nf-kb dimer


title: EMSA-Seq of RELAp52