title: DNA_Methylation_E14_adapted_2i_replica

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

data_processing:
FASTQ sequence files were aligned using RMAPBS (Smith et al., 2009; Smith et al., in prep) allowing a maximum of 10 mismatches for efficient mapping of reads containing bisulfite converted unmethylated cytosines. Cytosine methylation levels were determined using the standard new pipeline within RMAPBS (Methpipe; Andrew Smith, in prep).
In short, both mates of the paired-end sequencing were mapped separately by RMAPBS. If mated reads mapped within 300 bp, the reads were merged and included for analysis. Mated reads mapping with a distance of more than 300 bp were excluded from further analysis. Mated reads mapped within 300 bp, but mapping equally well on multiple positions on the genome, were discarded. If multiple mated reads mapped on exactly the same genomic coordinates, all but one (at random) were discarded. Symmetric cytosines (within a CpG context) on both forward and reverse strands were combined. Cytosine methylation level was called per individual C as: #C/(#C+#T).
Genome_build: mm9
Supplementary_files_format_and_content: Cytosine methylation levels within CpG context are present in the methcounts bedGraph files; Coverage over the cytosines within CpG context are present in the coverage bedGraph files. These files can be used as tables, but can also be directly uploaded in the UCSC genome browser.

source_name: Embryonic Stem cells

growth_protocol: Embryonic stem cells were cultured without feeders in the presence of leukaemia inhibitory factor (LIF) either in medium containing 10% foetal calf serum or in serum-free medium containing the MEK inhibitor PD0325901 (1mM) and the Gsk3 inhibitor CH99021 (3mM), together known as 2i. Rex-GFP cells are heterozygous for knock-in of a destabalized form of GFP to the Rex gene.

extract_protocol:
Pelleted ES cells were resuspended in 5 ml digestion buffer (100mM NaCl, 10mM Tris-HCl pH8, 15mM EDTA pH8, 0.5% SDS, 0.1mg/ml Proteinase K) per collected confluent 10 cm plate, and incubated at 55°C for 12-18 hr. DNA was isolated by two times extraction with 5 ml phenol/chloroform/isoamyl alcohol, and the aqueous top layer was transferred to a new tube. To precipitate DNA, 1/2 volume 7.5M ammonium acetate and 2 volumes 100% ethanol were added. After spinning, the supernatant was discarded, the DNA pellet washed with 70% ethanol, dried, and resuspended in water.
Library construction was performed according to Kulis et al. (2012; Nature Genetics). In short: We spiked genomic DNA (1 or 2 μg) with unmethylated λ DNA (5 ng of λ DNA per μg of genomic DNA) (Promega). We sheared DNA by sonication to 50–500 bp with a Covaris E220 and selected 150- to 300-bp fragments using AMPure XP beads (Agencourt Bioscience Corp.). We constructed genomic DNA libraries using the TruSeq Sample Preparation kit (Illumina Inc.) following the Illumina standard protocol: the ends of the fragments were repaired, an adenine was added at the 3′ extremities of the fragments and Illumina TruSeq adapters were ligated at each extremity. After adaptor ligation, we treated DNA with sodium bisulfite using the EpiTect Bisulfite kit (Qiagen) following the manufacturer’s instructions for formalin-fixed and paraffin-embedded (FFPE) tissue samples. We performed two rounds of conversion to get >99% conversion. We enriched adaptor-ligated DNA through seven cycles of PCR using the PfuTurboCx Hotstart DNA polymerase (Stratagene). We monitored library quality using the Agilent 2100 BioAnalyzer (Agilent) and determined the concentration of viable sequencing fragments (molecules carrying adapters at both extremities) by quantitative PCR using the Library Quantification Kit from KAPA Biosystem. We performed paired-end DNA sequencing (two reads of 100 bp each) using the Illumina Hi-Seq 2000.

treatment_protocol: The 2i adapted cells were released from serum and LIF and cultured on 2i and LIF for at least 8 passages

tag: line

value: ES-cells

tag: measurement

value: DNA methylation

tag: growth


title: M8_081711

status: Public on Jul 12 2013

type: SRA

city: St Louis

first: Federico

middle: E

last: Rey

state: MO

address: 4444 Forest Park Blvd

department: Pathology

country: USA

institute: Washington University

library_source: genomic

data_processing:
Library strategy: COPRO-Seq
Demultiplexing: sequences were demultiplexed by 4 nt barcode, requiring an exact match (sequences without a barcode match were excluded from the analysis)
Trimming: after demultiplexing, all sequences were trimmed to 25 bases to eliminate low-quality bases at the ends of each read
Mapping: sequences were aligned to the reference genomes of the 12 bacteria included in the study using Illumina's ELAND aligner (as provided in GAPipeline-1.4.0). Only perfect, non-redundant matches were carried forward in the analysis.
Normalization: raw counts were normalized based on the informative genome size (IGS) of each organism included in the analysis, as described by McNulty et al (PMID: 22030749).
Summarization: the proportional representation of each organism in the analysis was determined by dividing its normalized counts within a sample by the total normalized counts for all organisms within that sample.
Genome_build: AAVM00000000;  AE015928.1; AAVN00000000; ACCL00000000; NC_000913.2;  NZ_AAXF00000000.2; NC_012781.1; assembly for C. symbiosum can be found at http://genome.wustl.edu/pub/organism/Microbes/Human_Gut_Microbiome; for D. piger: PRJNA30377
Supplementary_files_format_and_content: Tab-delimited text file. The file header (in angle brackets, <>) specifies the sample from which data were derived. Subsequent rows specify the organism/reference genome, raw counts, normalized counts, and normalized relative proportion for each taxon included in the alignment. Additional details are available in the accompanying 'README.txt' file.

