title: Control 1

data_processing:
Basecalls performed using CASAVA version 1.2
Reads aligned to reference transcriptome with Bowtie v0.12.7
Counts per reference were summarised using in-house scripts
Genome_build: NCBI Transcriptome Shotgun Assembly Database numbers JR970414–JR999999 and JT000001–JT023377
Supplementary_files_format_and_content: Reference trancript name, TAB, count

source_name: Branch

tag: developmental stage

value: Adult

tag: immunogen treatment

value: Sea water

tag: time after exposure

value: 1 hour


title: HA-BmTdrd12 IP

status: Public on Nov 04 2013

type: SRA

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description: HA-IP from transfected BmN4 cells

library_source: transcriptomic

data_processing:
Illumina CASAVA version 1.7 used for basecalling (?)
The adapter sequences of smallRNA reads were clipped. Both smallRNA and mRNA sequencing reads were then mapped to the respective genomes.
Genome_build: mm9 for mouse, bombyx mori genome from KAIKOGAAS
Supplementary_files_format_and_content: Tab-delimted text file includes reads and their frequencies.

molecule: total RNA

organism: Bombyx mori

source_name: Bombyx mori, BmN4 cells

extract_protocol: Detailed protocol can be found in Pandey et al. 2013

tag: antibody

tag: cell line

tag: sample type

value: HA-IP from transfected BmN4 cells

tag: genetic background

value: C57BL/6;129S4/SvJae mixed


title: H9 Embryonic stem (ES) cells hMeDIP-Seq

city: Daejeon

first: Mirang

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: KRIBB(Korea Research Institute of Bioscience and Biotechnology

library_source: genomic

data_processing:
The sequences were mapped to the human genome (UCSC hg18) using the Illumina Genome Analyzer data analysis pipeline.
The entire genome was divided into 200-bp segments, and the number of reads was counted in each segment. The number of reads was normalized in MES (methylation enrichement score). MES is a normalized abundance measurement for 5hmC or 5mC reads aligned on each 200-bp bin of the genome and was calculated from the number of mapped 5hmC or 5mC reads on each bin divided by the bin size (200bp) and the total number of mapped sequence reads on the genome and multiplied by the human genome size.
Genome_build: hg18
Supplementary_files_format_and_content: BED files were generated based-on the normalized read depth mapped on each 200-bp bin of the genome.

molecule: genomic DNA

organism: Homo sapiens

source_name: Embryonic stem cells

growth_protocol: Differentiation of the hES cell line H9 (WiCell, Madison, WI, USA; passages 35-38) into NP cells and terminally into DA neurons was performed as described (Ko et al., 2007).

extract_protocol:
MBD-Seq: Genomic DNA was fragmented to 100–500 bp using nebulizer (Illumina) and then subjected to methylated DNA enrichment using the MethylMiner methylated DNA enrichment kit (Invitrogen). Briefly, methylated DNA was precipitated from 1 µg fragmented genomic DNA via binding to the methyl-CpG binding domain of human MBD2 protein, which was coupled to magnetic Dynabeads. The purified methylated DNA fragments were ligated to a pair of adaptors for sequencing on the Illumina Genome Analyzer. The ligation products were size fractioned to obtain 200–300 bp fragments on a 2% agarose gel and subjected to 18 cycles of PCR amplification.
hMeDIP-Seq: Genomic DNA was fragmented to 150–250 bp by 60 psi of nitrogen gas for 7 minute through a nebulizer (Illumina) and then subjected to library preparation using genomic DNA sample prep kit (Illumina). Briefly, 5 µg fragmented DNA was end-repaired, A-tailed and ligated to paired-end adapters. The pre-adapted DNA was subjected to immunoprecipitation using hMeDIP kit (Diagenode, Catalog No. AF-110-0016). Briefly, 1 µg of the pre-adapted DNA was denatured for 10 minutes at 95 oC and incubated with the 2.5 µg of mouse monoclonal anti-5hmC antibody (Diagenode) for 2 hours at 4 oC. The immunoabsorbed DNA was recovered after incubating with anti-mouse IgG-coated magnetic beads (Diagenode) at 4 oC for overnight. The immunoprecipitated DNA was amplified by 18 cycles of PCR using illumina PCR primers and then size fractioned to obtain 200–300 bp fragments on a 2% agarose.
Cluster generation and 72 cycles of single-read sequencing were done.

tag: cell type

value: Embryonic stem cells H9

tag: passages

tag: antibody manufacturer

value: Diagenode

tag: quantification

value: MethylFlash hydroxymethylated DNA quantification kit (Epigentek, Catalog No. P-1036)


title: Osr1f/+ tongue

city: cincinnati

first: HAN

last: LIU

state: oh

address: 3333 burnet avenue

department: DEVELOPMENTAL BIOLOGY

country: USA

institute: CINCINNATI CHILDREN'S HOSPITAL

data_processing:
Illumina offline basecaller v1.9.0.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.Implanted in tophat 1.4.1 using parameters:tophat -G mm9.gtf -o tophat -p 4 -r 0 mm9 reads.fastq. In short, exons from 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 size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: control mouse embryonic tongue

extract_protocol:
E12 mouse embryonic tongues were micro-dissected in cold PBS, immediately frozen at -80℃, total RNA was extracted by using RNeasy micro kit from Qiagen.
cDNA was made by the NuGEN Ovation RNA-Seq v2 Assay.

tag: strain

value: mixed background

tag: tissue

value: embryonic tongue

tag: genotype/variation

tag: age

value: emrbyonic day 12


title: DZ025_input_spe11YA

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
All C. elegans reads were subsequently trimmed to the first 27 bases and aligned to the ce10 reference genome using Bowtie, accepting only uniquely mapped reads with up to two mismatches. For C. briggsae, 48-base reads were aligned using the same Bowtie program settings to the cb4 reference genome.
Aligned reads were extended to 200 bases, and the number of reads overlapping with each base of the genome was counted using Bedtools (Quinlan & Hall, Bioinformatics, 2010).
The per-base read counts were then normalized to the genome-wide average in order to take the sequencing depth into account.
Genome_build: ce10
Genome_build: cb4
Supplementary_files_format_and_content: Processed data files are in bigwig format representing overlappaing read counts at each base in the genome.

organism: Caenorhabditis elegans

source_name: spe-11(hc77) yound adult

growth_protocol: Gravid hermaphrodites were bleached and their eggs were  collected and allowed to hatch overnight in M9. Synchronized animals were then grown in  standard liquid culture conditions (wormbook.org) using HB101 bacteria as a food source, and  staged by gonad migration and time. N2, AF16, and tra-1(e1834)/hT2[bli-4(e937) let-?(q782)  qIs48] animals were grown at 20°C; spe-11(hc77) and glp-4(bn2) animals were grown at 25°C.  tra-1(e1834) homozygotes were sorted from tra-1(e1834)/hT2[bli-4(e937) let-?(q782) qIs48]  siblings using a COPAS BIOSORT SELECT (Union Biometrica, 350-5000-000) to collect GFPnegative  animals. Two consecutive rounds of sorting were used to ensure a pure population of  tra-1(e1834) homozygotes. Collected animals were separated from residual bacteria by sucrose  flotation and washes in M9, and then frozen in liquid nitrogen.

extract_protocol:
Insoluble material was pelleted at 12000g at 4C for 10 min. 1mL of supernatant was added to 9mL of dilution buffer. 300uL of this was set aside as an “input” sample. 2ug of TRA-1 antibody UMN163 was added to the remaining sample and incubated in a 15mL conical with rotation at 4C o/n. Samples were spun at 15000g at 4C for 15 min and supernatant was decanted into a fresh 15mL conical tube. 50ul of blocked 50% PAS beads were added and incubated with rotation at 4C for 1 hr. PAS beads were pelleted at 1000g for 30 sec and supernatant was removed. Beads were then washed once in each of the following buffers; low salt buffer, high salt buffer, LiCl buffer, Morohashi RIPA, DOC lysis buffer, and TE. Beads were then transferred to a fresh tube and washed again with TE. Each wash consisted of adding 1mL of 4C buffer, inverting for 30 seconds, spinning at 1000g at 4C for 30 sec, and then discarding the supernatant. After the final wash, residual TE was removed with a small bore pipette tip. 130uL of elution buffer was added to each sample and incubated with rotation at RT for 15 min. Beads were spun down at 1000g for 30 sec and 100uL of supernatant was transferred into a new 1.5mL tube. An additional 100uL of elution buffer was added to each sample and incubated with rotation at RT for an additional 15 min. Again, beads were spun down at 1000g for 30 sec and another 100uL of supernatant was transferred into the same 1.5mL tube, making 200uL total volume per sample. At this point, 200uL of the “input” sample was processed in parallel to the IP samples for the rest of the protocol. 10uL of 4M NaCl was added to each sample and incubated o/n at 65C. Samples were then cooled to RT, and 1uL of 10 mg/mL RNAse A was added to each sample and incubated at 37C for 30 min. Then 4uL of .5M EDTA, 8uL Tris (pH=6.5), and 1uL of PCR grade proteinase K were added to each sample and incubated at 50C for 1 hr. Samples were then purified using Qiagen PCR purification columns and eluted in 50-100uL of Qiagen EB.
DNA were blunt-ended, A-overhanged, and then ligated with adaptors. DNA libraries were amplified by PCR with single-end primers. Amplicons in the size range between 200 and 500 bp were recovered from agarose gel.

