title: Sven_long_read

city: Hamilton

first: Matthew

middle: John

last: Moody

state: ON

address: Life Sciences Building Rm 323, McMaster University, 1280 Main St W

department: Biology

institute: McMaster University

description: Sample 3

data_processing:
Base-calling pipeline: HiSeq Control Soft. v. 1.4.8, RTA 1.12.4.2, CASAVA 1.8.2
*txt files showing read-depth for each gene are separated into positive and negative strands to facilitate antisense RNA identification.
The processed files were generated using BEDTools with a .bam file used as an input. The .bam file was created by aligning the .fastq reads to the respective genome using Bowtie/Samtools.
The *txt files were generated using the BEDtools suite, using the coverageBed function. Specifically, it looks for overlap between features (genes, mRNAs, rRNASs, tRNAs) in a general features file (GFF), and an alignment. Here is a description of the columns: 1 - genome assession number, 2 - Genbank, 3  - feature type (mRNA, tRNA etc), 4 - chromosomal start location, 5 -chromosomal stop location, 6 - N/ap, 7 - strand (+/-) of the feature, 8 - N/ap, 9 - description of the mRNA, tRNA found in column 3, 10 - number of reads mapping to this chromosomal region, 11 - number of nucleotidesm covered by the reads mapping to the region, 12 - size of the region, 13 - the percent coverage (column 11/12) of the reads aligning to the region.
Genome_build: NC_003888.3
Genome_build: NC_003155.4
Genome_build: FR845719.1
Supplementary_files_format_and_content: custom-text file created by BedTools

organism: Streptomyces venezuelae

source_name: bacterial cells

growth_protocol: grown on maltose, yeast extract, malt extract media (MYM) and isolated at various timepoints encompasing vegetative growth, aerial hyphae development, and sporulation

extract_protocol:
Guanidium thiocyanate / phenol:chloroform RNA isolation protocol
For each species, RNA samples were divided in two, with one half being subjected to rRNA depletion using the MICROBExpressTM Bacterial mRNA Enrichment Kit (Ambion) as per the manufacturer’s instructions.  rRNA depleted samples were then pooled such that each pool contained equal amounts of RNA from each time-point (vegetative growth, aerial growth/fragmentation, sporulation).  Equivalent pools were created for the untreated (total) RNA samples.  The two pools were destined to become two separate libraries: the rRNA-depleted pools were to be sequenced using a protocol optimized for full length transcripts, while the total RNA samples were to be size fractionated and enriched for sRNAs prior to sequencing.  All samples were treated with tobacco acid pyrophosphatase to create 5′ ends amenable for adapter ligation. To enrich for small RNAs, the total RNA samples were size selected (40 to 300 nucleotides) following polyacrylamide gel electrophoresis. RNAs for both libraries were then fragmented in a buffered zinc solution and single stranded RNA adapters were ligated to the 5′ and 3′ ends to maintain strand specificity, prior to re-purifying on a polyacrylamide gel. Each pool was then reverse transcribed and PCR amplified to generate DNA colonies and sequenced using an Illumina HiSeq 2000 sequencer.

tag: growth stages

value: pooled (vegetative, aerial growth, sporulation)

tag: tissue

value: bacterial cells

value: total RNA, rRNA-depleted


title: Sven_short_read

status: Public on Aug 01 2013

type: SRA

country: Canada

description: Sample 6

library_source: transcriptomic

molecule: total RNA

tag: molecule subtype

value: ~30-400 size selected RNA


title: RNAPb_ChIP_seq_2

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

country: USA

institute: Memorial SLoan-Kettering Cancer Center

library_source: genomic

data_processing:
The number of sequence reads per base pair was normalized to the total number of reads and expressed as a log2 value.
ChIP-seq reads were alligned to the M. smegmatis Mc2155 genome. Sequences that alligned more than once were discarded except for those corresponding to the ribosomal RNA operons. In this case the reads for the ribosomal RNA were split between operons.
Genome_build: NC_008596.1
Supplementary_files_format_and_content: wig files were generated and the scores represent number of sequence reads per base pair was normalized to the total number of reads and expressed as a log2 value.

molecule: genomic DNA

organism: Mycolicibacterium smegmatis

growth_protocol: All M. smegmatis strains were isogenic to mc2155 and were grown at 37 oC in LB supplemented with 0.5% dextrose, 0.5% glycerol, and 0.05% Tween 80 to late log phase (OD600 of 1.0) before crosslinking the protein-nucleic acid complexes.

extract_protocol:
1. Monoclonal antibodies specific for HA from Sigma Aldrich and the catalog number is 89658
2. Monoclonal antibodies specific for RNAP beta subunit from Neoclone, Madison, WI. The antibody clone was 8RB13 and the catalog number is WP023
3. Monoclonal antibodies specific for RNAP sigma subunit from Neoclone, Madison, WI. The antibody clone was 2G10 and the catalog number is W0004
The cell pellet was resuspended in TE with protease inhibitors. Cells were lysed and DNA was sheered to 100bp fragments in the Covaris focused ultrasonicator.
Cell lysates (in 50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100) containing protein-nucleic acid complexes were incubated with immobilized HA specific antibodies to immunoprecipitate CarD containing complexes from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain and unfused HA from the Mc2155 attB::pmsg431. RNAPb and RNAPs containing complexes were immunoprecipitated  from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain using specific monoclonal antibodies immobilized on Gammabind sepharose. Co-precipitated  complexes were washed 4 times in 10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA with increasing salt. Co-precipitated complexes were eluted in 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% sodium dodecyl sulfate at 65 oC. Eluate crosslinks were reversed by incubating overnight at 65 oC. The samples were treated with 100 ug/ml of proteinase K to each sample and incubate at 37 oC for 2 hours. DNA was extracted by phenol:chloroform:IAA (25:24:1) extraction, precipitated with ethanol, and resuspended in water.

treatment_protocol: 2% Formaldehyde was added to each culture, which was then incubated shaking at RT for 30 minutes to crosslink DNA and proteins. Glycine was then added to quench the crosslinking and the cells were spun down cells at 4 oC for 10 minutes at 3700 rpm

tag: strain

value: Mc2155 delta-carD attB::tetcarD-HA

tag: growth phase

value: Log


title: MED1 ChIP-seq, 3T3-L1 Day7 1h Rosi

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Quality of all libraries were assessed using FastQC (Babraham Bioinformatics). Reads were trimmed and/or filtered using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Sequenced reads were aligned to the genome (mm9) using bowtie (Langmead B, et al. 2009. Genome Biol. 10:R25) with the options: -m 1 --best --strata
Reads from paired Rosi and DMSO libraries were combined into one library and peaks were called using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576–589) with the default settings, and using sonicated input samples as control.
Binding intensity was scored using HOMER for each factor and each condition by counting tags aligning within detected peaks, and normalizing to a total read depth of 10^7 aligned reads.
Expression was scored by counting RNAPII ChIP-seq reads mapping within RefSeq gene bodies longer than 1 kb (omitting the initial 250 bp) using HOMER. Differential expression was called using edgeR (Robinson MD, et al. 2010. Bioinformatics 26:139-140)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files created using HOMER for visualization of binding profiles in the UCSC genome browser. HOMER peak files with tag counts were generated using the HOMER annotatePeaks.pl script using the -d option. The files contain read counts of PPARγ, C/EBPα, MED1, and CBP ChIP-seq libraries (from both conditions). The read counts were normalized to a total read depth of 10^7 aligned reads.

organism: Mus musculus

source_name: 3T3-L1 adipocytes (Day 7)

growth_protocol: 3T3-L1 cells were maintained in DMEM supplemented with calf serum. Two days post confluency (day 0), the cells were induced to differentiate into adipocytes using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS). Two days post induction, medium was changed to DMEM supplemented with FCS and insulin, and four days post induction the medium was changed to DMEM supplemented with FCS. The medium was changed a final time at day 6 post induction and all experiments were performed on day 7.

extract_protocol:
Chromatin was prepared from 149 mm culture dishes first by crosslinking in 1% formaldehyde in PBS (10 minutes, RT). Cross-linking was stopped by adding glycine to a final concentration of 1 M (10 minutes, RT). The cells were washed twice in ice-cold PBS, and harvested in ice-cold lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0,5% NP-40). Nuclei were subsequently released using a Dounce homogenizer, and crude nuclei were resuspended at 10^7 nuclei / mL in RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) and sonicated at high setting in a Bioruptor-Twin (Diagenode) at a volume of 300 μL in 1.5-mL tubes for 40 cycles of 30 seconds on and 30 seconds off. The chromatin IPs were performed as described in (Siersbæk MS, et al. 2012. Mol Cell Biol. 32:3452-3463).
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina).

treatment_protocol: Day 7 3T3-L1 adipocytes were treated directly in incubators, by supplementing the culture media with either 1 μM rosiglitazone or 0.1% DMSO (vehicle). Chromatin was harvested after 1 hour of treatment.