molecule: genomic DNA

organism:
[Clostridium] symbiosum
Bacteroides thetaiotaomicron VPI-5482
Bacteroides ovatus ATCC 8483
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Marvinbryantia formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Agathobacter rectalis ATCC 33656
Desulfovibrio piger GOR1

source_name: Defined bacterial assemblage from the feces of a gnotobiotic mouse

growth_protocol: Bacteria from frozen culture stocks were introduced as an artificial community (AC) into 7-8 week-old male gnotobiotic NMRI mice.  Cells were therefore maintained over the course of the experiment within mice until sampling occurred.

extract_protocol:
DNA was extracted from fecal samples using mechanical disruption (bead-beating with 0.1 mm zirconium beads) in phenol:chloroform:IAA in the same manner as described by McNulty et al. in a previous publication (PMID: 22030749).
Libraries were prepared according to a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, total bacterial gDNA was sonicated in a BioRuptor XL water bath sonicator, cleaned up and concentrated using a Qiagen PCR Purification column, and end-repaired using Klenow DNA polymerase. The blunt DNA was treated with Klenow fragment (exo minus) to add an adenine overhang, and the A-tailed molecules were ligated to the relevant barcoded Illumina adapter sequence.  Adaptered-DNA was then size-selected by agarose gel electrophoresis.  Fragments of the appropriate size were PCR amplified and purified, after which the purified PCR products were loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer I, II or IIx following the manufacturer's protocols.

treatment_protocol: Immediately after collection, samples were subjected to flash-freezing in liquid nitrogen and storage at -80 C until total community DNA extractions could be performed.

tag: experiment

tag: group/diet

value: HF/HS (control diet; 0.12% SO4)

tag: collection site

value: Feces

tag: days after colonization


title: DNA_Methylation_female_XT67E1_serum_LIF

organism: Mus musculus

tag: strain

tag: cell type


title: M10_090711


title: DNA_Methylation_E14_2i_to_serum_p2


title: Dp8

description: mice colonized with 8 human gut bacterial species plus Desulfovibrio piger

library_source: transcriptomic

data_processing:
Splitting barcodes - Sequence runs were split into their respective experiments using the 4-bp barcode at the beginning of each sequencing read.
Mapping reads - After trimming reads to 42nt and dividing sequence runs by barcode, we mapped the reads to the mouse genome using the TopHat and  Bowtie algorithm
Counts were normalized to upper quartile and significance between groups was assessed using CyberT
Genome_build: genome mm37.63 (from ENSEMBL).

molecule: total RNA

source_name: Proximal colon from gnotobiotic mice colonized with defined bacterial assemblage

extract_protocol:
Proximal colon samples were homogenized in trizol and purified using the Qiagen Rneasy kit including the in column DNAse treatment. mRNA was furter purified using Dynabeads mRNA purification kit (Invitrogen) following manufacters protocol
cDNA libraries were prepared for sequencing using a modified version of Illumina's sample preparation protocol

treatment_protocol: proximal colon samples obtained from mice were immediately frozen at -80C and maintained at this temperature prior to processing.

tag: age

value: 7-8 weeks old

value: NMRI

tag: diet

value: High fat/ High sugar supplemented with 3% chondroitin sulfate

tag: colonization


title: DNA_Methylation_E14_serum_LIF_replica


title: DNA_Methylation_E14_2i_to_serum_24h


title: DNA_Methylation_E14_serum_to_2i_p3


title: DNA_Methylation_E14_2i_to_serum_p1


title: DNA_Methylation_Rex_GFP_2i_LIF


title: Dp6

value: mice colonized with 8 human gut bacterial species plus Desulfovibrio piger


title: DNA_Methylation_E14_serum_to_2i_24h


title: GI-DR

city: Shanghai

first: Yingying

last: Han

address: 220 Handan Road

department: Institute of Genetics

country: China

institute: Fudan Univeisity

description: gi mutant,drought

data_processing:
3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 35nt long, raw sequences are with 3' adaptor sequences；Empty reads removal (reads with only 3' adaptor sequences but no tags)；Low quality Tags removal (Tags with unknown sequences 'N')；Removal of Tags which are too long or too short, leaving Tags of 21nt long；Removal of Tags with a copy number of 1 (probably be sequencing error)；Generate Clean Tags
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include sequence，copynumber and TPM values for each Sample

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown in a controlled culture room set at 23–25°C with a RH of 40- 60% in long-day (L/D, 16/8h).

extract_protocol:
Extract 6 μg of the total RNA, use Oligo (dT) magnetic beads adsorption to purify mRNA, and then use Oligo (dT) to guide reverse transcription to synthesize double-stranded cDNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ler-0 wild type and gi plants with 10d age were deprived of watering for 10d.

tag: tissue

value: leaf

tag: genetic background

tag: genotype

value: gi mutant

tag: treatment

value: Drought


title: GI-CK

description: gi mutant,normal condirion

value: CK


title: DNA_Methylation_2i_LIF_Rex_GFP_E14


title: WT-DR

description: wild type,drought

value: wild type


title: WTC3

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

country: Belgium

institute: KULeuven

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome using bowtie2 version 2.0.5 with default parameters.
ecoli NC_000913.2
Genome_build: ASM584v1
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

extract_protocol:
DNA was extracted in the same manner as described by McNulty et al. (PMID: 22030749).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation


title: NoDp1

description: mice colonized with 8 human gut bacterial species


title: 39C1

organism: Escherichia coli str. K-12 substr. MG1655

value: yjiR (b4340) MUTANT


title: WTA1


title: WT-CK

description: wild type,normal condition


title: DNA_Methylation_E14_adapted_2i

tag: line


title: DNA_Methylation_serum_LIF_E14

tag: measurement


title: NoDp8_d14_CS_S24

organism:
[Clostridium] symbiosum
Bacteroides thetaiotaomicron VPI-5482
Bacteroides ovatus ATCC 8483
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Marvinbryantia formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Agathobacter rectalis ATCC 33656


title: 39B1


title: DNA_Methylation_female_XT67E1_adapted_2i

tag: growth


title: DNA_Methylation_E14_2i_to_serum_p3


title: NoDp9_d14_CS_S25

tag: experiment


title: NoDp10_d14_CS_S26

tag: group/diet


title: 23C3

value: ydcR (b1439) MUTANT


title: 39A1


title: NoDp6_d14_CS_S22

tag: collection site


title: NoDp3

value: mice colonized with 8 human gut bacterial species


title: WTB1


title: 23B1


title: NoDp7_d14_CS_S23

tag: days after colonization


title: NoDp3_d14_CS_S3


title: 23A1

tag: strain


title: A_adipose_preLPS (Sample 1)

city: Philadelphia

first: Yichuan

last: Liu

address: 423 Guardian Drive

institute: University of Pennsylvania

data_processing:
Generate gene expression by cufflink v1.3.0
Generate alternative splicing files by MATS2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: Standard cufflink outputs, tab-delimited text files including FPKM values and FDR adjusted p-values.
Supplementary_files_format_and_content: A_adipose_gene_exp.xls contains the differentially expressed genes from cuffdiff at variant read depths. The read depths were ranged from 5M reads to 500M reads (full set). In the excel file one tab has the cuffdiff result for one read depth, e.g. adipose_100M indicates the differentially expressed gene results for adipose tissue at read depth 100M reads.
Supplementary_files_format_and_content: A_adipose_gene_exp_simluation_100M.xls contains the differentially expressed genes for certain read depth (100M reads here) for 10 times simulation. The purpose is to evaluate sampling variations and to see whether the sequenced reads are representative. Each tab in the excel file contains the differentially expressed genes for each simulation rounds, as a result, 10 tabs in this file. Similar description for A_adipose_gene_exp_simulation_10M.xls file, the only difference is the read depth in simulation is 10M reads.
Supplementary_files_format_and_content: MATS_A_adipose.xls represents the alternative-splicing (AS) results from Multivariate Analysis of Transcript Splicing (MATS). Similar to A_adipose_gene_exp.xls, it contains the AS results for adipose tissue at variant depths from 5M to 500M reads. Each tab represents the AS results for one depth.
Supplementary_files_format_and_content: MATS_A_adipose_simulation_100M.xls and MATS_A_adipose_simulation_10M.xls represents the AS results for 10 times simulation at read depths 100M and 10M reads. Similar to A_adipose_gene_exp_simulation_100M.xls and A_adipose_gene_exp_simulation_10M.xls, each tab contains the AS result for one simulation rounds, as a result, totally 10 tabs.

organism: Homo sapiens

extract_protocol: For adipose tissue, the RNA was extracted using RNeasy lipid total RNA mini kit (Qiagen, Valencia, CA). Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA). Poly-A library preparation and RNA sequencing were performed at the Penn Genome Frontiers Institute’s High-Throughput Sequencing Facility per Illumina’s (San Diego, CA) standard protocols. Briefly, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the Illumina paired-end sample preparation kit. Fragments of ~350 bp were selected gel electrophoresis, followed by 15 cycles of PCR amplification. The prepared libraries were then sequenced using Illumina’s HiSeq 2000 at four lanes per sample (~456 million to 701 million 2 × 101 bp paired-end reads per sample).

value: adipose

value: control


title: A_adipose_postLPS (Sample 2)

value: LPS


title: NoDp7_d14_CS_S7


title: NoDp4_d14_CS_S4


title: NoDp9_d14_CS_S9


title: NoDp8_d14_CS_S8


title: NoDp1_d14_CS_S1


title: NoDp6_d14_CS_S6


title: E12_FP010912_NoDp_m4


title: E12_FP010912_NoDp_m5


title: E12_FP010912_Dp_m7


title: E12_FP010912_Dp_m6


title: Snyder_MAB-5_GFP_Embryo_Input_Rep2

status: Public on Jul 11 2013

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

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

organism: Caenorhabditis elegans

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: OP27(official name :OP27 genotype :unc-119(ed3); wgIs27(mab-5::TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The MAB-5::EGFP fusion protein is expressed in the correct mab-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MAB-5 transcription factor. made_by :Bob Waterston's lab from UW )

tag: developmental stage

value: embryo

tag: sex type

value: mixed Male and Hermaphrodite population


title: Snyder_MAB-5_GFP_Embryo_ChIP_Rep2

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. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control 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

value: unc-119(ed3); wgIs27(mab-5::TY1 EGFP FLAG; unc-119)


title: E12_FP010912_NoDp_m2

value: Feces


title: Snyder_MAB-5_GFP_Embryo_Input_Rep1

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. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control 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


title: Snyder_SKN-1_GFP_L3_Input_Rep2

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. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control 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 WS180

value: OP342(official name :OP342 genotype :unc119(ed3);wgIs341(skn-1::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by :Bob Waterston's lab from UW )

tag: Sex

value: Hermaphrodite


title: Snyder_SKN-1_GFP_L3_ChIP_Rep2


title: Snyder_F23F12.9_GFP_Emb_Input_Rep1

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. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control 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 WS180

value: OP327(official name :OP327 genotype :unc327(ed3);wgIs102(F23F12.::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by :Bob Waterston's lab from UW )


title: NoDp2_d14_CS_S2


title: Snyder_F23F12.9_GFP_Emb_ChIP_Rep1


title: Snyder_SKN-1_GFP_L3_Input_Rep1


title: Snyder_MAB-5_GFP_Embryo_ChIP_Rep1


title: Snyder_NHR-23_GFP_L3_Input_Rep2

value: OP43(official name :OP43 genotype :unc-119(ed3); wgIs43(nhr-23::TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The NHR-23::EGFP fusion protein is expressed in the correct nhr-23 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-223 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_NHR-23_GFP_L3_ChIP_Rep2