treatment_protocol: Frozen animals were physically disrupted by grinding in liquid nitrogen in a mortar and pestle,  fixed in 1%PFA in PBS for 15 min at RT and post-fixed with 50mM glycine for 5 min at RT. All  subsequent steps were performed at 4°C. Material was pelleted, washed 3x in PBS with  protease inhibitors, and resuspended in 1%SDS lysis buffer. Fixed chromatin was sheared with  a Diagenode Bioruptor Standard, on the high setting for 7.5 min total on time (15 min of 30 sec  on, 30 sec off cycles).

tag: treatment

value: no treatment

tag: chip antibody


title: H1371_exp

status: Public on Nov 03 2013

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

description: In the processed data file the values for each chromosome were generated by dividing by the following factors, main chromosome: 0.65; pHV1: 0.82; pHV3: 1.105.

data_processing:
Sequence reads were mapped to the H. volcanii reference genome (Accession numbers: CP001953-CP001957) using BioScope (version 1.3.1).
Sequence reads mapping to a single genomic location were summed in 1 kb bins.
Normalised copy numbers were generated by dividing the sequence read counts from the exponential (replicating) sample by counts from the stationary (non-replicating) sample for each strain.
Normalised copy numbers were manually adjusted to give a minimum ratio of ~1 for each chromosome.
Genome_build: CP001953-CP001957
Supplementary_files_format_and_content: Wig file containing normalised replication profile for the main chromosome (reconstructed where appropriate), pHV1,  pHV3 and (where appropriate) pHV4. Each chromosome is individually normalised to give a minimum of ~1.

organism: Haloferax volcanii

source_name: Genome DNA from cells in exponential phase (A650 =~ 0.1)

growth_protocol: H. volcanii strains were grown as described previously [PMID: 14766575]. Genomic DNA was isolated from 100 ml culture in stationary phase (A650 >1) or ~1 L in exponential phase (A650 ~0.1).

extract_protocol:
SDS lysis, ethanol precipitation, RNaseA treatment, phenol-chloroform extraction as described previously [PMID: 14766575].
Library preparation and sequencing was carried out according to SOLiD instructions.

tag: relevant genotype

value: ∆pyrE2 ∆trpA ∆oriC3::trpA+

tag: growth phase

value: exponential


title: H1269_stat

description: In the processed data file the values for each chromosome were generated by dividing by the following factors, main chromosome: 0.7; pHV1: 0.525; pHV3: 1.2.

source_name: Genome DNA from cells in stationary phase (A650 > 1)

value: ∆pyrE2 ∆trpA ∆oriC1

value: stationary


title: H1269_exp


title: DS2_stat

description: In the processed data file the values for each chromosome were generated by dividing by the following factors, main chromosome: 1.1; pHV1: 0.66; pHV3: 1.43; pHV4: 0.9.

value: Wild-type


title: DS2_exp


title: H26_stat

description: In the processed data file the values for each chromosome were generated by dividing by the following factors, main chromosome: 0.90; pHV1: 0.66; pHV3: 1.4.


title: H1371_stat


title: H26_exp


title: Input

status: Public on Nov 02 2013

city: Houston

first: Francesco

middle: J

last: DeMayo

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Endometrial biopsy from healthy women

data_processing:
Sequence Aanlysis: DNA libraries were sequenced by Illumina’s Hi-Seq Sequencing Service. The 50-nucleotide (nt) sequence reads were mapped to the human genome (GRCh Build 37, February 2009) using the BWA algorithm with default settings. Alignment information for each read was stored in the BAM/SAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
Determination of Fragment Density: Since the 5 ́-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3 ́- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 150 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a Wig file.
Genome_build: hg19
Supplementary_files_format_and_content: wig

source_name: Endometrial stromal cells

growth_protocol: Human endometrial stromal cells (HESCs) were cultured in 150-mm culture dishes with HESC growth media (DMEM/F12 containing 10% of fetal bovine serum and 1% antibiotic-antimycotic)

extract_protocol:
Cells were fixed for 15 min with 1/10 volume of freshly prepared formaldehyde solution (11% formaldehyde, 0.1 M NaCl, 1 mM EDTA, and 50 mM HEPES). The fixation was stopped by adding 1/20 volume 2.5 M glycine for 5 min. Fixed HESCs were collected and pelleted at 800 x g for 10 min at 4 oC. Cell pellets were washed two times with cold PBS-Igepal (0.5% Igepal, 1 mM PMSF).  HESCs from six patients were pooled before genomic DNA isolation. NR2F2 immunoprecipitation and DNA library generation were performed by Active Motif.
ChIP and input DNA were amplified using the Illumina ChIP-Seq DNA Sample Prep Kit. Briefly, DNA ends were polished and 59-phosphorylated using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. Addition of 3’-adenine to blunt ends using Klenow fragment (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was size fractionated to 175–225 bp on a 2% agarose gel. After amplification for 18 cycles with Phusion polymerase, the resultingDNAlibraries were tested by RT-qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.

treatment_protocol: Cells grow to reach approximately 90% confluency, starting to treat with decidual media (Opti-MEM media containing 2% charcoal-stripped FBS, 1% antibiotic-antimycotic, 1 µM Medroxyprogesterone acetate, 10 nM E2, and 50 µM cAMP). Decidual media was changed every 48 h. After 72h of treatment, cells were fixed.

value: Primary endometrial stromal cells

tag: passage


title: NR2F2_ChIP-seq

description: Endometrial biopsy from healthy women

value: NR2F2 (Active Motif, Cat#61213)


title: Input

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

data_processing:
Input.aligned.bed; genome build: hg19
Mapping: raw Illumina sequencing reads in the FASTQ format were cleaned using in-house scripts by trimming sequencing adaptors and low quality bases in both ends (Q<67 in Illumina 1.5).  Cleaned sequences were then mapped to the human genome (hg19) using Novoalign v2.07.
Peak: The reads mapped uniquely to a single genomic locus were used for peak finding with Model-based Analysis of ChIP-Seq (MACS v1.4).

growth_protocol: BE(2)-C/Tet-Off/Myc-HOXC9 cells were cultured in a 1:1 mixture of DMEM and Ham’s nutrient mixture F12 supplemented with 10% fetal bovine serum (Invitrogen) in the presence or absence of doxycycline for 6 days.

extract_protocol: ChIP was conducted according to the published procedure (Lee, et al., Nat. Protocols 1:729-748, 2006). ChIP-seq libraries were generated from ChIP DNA samples according to the Illumina ChIP-seq library construction procedure. DNA fragments of ~250 bp in size were gel-isolated and purified, and the libraries were amplified by 18 cycles of PCR and sequenced using Illumina Genome Analyzer IIx with a read length of 76 bp.

tag: tumor cell type

value: Neuroblastoma

tag: tissue origin

value: Sympathetic nervous system


title: HOXC9_ChIP-seq_rep2

data_processing:
HOXC9_IP4.aligned.bed; genome build: hg19
HOXC9_IP4.aligned.wig; genome build: hg19
HOXC9_IP4.peaks.bed; genome build: hg19
Mapping: raw Illumina sequencing reads in the FASTQ format were cleaned using in-house scripts by trimming sequencing adaptors and low quality bases in both ends (Q<67 in Illumina 1.5).  Cleaned sequences were then mapped to the human genome (hg19) using Novoalign v2.07.
Peak: The reads mapped uniquely to a single genomic locus were used for peak finding with Model-based Analysis of ChIP-Seq (MACS v1.4).

tag: cell line

value: anti-Myc tag (clone 4A6, Millipore)


title: HOXC9_ChIP-seq_rep1

data_processing:
HOXC9_IP3.aligned.bed; genome build: hg19
HOXC9_IP3.aligned.wig; genome build: hg19
HOXC9_IP3.peaks.bed; genome build: hg19
Mapping: raw Illumina sequencing reads in the FASTQ format were cleaned using in-house scripts by trimming sequencing adaptors and low quality bases in both ends (Q<67 in Illumina 1.5).  Cleaned sequences were then mapped to the human genome (hg19) using Novoalign v2.07.
Peak: The reads mapped uniquely to a single genomic locus were used for peak finding with Model-based Analysis of ChIP-Seq (MACS v1.4).


title: Old_3_MeDIP

status: Public on Nov 01 2013

city: London

first: Gareth

last: Wilson

address: 23 Huntley Street

institute: UCL Cancer Institute

description: DNA IP against 5-Methylcytosine

data_processing:
The MeDIP-seq data were analysed within the MeDUSA pipeline (Wilson et al. 2012)
Alignment was performed using BWA v0.5.8 with default parameters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Wig files were created using the MEDIPS v1.0 bioconductor package. Bigwig files generated by converting wig files generated in MEDIPS using wigToBigWig from UCSC.
The RNA-Seq data were analysed using RSEM v1.1.21
RNA-seq data was aligned against a transcriptome library using BOWTIE v0.12.7 with default parameters. Transcript library built using RSEM v1.1.21 utilising UCSC mm9 annotation (from UCSC table 'knownGene')
Isoform counts were generated from the aligned RNA-seq data using RSEM (http://deweylab.biostat.wisc.edu/rsem/)  utilising the UCSC known gene table for mm9.
Gene counts and isoform counts .results files output from RSEM
Genome_build: mm9
Supplementary_files_format_and_content: .bw file scores represent normalised (reads per million) read depth across the genome.
Supplementary_files_format_and_content: .results files represent gene counts and isoform counts. Headers for the output genes.results are 'internal_gene_id', 'expected_counts', 'tau_value', 'ucsc_transcript_id_list'. Headers for the output isoforms.results are 'ucsc transcript_id', 'expected_counts', 'tau_value', 'internal_gene_id'.