tag: cell type

value: 3T3-L1 adipocytes

tag: chip antibody

value: anti-MED1 (sc-8998; Santa Cruz)

tag: treatment

value: 1 μM rosiglitazone / 0.1% DMSO for 1 hour


title: MED1 ChIP-seq, 3T3-L1 Day7 1h DMSO

value: 0.1% DMSO (Vehicle) for 1 hour


title: RNAPb_ChIP_seq_1


title: HA_ChIP_seq_2

value: Mc2155 attB::pmsg431


title: Scoel_long_read

description: Sample 1

organism: Streptomyces coelicolor


title: HA_ChIP_seq_1


title: Scoel_short_read

description: Sample 4


title: CarD_HA_ChIP_seq_2


title: PPARγ ChIP-seq, 3T3-L1 Day7 1h DMSO rep2

value: anti-PPARγ (sc-7196; Santa Cruz)


title: PPARγ ChIP-seq, 3T3-L1 Day7 1h Rosi rep1


title: Saver_short_read

description: Sample 5

organism: Streptomyces avermitilis


title: CarD_HA_ChIP_seq_1


title: PPARγ ChIP-seq, 3T3-L1 Day7 1h DMSO rep1


title: RNA in the female germ cells at 15.5 dpc

status: Public on Jul 31 2013

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
B_FGC
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).
RNA-seq in the female germ cells at 15.5 dpc.
Strand-specific RNA-Seq.

data_processing:
Illumina Casava 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v1.2.0 with default settings.
Read counts for each RefSeq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the TMM method implemented in Bioconductor package "edgeR" .
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text files include normalized read counts for each RefSeq gene.
Supplementary_files_format_and_content: Two bedGraph files (forward and reverse strand separately) for each sample.

source_name: fetal female germ cells at 15.5 dpc

growth_protocol: in vivo

extract_protocol:
GFP+ germ cells and GFP- gonadal somatic cells were flow sorted based on Oct4 promoter-driven EGFP expression in germ cells from CF1XOG2 embryo and fetus gonads using a MoFlo or Aria II flow cytometer. Total RNA was extracted using RNA Bee (Tel Test Inc.). Contaminating DNA was removed with the DNA-free Kit (Ambion). The amount of RNA was monitored using a Nanodrop spectrophotometer followed by a quality check using the Bioanalyzer. All RNA samples had a RIN>9.0. 2µg total RNA samples were depleted for rRNA using the RiboZero Kit (Epicenter, Illumina).
RNA-seq libraries were prepared and paired-end sequencing was performed using the IntegenX RNA kit (Illumina) with read length/coverage of 2x100.

tag: strain/background

value: CF1 x TgOG2

value: germ cells

tag: gender

value: female

tag: age


title: Saver_long_read

description: Sample 2


title: EBNALP rep2

city: Boston

first: Hufeng

last: Zhou

address: 181 Longwood Ave,

department: Department of Microbiology and Molecular Genetics

institute: Harvard Medical School

data_processing:
Chip-Seq reads were mapped to hg19 using Bowtie (v.0.12.9) allowing 1-missmatch in the alignment seed-region (parameters –m1)
HOMER was used to call peaks using default criteria of FDR < 0.001, a four-fold enrichment over input, and other default filters.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq reads were mapped to the human genome hg19 and they are converted to the bam file format. HOMER was used to call peaks and the peak file are in txt format.

organism: Homo sapiens

source_name: Lymphoblastoid Cell Lines (IB4 LCL)

extract_protocol:
EBNALP-DNA complexes were captured with the addition of protein A-Agarose/Salmon sperm DNA and then washed 1x for 15’ at 4°C with rotation, with  Low Salt Wash Buffer (20mM Tris-HCl pH 8.1, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 1% SDS), 1x with High Salt Wash Buffer (20mM Tris-HCl pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 1% SDS), 1x with LiCl Wash Buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA, 0.25 M LiCl, 1% NP40, 1% Deoxycholate acid), and 2x TE buffer. EBNALP-DNA complexes were eluted from the protein A-beads by rotating at room temperature 2x for 15’ in Elution Buffer (100 mM NaHCO3, 1% SDS). DNA-protein cross-link was reversed by the addition of NaCl and incubation at 65°C for 4 h. DNA was purified using a PCR purification column (Qiagen®).
ChIP-seq DNA libraries were prepared and sequenced, using Illumina HiSeq 2000. Libraries were prepared according to Illumina's instructions

treatment_protocol: IB4 LCL cells were cross-linked in 1% formaldehyde, lysed in Lysis Buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS and protease inhibitors (Roche®) and sonicated 20x20” cycles on ice. Lysate was diluted 10 fold with Dilution Buffer (16.7 mM Tris-HCl pH 8.1, 1.2 mM EDTA, 167 mM NaCl, 1.1% Triton X-100, 0.01% SDS and protease inhibitors) and monoclonal EBNALP antibodies (JF186) were added to immune precipitate EBNALP-DNA complexes.

tag: cell line

value: IB4 LCL

value: monoclonal anti-EBNALP (JF186)


title: EBNALP rep1


title: RNA in the male somatic cells at 15.5 dpc

description:
C_MSC
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).
RNA-seq in the male somatic cells at 15.5 dpc.
Strand-specific RNA-Seq.

source_name: fetal male somatic gonadal cells at 15.5 dpc

value: gonadal somatic cells

value: male


title: RNA in the female somatic cells at 15.5 dpc

description:
D_FSC
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).
RNA-seq in the female somatic cells at 15.5 dpc.
Strand-specific RNA-Seq.

source_name: fetal female somatic gonadal cells at 15.5 dpc


title: S. mansoni male, AB SOLiD 4

city: Colchester

first: Antonio

last: Marco

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

data_processing:
Reads were mapped to the Schistosoma mansoni reference genome version 4.1 using Bowtie and SeqTrimMap (see paper for details).
Genome_build: Schistosoma mansoni reference genome version 4.1
Supplementary_files_format_and_content: Tab-delimited text file shows chromosome coordinates, sequences and read counts.

organism: Schistosoma mansoni

source_name: Schistosoma mansoni male individuals

extract_protocol: SOLiD Small RNA Expression Kit (Ambion).

value: whole body


title: S. mansoni female, AB SOLiD 4

source_name: Schistosoma mansoni female individuals


title: S. mansoni female, MiSeq

data_processing:
Linker sequences were removed with CutAdapt.
Genome_build: Schistosoma mansoni reference genome version 4.1
Supplementary_files_format_and_content: Tab-delimited text file shows unique sequences and read counts.

extract_protocol: MirVana Small RNA Expression Kit (Ambion).


title: RNA in the male germ cells at 15.5 dpc

description:
A_MGC
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).
RNA-seq in the male germ cells at 15.5 dpc.
Strand-specific RNA-Seq.

source_name: fetal male germ cells at 15.5 dpc


title: S. mansoni male, MiSeq


title: synovial membrane LPS stimulated

status: Public on Jul 30 2013

city: Fort Collins

first: Stephen

middle: J

last: Coleman

state: CO

address: 1682 Campus Delivery

department: MIP

institute: Colorado State University

description: joint received four 0.5ng LPS injections over eight days prior to collection

data_processing: basecalls performed by Illumina pipeline

organism: Equus caballus

source_name: left carpal joint articular cartilage

extract_protocol:
Total RNA was isolated from the eight samples using variations of guanidinium-based protocols. RNA was purified from the articular cartilage samples as described in MacLeod et al. 1996 (PMID 8702559), from control synovial membrane, cerebellum, testis and placenta villous using acid guanidinium thiocyanate/phenol/chloroform extraction with alcohol and salt precipitations (Chomczynski & Sacchi 1987, PMID 2440339), and from LPS-stimulated synovial membrane and whole embryo with RNeasy mini kits (Cat# 74104; Qiagen). All samples were processed with a final RNeasy (Qiagen) silica gel spin column clean up, ethanol precipitation and solubilization in nuclease-free water (Cat# AM9937; Ambion). Quantitative and qualitative parameters of the RNA preparations were assessed using a NanoDrop ND-1000 and Bioanalyzer 2100 (Agilent, Eukaryotic Total RNA Nano Series II). All samples had 260/280 ratios ≥1.93, 260/230 ratios ≥1.75 and an Agilent RNA integrity number (RIN) ≥8.1.
Library preparation and subsequent nucleotide sequencing was performed according to Illumina’s standard mRNA-seq kit protocol (Transcriptome Analysis: mRNA-seq, http://www.illumina.com/pages.ilmn?D=291). Messenger RNA was selected with PolyT capture beads from 3.5 to 10.0 μg of total RNA and fragmented by zinc metal ion hydrolysis. RNA fragments were converted into cDNA using random hexamer primers and made double stranded using RNase H and DNA polymerase. The cDNA fragments were ligated to sequencing adaptors using Illumina’s Genomic DNA sample prep. Fragments between 100 and 300 bp were size selected by gel electrophoresis, applied to sequencing flow cells and enriched by PCR to grow fragment clusters.

tag: Sex

tag: breed

value: pony

value: 3 years old

value: synovial membrane


title: synovial membrane normal

description: joint received four control PBS injections over eight days prior to collection

source_name: right carpal joint articular cartilage


title: Pancreatic cancer case 2 mc

city: Bronx

first: Yiting

last: Yu

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: HpaII test for HELP-GT

data_processing:
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions 1.3-1.4).  Initial data processing was performed using the default read length of 36 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).  The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg18 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.  To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylation scores (5-mc) and hydroxymethylation scores (5-hmc) for each Sample

source_name: low-passage patient-derived cell lines Pa03C

extract_protocol:
Genomic DNA from cell lines were isolated by Puregene Core Kit A (Qiagen)
Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  Five micrograms of genomic DNA were digested with HpaII and MspI in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA or 1 μg of MspI-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).