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 WS180

value: unc-119(ed3); wgIs43(nhr-23::TY1 EGFP FLAG; unc-119)


title: NoDp5_d14_CS_S5


title: Snyder_F23F12.9_GFP_Emb_Input_Rep2


title: Snyder_NHR-23_GFP_L3_Input_Rep1


title: NoDp10_d14_CS_S10


title: Snyder_F23F12.9_GFP_Emb_ChIP_Rep2


title: Snyder_NHR-6_GFP_L4_Input_Rep2

value: OP90(official name :OP90 genotype :unc-119(ed3) III; wgIs90 [unc-119(+) nhr-6::TY1::EGFP::3xFLAG] outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-6::EGFP fusion protein is expressed in neurons surrounding pharynx at L2 stage.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-6 transcription factor. made_by :R. Waterston )


title: Snyder_NHR-23_GFP_L3_ChIP_Rep1


title: Snyder_NHR-6_GFP_L4_ChIP_Rep2

value: unc-119(ed3) III; wgIs90 [unc-119(+) nhr-6::TY1::EGFP::3xFLAG]


title: E12_FP010912_NoDp_m3


title: Snyder_SKN-1_GFP_L3_ChIP_Rep1


title: Snyder_NHR-6_GFP_L4_Input_Rep1


title: Snyder_NHR-6_GFP_L4_ChIP_Rep1


title: Snyder_NHR-25_GFP_L2_ChIP_Rep3

value: OP33(official name :OP33 genotype :unc119(ed3);wgIs33(nhr-25::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by :Bob Waterston's lab from UW )


title: Snyder_NHR-25_GFP_L2_Input_Rep2


title: Snyder_NHR-25_GFP_L2_Input_Rep3


title: Snyder_NHR-25_GFP_L2_ChIP_Rep2


title: Snyder_NHR-25_GFP_L2_Input_Rep1


title: Snyder_NHR-25_GFP_L2_ChIP_Rep1


title: Snyder_pGES_HPL-2_lin-35_YL474_L1_ChIP_Rep2

value: YL474(official name :YL474 genotype :lin-35(n745) I; unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG:HPL-2 3-UTR genotype :unc-119 (+)] outcross :0 mutagen :None tags :GFP::3xFlag description :The HPL-2::GFP fusion protein is driven by the ges-1 promoter and expressed in the intestine. The original transgene was subsequently crossed into a lin-35 mutant. made_by :Michelle Kudron in Reinke lab )

value: starved L1


title: Snyder_pGES_HPL-2_lin-35_YL474_L1_Input_Rep2

value: lin-35(n745) I; unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG:HPL-2 3-UTR


title: Snyder_pGES_HPL-2_lin-35_YL474_L1_ChIP_Rep1


title: Snyder_pGES_HPL-2_lin-35_YL474_L1_Input_Rep1


title: Snyder_Pmex-5_LIN-35_YL468_yAd_ChIP_Rep2

value: YL468(official name :YL468 genotype :unc-119(ed3) III; vrIs93 [pMEX-5::LIN-35:GFP:FLAG::LIN-35 3-UTR genotype :unc-119 (+)]) outcross :0 mutagen :None tags :GFP::3xFlag description :LIN-35 expressed under the germline-specific promoter MEX-5. made_by :Michelle Kudron in Reinke lab )

value: Young adult


title: Snyder_Pmex-5_LIN-35_YL468_yAd_Input_Rep1

value: unc-119(ed3) III; vrIs93 [pMEX-5::LIN-35:GFP:FLAG::LIN-35 3-UTR


title: Snyder_Pmex-5_LIN-35_YL468_yAd_ChIP_Rep1


title: Snyder_SEM-4_GFP_L2_ChIP_Rep2

value: OP57(official name :OP57 genotype :unc-119(ed3); wgIs57(sem-4::TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The SEM-4::EGFP fusion protein is expressed in the correct sem-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sem-4 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_SEM-4_GFP_L2_Input_Rep2

value: unc-119(ed3); wgIs57(sem-4::TY1 EGFP FLAG; unc-119)


title: Snyder_SEM-4_GFP_L2_Input_Rep1


title: Snyder_N2_EFL-1_Ab_Input_Rep1

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 26ºC 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: DevStageWorm:L1 26dC:MS:1(official name :L1 26dC )

value: L1 larva

value: wild type


title: Snyder_SEM-4_GFP_L2_ChIP_Rep1

value: Hermaphrodite


title: Snyder_N2_EFL-1_Ab_ChIP_Rep1


title: Snyder_N2_EFL-1_Ab_Input_Rep2


title: Snyder_N2_EFL-1_Ab_ChIP_Rep2


title: Snyder_NHR-129_GFP_L2_Input_Rep2

value: OP339(official name :OP339 genotype :unc119(ed3);wgIs339(nhr-129::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain.  The NHR-129::EGFP fusion protein was expressed in seam cells description :pharynx description :head neurons at L2 stage.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-129 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_GEI-11_GFP_L1_Input_Rep1

value: OP179(official name :OP179 genotype :unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by :R. Waterston )