source_name: Bone Marrow

extract_protocol: We sorted lower side population cells (LSPs) from adult female wild-type C57b/6 mice at different time points and extracted DNA and RNA simultaneously from the same cells. DNA library prep was performed using NEB library prep kits for illumina and mRNA library prep was completed using the Illumina Tru-seq library prep kit

value: Haematopoietic Stem Cells

value: Old - ~24 months

tag: medip antibody

value: 5-mC monoclonal antibody 33D3 (Diagenode, catalog# mAb-081, lot# 03000A)


title: Mid_1_RNAseq

description: RNA-(Tru)seq

data_processing:
The MeDIP-seq data were analysed within the MeDUSA pipeline (Wilson et al. 2012)
Alignment was performed using BWA v0.5.8 with default parameters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Wig files were created using the MEDIPS v1.0 bioconductor package. Bigwig files generated by converting wig files generated in MEDIPS using wigToBigWig from UCSC.
The RNA-Seq data were analysed using RSEM v1.1.21
RNA-seq data was aligned against a transcriptome library using BOWTIE v0.12.7 with default parameters. Transcript library built using RSEM v1.1.21 utilising UCSC mm9 annotation (from UCSC table 'knownGene')
Isoform counts were generated from the aligned RNA-seq data using RSEM (http://deweylab.biostat.wisc.edu/rsem/)  utilising the UCSC known gene table for mm9.
Gene counts and isoform counts .results files output from RSEM
Genome_build: mm9
Supplementary_files_format_and_content: .bw file scores represent normalised (reads per million) read depth across the genome.
Supplementary_files_format_and_content: .results files represent gene counts and isoform counts. Headers for the output genes.results are 'internal_gene_id', 'expected_counts', 'tau_value', 'ucsc_transcript_id_list'. Headers for the output isoforms.results are 'ucsc transcript_id', 'expected_counts', 'tau_value', 'internal_gene_id'.

Mapping of processed files to raw files:
Files *1_out* generated from SRA run SRR594994.
Files *1_120417_out* generated from SRA run SRR594995.

molecule: polyA RNA

tag: cell type

value: Middle-aged - ~12 months


title: Old_2_RNAseq

description: RNA-(Tru)seq

data_processing:
The MeDIP-seq data were analysed within the MeDUSA pipeline (Wilson et al. 2012)
Alignment was performed using BWA v0.5.8 with default parameters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Wig files were created using the MEDIPS v1.0 bioconductor package. Bigwig files generated by converting wig files generated in MEDIPS using wigToBigWig from UCSC.
The RNA-Seq data were analysed using RSEM v1.1.21
RNA-seq data was aligned against a transcriptome library using BOWTIE v0.12.7 with default parameters. Transcript library built using RSEM v1.1.21 utilising UCSC mm9 annotation (from UCSC table 'knownGene')
Isoform counts were generated from the aligned RNA-seq data using RSEM (http://deweylab.biostat.wisc.edu/rsem/)  utilising the UCSC known gene table for mm9.
Gene counts and isoform counts .results files output from RSEM
Genome_build: mm9
Supplementary_files_format_and_content: .bw file scores represent normalised (reads per million) read depth across the genome.
Supplementary_files_format_and_content: .results files represent gene counts and isoform counts. Headers for the output genes.results are 'internal_gene_id', 'expected_counts', 'tau_value', 'ucsc_transcript_id_list'. Headers for the output isoforms.results are 'ucsc transcript_id', 'expected_counts', 'tau_value', 'internal_gene_id'.

Mapping of processed files to raw files:
Files *2_out* generated from SRA runs SRR595006 SRR595007.
Files *2_120417_out* generated from SRA runs SRR595008 SRR595009.


title: Old_3_RNAseq

description: RNA-(Tru)seq

data_processing:
The MeDIP-seq data were analysed within the MeDUSA pipeline (Wilson et al. 2012)
Alignment was performed using BWA v0.5.8 with default parameters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Wig files were created using the MEDIPS v1.0 bioconductor package. Bigwig files generated by converting wig files generated in MEDIPS using wigToBigWig from UCSC.
The RNA-Seq data were analysed using RSEM v1.1.21
RNA-seq data was aligned against a transcriptome library using BOWTIE v0.12.7 with default parameters. Transcript library built using RSEM v1.1.21 utilising UCSC mm9 annotation (from UCSC table 'knownGene')
Isoform counts were generated from the aligned RNA-seq data using RSEM (http://deweylab.biostat.wisc.edu/rsem/)  utilising the UCSC known gene table for mm9.
Gene counts and isoform counts .results files output from RSEM
Genome_build: mm9
Supplementary_files_format_and_content: .bw file scores represent normalised (reads per million) read depth across the genome.
Supplementary_files_format_and_content: .results files represent gene counts and isoform counts. Headers for the output genes.results are 'internal_gene_id', 'expected_counts', 'tau_value', 'ucsc_transcript_id_list'. Headers for the output isoforms.results are 'ucsc transcript_id', 'expected_counts', 'tau_value', 'internal_gene_id'.

Mapping of processed files to raw files:
Files *3_out* generated from SRA run SRR595010.
Files *3_120417_out* generated from SRA run SRR595011.


title: H1267_stat

description: In the processed data file the values for each chromosome were generated by dividing by the following factors, main chromosome: 1.0; pHV1: 1.08; pHV3: 1.6.

value: ∆pyrE2 ∆trpA ∆oriC2


title: Mid_3_RNAseq

description: RNA-(Tru)seq

data_processing:
The MeDIP-seq data were analysed within the MeDUSA pipeline (Wilson et al. 2012)
Alignment was performed using BWA v0.5.8 with default parameters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Wig files were created using the MEDIPS v1.0 bioconductor package. Bigwig files generated by converting wig files generated in MEDIPS using wigToBigWig from UCSC.
The RNA-Seq data were analysed using RSEM v1.1.21
RNA-seq data was aligned against a transcriptome library using BOWTIE v0.12.7 with default parameters. Transcript library built using RSEM v1.1.21 utilising UCSC mm9 annotation (from UCSC table 'knownGene')
Isoform counts were generated from the aligned RNA-seq data using RSEM (http://deweylab.biostat.wisc.edu/rsem/)  utilising the UCSC known gene table for mm9.
Gene counts and isoform counts .results files output from RSEM
Genome_build: mm9
Supplementary_files_format_and_content: .bw file scores represent normalised (reads per million) read depth across the genome.
Supplementary_files_format_and_content: .results files represent gene counts and isoform counts. Headers for the output genes.results are 'internal_gene_id', 'expected_counts', 'tau_value', 'ucsc_transcript_id_list'. Headers for the output isoforms.results are 'ucsc transcript_id', 'expected_counts', 'tau_value', 'internal_gene_id'.

Mapping of processed files to raw files:
Files *3_out* generated from SRA run SRR595000.
Files *3_120417_out* generated from SRA run SRR595001.


title: Mid_2_RNAseq

description: RNA-(Tru)seq

data_processing:
The MeDIP-seq data were analysed within the MeDUSA pipeline (Wilson et al. 2012)
Alignment was performed using BWA v0.5.8 with default parameters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Wig files were created using the MEDIPS v1.0 bioconductor package. Bigwig files generated by converting wig files generated in MEDIPS using wigToBigWig from UCSC.
The RNA-Seq data were analysed using RSEM v1.1.21
RNA-seq data was aligned against a transcriptome library using BOWTIE v0.12.7 with default parameters. Transcript library built using RSEM v1.1.21 utilising UCSC mm9 annotation (from UCSC table 'knownGene')
Isoform counts were generated from the aligned RNA-seq data using RSEM (http://deweylab.biostat.wisc.edu/rsem/)  utilising the UCSC known gene table for mm9.
Gene counts and isoform counts .results files output from RSEM
Genome_build: mm9
Supplementary_files_format_and_content: .bw file scores represent normalised (reads per million) read depth across the genome.
Supplementary_files_format_and_content: .results files represent gene counts and isoform counts. Headers for the output genes.results are 'internal_gene_id', 'expected_counts', 'tau_value', 'ucsc_transcript_id_list'. Headers for the output isoforms.results are 'ucsc transcript_id', 'expected_counts', 'tau_value', 'internal_gene_id'.