tag: sample type

tag: disease state

value: pancreatic cancer


title: control mc

description: HpaII test for HELP-GT

source_name: immortalized healthy pancreatic cells

value: immortalized healthy pancreatic cells

value: healthy


title: control hmc

description: GTM test for HELP-GT


title: Pancreatic cancer case 1 mc

description: HpaII test for HELP-GT

source_name: low-passage patient-derived cell lines Pa04C


title: 34-day embryo normal

description: apparent normal gross morphology

source_name: whole embryo

value: thoroughbred

value: 34 days gestation

value: embryo


title: cerebellum normal

description: apparent normal gross morphology

source_name: cerebellum

value: 2 years old

value: cerebellum


title: full thickness articular cartilage normal

value: full thickness articular cartilage


title: full thickness articular cartilage LPS stimulated


title: testes normal

description: apparent normal gross morphology

source_name: testes

value: 4 years old

value: testes


title: placental villous normal

description: apparent normal gross morphology

source_name: full term placental villous

value: female

value: full term

value: placental villous


title: Namalwa_2_Input

city: Berlin

first: Lora

last: Dimitrova

state: Berlin

address: Hindenburgdamm 30

department: Institute of Pathology

country: Germany

institute: Charité-University Medicine Berlin

description: Input control

data_processing:
Basecalls performed using CASAVA version 1.3 and CASAVA 1.8
ChIP-seq reads were reduced to a set of unique reads, where reads with the best average quality were kept. Reads with an average phred-score lower than 30 were discarded.
ChIP-seq reads were aligned to the galGal3 genome assembly using bwa version 0.5.9-r16 with default parameters. Non-unique hits were discarded
Peaks were called using  PeakRanger (Version 1.14) with default settings except the p-value cutoff which was set to 10-5 (instead of default 10-4).
Genome_build: hg19
Supplementary_files_format_and_content: peak files for individual experiments are given as standard .bed format files

source_name: Burkitt lymphoma cell line

growth_protocol: The Burkitt lymphoma cell lines Raji and Namalwa (designated as B-cell lines throughout the manuscript) and the Hodgkin cell line L428 were grown in RPMI 1640 (PAA Laboratories) supplemented with 10% fetal calf serum (PAN-Biotech). For the cultivation of the cell line L428-PAX5, 25 mM HEPES (Life Technologies/Invitrogen) was added supplementary. The cell lines were incubated at 37 °C and 5% CO2.

extract_protocol:
Chromatin immunoprecipitation was performed as described by Lee et al. (2006) with slight modifications. 1E8 cells were fixed with 1% formaldehyde (20 min, room temperature). After fixation was stopped with 0.125 M glycine, cells were washed with ice-cold PBS (4 times) and stored at – 80°C. 100 µl Dynabeads® Protein G (Life Technologies/Invitrogen) were preblocked with blocking solution (PBS containing 0.5% BSA) and resuspended in 250 µl blocking solution. 10 µg of PAX5 (C-20) antibody (sc-1974, Santa Cruz Biotechnology) were added to the beads. The beads were incubated with the antibody overnight at 4°C on a lab rotator. The beads were washed after incubation with blocking solution (3 times) and resuspended in 100 µl blocking solution. The cell pellet was lysed in buffer LB1 (50 mM Hepes-KOH, pH 7.2; 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% IGEPAL® CA-630, 0,25 % Triton® X-100, Complete EDTA-free Protease Inhibitor Cocktail (F. Hoffmann-La Roche Ltd.)) for 10 min at 4°C. After centrifugation the pellet was resuspended in buffer LB2 (10 mM Tris-HCl, pH 8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, Complete EDTA-free Protease Inhibitor Cocktail) and incubated for 10 min at room temperature on a rocking platform. Following centrifugation, the pellet was resuspended in 3 ml buffer LB3 (10 mM Tris-HCl, pH 8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine sodium salt, Complete EDTA-free Protease Inhibitor Cocktail) and sonicated (Bioruptor® Sonicator, 3 cycles of 15 minutes at high power in pulsed modus (30 sec on, 30 sec off)). 300 µl of 10% Triton X-100 was added and the sample was centrifuged at 13000 rpm for 10 min (4°C). The supernatant was removed and 50 µl were saved as input DNA sample. 1 ml of the supernatant was mixed with 100 µl of the Dynabeads®-PAX5-antibody complex and incubated on a lab rotator at 4°C overnight. After incubation the beads were separated from the supernatant using a Dynal® magnet and washed four times with RIPA buffer (50 mM Hepes-KOH, pH 7.6; 750 mM LiCl; 1 mM EDTA; 1% IGEPAL® CA-630; 0.7% Na-Deoxycholate, Complete EDTA-free Protease Inhibitor Cocktail) and once with TE containing 50 mM NaCl. Next, an incubation with elution buffer (50 mM Tris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) at 65°C for 15 minutes was followed by centrifugation. The supernatant was removed and incubated at 65°C overnight for reverse-crosslinking of the DNA. Elution buffer was added to the input DNA sample too and this sample experienced the same incubation. The next day TE buffer containing 0.25 mg/ml RNaseA was added to the samples and they were incubated at 37°C for 2 hours. Afterwards proteinase K (0.2 mg/ml) was added and an incubation at 55°C for 2 hours followed. The DNA was phenol/chloroform extracted and precipitated by ethanol. The DNA pellets were air-dried and dissolved in 30 µl of 10 mM Tris-HCl (pH 8.0). For each cell line two independent ChIP experiments were performed. Extensive controls by real-time DNA-PCR for successful enrichment of selected known PAX5 target genes were carried out with the precipitated genomic DNA-fragments prior to Illumina sequencing. Two IPs from each ChIP experiment were pooled and subjected to next generation sequencing together with the input sample (ChIP-Seq).
Libraries from ChIP-DNA were constructed using NEBnext ChIP-Seq Library Prep Master Mix for Illumina (New England Biolabs) selecting for a fragment size range of 300-450 bp according to manufacturer’s instructions.Sequencing was performed on an Illumina GAIIx sequencer with 36 bp single reads.

treatment_protocol: PAX5 overexpression in the cell line L428-PAX5 was induced 48 h before fixation of the cells. Successful PAX5 overexpression was checked by PAX5 immunocytochemistry.

value: Namalwa


title: Namalwa_1_Input

description: Input control


title: L428-PAX5_1_Input

description: Input control

source_name: Hodgkin lymphoma cell line

value: Mifepristone


title: L428-PAX5_2_Input

description: Input control


title: Raji_2_Input

description: Input control

value: Raji


title: Raji_1_Input

description: Input control


title: Namalwa_1_IP

description: Chromatin IP against PAX5

value: Pax-5 antibody (C-20)

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #


title: L428-PAX5_1_IP

description: Chromatin IP against PAX5


title: Namalwa_2_IP

description: Chromatin IP against PAX5


title: L428-PAX5_2_IP

description: Chromatin IP against PAX5


title: Raji_2_IP

description: Chromatin IP against PAX5


title: Pancreatic cancer case 2 hmc

description: GTM test for HELP-GT

value: low-passage patient-derived cell lines Pa03C

value: pancreatic cancer


title: Pancreatic cancer case 1 hmc

description: GTM test for HELP-GT

value: low-passage patient-derived cell lines Pa04C


title: HRN2

first: Eric

last: Pierce

state: MA

address: 243 Charles Street

department: Ophthalmology

institute: Massachusetts Eye and Ear Infirmary

description: supplier: Biochain

data_processing:
fastq files generated using CASAVA v1.8
The fastq files were first concatenated, and alignment and post-processing of the fastq was performed using the RNA-Seq Unified Mapper v1.10 using default parameters
novel splicing was determined by parsing the junctions_high-quality.bed (output from RUM post-processing) using custom scripts.
Genome_build: hg19

source_name: retina

extract_protocol: Normal human retina total RNA was purchased from Biochain.  RNA-Seq libraries were prepared from 5 μg total RNA following a modified Illumina mRNA-Seq protocol (Illumina).  Briefly, mRNA was purified using oligo-dT beads (Invitrogen).  The purified mRNA was then fragmented for 2 minutes at 94°C on a thermalcycler with the addition of 2 μl of 10X fragmentation buffer (1 mM ZnCl2, 1 mM Tris-HCl, pH 7.0).  The reaction was stopped with the addition of 4 μl of 100 mM EDTA, pH 8.0.  First strand cDNA was synthesized using SuperScript II reagents following manufacturers instructions (Invitrogen).  The remaining steps: second strand cDNA synthesis, end-repair, monoadenylation, and adapter ligation were performed following Illumina’s mRNA-Seq protocol.  All reagents, excluding paired-end adapters, were purchased from New England Biolabs.  Paired-end adapters and PCR primers were purchased from Illumina.  cDNA libraries were size selected using a 2% agarose gel and fragments between 300-350 bp were selected.  Size selected samples were then PCR amplified using 15 cycles.  cDNA library quantity and quality were determined using DNA 1000 chips on a Bioanalyzer 2100 (Agilent)

tag: disease status

value: normal

tag: tissue

value: retina


title: HRN1

description: supplier: Biochain


title: Adult liver 7_non-enriched control

status: Public on Jul 29 2013

city: Tartu

first: Mart

last: Kals

address: Riia 23b

country: Estonia

institute: Estonian Genome Center

description: Control for Adult liver 7_5hmC

data_processing:
CASAVA 1.8.2 software were used for basecalling.
FASTQ sequences of all samples were aligned to NCBI37/hg19 using Burrows-Wheeler Aligner (BWA). Parameter -q 20 was used for read trimming, and all reads with mapping quality less than 20 were filtered out.
Duplicate reads generated during the PCR amplification were removed using SAMtools.
5hmC peak identification was performed using MACS with the following parameters: tag size = 100; effective genome size = 2.70e+09; band width = 200; model fold = 10, 30; P-value cutoff = 1.00e-05; ranges for calculating regional lambda: 1,000 bps and 10,000 bps.
Genome_build: GRCh37
Supplementary_files_format_and_content: The .bed files report 5hmC peaks identified using MACS.