value: fed L1


title: Snyder_GEI-11_GFP_L1_ChIP_Rep1


title: Snyder_NHR-129_GFP_L2_ChIP_Rep2


title: Snyder_NHR-129_GFP_L2_Input_Rep1


title: Snyder_GEI-11_GFP_L1_Input_Rep2


title: Snyder_SMA-9_GFP_L2_Input_Rep1

value: OP130(official name :OP130 genotype :unc119(ed3);wgIs130(sma-9::TY1 EGFP FLAG C;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The SMA-9::EGFP fusion protein is expressed in the correct sma-9 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SMA-9 transcription factor. made_by :S Kim )


title: Snyder_GEI-11_GFP_L1_ChIP_Rep2


title: Snyder_SMA-9_GFP_L2_Input_Rep2

value: unc119(ed3);wgIs130(sma-9::TY1 EGFP FLAG C;unc119)


title: Snyder_NHR-129_GFP_L2_ChIP_Rep1


title: Snyder_SMA-9_GFP_L2_ChIP_Rep2


title: Snyder_PEB-1_GFP_L2_ChIP_Rep2

value: OP86(official name :OP86 genotype :unc119(ed3);wgIs86(peb-1::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PEB-1::EGFP fusion protein is expressed in the correct peb-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PEB-1 transcription factor. made_by :R Waterston )


title: Snyder_PEB-1_GFP_L2_Input_Rep2


title: Snyder_Pmex-5_LIN-35_YL468_yAd_Input_Rep2


title: Snyder_PEB-1_GFP_L2_Input_Rep1


title: Snyder_PEB-1_GFP_L2_ChIP_Rep1


title: Snyder_NHR-12_GFP_L2_ChIP_Rep2

value: OP318(official name :OP318 genotype :unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)) outcross :3 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of NHR-12::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-12 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_NHR-12_GFP_L2_Input_Rep2


title: Snyder_LIN-35_GFP_L1_Input_Rep2

value: YL409(official name :YL409 genotype :unc-119(ed3) III; vrIs60 [pLIN-35::LIN-35:GFP:FLAG::DPL-1 3'-UTR genotype :unc-119 (+)]) outcross :0 mutagen :None tags :GFP::3xFlag description :The LIN-35::GFP fusion protein is driven by its own lin-35 promoter. made_by :Michelle Kudron (Valerie Reinke's lab) )


title: Snyder_NHR-12_GFP_L2_Input_Rep1


title: Snyder_LIN-35_GFP_L1_Input_Rep1

value: unc-119(ed3) III; vrIs60 [pLIN-35::LIN-35:GFP:FLAG::DPL-1 3'-UTR


title: Snyder_DPL-1_GFP_L1_ChIP_Rep2

value: YL448(official name :YL448 genotype :unc-119(ed3) III; vrIs83 [pGES-1::DPL-1::GFP FLAG:DPL-1 3'UTR genotype :unc-119 (+)] outcross :0 mutagen :None tags :GFP::3xFlag made_by :Michelle Kudron (Valerie Reinke's lab) )


title: Snyder_LIN-35_GFP_L1_ChIP_Rep2


title: Snyder_NHR-12_GFP_L2_ChIP_Rep1


title: Snyder_LIN-35_GFP_L1_ChIP_Rep1


title: Snyder_SMA-9_GFP_L2_ChIP_Rep1


title: Snyder_CEH-16_GFP_L2_Input_Rep2

value: OP82(official name :OP82 genotype :unc119(ed3);wgIs82(ceh-16::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-16::EGFP fusion protein is expressed in the correct CEH-16 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-16 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_DPL-1_GFP_L1_ChIP_Rep1

value: unc-119(ed3) III; vrIs83 [pGES-1::DPL-1::GFP FLAG:DPL-1 3'UTR


title: Snyder_DPL-1_GFP_L1_Input_Rep1


title: Snyder_CEH-16_GFP_L2_ChIP_Rep2


title: Snyder_CEH-16_GFP_L2_Input_Rep1


title: Snyder_CEH-16_GFP_L2_ChIP_Rep1


title: Snyder_C34F6.9_GFP_L2_Input_Rep2

value: OP324(official name :OP324 genotype :unc119(ed3);wgIs324(C34F6.9::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of C34F6.9::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the C34F6.9 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_C34F6.9_GFP_L2_Input_Rep1


title: Snyder_HAM-1_GFP_L1_Input_Rep2

value: OP102(official name :OP102 genotype :unc-119 (ed3); wgIs102 (ham-1::TY1 EGFP FLAG; unc-119(+)) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The HAM-1::EGFP fusion protein is expressed in the correct ham-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HAM-1 transcription factor. made_by :R Waterston )


title: Snyder_C34F6.9_GFP_L2_ChIP_Rep1


title: Snyder_HAM-1_GFP_L1_ChIP_Rep2


title: Snyder_C34F6.9_GFP_L2_ChIP_Rep2


title: Snyder_HAM-1_GFP_L1_Input_Rep1


title: Snyder_R02D3.7_GFP_L4_Input_Rep2

value: OP218(official name :OP218 genotype :unc-119(ed3); wgIs218(R02D3.7:TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The R02D3.7::EGFP fusion protein is expressed in the correct R02D3.7 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the RO2D3.7 transcription factor. made_by : )