Mapping of processed files to raw files:
Files *2_out* generated from SRA runs SRR594996 SRR594997.
Files *2_120417_out* generated from SRA runs SRR594998 SRR594999.


title: Young_2_RNAseq

description: RNA-(Tru)seq

data_processing:
The MeDIP-seq data were analysed within the MeDUSA pipeline (Wilson et al. 2012)
Alignment was performed using BWA v0.5.8 with default parameters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Wig files were created using the MEDIPS v1.0 bioconductor package. Bigwig files generated by converting wig files generated in MEDIPS using wigToBigWig from UCSC.
The RNA-Seq data were analysed using RSEM v1.1.21
RNA-seq data was aligned against a transcriptome library using BOWTIE v0.12.7 with default parameters. Transcript library built using RSEM v1.1.21 utilising UCSC mm9 annotation (from UCSC table 'knownGene')
Isoform counts were generated from the aligned RNA-seq data using RSEM (http://deweylab.biostat.wisc.edu/rsem/)  utilising the UCSC known gene table for mm9.
Gene counts and isoform counts .results files output from RSEM
Genome_build: mm9
Supplementary_files_format_and_content: .bw file scores represent normalised (reads per million) read depth across the genome.
Supplementary_files_format_and_content: .results files represent gene counts and isoform counts. Headers for the output genes.results are 'internal_gene_id', 'expected_counts', 'tau_value', 'ucsc_transcript_id_list'. Headers for the output isoforms.results are 'ucsc transcript_id', 'expected_counts', 'tau_value', 'internal_gene_id'.

Mapping of processed files to raw files:
Files *2_out* generated from SRA runs SRR594988 SRR594989.
Files *2_120417_out* generated from SRA runs SRR594990 SRR594991.

value: Young - 8 - 12 weeks


title: Young_3_MeDIP

description: DNA IP against 5-Methylcytosine


title: Mid_3_MeDIP

description: DNA IP against 5-Methylcytosine


title: Young_3_RNAseq

description: RNA-(Tru)seq

data_processing:
The MeDIP-seq data were analysed within the MeDUSA pipeline (Wilson et al. 2012)
Alignment was performed using BWA v0.5.8 with default parameters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Wig files were created using the MEDIPS v1.0 bioconductor package. Bigwig files generated by converting wig files generated in MEDIPS using wigToBigWig from UCSC.
The RNA-Seq data were analysed using RSEM v1.1.21
RNA-seq data was aligned against a transcriptome library using BOWTIE v0.12.7 with default parameters. Transcript library built using RSEM v1.1.21 utilising UCSC mm9 annotation (from UCSC table 'knownGene')
Isoform counts were generated from the aligned RNA-seq data using RSEM (http://deweylab.biostat.wisc.edu/rsem/)  utilising the UCSC known gene table for mm9.
Gene counts and isoform counts .results files output from RSEM
Genome_build: mm9
Supplementary_files_format_and_content: .bw file scores represent normalised (reads per million) read depth across the genome.
Supplementary_files_format_and_content: .results files represent gene counts and isoform counts. Headers for the output genes.results are 'internal_gene_id', 'expected_counts', 'tau_value', 'ucsc_transcript_id_list'. Headers for the output isoforms.results are 'ucsc transcript_id', 'expected_counts', 'tau_value', 'internal_gene_id'.

Mapping of processed files to raw files:
Files *3_out* generated from SRA run SRR594992.
Files *3_120417_out* generated from SRA run SRR594993.


title: Mid_1_MeDIP

description: DNA IP against 5-Methylcytosine


title: Snyder Pmex-5 HPL-2 eGFP YL472 yAd C.elegans ChIP Rep2

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: eGFP;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.;input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

source_name: Snyder Pmex-5 HPL-2 eGFP YL472 yAd ChIP Rep.2

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
The current ChIP Protocol is modified from Ercan et al., Nature Genetics 39: 403-408 (2007). Worm samples are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents. The cellular debris is removed by centrifugation and the supernatant containing any formaldehyde crosslinked chromatin is saved for preparing input DNA and collecting immunocomplexes. 10% (or 50 ul) of the above supernatant from each sample is saved as input sample (control). Input sample (also known as whole cell extract) represents the total genomic DNA and is processed later (treated with RNAase A, proteinase K and reverse crosslink steps) along with the ChIPed samples to isolate genomic DNA (input DNA). The remaining supernatant is incubated with affinity-purified anti-GFP antibodies and Protein G-sepharose beads to collect the immunocomplexes containing a targeted transcription factor that is C-terminally tagged with GFP and its genomic binding fragments. Alternatively, the 8WG16 mouse monoclonal antibodies and Protein A-sepharose beads are used to collect the immunocomplexes containing RNA polymerase II. After extensive washing, any immunocomplexes are eluted and the protein-DNA crosslinks are reversed. The degree of sonication is assessed by running a small aliquot of DNA on a 2% agarose gel. Quantitative PCR is used to check if the ChIPed sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

value: YL472(official name :YL472 genotype :unc-119(ed3) III; vrEx66 [pMEX-5::HPL-2:GFP:FLAG::HPL-2 3?UTR genotype :unc-119 (+)]) outcross :0 mutagen :None tags :GFP::3xFlag description :It is actually extrachromosomal line by bombardment. made_by :Michelle Kudron in Reinke lab )

tag: developmental stage

value: Young adult

tag: genotype

tag: Sex

value: Hermaphrodite


title: Mid_2_MeDIP

description: DNA IP against 5-Methylcytosine

tag: strain


title: H1267_exp

value: exponential


title: Young_2_MeDIP

description: DNA IP against 5-Methylcytosine


title: Snyder Pmex-5 HPL-2 eGFP YL472 yAd C.elegans Input Rep2

description: input DNA

source_name: Snyder Pmex-5 HPL-2 eGFP YL472 yAd Input Rep.2

value: unc-119(ed3) III; vrEx66 [pMEX-5::HPL-2:GFP:FLAG::HPL-2 3?UTR


title: Snyder lin-35 n745 EFL-1 Ab L1 26dC C.elegans Input Rep2

description: input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

source_name: Snyder lin-35 n745 EFL-1 Ab L1 Input Rep.2

value: MT10430(official name :MT10430 genotype :lin-35(n745) I. )

value: L1 26dC


title: Snyder Pmex-5 HPL-2 eGFP YL472 yAd C.elegans Input Rep1

description: input DNA

source_name: Snyder Pmex-5 HPL-2 eGFP YL472 yAd Input Rep.1


title: Snyder Pmex-5 HPL-2 eGFP YL472 yAd C.elegans ChIP Rep1

source_name: Snyder Pmex-5 HPL-2 eGFP YL472 yAd ChIP Rep.1


title: Young_1_RNAseq

description: RNA-(Tru)seq


title: Snyder lin-35 n745 EFL-1 Ab L1 26dC C.elegans Input Rep1

description: input DNA

source_name: Snyder lin-35 n745 EFL-1 Ab L1 Input Rep.1


title: Snyder lin-35 n745 EFL-1 Ab L1 26dC C.elegans ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: EFL-1 antibody (44960002);target name: EFL-1;host: Rabbit;antigen: MEDSYNDMEDPGFRQLSDMELQKALEMTKQSSIKNNLMLGLDNELDFDFDFDEDEDLDQPQMGTRADKSLGLLAKRFIRMIQYSPYGRCD LNTAAEALNV;clonal: Polyclonal;purified: Affinity;company: Other;catalog: NOVUS 44960002;short description: This product was created from the ModEncode Project a part of the NHGRI and is sold by SDIX and Novus Biologicals. This antibody is available from different lot and animal productions. These C. elegans antibodies were generated in the labs of Jason Lieb Susan Strome Julie Ahringer Arshad Desai and Abby Dernburg. Lot # G3048-110A01 Animal number SDQ3590;input DNA

source_name: Snyder lin-35 n745 EFL-1 Ab L1 ChIP Rep.2


title: Snyder lin-35 n745 EFL-1 Ab L1 26dC C.elegans ChIP Rep1

source_name: Snyder lin-35 n745 EFL-1 Ab L1 ChIP Rep.1


title: Old_1_MeDIP

description: DNA IP against 5-Methylcytosine


title: Old_2_MeDIP

description: DNA IP against 5-Methylcytosine


title: Young_1_MeDIP

description: DNA IP against 5-Methylcytosine


title: H3K36me2 W ML-DmBG3-c2 D.melanogaster ChIP Rep2

description: ChIP DNA; Antibody information listed below: official name: H3K36me2 W;target name: H3K36me2;host: Mouse;antigen: KSAPATGGV(me2-K)KPHRYRPGTC;clonal: Monoclonal;purified: Crude;company: Lab;catalog: 2C3;reference: http://genome.cshlp.org/content/21/2/227.full;short description: Monoclonal H3K36me2 from Kimura lab;input DNA