source_name: Adult liver

extract_protocol:
AllPrep DNA/RNA/Protein Mini kit (QIAgen, Cat. # 80004)
1) gDNA samples (3 µg in 120 µl) were sonicated using a Covaris S2 (Duty Cycle = 10%, Intensity = 5, Cycles per Burst = 200, Time = 6 cycles (60s each), Mode = Frequency Sweeping, Temperature = 4°C). Sonicated DNA was purified once with 180 µl of Agencourt AMPure XP beads (Beckman-Coulter, Cat. # A63880);
2) Sheared DNA samples were enriched for the 5hmC-containing fraction with the Hydroxymethyl Collector kit (ActiveMotif, Cat. # 55013) following manufacturer’s instructions. In parallel, non-enriched aliquots of sheared DNA were diluted 1:100;
3) 10 ng of sonicated gDNA (either 5hmC-enriched or non-enriched) were processed with NEBNext End Repair Module (New England Biolabs, Cat. # E6050S) and then purified with MinElute Reaction Cleanup kit (QIAgen, Cat. # 28204);
4) End repaired samples were treated with NEBNext dA-Tailing Module (New England Biolabs, Cat. # E6053S) and then purified with MinElute Reaction Cleanup kit;
5) dA tailed samples were ligated to TruSeq adapters (1.5 ul) using NEBNext Quick Ligation Module (New England Biolabs, Cat. # E6056S). The adapters were diluted 1:50 with 0.1x TE from TruSeq DNA Sample Prep kit v2 (Illumina Inc., Cat. # FC-121-2001);
6) Adapter ligated samples were purified twice with Agencourt AMPure XP beads (50 ul DNA + 30 ul beads);
7) Purified samples were PCR amplified: 37 ul DNA + 1 ul TruSeq primer 1.0 + 1 ul TruSeq primer 2.0 + 0.5 µl dNTPs mix (25 mM each) + 10 µl Herculase II Buffer + 1 µl Herculase II Fusion DNA polymerase (Agilent, Cat. # 600675). Program: 95°C, 5' (1 cycle); 98°C, 30” (1 cycle); 98°C, 10” -> 63°C, 30” -> 72°C, 30” (14 cycles); 72°C, 5’ (1 cycle);
8) Amplified NGS libraries were purified once with Agencourt AMPure XP beads (50 ul DNA + 50 ul beads), quantified with QPCR NGS Library Quantification kit for Illumina GA (Agilent, Cat. #G4880A), pooled and sequenced on Illumina HiSeq2000;

value: Liver

tag: developmental stage

value: adult

value: unknown age

value: M

value: control (non-enriched  DNA)


title: Adult liver 5_non-enriched control

description: Control for Adult liver 5_5hmC

value: 25 years

value: F


title: Adult liver 4_non-enriched control

description: Control for Adult liver 4_5hmC

value: 45 years


title: Adult liver 6_non-enriched control

description: Control for Adult liver 6_5hmC

value: 59 years


title: Adult liver 2_non-enriched control

description: Control for Adult liver 2_5hmC


title: Fetal liver 8_non-enriched control

description: Control for Fetal liver 8_5hmC

source_name: Fetal liver

value: fetus

value: 10 weeks + 2 days


title: Adult liver 1_non-enriched control

description: Control for Adult liver 1_5hmC

value: 56 years


title: Fetal liver 7_non-enriched control

description: Control for Fetal liver 7_5hmC

value: 7 weeks + 6 days


title: Fetal liver 6_non-enriched control

description: Control for Fetal liver 6_5hmC

value: 12 weeks + 1 day


title: Fetal liver 4_non-enriched control

description: Control for Fetal liver 4_5hmC

value: 11 weeks + 1 day


title: Fetal liver 3_non-enriched control

description: Control for Fetal liver 3_5hmC

value: 11 weeks


title: Fetal liver 1_non-enriched control

description: Control for Fetal liver 1_5hmC

value: 8 weeks + 3 days


title: Fetal liver 2_non-enriched control

description: Control for Fetal liver 2_5hmC

value: Liver

value: 11 weeks + 6 days


title: HRN3

description: supplier: Biochain

value: normal

value: retina


title: Raji_1_IP

description: Chromatin IP against PAX5

value: Raji

value: Pax-5 antibody (C-20)

value: Santa Cruz


title: Fetal liver 5_non-enriched control

description: Control for Fetal liver 5_5hmC

value: 11 weeks + 2 days

value: F

value: control (non-enriched  DNA)


title: mouse 8-cell 3

city: Los Angeles

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

description: processed data file = mouse_expression_mat.txt

data_processing:
Raw reads from the Illumina HiSeq2000 were mapped to the mm9 genome using default parameters in BWA
Mapped transcripts reads were transformed using the reads per kilobase per million (RPKM) metric
Genes with low expression in all stages (average RPKM<0.1) were filtered out, followed by quantile normalization.
mm9
mouse_expression_mat.txt: matrix listing normalized RPKM

molecule: polyA RNA

source_name: 8-cell blastomere

growth_protocol: Single blastomeres were isolated by removing the zona pellucida using acidic tyrode solution (Sigma, cat. no. T1788), then separated by gentle mouth pipetting in a calcium-free medium.

extract_protocol:
RNA was isolated from single cells or single morula embryos and amplified as previously described (Tang et al., 2010, Nat Protoc)
Library construction was performed following Illumina manufacturer suggestions.

treatment_protocol: Single cells were washed twice with 1x PBS containing 0.1% BSA before placing in lysis buffer.

value: 8-cell blastomere

tag: strain


title: mouse morula 3

source_name: morula

tag: cell type

value: morula


title: mouse morula 1


title: Adult liver 7_5hmC

description: Bed file generated from the raw files in Samples Adult liver 7_5hmC and Adult liver 7_non-enriched control

value: adult

value: unknown age

value: M

value: 5hmC enriched DNA


title: mouse 8-cell 1


title: mouse morula 2


title: Adult liver 6_5hmC

description: Bed file generated from the raw files in Samples Adult liver 6_5hmC and Adult liver 6_non-enriched control

value: 59 years


title: Adult liver 4_5hmC

description: Bed file generated from the raw files in Samples Adult liver 4_5hmC and Adult liver 4_non-enriched control

value: Liver

value: 45 years


title: mouse 4-cell 3

source_name: 4-cell blastomere

value: 4-cell blastomere


title: mouse 8-cell 2


title: Adult liver 3_5hmC

description: Bed file generated from the raw files in Samples Adult liver 3_5hmC and Adult liver 3_non-enriched control

value: 58 years


title: Adult liver 3_non-enriched control

description: Control for Adult liver 3_5hmC


title: mouse 4-cell 2


title: mouse 4-cell 1


title: Adult liver 2_5hmC

description: Bed file generated from the raw files in Samples Adult liver 2_5hmC and Adult liver 2_non-enriched control


title: mouse 2-cell 3

source_name: 2-cell blastomere

value: 2-cell blastomere


title: Fetal liver 8_5hmC

description: Bed file generated from the raw files in Samples Fetal liver 8_5hmC and Fetal liver 8_non-enriched control

value: fetus

value: 10 weeks + 2 days


title: Fetal liver 7_5hmC

description: Bed file generated from the raw files in Samples Fetal liver 7_5hmC and Fetal liver 7_non-enriched control

value: 7 weeks + 6 days


title: mouse pronuclei 3

source_name: pronucleus

value: pronucleus


title: mouse 2-cell 1


title: Fetal liver 5_5hmC

description: Bed file generated from the raw files in Samples Fetal liver 5_5hmC and Fetal liver 5_non-enriched control

value: 11 weeks + 2 days

value: F


title: Adult liver 5_5hmC

description: Bed file generated from the raw files in Samples Adult liver 5_5hmC and Adult liver 5_non-enriched control

value: 25 years


title: Fetal liver 6_5hmC

description: Bed file generated from the raw files in Samples Fetal liver 6_5hmC and Fetal liver 6_non-enriched control

value: 12 weeks + 1 day


title: mouse pronuclei 1


title: Fetal liver 3_5hmC

description: Bed file generated from the raw files in Samples Fetal liver 3_5hmC and Fetal liver 3_non-enriched control

value: 11 weeks


title: Fetal liver 4_5hmC

description: Bed file generated from the raw files in Samples Fetal liver 4_5hmC and Fetal liver 4_non-enriched control

value: 11 weeks + 1 day

value: M


title: human morula 5

data_processing:
Raw reads from the Illumina HiSeq2000 were mapped to the hg19 genome using default parameters in BWA
Mapped transcripts reads were transformed using the reads per kilobase per million (RPKM) metric
Genes with low expression in all stages (average RPKM<0.5) were filtered out, followed by quantile normalization.
Genome_build: hg19
Supplementary_files_format_and_content: human_expression_mat.txt: matrix listing normalized RPKM

value: morula

tag: ethnicity

value: Han Chinese

tag: supplementary file


title: Fetal liver 1_5hmC

description: Bed file generated from the raw files in Samples Fetal liver 1_5hmC and Fetal liver 1_non-enriched control