title: Snyder_R02D3.7_GFP_L4_ChIP_Rep2


title: Snyder_R02D3.7_GFP_L4_Input_Rep1


title: Snyder_R02D3.7_GFP_L4_ChIP_Rep1


title: Snyder_GEI-11_GFP_YA_ChIP_Rep2

value: Young Adult


title: Snyder_GEI-11_GFP_YA_Input_Rep2

value: Hermaphrodite


title: Snyder_GEI-11_GFP_YA_ChIP_Rep1


title: Snyder_DPL-1_GFP_L1_Input_Rep2


title: Snyder_GEI-11_GFP_YA_Input_Rep1


title: Snyder_PHA-4_GFP_L4_ChIP_Rep2

value: OP37(official name :OP37 genotype :unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by :R. Waterston and S. Kim )


title: Snyder_PHA-4_GFP_L4_Input_Rep1

value: unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG]


title: Snyder_NHR-76_GFP_L3_Input_Rep1

value: OP203(official name :OP203 genotype :unc-119(ed3); wgIs203(nhr-76::TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-76::EGFP fusion protein is expressed in the correct nhr-76 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-76 transcription factor. made_by :R. Waterston )


title: Snyder_NHR-76_GFP_L3_ChIP_Rep1

value: unc-119(ed3); wgIs203(nhr-76::TY1 EGFP FLAG; unc-119)


title: Snyder_PHA-4_GFP_L4_ChIP_Rep1


title: Snyder_PHA-4_GFP_L4_Input_Rep2


title: Snyder_NHR-76_GFP_L3_ChIP_Rep2


title: Snyder_HAM-1_GFP_L1_ChIP_Rep1

value: fed L1


title: Snyder_MML-1_GFP_L3_ChIP_Rep2

value: OP198(official name :OP198 genotype :unc-119(ed3); wgIs198(mml-1::TY1 EGFP FLAG C; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The MML-1::EGFP fusion protein is expressed in the correct mml-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MML-1 transcription factor. made_by :R Waterston )


title: Snyder_MML-1_GFP_L3_Input_Rep1

value: unc-119(ed3); wgIs198(mml-1::TY1 EGFP FLAG C; unc-119)


title: Snyder_MML-1_GFP_L3_ChIP_Rep1


title: Snyder_FKH-2_GFP_L3_Input_Rep2

value: OP185(official name :OP185 genotype :unc-119(ed3); wgIs185(fkh-2::TY1 EGFP FLAG C; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The FKH-1::EGFP fusion protein is expressed in the correct fkh-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FKH-2 transcription factor. made_by :R Waterston )


title: Snyder_MML-1_GFP_L3_Input_Rep2


title: Snyder_FKH-2_GFP_L3_ChIP_Rep2

value: unc-119(ed3); wgIs185(fkh-2::TY1 EGFP FLAG C; unc-119)


title: Snyder_FKH-2_GFP_L3_Input_Rep1


title: Snyder_FKH-2_GFP_L3_ChIP_Rep1


title: Snyder_AHA-1_GFP_L1_ChIP_Rep2

value: OP124(official name :OP124 genotype :unc-119(ed3); wgIs124(aha-1::TY1 EGFP FLAG;unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The AHA-1::EGFP fusion protein is expressed in the correct aha-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the AHA-1 transcription factor. made_by :R. Waterston and S. Kim )


title: Snyder_NFYA-1_GFP_YA_Input_Rep1

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

value: OP404(official name :OP404 genotype :unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description :using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by :Unknown )

value: Young adult


title: Snyder_NFYA-1_GFP_YA_ChIP_Rep1


title: Snyder_NFYA-1_GFP_YA_Input_Rep2


title: Snyder_NFYA-1_GFP_YA_ChIP_Rep2


title: Snyder_AHA-1_GFP_L1_Input_Rep1

value: unc-119(ed3); wgIs124(aha-1::TY1 EGFP FLAG;unc-119)


title: Snyder_NFYA-1_GFP_LateEMB_Input_Rep2

value: Late Embryo


title: Snyder_NFYA-1_GFP_LateEMB_ChIP_Rep2


title: Snyder_NHR-76_GFP_L3_Input_Rep2


title: Snyder_AHA-1_GFP_L1_Input_Rep2


title: Snyder_AHA-1_GFP_L1_ChIP_Rep1


title: Snyder_NFYA-1_GFP_LateEMB_Input_Rep1


title: Snyder_NFYA-1_GFP_LateEMB_ChIP_Rep1


title: Snyder_NFYA-1_GFP_L3_ChIP_Rep2


title: Snyder_NFYA-1_GFP_L3_Input_Rep2


title: Snyder_NFYA-1_GFP_L3_ChIP_Rep1


title: Snyder_HLH-30_GFP_LateEMB_ChIP_Rep2

value: OP433(official name :OP433 genotype :unc-119(ed3) III; wgIs433(hlh-30::TY1 EGFP FLAG; unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description :using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The HLH-30::EGFP fusion protein is expressed in the correct hlh-30 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HLH-30 transcription factor. made_by :Unknown )


title: Snyder_MED-1_GFP_MIDEMB_Input_Rep1

value: OP391(official name :OP391 genotype :unc-119(ed3) III; wgIs391(med-1::TY1 EGFP FLAG C; unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description :using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The MED-1::EGFP fusion protein is expressed in the correct med-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MED-1 transcription factor. made_by :Unknown )

value: embryo

value: mixed Male and Hermaphrodite population


title: Snyder_MED-1_GFP_MIDEMB_ChIP_Rep2

value: unc-119(ed3) III; wgIs391(med-1::TY1 EGFP FLAG C; unc-119(+))


title: Snyder_HLH-30_GFP_LateEMB_Input_Rep2

value: unc-119(ed3) III; wgIs433(hlh-30::TY1 EGFP FLAG; unc-119(+))