data_processing: Bowtie alignment protocol. Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.Reads that passed default parameters of the Illumina quality filter were mapped with Bowtie 0.12.7. The reference sequence used to built an index for mapping was the Flybase reference r5.22. The reference index was created using the bowtie-build function with default parameters. Reads were mapped using  -n 2 -l 28 -e 70 -k 1 -m 10 --best in Bowtie (-n 2, -l 28, -e 70 default). Parameters-n INT number of allowed mismatch-l INT seed length-e INT maximum permitted total of quality values at all mismatched read positions-m INT suppress all alignments for a particular read or pair if more than INT reportable alignments-k INT report up to INT valid alignments--best report alignments in best-to worst orderReads were converted to SAM formant using the bowtie2sam.pl script provided by the DCC. SPP Peak calling protocol. The aligned reads were called using SPP R package (ver.1.10, Kharchenko et al., Nat.Biotech 2008). The binding characteristics and tag shift were estimated using SPP get.binding.characteristics() function. The reads showing abnormality were removed using SPP remove.local.tag.anomalies() function. The regions of enrichment were identified as continuous blocks of positions that exhibit significant enrichment of IP over input reads. The significance of enrichment was assessed within a 1Kb window around each point using a Poisson model. A position was considered significantly enriched if the number of IP read counts was significantly higher (Z-score > 3) than the number of input read counts, after adjusting for the total number of reads sequenced in IP and input measurements. For each replicate set, if replicates were consistent (>80% agreement for top 40% of peaks/enrichment clusters), reads in each replicates were combined and enrichment regions were called as described above.  Processed data are obtained using following parameters: genome version is FlyBase r5

organism: Drosophila melanogaster

source_name: H3K36me2 W BG3 ChIP expt.2392

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

tag: tissue

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

value: Unknown


title: 35S>>SlDCL1IR-1

city: Bet Dagan

first: Tzahi

last: Arazi

state: ISRAEL

address: Institute of Plant Sciences, ARO the Volcani Center

department: Institute of Plant Sciences

country: Israel

institute: ARO - Volcani Center

description: Sample 3

data_processing:
The Cache ASsisted Hash Search with Xor logic (CASHX) Pipeline (release 2.3)  was used to parse and map the small sequences to the tomato genome SGN release version SL2.40
Reads in the size range of 18-26 nts and perfectly matched to the tomato genome were retained.
The small RNA CASHX database was annotated with the Repeats Master version 5.0 (ftp://ftp.solgenomics.net/tomato_genome/repeats/), Plant snoRNAs Database (version 1.2; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home), SILVA rRNA database (http://www.arb-silva.de/), miRbase (release 19)http://www.mirbase.org/);
After annotation, only "clean" reads not matching tRNAs, rRNAs, snRNA and SnoRNA were used for further analysis.
Genome_build: tomato genome (SGN release version SL2.40; http://solgenomics.net/organism/Solanum_lycopersicum/genome)
Supplementary_files_format_and_content: tab delimited values (txt) files include RPM values for each Sample

organism: Solanum lycopersicum

source_name: seedlings shoots

growth_protocol: growth chamber with a 16 h light period and 8 h dark period 24 °C

extract_protocol:
Tri-reagent extraction
Total RNA samples were used to construct small RNA libraries using the TruSeq small RNA kit as described by the manufacturer (Illumina, San Diego, CA, USA).

tag: cultivar

tag: genotype/variation

value: SlDCL1 silenced (35S>>SlDCL1IR)

value: 14 days after sowing

value: seedling shoots


title: H3K36me2 W ML-DmBG3-c2 D.melanogaster ChIP Rep1

description: input DNA

source_name: H3K36me2 W BG3 ChIP expt.2393


title: H3K36me2 W ML-DmBG3-c2 D.melanogaster Input Rep1

source_name: H3K36me2 W BG3 Input expt.2435


title: H2AV 9751 S2-DRSC GFP RNAi D.melanogaster ChIP Rep2

description: input DNA

source_name: H2AV 9751 S2 GFP RNAi ChIP expt.2579

extract_protocol:
The template for the dsRNA synthesis was PCR amplified from Drosophila genomic DNA using specific primers extended with 5? T7-promoter tails. The sequence of the T7-promoter tails is as follows: 5?- CTAATACGACTCACTATAGGGAG-3?. The amplicon was selected such that it is contained within single exon. Following PCR the template was purified using PCR purification Kit from Qiagen. 2.5ug of purified template was used to synthesize dsRNA with Ribomax T7 RNA transcription kit from Promega. The dsRNA was precipitated with ethanol, dissolved in 300ul of pure water, denatured by heating to 65C for 30min and re-annealed by slow cooling to room temperature.2x10^6cells were treated with 50ug of dsRNA in 25cm2 T-flask for 1 hour in serum-free Schneider?s media. They were further brought up 6ml of Schneider?s media supplemented with 10% FBS and grown to confluence (~4 days). The cells were passaged to a 75cm2 T-flask and treated the second time with 200ug of dsRNA as described above. Following the treatment the cells were grown to confluence in 15ml Schneider?s media. 1ml of resulted culture was taken for preparation of nuclear and cytoplasmic protein extracts and the rest was in vivo crosslinked with formaldehyde. The protocol typically yields about 7x10^7 crosslinked cells, which is enough for about 7 ChIPs. And the RNAi treated cells were treated with formaldehyde as in normal cultured cell.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

value: embryo-derived cell-line

value: late embryonic stage

value: Male


title: H3K36me2 W ML-DmBG3-c2 D.melanogaster Input Rep2

description: input DNA

source_name: H3K36me2 W BG3 Input expt.2436


title: 35S:LhG4-1

description: Sample 1

value: control (35S:LhG4)

tag: age


title: H2AV 9751 S2-DRSC GFP RNAi D.melanogaster ChIP Rep1

description: ChIP DNA; Antibody information listed below: official name: H2AV 9751;target name: H2AV;host: Rabbit;antigen: QDPQRKGNVILSQAY;clonal: Polyclonal;purified: Affinity;company: Lake Placid;catalog: Rabbit 9751;short description: Raised against peptide;input DNA

source_name: H2AV 9751 S2 GFP RNAi ChIP expt.2577


title: H2AV 9751 S2-DRSC H2AV RNAi D.melanogaster Input Rep2

description: input DNA

source_name: H2AV 9751 S2 H2AV RNAi Input expt.2573


title: H2AV 9751 S2-DRSC H2AV RNAi D.melanogaster ChIP Rep1

source_name: H2AV 9751 S2 H2AV RNAi ChIP expt.2576


title: 35S>>SlDCL1IR-2

description: Sample 4


title: Old_1_RNAseq

description: RNA-(Tru)seq

source_name: Bone Marrow

value: Haematopoietic Stem Cells

value: Old - ~24 months


title: Brg1_ChIP_Seq

city: Bradford

first: Michael Y

last: Fessing

address: Richmond Road

institute: University of Bradford

description: Sample 1

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 1.1.2
Data were filtered using the following specifications…
peaks were called using Sicer version 0.0.1 with the following setting:FDR 0.01
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using Sicer

source_name: mouse primary epidermal keratinocytes

growth_protocol: Skin from the newborn mice has been treated with 1% Trypsin in PBS buffer at 4 C overnight, dermis was separated from epidermis and the single cell suspension was prepared from the epidermis.

extract_protocol:
Cell were fixed with 1% formaldehyde in PBS, the nuclei were isolated, chromatin was sonicated and immuno-precipitated using anti-Brg1 anti-bodies (Santa Cruz Biotechnologies). The DNA has been isolated from the immuno-precipitated and input chromatin
Indexed ChIP-seq libraries were generated using NEBNext reagents (New England Biolabs) and

value: newborn

value: skin

value: mouse primary epidermal keratinocytes

tag: chip antibody

value: anti-Brg1 (H-88)

tag: chip antibody vendor

value: Santa Cruz Biotechnologies

tag: chip antibody cat. #

tag: chip antibody lot #


title: input DNA

description: Sample 2


title: H2AV 9751 S2-DRSC H2AV RNAi D.melanogaster Input Rep1

source_name: H2AV 9751 S2 H2AV RNAi Input expt.2572


title: Smc3 Q2580 3rd Instar Larvae D.melanogaster ChIP Rep2

description: input DNA

source_name: Smc3 Q2580 3rd Instar D.mel ChIP expt.2498

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

value: 3rd Instar Larvae

value: wild type


title: POF (MO 459) 3rd Instar Larvae D.melanogaster Input Rep2

description: input DNA

source_name: POF (MO 459) 3rd Instar D.mel Input expt.2223


title: POF (MO 459) 3rd Instar Larvae D.melanogaster ChIP Rep2

description: input DNA

source_name: POF (MO 459) 3rd Instar D.mel ChIP expt.2238


title: Smc3 Q2580 3rd Instar Larvae D.melanogaster Input Rep1

description: ChIP DNA; Antibody information listed below: official name: Smc3 Q2580;target name: Smc3;host: Rabbit;antigen: aa 321-420;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2580;short description: Smc3/Cap (CG9802) aa 321-420;input DNA

source_name: Smc3 Q2580 3rd Instar D.mel Input expt.2493


title: H2AV 9751 S2-DRSC GFP RNAi D.melanogaster Input Rep2

description: input DNA

source_name: H2AV 9751 S2 GFP RNAi Input expt.2575


title: POF (MO 459) 3rd Instar Larvae D.melanogaster Input Rep1

description: ChIP DNA; Antibody information listed below: official name: POF (MO 459);target name: POF;host: Rabbit;antigen: aa1-150;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: MO 459;short description: Custom produced by Covance;input DNA

source_name: POF (MO 459) 3rd Instar D.mel Input expt.2221


title: Smc3 Q2580 3rd Instar Larvae D.melanogaster ChIP Rep1

source_name: Smc3 Q2580 3rd Instar D.mel ChIP expt.2497


title: JMJD2A-KDM4A Q2541 3rd Instar Larvae D.melanogaster ChIP Rep1

description: ChIP DNA; Antibody information listed below: official name: JMJD2A-KDM4A Q2541;target name: JMJD2A/KDM4A;host: Rabbit;antigen: aa 350-449;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2541;short description: JMJD2A demethylase (CG15835) KDM4A;input DNA