value: Liver

value: 8 weeks + 3 days

value: 5hmC enriched DNA


title: mouse oocyte 2

source_name: oocyte

value: oocyte


title: mouse oocyte 1


title: human 8-cell pooled

source_name: 8-cell embryo

value: 8-cell blastomere


title: Fetal liver 2_5hmC

description: Bed file generated from the raw files in Samples Fetal liver 2_5hmC and Fetal liver 2_non-enriched control

value: fetus

value: 11 weeks + 6 days


title: human morula 4


title: human 8-cell 5c


title: human 8-cell 5b


title: Adult liver 1_5hmC

description: Bed file generated from the raw files in Samples Adult liver 1_5hmC and Adult liver 1_non-enriched control

value: adult

value: 56 years


title: human 8-cell 4b


title: human 8-cell 3b


title: human 8-cell 2b


title: human 8-cell 3c


title: mouse 2-cell 2

value: 2-cell blastomere


title: human 8-cell 1b


title: human 8-cell 6a


title: human 8-cell 7a


title: mouse pronuclei 2

value: pronucleus


title: human 8-cell 3a


title: human 4-cell 3

value: 4-cell blastomere


title: human 4-cell 1


title: human 4-cell 2


title: human 2-cell 6


title: human 2-cell 5


title: human morula 1


title: human zygote 1

source_name: zygote

value: zygote


title: human pronuclei 4


title: human zygote 2


title: human oocyte 1


title: human paternal exome

data_processing:
Library strategy: Exome-Seq
Raw reads from the Illumina HiSeq2000 were mapped to the hg19 genome using default parameters in BWA
hg19
exome.wig: wiggle files represent the read depth every 10bp along the hg19 genome

source_name: blood

growth_protocol: Genomic DNA was obtained from blood of the father for exome sequencing analysis

extract_protocol:
Targeted enrichment was performed with Agilent 50M kit
Libraries were prepared using an Illumina paired-end DNA sample prep kit (Illumina) following the manufacturer's protocols

value: primary blood

tag: exome capture

value: Agilent 50M kit was used to capture the genome


title: human oocyte 4


title: human pronuclei 2


title: Mutant-Mar-S-3

status: Public on Jul 28 2013

city: Anyang

first: Ming ming

last: Wei

address: Huang he road 38

country: China

institute: Cotton Research Institute, Chinese Academy of Agriculture Sciences (CAAS)

description:
Small RNA
Sample 6

data_processing:
Raw sequence reads were produced using an Illumina 1G Genome Analyzer at BGI (Shenzhen, China) and processed into clean full-length reads through the BGI small RNA pipelines.
During this procedure, all low quality reads were removed, such as reads with 3’ and 5’ adapter contaminants, those without insert tags, and those with poly A sequences.
The remaining high-quality sequences were trimmed of their adapter sequences, and those larger than 30 nt or smaller than 18 nt were discarded. All high-quality sequences, even those with only a single unique read, were considered significant and used for further analysis.
The small RNAs were aligned to miRNA precursors/mature miRNAs in the miRBase (http://www.mirbase.org/index.shtml, release 15.0). The following criteria were used to determine the sequence counts of miRNA families in the different tissue samples: (1) if there was cotton miRNA information in the miRBase, the small RNAs were aligned to the corresponding cotton miRNA precursor/mature miRNA; and (2) if there was no cotton miRNA information in the miRBase, the small RNAs were aligned to the miRNA precursors/mature miRNAs of all plants in the database.
To identify potentially novel miRNAs among the six small RNA libraries, cotton transcript assemblies (ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Gossypium) from the Dana Farber Cancer Institute were chosen to map unique small RNA sequences. The characteristic hairpin structure of miRNA precursors was used to predict possible novel miRNAs. The miRNA prediction software, mireap, was also used to predict novel miRNA based on the secondary structure, the Dicer cleavage site, and the minimum free energy (http://sourceforge.net/projects/mireap/).
Genome_build: CGI.release_11.zip at ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Gossypium
Supplementary_files_format_and_content: Text files include lengths and counts of each distinct reads.

organism: Gossypium hirsutum

growth_protocol: Upland cotton (G. hirsutum) ‘Dong A’ (WT) plants and the GMS mutant in the ‘Dong A’ background were grown under regular field conditions at the experimental farm of the Cotton Research Institute in China Agricultural Academy of Science.

extract_protocol:
Total RNA was extracted from anthers using the pBiozol Total RNA Extraction Reagent (BioFlux), in accordance with the manufacturer’s instructions. The RNA was then precipitated with ethanol, dissolved in diethypyrocarbonate (DEPC) water and stored at −80°C. All RNA samples were examined for protein contamination (A260/A280 ratios) and reagent contamination (A260/A230 ratios) using a Nanodrop ND 1000 spectrophotometer (NanoDrop, Wilmington, DE).
The samples from the WT and GMS mutant anthers were quantified and equalized so that equivalent amounts of RNA were analyzed. The extracted total RNA was resolved on denatured 15% polyacrylamide gels. Gel fragments with a size range of 18–30 nt were excised, and the small RNA fragments were eluted overnight with 0.5 M NaCl at 4°C, and precipitated with ethanol. These 18–30 nt small RNAs were given 5’ and 3’ RNA adapters that were ligated with T4 RNA ligase. The adapter-ligated small RNAs were subsequently transcribed into cDNA by Super-Script II Reverse Transcriptase (Invitrogen) and amplified with the polymerase chain reaction, using primers that were annealed to the ends of the adapters. The amplified cDNA products were purified and recovered. Finally, Solexa sequencing technology was employed to sequence the small RNA samples (BGI, Shenzhen, China).

treatment_protocol: According to this sampling criterion and combined with microscopic examination, developing anthers at these three different growth stages were collected during early mornings.

tag: background

value: Dong A

tag: genotype/variation

value: Genetic male sterility (GMS) mutant

value: uninucleate stage

value: anthers


title: Mutant-Mar-S-2

description:
Small RNA
Sample 5

value: tetrad stage


title: uH2B ChIP-Seq Control

city: Richmond

first: Hengbin

last: Wang

state: VA

address: 401 College Street

department: Massey Cancer Institute

institute: Virginia Commonwealth University

data_processing:
Basecalls for both RNA-Seq and ChIP-Seq were performed in Illumina 1.5 software.
RNA-Seq and ChIP-seq files were filtered to retain reads with at least 90% of bases having a quality score greater than or equal to 20.  RNA-Seq results were mapped to hg18 using TopHat default paramenters.  ChIP-Seq results were mapped to hg18 using Bowtie with default settings.
FPKM and transcript sizes were determined using Cufflinks with default settings.
Genome_build: hg18
Supplementary_files_format_and_content: Mapped reads were converted to bedgraph format (BEDTools) and normalized as reads per million total unique mapped reads using the -scale parameter. GTF files for control assembled transcripts and Usp49 knockdown assembled transcripts.  BED files containing retained and unaffected transcribed introns.

source_name: uH2B ChIP-Seq Control

growth_protocol: HCT116 USP49 tetracycline inducible knockdown cells (T-Rex Expression System) were grown in DMEM supplemented with 10% FBS, 1% Pennicillin and Streptomycine, blasticidin and puromycin.

extract_protocol: For RNA-Seq, mRNA was specifically enriched from total RNA using oligo(dT) beads and sheared into small pieces.  The fragments were then reverse-transcribed into first-strand cDNA using random hexamer primers, followed by second strand synthesis using DNA polymerase I.  The short cDNA strands were ligated with 3' and 5' adapters for amplification and sequencing.  For ChIP-seq, uninduced control and induced knockdown cells were crosslinked with 1% formaldehyde and chromatin was disrupted into 100-400 bp fragments by sonication and precipitated with either anti-uH2B or anti-H2B antibodies.  After elution from the beads and reverse cross-linking, the DNA fragments were extracted with phenol/chloroform and recovered by ethanol precipitation.  Immunoprecipitated DNA was ligated with 3' and 5' adapters for amplification and sequencing.

treatment_protocol: USP49 knockdown was induced by adding doxycycline to growth media.  Cells were harvested 36 hours after doxycycline induction.

tag: cell line

value: colorectal carcinoma

tag: chip antibody

value: anti-uH2B (Millipore Cat# 05-1312)


title: uH2b ChIP-Seq USP49 knockdown

source_name: uH2b ChIP-Seq USP49 knockdown


title: H2B ChIP-Seq Control

source_name: H2B ChIP-Seq Control

value: anti-H2B (Abcam Cat# ab1790)


title: ChIP-Seq H3 Control

data_processing:
Basecalls for both RNA-Seq and ChIP-Seq were performed in Illumina 1.5 software.
RNA-Seq and ChIP-seq files were were mapped to hg18 using TopHat (RNA-seq) or Bowtie (ChIP-seq).  Samtools and Picard were used for post alignment processing.
FPKM and transcript sizes were determined using Cufflinks with default settings.
Genome_build: hg18
Supplementary_files_format_and_content: Mapped reads were converted to bedgraph format (BEDTools) and normalized as reads per million total unique mapped reads using the -scale parameter. GTF files for control assembled transcripts and Usp49 knockdown assembled transcripts.