value: Hermaphrodite


title: Snyder_MED-1_GFP_MIDEMB_Input_Rep2


title: Snyder_HLH-30_GFP_L4_ChIP_Rep2


title: Snyder_HLH-30_GFP_L4_Input_Rep1


title: Snyder_F23B12.7_GFP_YA_ChIP_Rep2

value: OP429(official name :OP429 genotype :unc-119(ed3) III; wgIs429(F23B12.7::TY1GFP-3xFLA; unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description :using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The F23B12.7::EGFP fusion protein is expressed in the correct F23B12.7 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F23B12.7 transcription factor. made_by :Unknown )


title: Snyder_HLH-30_GFP_LateEMB_Input_Rep1


title: Snyder_F23B12.7_GFP_YA_Input_Rep2


title: Snyder_DVE-1_GFP_LateEMB_Input_Rep2

value: OP398(official name :OP398 genotype :unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description :using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The DVE-1::EGFP fusion protein is expressed in the correct dve-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DVE-1 transcription factor. made_by :Unknown )


title: Snyder_F23B12.7_GFP_YA_ChIP_Rep1


title: Snyder_F23B12.7_GFP_YA_Input_Rep1


title: Snyder_DVE-1_GFP_L4_Input_Rep1

value: unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+))


title: Snyder_DVE-1_GFP_LateEMB_ChIP_Rep1


title: Snyder_NFYA-1_GFP_L3_Input_Rep1


title: Snyder_DVE-1_GFP_LateEMB_Input_Rep1


title: Snyder_ZIP-2_GFP_L4_ChIP_Rep2

value: OP432(official name :OP432 genotype :unc-119(ed3) III; wgIs432(zip-2::TY1-GFP-3xFLA;unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description :using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZIP-2::EGFP fusion protein is expressed in the correct zip-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZIP-2 transcription factor. made_by :Unknown )


title: Snyder_DVE-1_GFP_L4_ChIP_Rep1


title: Snyder_ZIP-2_GFP_L4_ChIP_Rep1


title: Snyder_DVE-1_GFP_L4_ChIP_Rep2


title: Snyder_MED-1_GFP_MIDEMB_ChIP_Rep1


title: Snyder_ZTF-11_GFP_EMB_Input_Rep2

value: OP236(official name :OP236 genotype :unc-119(ed3) III; wgIs236(ekl-2::TY1 EGFP FLAG; unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description :using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by :Unknown )


title: Snyder_HLH-30_GFP_LateEMB_ChIP_Rep1


title: Snyder_HLH-30_GFP_L4_ChIP_Rep1


title: Snyder_ZTF-11_GFP_EMB_Input_Rep1

value: unc-119(ed3) III; wgIs236(ekl-2::TY1 EGFP FLAG; unc-119(+))


title: Snyder_ZTF-11_GFP_EMB_ChIP_Rep1


title: Snyder_MAB-5_GFP_L2_ChIP_Rep2

value: OP27(official name :OP27 genotype :unc-119(ed3); wgIs27(mab-5::TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The MAB-5::EGFP fusion protein is expressed in the correct mab-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MAB-5 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_ZTF-11_GFP_EMB_ChIP_Rep2


title: Snyder_MAB-5_GFP_L2_Input_Rep2

value: unc-119(ed3); wgIs27(mab-5::TY1 EGFP FLAG; unc-119)


title: Snyder_DVE-1_GFP_L4_Input_Rep2


title: Snyder_HLH-30_GFP_L4_Input_Rep2


title: Snyder_MAB-5_GFP_L2_Input_Rep1


title: Snyder_MAB-5_GFP_L2_ChIP_Rep1


title: Snyder_GEI-11_GFP_Emb_ChIP_Rep1

value: OP179(official name :OP179 genotype :unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by :R. Waterston )


title: Snyder_GEI-11_GFP_Emb_Input_Rep1


title: Snyder_BLMP-1_GFP_Emb_Input_Rep2

value: OP109(official name :OP109 genotype :unc-119 (ed3) III; wgIs109 [blmp-1::TY1::EGFP::FLAG; unc-119 (+)] outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The BLMP-1::EGFP fusion protein is expressed in the correct blmp-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the BLMP-1 transcription factor. made_by :R Waterston )


title: Snyder_ZIP-2_GFP_L4_Input_Rep1


title: Snyder_BLMP-1_GFP_Emb_ChIP_Rep2


title: Snyder_BLMP-1_GFP_Emb_ChIP_Rep1


title: Snyder_UNC-55_GFP_L2_ChIP_Rep3

value: NC1639(official name :NC1639 genotype :[wdIs49 (pttr39::UNC-55a::GFP; dpy-20+) III outcross :0 mutagen :None tags :GFP description :Expresses functional *GFP-tagged UNC-55* (COUP-TF) in ventral cord GABA motor neurons (also some ectopic expression in other cells). This line is integrated and shows strong GFP expression. made_by :David Miller lab )


title: Snyder_UNC-55_GFP_L2_Input_Rep2

value: [wdIs49 (pttr39::UNC-55a::GFP; dpy-20+) III


title: Snyder_UNC-55_GFP_L2_Input_Rep1


title: Snyder_UNC-55_GFP_L2_ChIP_Rep2


title: Snyder_N2_POLIII_YA_ChIP_Rep2

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 WS180

value: N2(official name :N2 genotype :wild type genotype :DR subclone of DB original (Tc1 pattern I) )

value: Young adult

value: wild type


title: Snyder_N2_POLIII_YA_Input_Rep2


title: Snyder_BLMP-1_GFP_Emb_Input_Rep1

value: embryo


title: Snyder_N2_POLIII_YA_Input_Rep1

value: Hermaphrodite


title: Snyder_N2_POLIII_YA_ChIP_Rep1


title: Snyder_PHA-4_Male_L4_ChIP_Rep3

value: OP37(official name :OP37 genotype :unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by :R. Waterston and S. Kim )