source_name: JMJD2A-KDM4A Q2541 3rd Instar D.mel ChIP expt.2384


title: Smc3 Q2580 3rd Instar Larvae D.melanogaster Input Rep2

description: input DNA

source_name: Smc3 Q2580 3rd Instar D.mel Input expt.2494


title: H2AV 9751 S2-DRSC H2AV RNAi D.melanogaster ChIP Rep2

description: input DNA

source_name: H2AV 9751 S2 H2AV RNAi ChIP expt.2578


title: JMJD2A-KDM4A Q2541 3rd Instar Larvae D.melanogaster ChIP Rep2

description: input DNA

source_name: JMJD2A-KDM4A Q2541 3rd Instar D.mel ChIP expt.2385


title: H2AV 9751 S2-DRSC GFP RNAi D.melanogaster Input Rep1

source_name: H2AV 9751 S2 GFP RNAi Input expt.2574


title: BEAF-HB.14-16 hr OR embryo D.melanogaster ChIP Rep1

description: input DNA

source_name: BEAF-HB.14-16 hr OR emb ChIP expt.1972

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit.http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

value: Embryo 14-16hr OR


title: POF (MO 459) 3rd Instar Larvae D.melanogaster ChIP Rep1

source_name: POF (MO 459) 3rd Instar D.mel ChIP expt.2237


title: JMJD2A-KDM4A Q2541 3rd Instar Larvae D.melanogaster Input Rep1

source_name: JMJD2A-KDM4A Q2541 3rd Instar D.mel Input expt.2316


title: BEAF-HB.14-16 hr OR embryo D.melanogaster Input Rep2

description: input DNA

source_name: BEAF-HB.14-16 hr OR emb Input expt.1962


title: BEAF-HB.14-16 hr OR embryo D.melanogaster Input Rep1

description: ChIP DNA; Antibody information listed below: official name: BEAF-HB;target name: BEAF32A and BEAF42B;host: Rabbit;antigen: Peptide based on aa 88-282 of the BEAF protein;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: VP Lab;short description: antibody against BEAF32A and BEAF32B;input DNA

source_name: BEAF-HB.14-16 hr OR emb Input expt.1823


title: hk4s_A

city: Zurich

first: Stefan

last: Grob

address: Zollikerstrasse 107

department: Institute of Plant Biology

institute: University of Zurich

description: 4C PCR product

data_processing:
sample separation according to 4C primer sequence: Custom Python script
alignment: bowtie version 0.12.7
sequences distal from restriction sites were discarded: Custom Python script
addition of diverse tracks: Custom Python script
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include number of reads per 4C fragment

organism: Arabidopsis thaliana

source_name: Aerial tissue

growth_protocol: Arabidopsis seedlings were grown for 14 days on MS medium in long day condidtion (16h light, 8h dark; 22°C day, 18°C night)

extract_protocol:
4C PCR product was purified using QIAquick PCR Purification Kit.
PCR product of individual replicates were pooled. The library was constructed using standard Illumina DNA-seq protocol

tag: ecotype

value: 14 days old seedlings


title: SWN_A

description: 4C PCR product


title: SWN_B

description: 4C PCR product


title: AT3G44380_A

description: 4C PCR product


title: YAO_A

description: 4C PCR product


title: FLC_B

description: 4C PCR product


title: YAO_B

description: 4C PCR product


title: BEAF-HB.14-16 hr OR embryo D.melanogaster ChIP Rep2

source_name: BEAF-HB.14-16 hr OR emb ChIP expt.1964


title: AT3G44380_B

description: 4C PCR product


title: AT1G51860_B

description: 4C PCR product


title: FLC_A

description: 4C PCR product


title: FWA_B

description: 4C PCR product


title: AG_B

description: 4C PCR product


title: hk4s_B

description: 4C PCR product


title: AT1G51860_A

description: 4C PCR product


title: AG_A

description: 4C PCR product


title: CKI1_A

description: 4C PCR product


title: JMJD2A-KDM4A Q2541 3rd Instar Larvae D.melanogaster Input Rep2

description: input DNA

source_name: JMJD2A-KDM4A Q2541 3rd Instar D.mel Input expt.2317


title: FWA_A

description: 4C PCR product


title: FIS_B

description: 4C PCR product


title: CKI1_B

description: 4C PCR product


title: FIS_A

description: 4C PCR product


title: PHE_A

description: 4C PCR product


title: MEA F6_B

description: 4C PCR product


title: MEA F8_B

description: 4C PCR product


title: MEA F8_A

description: 4C PCR product


title: jmj14 ldl1 ldl2 BSseq

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

data_processing:
Raw file content: quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane
BS-seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics), allowing up to 2 mismatches and retaining only uniquely mapping reads. The drm2 and nrpe1 libraries used in this study were previously published (GSE39901), as were the 3 other Col replicates used (GSE39901 - WT replicate 2 ; GSE38286 ; GSE36129).
Genome_build: TAIR10
Supplementary_files_format_and_content: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (#methylated cytosines sequenced/#total cytosines sequenced).

source_name: 3 week leaf tissue

growth_protocol: All plants were grown at 22 degrees celsius in constant light.

extract_protocol:
phenol-chloroform extraction followed by bisulfite treatment
converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013
genomic DNA isolated by phenol/chloroform and bisulfite treated

value: jmj14-1 ldl1-2 ldl2

value: Columbia


title: ldl1 ldl2 BSseq

value: ldl1-2 ldl2


title: MEA F6_A

description: 4C PCR product


title: nrpe1 sRNA

data_processing:
Raw file content: quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/8 lane
RNA-seq (size fractionation) - Reads were demultiplexed (perfect matches to each index were required). Adapter sequences (identified by at least a 13 nt perfect match) were trimmed and reads >18 nt and <28 nt in length after trimming were retained. Reads with no identifiable adapter were discarded. Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch. Both unique and non-uniquely mapping reads were retained for normalization purposes but only uniquely mapping reads were used for downstream analysis. For downstream analyses up to 100 identical mapping reads were allowed to be counted at any given region, locations with more than 100 siblings were flattened to 100 mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome for 24nt class of small RNAs with each bin given a value corresponding to the relative 24 nt read density at that location (24nt reads in 25bp bins / total mapping small RNA reads of all size classes - unique and non-uniquely mapping)

source_name: floral tissue

extract_protocol:
Trizol extraction followed by PEG and then urea-PAGE fractionation
Illumina TruSeq small RNA
18-28nt isolated small RNAs from total RNA Trizol preparation


title: Col BS-seq

value: Wild type


title: jmj14 BSseq


title: shh1 sRNA


title: jmj14 ldl1 ldl2 sRNA


title: PHE_B

description: 4C PCR product


title: drm2 sRNA


title: ldl1 ldl2 sRNA


title: jmj14 sRNA


title: Col sRNA


title: HT_High_3

city: Madrid

first: Dafne

last: Pérez Montarelo

state: Madrid

address: Crta. de la Coruña Km 7.5

department: Animals Genetics

country: Spain

institute: INIA

description: mRNA

data_processing:
Illumina Casava software was used for base calling.
FastQC was used to assess the quality of the raw sequencing data.
Trim Galore was used to quality trim the data and remove sequencing adaptors.
Reads were mapped against the reference genome using TopHat v.2.0.5 with Bowtie2.
Transcripts were assembled and quantified in FPKM by Cufflinks v.2.0.2.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Text file with the RPKM normalized expression values of each gene per group (high or low growth and fatness).

organism: Sus scrofa

source_name: hypothalamus, high growth and fatness

extract_protocol:
RiboPure TM of High Quality total RNA kit.
Paired-end libraries with fragments of 300 bp were prepared using the TrueSeq RNA sample Prep kit v2 (Illumina).
Multiplex sequencing of the libraries was performed on an Illumina HiSeq 2000 with three samples per lane.

tag: breed

value: Iberian x Landrace backcross

value: hypothalamus

tag: phenotype

value: high growth and fatness


title: HT_Low_4

description: mRNA

source_name: hypothalamus, low growth and fatness

value: low growth and fatness


title: HT_Low_2

description: mRNA


title: HT_High_4

description: mRNA


title: HT_High_1

description: mRNA


title: HT_Low_5

description: mRNA


title: ldl1 ldl2 RNA-seq

data_processing:
RNA-seq -- Reads were filtered for full-length (50bp) reads. Reads containing adapter were discarded. Reads were mapped with Tophat2 (Kim et al. 2011 Genome Bio) to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads. Identical reads (potential PCR or optical duplicates) were flattened to 1 read.
Genome_build: TAIR10
Supplementary_files_format_and_content: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 25bp bins / total unique mapping reads)

extract_protocol:
Trizol (Life Technologies)
Illumina TruSeq mRNA
Total RNA isolated by a standard Trizol (Life Technologies) extraction. mRNA was selectively sequenced by bead purification as part of library generation.
Total RNA Trizol extracted from leaf tissue\n\!Sample_data_processing = Raw file content: quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 lane


title: HT_High_2

description: mRNA


title: HT_Low_1

description: mRNA


title: HT_Low_3

description: mRNA


title: nrpd1 sRNA


title: 35S:LhG4-2

description: Sample 2

source_name: seedlings shoots

value: control (35S:LhG4)

value: 14 days after sowing

value: seedling shoots


title: jmj14 ldl1 ldl2 RNA-seq


title: HT_High_5

description: mRNA


title: iPSC6

city: Bronx

first: Herb

last: Lachman

state: NY

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

description: Sample 6

data_processing:
Paired-end RNA-seq was carried out on an Illumina HiSeq 2000. We obtained 90-101 bp mate-paired reads from cDNA fragments with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8) [PMID:19289445]. We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18), which included multiple categories of annotated transcripts, and quantified transcript abundance as FPKM (fragments per kilobase of exon per million fragments mapped).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: text file including FPKM for each sample.