source_name: colorectal carcinoma

value: anti-H3 (Abcam #1791)


title: H2B ChIP-Seq USP49 knockdown

source_name: H2B ChIP-Seq USP49 knockdown


title: ChIP-Seq FLAG-USP49 knockdown

value: anti-FLAG (Sigma Cat# F3165)


title: human 4-cell 4

value: Han Chinese


title: Degradome library

data_processing:
Low quality sequences and adapters were removed before sequence analysis.
Unique sequence signatures were aligned to the database of cotton transcript assemblies in Cotton Gene Index (Release 11.0, http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=cotton).
The CleaveLand was used to detect potentially cleaved targets based on degradome sequences. The 20 and 21 nt distinct reads were subjected to the CleaveLand pipeline for small RNA targets identification as previously described [Addo-Quaye C, Miller W, Axtell MJ: CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 2009, 25: 130-131].
the 20 and 21 nt distinct reads were first normalized to give 'reads per million' (RPM). Subsequently, the degradome reads were mapped to the cotton annotated cDNA (DFCI-Cotton Gene Index, release 11.0) and the cDNA hit number of each degradome read was recorded.
All alignments with scores not exceeding 4 and having the 5’ end of the degradome sequence coincident with the tenth and eleventh nucleotides of complementarity to the small RNA were retained.
Genome_build: DFCI-Cotton Gene Index Release 11.0 at http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=cotton
Supplementary_files_format_and_content: Text files include lengths and counts of each distinct reads.

source_name: Upland cotton_anthers pooled

extract_protocol:
In this study, in order to dissect miRNA-guided gene regulation in the WT and GMS mutant anthers, a degradome library suitable for miRNA target identification was constructed as described previously.
Briefly, total RNAs, which were extracted from the WT and GMS mutant anthers representing three stages of development, respectively, were mixed at an equal molar ratio as one sample. Approximately 200 μg of the mixed total RNA was used for polyadenylation using the Oligotex mRNA mini kit (Qiagen). Using T4 RNA ligase (Takara), a 5’ RNA adapter was added to the cleavage products, which possessed a free 5’-monophosphate at their 3’ termini. The ligated products were then purified using Oligotex mRNA mini kit (Qiagen) for reverse transcription to generate the first strand of cDNA using an oligo dT primer via SuperScript II RT (Invitrogen). After the cDNA library was amplified for 6 cycles (94°C for 30 s, 60°C for 20 s, and 72°C for 3 min) using Phusion Taq (NEB), the PCR products were digested with restriction enzyme Mme I (NEB). A double-stranded DNA adapter was then ligated to the digested products using T4 DNA ligase (NEB). The ligated products were selected based on size by running 10% polyacrylamide gel and purified for the final PCR amplification (94°C for 30 s, 60°C for 20 s, and 72°C for 20 s) for 20 cycles. The PCR products were gel purified and used for high-throughput sequencing using Illumina HiSeq 2000.

tag: line background

value: mixture of WT and GMS mutant

value: Anthers of the WT and GMS mutant representing three stages of development

tag: develpmental stage

value: mixed (meiosis, tetrad,and uninucleate microspore stage)


title: PPARγ ChIP-seq, 3T3-L1 Day7 1h Rosi rep2

data_processing:
Quality of all libraries were assessed using FastQC (Babraham Bioinformatics). Reads were trimmed and/or filtered using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Sequenced reads were aligned to the genome (mm9) using bowtie (Langmead B, et al. 2009. Genome Biol. 10:R25) with the options: -m 1 --best --strata
Reads from paired Rosi and DMSO libraries were combined into one library and peaks were called using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576–589) with the default settings, and using sonicated input samples as control.
Binding intensity was scored using HOMER for each factor and each condition by counting tags aligning within detected peaks, and normalizing to a total read depth of 10^7 aligned reads.
Expression was scored by counting RNAPII ChIP-seq reads mapping within RefSeq gene bodies longer than 1 kb (omitting the initial 250 bp) using HOMER. Differential expression was called using edgeR (Robinson MD, et al. 2010. Bioinformatics 26:139-140)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files created using HOMER for visualization of binding profiles in the UCSC genome browser. HOMER peak files with tag counts were generated using the HOMER annotatePeaks.pl script using the -d option. The files contain read counts of PPARγ, C/EBPα, MED1, and CBP ChIP-seq libraries (from both conditions). The read counts were normalized to a total read depth of 10^7 aligned reads.

source_name: 3T3-L1 adipocytes (Day 7)

value: 3T3-L1 adipocytes

value: anti-PPARγ (sc-7196; Santa Cruz)

tag: treatment

value: 1 μM rosiglitazone / 0.1% DMSO for 1 hour


title: ChIP-Seq FLAG-USP49


title: WT-Mar-F-2

description:
Small RNA
Sample 2

value: Dong A

value: fertile wild type (WT)


title: human 2-cell 1

value: 2-cell blastomere


title: WT-Mar-F-1

description:
Small RNA
Sample 1

value: meiosis stage

value: anthers


title: RNA-Seq USP49 knockdown

value: USP49 knockdown


title: RNA-Seq Control

value: control


title: human oocyte 3

value: oocyte


title: human pronuclei 3

value: pronucleus


title: 24hpf Sample3_71

status: Public on Jul 27 2013

city: Eggenstein-Leopoldshafen

first: olivier

last: armant

address: Hermann-von-Helmholtz-Platz 1

institute: ITG

description: Technical replicate of Sample3 read1

data_processing:
Basecalls performed using CASAVA version 1.4
Reads aligned to zebrafish genome Zv9 (Ensembl) with Tophat v 1.4.1 and Bowtie v 0.12.7  options: butterfly-search,coverage-search, microexon-search, min-anchor-length 5, -G GTF
Determination of raw reads aligned to ZV9 with HTSeq v0.5.3p3 and gtf file (ensembl zv9 release 60)
Determination of RPKM/FPKM with cufflinks v 1.3.0 with the options -u -b -M rRNA/Mtgenes mask -G gtf
Genome_build: Zv9 v 60
Supplementary_files_format_and_content: *.count file are the output of Htseq reads quantification. *.fpkm files are the output of cufflinks quantification

organism: Danio rerio

source_name: whole embryos

extract_protocol: Extraction of total RNA with Trizol following manufacturer's instruction. Generation of mRNA libraries with Trueseq RNA kit following Illumina's instructions

tag: genotype

value: Wild type

value: AB

tag: Stage

value: 24hpf embryos


title: 24hpf Sample1_22

description: Technical replicate of Sample1 read2


title: 24hpf Sample3_62

description: Biological sample  3 read2


title: 24hpf Sample2_51

description: Technical replicate of Sample2 read1


title: 24hpf Sample2_52

description: Technical replicate of Sample2 read2


title: 24hpf Sample2_32

description: Biological sample  2 read2


title: 24hpf Sample2_31

description: Biological sample  2 read1


title: 24hpf Sample3_72

description: Technical replicate of Sample3 read2


title: 24hpf Sample3_61

description: Biological sample  3 read1


title: 24hpf Sample1_21

description: Technical replicate of Sample1 read1


title: 24hpf Sample1_11

description: Biological sample  1 read1


title: head

description: Wild type adult head

source_name: entire adult head

value: adult head


title: 5days

description: Wild type larvea

source_name: whole larvae

value: 5 days old


title: 16-36hpf

description: Wild type embryos

value: 16 somites to 24hpf old embryos


title: TALE-3XFlag rep 2

status: Public on Jul 26 2013

city: Cambridge

last: Mendenhall

address: 7 CC

institute: Broad Institute

description: Sample 3

data_processing:
imaging and basecalls from MiSeq RTA
Fastq files were aligned to hg19 using Bowtie
Duplicate reads were removed from BAM files using BAM tools
BAM was converted to WIG files using IGVtools
Genome_build: hg19
Supplementary_files_format_and_content: wig files generated using IGVtools

growth_protocol: K562 erythrocytic leukaemia cells (ATCC CCL-243) were grown according to standard protocols in RPMI 1640 media (Invitrogen, 22400105) supplemented with 10% fetal bovine serum (FBS, Atlas Biologicals, F-0500-A) and 10% Penicillin/Streptomycin (Invitrogen, 15140122)

extract_protocol:
Cells were harvested at 72 hours for Sonication (flag) and ChIP
Library construction protocol: Single read - Illumina

treatment_protocol: For transfection, 5 X 10^6 cells per transfection were washed once with PBS.Cells were then transfected with 20 ug of TALE plasmid DNA or control mCherry plasmid by nucleofection with Lonza Kit V, as described by the manufacturer (Program T-016). Cells were immediately resuspended in K562 media at a cell density of 0.25 X 10^6 cells/ml.

value: erythrocytic leukaemia cells

tag: transfected with

value: 20ug TALE:3X Flag Plasmid

value: FLAG M2

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat. #


title: TALE-3XFlag rep 1

description: Sample 2


title: WT-Mar-F-3

description:
Small RNA
Sample 3

value: Dong A

value: fertile wild type (WT)

tag: developmental stage

value: uninucleate stage

tag: tissue


title: T-reg Bcatenin

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using BWA package.
Genome_build: hg19
Supplementary_files_format_and_content: *.bed – chromosome, start end strand; multiple reads mapping to same location and strand have been collapsed to single read

source_name: Five pooled donors

extract_protocol:
An iTreg pool of 5 different donors were crosslinked with 2 mM disuccinimidyl glutarate (Thermo Fisher Scientific) and 1% formaldehyde, cells were lysed in pre-immunoprecipitation buffer (10 mM Tris, 10 mM NaCl, 3 mM MgCl2 and 1 mM CaCl2). Chromatin was prepared and ChIP was performed according to the Millipore online protocol using 15 μg of β-Catenin antibody #9562 (Cell signaling technology, Boston, MA).
Immunoprecipitated chromatin was sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by ligation mediated PCR (LMPCR). After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel.