source_name: control neurons

extract_protocol:
RNA-seq was carried out on and day 14 neurons at the Columbia Genome Center. Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2.
Briefly, total RNA was converted to cDNA using oligo dT, which was then used for Illumina sequencing library preparation.

tag: sample group

value: control

value: 14 day neurons


title: jmj14 RNA-seq


title: iPSC5

description: Sample 5


title: Col RNA-seq


title: nrpd1 H3K4m3 ChIP (replicate 2)

data_processing:
Raw file content: quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/6 lane
ChIP-seq -- Reads were filtered for full-length (50bp) reads. Reads containing adapter were discarded. Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads. Identical reads (potential PCR or optical duplicates) were flattened to 1 read. Technical sequencing replicates for each respective genotype to increase coverage.
Genome_build: TAIR10
Supplementary_files_format_and_content: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 25bp bins / total unique mapping reads)

source_name: seedling tissue (10-day)

extract_protocol:
extracted by ChIP followed by phenol-chloroform exctract as described
NuGen Ovation Ultralow DR sample prep kit
immunoprecipitated formaldehyde-crosslinked leaf tissue

tag: antibody

value: anti-H3K4m3 (Millipore 04-745)


title: 537

description: Sample 3

source_name: schizohrenia neurons

value: patients


title: 22q11-30

description: Sample 2


title: nrpe1 H3K4m3 ChIP (replicate 2)


title: drm2 H3K4m3 ChIP (replicate 2)


title: 1804

description: Sample 1


title: iPSC2

description: Sample 7


title: jmj14 ldl1 ldl2 H3K4m3 ChIP (replicate 2)


title: nrpe1 H3K4m2 ChIP (replicate 2)

value: anti-H3K4m2 (Millipore 07-030)


title: nrpd1 H3K4m2 ChIP (replicate 2)


title: A11

city: New York

first: Xin

last: Jin

state: New York

address: 417 East 68th Street

department: Cancer Biology and Genetics

institute: Memorial Sloan-Kettering Cancer Center

description: without MSC supplementation

data_processing:
Base-calling was performed with Illumina Casava v1.8.1
Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0
Gene-level expression counts were determined with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts

source_name: mammary tumor xenograft

growth_protocol: EGFP-L10a+ MDA-MB-231 cancer cells were orthotopically injected into the mammary fat pad with or without 1:1 ratio of human bone marrow derived mesenchymal stem cells (MSCs). The mammary tumors were retrieved for TRAP-RNAseq profiling after 3 weeks. Five biological replicates from different mice were included in the "with MSC" group (M), and four biological replicates from different mice were included in the "without MSC" group (A).

extract_protocol:
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, the whole tumor were harvested and cut into small pieces. Tumor slices were lysed in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).
RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).

tag: cell line

value: EGFP-10a+ MDA-MB-231

tag: protocol

value: without MSC supplementation


title: jmj14 ldl1 ldl2 H3K4m3 ChIP (replicate 1)

data_processing:
Raw file content: quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 lane
ChIP-seq -- Reads were filtered for full-length (50bp) reads. Reads containing adapter were discarded. Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads. Identical reads (potential PCR or optical duplicates) were flattened to 1 read. Technical sequencing replicates for each respective genotype to increase coverage.
Genome_build: TAIR10
Supplementary_files_format_and_content: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 25bp bins / total unique mapping reads)

extract_protocol:
extracted by ChIP followed by phenol-chloroform exctract as described
Illumina TruSeq DNA Prep Kit
immunoprecipitated formaldehyde-crosslinked leaf tissue

tag: genotype

value: jmj14-1 ldl1-2 ldl2

value: Columbia

value: anti-H3K4m3 (Diagenode pAb-003-050)


title: jmj14 ldl1 ldl2 H3K4m2 ChIP (replicate 2)


title: drm2 H3K4m2 ChIP (replicate 2)


title: M10

description: supplemented with 1:1 ratio of MSC

value: supplemented with 1:1 ratio of MSC


title: A13

description: without MSC supplementation


title: M15

description: supplemented with 1:1 ratio of MSC


title: A9

description: without MSC supplementation


title: M7

description: supplemented with 1:1 ratio of MSC


title: M6

description: supplemented with 1:1 ratio of MSC


title: ldl1 ldl2 H3K4m3 ChIP (replicate 1)

value: ldl1-2 ldl2


title: 22q11-15

description: Sample 4


title: M1

description: supplemented with 1:1 ratio of MSC


title: jmj14 H3K4m3 ChIP (replicate 1)


title: 300+100_b

source_name: cells in culture

extract_protocol:
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).
RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).

treatment_protocol: Cells were starved in 0.2% serum for 24hrs and treated with CXCL12 + IGF1 at two different concentrations for 6 hrs. Two biological replicates were included for each condition.

tag: treatment


title: 300+100_a


title: jmj14 ldl1 ldl2 H3K4m2 ChIP (replicate 1) A, B

description: 2 technical replicates

value: anti-H3K4m2 (Abcam AB32356)


title: A12

description: without MSC supplementation


title: 30+10_a

value: CXCL12 (30ng/mL) + IGF1 (10ng/mL)


title: 30+10_b


title: 0+0_b

value: CXCL12 (0ng/mL) + IGF1 (0ng/mL)


title: Col H3K4m2 ChIP (replicate 1) A, B, C

description: 3 technical replicates

data_processing:
Raw file content: quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 or 1/1 lane
ChIP-seq -- Reads were filtered for full-length (50bp) reads. Reads containing adapter were discarded. Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads. Identical reads (potential PCR or optical duplicates) were flattened to 1 read. Technical sequencing replicates for each respective genotype to increase coverage.
Genome_build: TAIR10
Supplementary_files_format_and_content: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 25bp bins / total unique mapping reads)

value: Wild type


title: jmj14 H3K4m2 ChIP (replicate 1) A, B

description: 2 technical replicates


title: 0+0_a


title: input

city: Sendai

first: Hozumi

last: Motohashi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Center for Radioisotope Science

country: Japan

institute: Tohoku University Graduate School of Medicine

data_processing:
Basecalls performed using illumina Pipeline v1.4.0
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND
peaks were called using MACS
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS; Scores represent -10*log10(pvalue)

source_name: primary megakaryocytes

growth_protocol: Whole livers were collected from mouse fetuses at embryonic day 13.5, and single-cell suspensions were prepared by successive passage through 25-gauge needles. The fetal liver cells were maintained in RPMI1640 (Wako, Osaka, Japan) supplemented with 20% charcoal-stripped FBS, 100 U/ml penicillin, 100 µg/ml streptomycin, and 50 ng/ml recombinant human thrombopoietin (generously provided by Kyowa Hakko Kirin Co. Ltd., Tokyo, Japan). Megakaryocytes were harvested for RNA purification and ChIP assay from a day-3 culture.

extract_protocol:
Primary megakaryocytes were fixed with 1% formaldehyde for 10 min at room temperature. After neutralization with 125 mM glycine, the cells were washed in cold PBS twice and lysed in cell lysis buffer (5 mM PIPES-KCl pH8.0, 85 mM KCl, 0.5% NP40, 1 mM PMSF, 1x Complete (Roche, Basel, Switzerland)) for ten minutes on ice. The chromatin was pelleted by centrifugation at 2,000 rpm for 5 min at 4Co, resuspended in nuclear lysis buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS, 1 mM PMSF, 1x Complete) and sonicated on ice. Chromatin was incubated with the anti-p45 antibody and immunoabsorbed using a mixture of protein A plus protein G-sepharose (GE Healthcare, Waukesha, WI).
Lysates were clarified from sonicated nuclei and protein-DNA complexe was isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the ChIP DNA Sample Prep Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3-'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 250~ bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina Flow Cell for cluster generation. Libraries were sequenced on the Illumina Genome Analyzer IIx following the manufacturer's protocols.

tag: cell type

value: primary megakaryocytes

tag: genetic background


title: HM2.2

status: Public on Oct 31 2013

city: Durham

first: Devjanee

last: Swain Lenz

state: NC

address: 130 Bioscience Drive

institute: Duke University

description: hybrid S. MATa S. MATalpha, developmental stage M2, replicate 2

data_processing:
original base-calling,quality control and trimming of indexes was performed by GTAC at Washington University
aligned sequencing reads using Bowtie v 0.12.7 with parameters -v 1 -m 0
used lab perl script to map alignments to ORFs that are shared between S. cerevisiae and S. paradoxus
used lab perl script to filter out ORFs in which all samples had 0 reads
For allele specific variance stabiliting, use DESeq v1.8.3 with command estimateDispersions(cds, method="pooled-CR", modelFormula=count~stage*allele*species)
For allele non-specific variance stabiliting, use DESeq v1.8.3 with command estimateDispersions(cds, method="pooled-CR", modelFormula=count~stage*species)
Genome_build: parental and hybrid indexes created from S. cerevisiae S288c (SGD) and S. paradoxus N17 (SGRP) genomes
Supplementary_files_format_and_content: 2013.02.06.1.mm.0.MA.all.species.high.counts.allele.non: read counts for all samples, hybrid counts are allele-nonspecific, this is count data for DESeq
Supplementary_files_format_and_content: 2013.02.06.1.mm.0.MA.all.species.high.counts.allele.sp: read counts for all samples, hybrid counts are allele-specific in which "c" designates S. cerevisiae allele and "p" designates S. paradoxus allele, this is count data for DESeq
Supplementary_files_format_and_content: 2013.02.06.allele.non.vsd: variance stabilized data for all samples derived from DESeq, hybrid data is allele-nonspecific
Supplementary_files_format_and_content: 2013.02.07.allele.specific.hybrid.high.counts.vsd: variance stabilized data for all samples derived from DESeq, hybrid counts are allele-specific in which "c" designates S. cerevisiae allele and "p" designates S. paradoxus allele

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

source_name: yeast culture

growth_protocol: We inoculated 100 ml of YPD (1% BactoTM yeast extract, 2% BactoTM peptone and 2% dextrose) in 250 ml Erlenmeyer flasks, and incubated the culture at 30ºC and 340 rpm for 15 hours. To sporulate cells we washed cells with water and resuspended the cells in 250 ml of SPO (1% potassium acetate, 0.1% BactoTM yeast extract, 0.05% dextrose) for a final concentration of 107 cells/ml. We incubated the cultures in 1 L baffled flasks at 30ºC at 340 rpm for 24 hours. We used distilled water for all media.

extract_protocol:
We extracted total RNA from samples using Ambion RiboPure-Yeast Kit. We purified mRNA from total RNA using Ambion Micro PolyPurist Kit, and reversed transcribed mRNA into cDNA using polyA primers.
We used T4 DNA Polymerase (NEB), T4 Polynucleotide Kinase (NEB), and Taq Polymerase (NEB) for end repair of the sheered cDNA.  We used T4 ligase (NEB) to ligate index adapters to the cDNA . We pooled each sample to an equal concentration and gel extracted 250 – 350 bp of ligated cDNA and used PCR to amplify the selected fragment to a final concentration of 1 nM.  We submitted our final cDNA library to GTAC at Washington University for sequencing on two Illumina HiSeq lanes. At a run concentration of 6 pM

treatment_protocol: We sampled, washed with distilled water and snap-froze 10 ml cultures prior to RNA extraction.

tag: developmental stage

tag: replicate

tag: index 1

value: GAATTAA


title: HM2.1

description: hybrid S. MATa S. MATalpha, developmental stage M2, replicate 1

value: TTACGAT


title: HM2.4

description: hybrid S. MATa S. MATalpha, developmental stage M2, replicate 4

value: ACGCGGG

tag: index 2

value: GCTATTG


title: HM1M2.2

description: hybrid S. MATa S. MATalpha, developmental stage M1M2, replicate 2

value: CAGTGCT


title: HM1.4

description: hybrid S. MATa S. MATalpha, developmental stage M1, replicate 4

value: CCGGACC


title: HM1M2.3

description: hybrid S. MATa S. MATalpha, developmental stage M1M2, replicate 3

value: GAAGAAC


title: HM2.3

description: hybrid S. MATa S. MATalpha, developmental stage M2, replicate 3

value: GGAGTCC


title: HM1M2.1

description: hybrid S. MATa S. MATalpha, developmental stage M1M2, replicate 1

value: GAGTACG


title: HM1M2.4

description: hybrid S. MATa S. MATalpha, developmental stage M1M2, replicate 4

value: CTAGCGC


title: MDA231_MBD3

city: RTP

first: Takashi

last: Shimbo

address: 111 TW Alexander Dr.

institute: NIH/NIEHS

description: Library was prepared by TruSeq DNA Sample Prep kit or Nextera XT kit.

data_processing:
Basecalls performed using CASAVA version 1.7
Raw data from the replicates were merged.
Raw data was filtered by the following steps:  reads were filtered if the average base quality score <20 and duplicate reads removed (based on identical sequences)
Reads were mapped against hg19 reference genome (excluding haplotype chromosomes) with Bowtie (v0.12.8 using the following parameters:  -v 2 -m 1); HeK4 data were mapped against hg18 reference genome with ELAND program
Mapped data was filtered to remove hits with >2 mismatches to the reference genome.
Genome_build: hg19; hg18 for H3K4 data
Supplementary_files_format_and_content: bigwig file per sample per strand showing mapped read coverage; generated by BEDtools genomeCoverageBed and bedGraphToBigWig.
Supplementary_files_format_and_content: MBD3 bed files were generated by SICER v1.1 (redundancy threshold=1, window size=200, gap size=600, fragment size=300, FDR=0.001)
Supplementary_files_format_and_content: H3k4 wig files were generated by MACS-1.3.3 with default parameters.

growth_protocol: Human breast cancer cell lines (MCF-7 and MDA-MB-231) were grown under standard conditions in DMEM/F12 supplemented with 10% fetal bovine serum and pen-strep.

extract_protocol:
Cells were fixed with DSG (Disuccinimidyl glutarate) followed by formaldehyde.  Chromatin was sonicated with Bioruptor to an average size of 0.3-0.6 kb. Chromatin was incubated with anti-MBD3 antibody (Abcam; ab91458) for 16hr followed by incubation with dynabeads A/G (Invitrogen). ChIP DNA was reverse-crosslinked and purified with Minelute PCR purification kit (Qiagen).
Library was prepared by TruSeq DNA Sample Prep kit (Illumina) or Nextera XT DNA sample prep kit (Illumina) according to the manufacturer's protocol.

value: anti-MBD3 antibody (Abcam; ab91458)


title: Col H3K4m3 ChIP (replicate 2)

value: Columbia

value: anti-H3K4m3 (Millipore 04-745)


title: HM1.3

description: hybrid S. MATa S. MATalpha, developmental stage M1, replicate 3

value: ACCCACT


title: HM1.2

description: hybrid S. MATa S. MATalpha, developmental stage M1, replicate 2

value: TGGCATA


title: Col H3K4m2 ChIP (replicate 2)

value: Wild type

value: anti-H3K4m2 (Millipore 07-030)


title: HM1.1

description: hybrid S. MATa S. MATalpha, developmental stage M1, replicate 1

value: CGCTACA


title: HC3

description: hybrid S. MATa S. MATalpha, developmental stage T0, replicate 3

value: CGTCGCT


title: ldl1 ldl2 H3K4m2 ChIP (replicate 1) A, B

description: 2 technical replicates

value: ldl1-2 ldl2

value: anti-H3K4m2 (Abcam AB32356)


title: HC1

description: hybrid S. MATa S. MATalpha, developmental stage T0, replicate 1

value: TTTAACT


title: HC4

description: hybrid S. MATa S. MATalpha, developmental stage T0, replicate 4

value: GTTCTCA


title: Col H3K4m3 ChIP (replicate 1)

value: anti-H3K4m3 (Diagenode pAb-003-050)


title: p45 ChIP-seq

tag: chip antibody

value: anti-p45 antibody by Bresnick EH

value: primary megakaryocytes


title: Zfp322a_ChIPSeq

city: Singapore

first: Qiang

last: Wu

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bwa with default parameter values
Data were filtered using the following specifications: PCR duplication
Peaks were called using Partek 6.6 software with an average fragment size of 300bps and 0.05 as the cutoff p-value of Mann-Whitney U test for separation of forward and reverse reads in a peak
Furthermore, peaks with peak height < 9 reads were discarded and enrichment fold of Zpf322 to IgG is set to be >=3.
Genome_build: mm9
Supplementary_files_format_and_content: bed files for the peaks were generated

source_name: E14 cells_Zfp322a_IP

growth_protocol: Murine ES cells (E14) were cultured in ES cell medium consisting of Glasgow Minimum Essential Medium (GMEM; Invitrogen), 15% ES cell qualified fetal bovine serum (FBS; Invitrogen), 0.055 mM β-mercaptoethanol (Sigma), 100 mM sodium pyruvate (Invitrogen), 0.1 mM MEM nonessential amino acid (NEAA, Invitrogen) and 1,000 units/ml of LIF (Millipore).

extract_protocol:
Lysates were clarified from sonicated nuclei and Zfp322a-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: E14 murine embryonic stem cells

value: anti-ZNF322 antibody (sc-102205, Santa Cruz)

tag: background strain


title: IgG_ChIPSeq

source_name: E14 cells_IgG_IP

value: anti-Rabbit IgG antibody (sc-2027, Santa Cruz)


title: HC2

description: hybrid S. MATa S. MATalpha, developmental stage T0, replicate 2

value: TGTAGTA