tag: cell type

value: Primary regulatory T cells

value: beta-catenin

tag: chip antibody catalog #

tag: chip antibody manufacturer

value: Cell Signaling


title: Mutant-Mar-S-1

description:
Small RNA
Sample 4

tag: background

value: Genetic male sterility (GMS) mutant

value: meiosis stage

value: anthers


title: tail

description: Wild type adult  tail

source_name: entire adult tail

value: Wild type

tag: strain

value: AB

value: adult tail


title: K562 input

description: Sample 1

tag: cell line


title: T-reg Input

tag: chip antibody


title: seq-ab9051_H4K20me1_N2_Mxemb_ChIP_Rep2

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: ab9051 H4K20me1:104513;target name: H4K20me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of human histone H4 mono methylated at K20;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9051;short description: An affinity purified rabbit antibody to H4K20me1 obtained from Abcam (ab9051 lot #104513). Used for ChIP.;input DNA

data_processing: to be updated

organism: Caenorhabditis elegans

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol:
Worm_embryo_extraction_v5. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131)+phosphatase inhibitors(Calbiochem cat#524624). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
DNA for Library Prep is incubated with an End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends. It is then purified and incubated with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends (a single A-overhang for more efficient and directed ligation of the adaptors). After a second purification, the DNA fragments is ligated with single-end ?Homebrew? adaptors which contain an index sequence within (Corbin Jones? lab). After ligation, the samples are purified TWICE using SPRI beads, allowing for a size selection step getting rid of excess adaptors. Samples are then amplified by PCR with single end primers. Depending on the original fragmentation of the DNA, samples can either be purified by SPRI or by separation and purification from an agarose gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: Mixed Embryo

value: wild type

tag: sex type

value: mixed Male and Hermaphrodite population


title: seq-ab9051_H4K20me1_N2_Mxemb_ChIP_Rep1


title: seq-ab9051_H4K20me1_N2_Mxemb_Input_Rep2

description: Input DNA


title: seq-AB46540_NIgG_N2_Mxemb_Input_Rep2

description: Input DNA

extract_protocol:
Worm_embryo_extraction_vSE3. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131) + phosphatase inhibitors (Calbiochem Cat# 524624), and dounced 30 times. Using samples were sonicated in Bioruptor using settings: high 30 sec on 30 sec off 15 minutes. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC, and taking the supernatant for ChIP. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_v3. 2mg extract was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
ChIP and input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated (concentrated T4 ligase) to annealed adaptors, size-selected, and amplified by PCR.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.


title: seq-AB46540_NIgG_N2_Mxemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: AB46540 NIgG;target name: N/A (negative control IgG);host: Rabbit;antigen: N/A;clonal: Polyclonal;purified: Affinity;company: Abcam ChIP grade;catalog: ab46540;short description: Rabbit Control IgG (ab46540) purchased from Abcam. An affinity purified rabbit polyclonal antibody to mouse whole IgG.;input DNA


title: seq-AB46540_NIgG_N2_Mxemb_Input_Rep1

description: Input DNA


title: seq-SDQ2966_MIS12_N2_Mxemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: MIS-12 SDQ2966;target name: MIS-12;host: Rabbit;antigen: IASAKEHKSLKQVEKEFDEKLEKIRQLRIKLAKRHDELEAVNNAIEVLHVMEKSQEQLISQKRIVPDSPTRMSPV;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ2966;short description: An Affinity purified Rabbit Polyclonal antibody to MIS-12 obtained from SDI (MIS-12 SDQ2966);input DNA


title: seq-SDQ2966_MIS12_N2_Mxemb_ChIP_Rep1


title: seq-HK72A9_H4K8ac_FEM2_AD_Input_Rep1

description: Input DNA

growth_protocol: Worm_adult_growth_and_harvest_vHP2.  Synchronized cultures of worms were grown until gravid in 400 mL batches.  Gravid adults were isolated through sucrose floatation, and frozen into pellets in liquid nitrogen with EBS (250 mM HEPES (pH 7.5), 1180 mM NaCl, 480 mM KCl, 20 mM EDTA, 5 mM EGTA, sucrose (final 340 mM) and protease/phosphatase inhibitors.  The pellets were stored at -80°C.

extract_protocol:
Worm extract was made from adult worms.  Frozen worm popcorn was ground up in a mixer mill.  Samples were then fixed with 1% formaldehyde for 10 minutes. Chromatin was then sheared by sonication in the Bioruptor, and the soluble fraction was collected and stored at -80°C for future use.
Worm extract from adult worms and 5 ?g of affinity purified antibody was used for ChIP. Dynal Protein A or G beads were used to recover the ChIPed DNA.  Samples were then treated with RNase A and Proteinase K, and reverse crosslinked at 65°C. ChIPed DNA was purified and then quantified using the Pico Green HS fluorescent assay.
Worm_ChIP-seq_ DNA_Library_Preparation_vSS2. ChIP and 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated (concentrated T4 ligase) to annealed adaptors, size-selected, and amplified by PCR.Changes: Ligate O/N at 16C. Use adapters and primer cocktail from Illumina TruSeq kit. Use AMPure cleanup in the place of Qiagne cleanup. Use Pippin prep for size selection .
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: Germline containing young adult

tag: Sex

value: Hermaphrodite


title: seq-HK72A9_H4K8ac_FEM2_AD_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: HK H4K8ac 72A9;target name: H4K8ac;host: Mouse;antigen: synthetic peptide of H4 acetylated at Lysine 8;clonal: Monoclonal;purified: Protein A/G;company: Lab;catalog: 4A7;short description: A Protein A/G purified Monoclonal Mouse antibody to H4K8ac obtained from Hiroshi Kimura (HK H4K8ac 72A9);input DNA


title: seq-HK72A9_H4K8ac_FEM2_AD_Input_Rep2

description: Input DNA


title: seq-SDQ2966_MIS12_N2_Mxemb_Input_Rep1

description: Input DNA


title: seq-SDQ2966_MIS12_N2_Mxemb_Input_Rep2

description: Input DNA


title: 24hpf Sample1_12

description: Biological sample  1

value: 24hpf embryos


title: seq-ab12181_H3K9acS10_873968_N2_L3_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: ab12181-H3K9acS10ph-873968;target name: H3K9acS10ph;host: Rabbit;antigen: ?;clonal: Polyclonal;purified: Affinity;company: abcam;catalog: ab12181;short description: a rabbit polyclonal antibody to H3K9acS10ph obtained from abcam (cat. #12181 lot #873968). used for ChIP;input DNA

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
ChIP or input DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads.  The protocol uses the Illuimina TruSeq DNA Sample Prep Kit.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: L3 Larva


title: seq-ab12181_H3K9acS10_873968_N2_L3_Input_Rep1

description: Input DNA


title: seq-ab12181_H3K9acS10_873968_N2_L3_Input_Rep2

description: Input DNA


title: seq-HK00009_H3K9me3_2F3_N2_Eemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: HK00009 H3K9me3:2F3;target name: H3K9me3;host: Mouse;antigen: ARTKQTAR(me3-K)STGGKAPRKQC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00009;short description: A protein G purified mouse monoclonal antibody to H3K9me3 (clone 2F3) obtained from Hiroshi Kimura. Used for ChIP.;input DNA

growth_protocol: Worm_embryo_growth_and_harvest_vSS5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
DNA for Library Prep is incubated with an End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends. It is then purified and incubated with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends (a single A-overhang for more efficient and directed ligation of the adaptors). After a second purification, the DNA fragments is ligated with single-end ?Homebrew? adaptors which contain an index sequence within (Corbin Jones? lab). After ligation, the samples are purified TWICE using SPRI beads, allowing for a size selection step getting rid of excess adaptors. Samples are then amplified by PCR with single end primers. Depending on the original fragmentation of the DNA, samples can either be purified by SPRI or by separation and purification from an agarose gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: Early Embryo


title: seq-Ab2621_H3K79me3_FEM2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: AB2621 H3K79me3:361576;target name: H3K79me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 tri methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2621;reference: http://www.abcam.com/Histone-H3-tri-methyl-K79-antibody-ChIP-Grade-ab2621.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide tri-methylated at K79.;input DNA


title: seq-Ab2621_H3K79me3_FEM2_AD_Input_Rep1

description: Input DNA


title: seq-ab9051_H4K20me1_N2_Mxemb_Input_Rep1

description: Input DNA


title: seq-HK00009_H3K9me3_2F3_N2_Eemb_Input_Rep2

description: Input DNA


title: seq-HK00009_H3K9me3_2F3_N2_Eemb_ChIP_Rep1


title: seq-AB46540_NIgG_N2_Mxemb_ChIP_Rep2


title: seq-ab8895_H3K4me1:733246_N2_L3_Input_Rep2

description: Input DNA


title: seq-ab8895_H3K4me1:733246_N2_L3_Input_Rep1

description: Input DNA


title: seq-HK00009_H3K9me3_2F3_N2_Eemb_Input_Rep1

description: Input DNA


title: seq-ab8895_H3K4me1:733246_N2_L3_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: ab8895 H3K4me1:733246;target name: H3K4me1;host: Rabbit;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8895;short description: A rabbit affinity purified antibody to H3K4me1 from Abcam (ab8895 lot #733246). Used for ChIP.;input DNA


title: seq-ab8895_H3K4me1:733246_N2_L3_ChIP_Rep1


title: seq-HK72A9_H4K8ac_FEM2_AD_ChIP_Rep2


title: seq-ab8896_H3K9me1_104560_N2_L3_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: ab8896 H3K9me1:104560;target name: H3K9me1;host: Rabbit;antigen: Synthetic peptide derived from within residues 1-100 of Histone H3;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8896;short description: An affinity purified rabbit antibody to H3K9me1 obtained from Abcam (ab8896 lot #104560). Used for ChIP.;input DNA


title: seq-ab8896_H3K9me1_104560_N2_L3_Input_Rep1

description: Input DNA


title: seq-ab8896_H3K9me1_104560_N2_L3_ChIP_Rep1


title: seq-ab12181_H3K9acS10_873968_N2_L3_ChIP_Rep2


title: seq-ab8896_H3K9me1_104560_N2_L3_Input_Rep2

description: Input DNA


title: seq-SDQ4501_T09A5.8_FEM2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: T09A5.8 SDQ4501;target name: T09A5.8;host: Rabbit;antigen: PSESPVASASSVIPTSKRKSINAETSNGRQRTLAPPVIVKDETTWTVDGIARHTDVDNTKTKLILMTNSATGERKVVEGREAFELDGWALAKYLLDRCEF;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4501;short description: An Affinity purified Rabbit Polyclonal antibody to T09A5.8 obtained from SDI (T09A5.8 SDQ4501);input DNA

extract_protocol:
Worm extract was made from adult worms.  Frozen worm popcorn was ground up in a mixer mill.  Samples were then fixed with 1% formaldehyde for 10 minutes. Chromatin was then sheared by sonication in the Bioruptor, and the soluble fraction was collected and stored at -80°C for future use.
Worm extract from adult worms and 5 ?g of affinity purified antibody was used for ChIP. Dynal Protein A or G beads were used to recover the ChIPed DNA.  Samples were then treated with RNase A and Proteinase K, and reverse crosslinked at 65°C. ChIPed DNA was purified and then quantified using the Pico Green HS fluorescent assay.
Libraries were prepared according to Illumina's instructions for ?Preparing Samples for ChIP Sequencing of DNA?, with some variation. DNA was end-repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 DNA polymerase.  A?s were then added to the 3? ends of the fragments using Kelow fragment (3? ? 5? exo minus). Paired-end adapters were then ligated onto the ends of the fragments.  DNA library was size selected by gel purification, fragments of 250-500 bp were band isolated from an agarose gel. DNA was PCR amplified for 18 cycles. The Bioanalyzer was used to verify fragment purification and quantify DNA.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.


title: seq-SDQ3166_LIN37_N2_LTemb_Input_Rep1

description: Input DNA

growth_protocol: Worm_embryo_growth_and_harvest_vSS7. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Embryos were incubated for 3.5 hours in M9 then frozen in liquid nitrogen.

extract_protocol:
Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later,washed pellets are resuspended in FA buffer and subjected to sonication in a DiagenodeBioruptor (40 pulses of 30 seconds with 1 minute rests in between at full power). Extractsare then spun down and the soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
Short description for UNC NimbleGen Database:Both ChIP and input DNA samples have their ends blunted and phosphorylated with KlenowDNAP, T4 DNAP, and T4 PNK. 3?-dA overhangs are then added with Klenow Fragment (3? to 5?exo minus), and Illumina adapters are subsequently ligated to the ends. Next, PCRamplification is performed using Illumina 1.1 and 2.1 primers, for a total of 18 cycles. AmplifiedDNA libraries are size-selected on a 2% agarose gel so that fragments sized between 250-350bp are obtained; gel extraction is carried out at room temperature.

value: Late Embryos


title: seq-SDQ4501_T09A5.8_FEM2_AD_Input_Rep1

description: Input DNA


title: seq-Ab2621_H3K79me3_FEM2_AD_Input_Rep2

description: Input DNA


title: seq-SDQ3166_LIN37_N2_LTemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: BH00003 LIN37;target name: LIN-37;host: Rabbit;antigen: Full length;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Bob Horvitz;input DNA


title: seq-SDQ4501_T09A5.8_FEM2_AD_Input_Rep2

description: Input DNA


title: seq-WA30932379_H3K9ac_N2_L3_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: WA30932379 H3K9ac;target name: H3K9Acetyl;host: Mouse;clonal: Monoclonal;purified: Protein A/G;company: Wako;catalog: blank;short description: A protein G purified mouse monoclonal antibody to H3K9ac (cat #309-32379) obtained from Waco. Used for ChIP.;input DNA

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
DNA was incubated with an enzyme mix (Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends. The DNA fragments were ligated with appropriate adaptor (Illumina) and then amplified by PCR. The amplicon was loaded into an agarose gel, and size-selected DNA was recovered from the gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.


title: seq-WA30932379_H3K9ac_N2_L3_ChIP_Rep1


title: seq-WA30932379_H3K9ac_N2_L3_Input_Rep2

description: Input DNA


title: seq-SDQ4501_T09A5.8_FEM2_AD_ChIP_Rep1


title: seq-AR0144_H3_144_N2_L3_Input_Rep2

description: Input DNA


title: seq-AR0144_H3_144_N2_L3_Input_Rep1

description: Input DNA


title: H2171_JQ1_POL2_ChipSeq

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against H2171_JQ1_POL2

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
01182013_C1FJWACXX_5.CCGTCC.wig.gz: hg18

source_name: Small Cell Lung Carcinoma

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: 500nM JQ1 for 6 hoursd

value: RNA Pol II (Rpb1 N-terminus)

tag: antibody catalog number

value: Santa Cruz SC-899

tag: duration

tag: concentration

tag: drug


title: seq-AR0144_H3_144_N2_L3_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: C. elegans  AR0144 H3 rabbit serum;target name: histone H3;host: Rabbit;antigen: C-terminal peptide of histone H3;clonal: Polyclonal;purified: Crude;company: Lake Placid Bio;catalog: AR-0144;short description: Rabbit serum to Histone H3 (lot# 144) obtained from LP Bio. Used for ChIP;input DNA

tag: genotype


title: H2171_DMSO_BRD4_ChipSeq

description: Chromatin IP against H2171_DMSO_BRD4

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
01182013_C1FJWACXX_4.AGTCAA.wig.gz: hg18

treatment_protocol: 0.05% DMSO for 6 hours

value: Bethyl A301-985A

value: DMSO


title: seq-AR0144_H3_144_N2_L3_ChIP_Rep2


title: H2171_DMSO_POL2_ChipSeq

description: Chromatin IP against H2171_DMSO_POL2

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
01182013_C1FJWACXX_5.AGTTCC.wig.gz: hg18


title: H2171_JQ1_WCE_ChipSeq

description: Chromatin IP against H2171_JQ1_WCE

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
01182013_C1FJWACXX_3.CAGATC.wig.gz: hg18

treatment_protocol: 500nM JQ1 for 6 hours

value: None WCE


title: seq-WA30932379_H3K9ac_N2_L3_Input_Rep1

description: Input DNA


title: HH_MM.1S_RNAPII_50nM_JQ1_ChipSeq

description: Chromatin IP against HH_MM.1S_RNAPII_50nM_JQ1

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
05242012_D0WUYACXX_4.GATCAG.wig.gz: hg18

source_name: Multiple myeloma

growth_protocol: RPMI 1640 supplemented with 10% FCS and 1% GlutaMAX

treatment_protocol: 50nM JQ1 treatment for 6hr

value: Plasma cell

tag: duration of treatment

value: 6 hr


title: HH_MM.1S_RNAPII_150nM_JQ1_ChipSeq

description: Chromatin IP against HH_MM.1S_RNAPII_150nM_JQ1

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
05242012_D0WUYACXX_5.TAGCTT.wig.gz: hg18

treatment_protocol: 150nM JQ1 treatment for 6hr


title: H2171_DMSO_WCE_ChipSeq

description: Chromatin IP against H2171_DMSO_WCE

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
01182013_C1FJWACXX_2.GCCAAT.wig.gz: hg18


title: seq-SDQ3166_LIN37_N2_LTemb_ChIP_Rep2

tag: developmental stage


title: H2171_JQ1_BRD4_ChipSeq

description: Chromatin IP against H2171_JQ1_BRD4

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
01182013_C1FJWACXX_5.ATGTCA.wig.gz: hg18


title: seq-SDQ3166_LIN37_N2_LTemb_Input_Rep2

description: Input DNA


title: HH_MM.1S_BRD4_150nM_JQ1_ChipSeq

description: Chromatin IP against HH_MM.1S_BRD4_150nM_JQ1

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
05242012_D0WUYACXX_3.TGACCA.wig.gz: hg18


title: MM1S_WT_IRF4_JL_ChipSeq

description: Chromatin IP against MM1S_WT_IRF4_JL

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
08282012_C1260ACXX_8.CGATGT.wig.gz: hg18

value: Santa Cruz SC-6059


title: MM1S_CDK9_JQ1_50nM_JL_ChipSeq

description: Chromatin IP against MM1S_CDK9_JQ1_50nM_JL

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
08282012_C1260ACXX_6.GTTTCG.wig.gz: hg18

treatment_protocol: 50nM JQ1 for 6h

value: Santa Cruz SC-484


title: MM1S_MED1_JQ1_5000nM_JL_ChipSeq

description: Chromatin IP against MM1S_MED1_JQ1_5000nM_JL

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
08282012_C1260ACXX_5.GTCCGC.wig.gz: hg18

treatment_protocol: 5000nM JQ1 for 6h

value: Bethyl A300-793A


title: MM1S_MED1_JQ1_50nM_JL_ChipSeq

description: Chromatin IP against MM1S_MED1_JQ1_50nM_JL

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
08282012_C1260ACXX_4.ATGTCA.wig.gz: hg18