title: Snyder_PHA-4_Male_L4_Input_Rep3

value: unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG]


title: Snyder_PHA-4_Male_L4_ChIP_Rep2


title: Snyder_PHA-4_Male_L4_Input_Rep2


title: Snyder_GEI-11_GFP_Emb_ChIP_Rep2


title: Snyder_PHA-4_Male_L4_ChIP_Rep1


title: Snyder_LIN-39_GFP_L1_ChIP_Rep2

value: OP18(official name :OP18 genotype :unc-119(ed3) III; wgIs18 [unc-119(+) lin-39::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-39::EGFP fusion protein is expressed in the correct lin-39 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-39 transcription factor. made_by :R. Waterston and S. Kim )

value: fed L1


title: Snyder_PHA-4_Male_L4_Input_Rep1


title: Snyder_LIN-39_GFP_L1_Input_Rep2


title: Snyder_UNC-55_GFP_L2_Input_Rep3


title: Snyder_NHR-67_GFP_L3_Input_Rep2

value: OP373(official name :OP373 genotype :unc119(ed3);wgIs373(nhr-67::TY1 EGFP FLAG;unc119 outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-67 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_NHR-67_GFP_L3_ChIP_Rep1


title: Snyder_LIN-39_GFP_L1_Input_Rep1


title: Snyder_FKH-10_GFP_L4_ChIP_Rep2

value: OP337(official name :OP337 genotype :unc119(ed3);wgIs377(fkh-10::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The FKH-10::EGFP fusion protein is expressed in the correct fkh-10 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FKH-10 transcription factor. made_by :Unknown )


title: Snyder_NHR-67_GFP_L3_Input_Rep1


title: Snyder_UNC-55_GFP_L2_ChIP_Rep1


title: Snyder_FKH-10_GFP_L4_Input_Rep2


title: Snyder_FKH-10_GFP_L4_ChIP_Rep1


title: Snyder_GEI-11_GFP_Emb_Input_Rep2


title: Snyder_FKH-10_GFP_LEMB_Input_Rep2

value: Late Embryo


title: Snyder_FKH-10_GFP_LEMB_ChIP_Rep2


title: Snyder_FKH-10_GFP_L4_Input_Rep1


title: Snyder_FKH-10_GFP_LEMB_ChIP_Rep1


title: Snyder_FKH-10_GFP_LEMB_Input_Rep1


title: Snyder_NHR-28_GFP_L1_ChIP_Rep2

value: OP317(official name :OP317 genotype :unc119(ed3);wgIs317(nhr-28::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-28::EGFP fusion protein is expressed in the correct nhr-28 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-28 transcription factor. made_by :R Waterston )

value: L1 26dC


title: Snyder_NHR-28_GFP_L1_ChIP_Rep1


title: Snyder_NHR-11_GFP_L1_ChIP_Rep2

value: OP305(official name :OP305 genotype :unc119(ed3);wgIs305(nhr-11::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-11::EGFP fusion protein is expressed in the correct nhr-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-11 transcription factor. made_by :R Waterston )


title: Snyder_NHR-11_GFP_L1_Input_Rep2


title: Snyder_LIN-39_GFP_L1_ChIP_Rep1


title: Snyder_NHR-11_GFP_L1_ChIP_Rep1


title: Snyder_NHR-11_GFP_L1_Input_Rep1


title: Snyder_NHR-11_GFP_LEMB_Input_Rep2


title: Snyder_NHR-11_GFP_LEMB_ChIP_Rep2


title: Snyder_NHR-28_GFP_L1_Input_Rep1


title: Snyder_NHR-11_GFP_LEMB_Input_Rep1


title: Snyder_NHR-67_GFP_L3_ChIP_Rep2


title: Snyder_NHR-28_GFP_EMB_Input_Rep1


title: Snyder_NHR-28_GFP_EMB_ChIP_Rep1


title: Snyder_UNC_62_GFP_EMB_Input_Rep2

value: OP600(official name :OP600 genotype :unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by :S Kim )


title: Snyder_UNC_62_GFP_EMB_ChIP_Rep2


title: Snyder_UNC_62_GFP_L4_Input_Rep2


title: Snyder_NHR-28_GFP_L1_Input_Rep2


title: Snyder_UNC_62_GFP_EMB_Input_Rep1


title: Snyder_UNC_62_GFP_L4_ChIP_Rep2


title: Snyder_NHR-28_GFP_EMB_ChIP_Rep2


title: Snyder_UNC_62_GFP_EMB_ChIP_Rep1


title: Snyder_LIN-39_GFP_L4_ChIP_Rep2


title: Snyder_UNC_62_GFP_L4_ChIP_Rep1


title: Snyder_LIN-39_GFP_L4_Input_Rep2


title: Snyder_LIN-39_GFP_L4_Input_Rep1


title: Snyder_LIN-39_GFP_L2_Input_Rep2


title: Snyder_LIN-39_GFP_L2_ChIP_Rep2


title: Snyder_NHR-11_GFP_LEMB_ChIP_Rep1


title: Snyder_LIN-39_GFP_L2_ChIP_Rep1


title: Snyder_LIN-39_GFP_L2_Input_Rep1


title: Snyder_NHR-11_GFP_L4_ChIP_Rep2


title: Snyder_LIN-39_GFP_L4_ChIP_Rep1


title: Snyder_NHR-11_GFP_L4_Input_Rep2


title: Snyder_UNC_62_GFP_L4_Input_Rep1


title: Snyder_NHR-11_GFP_L4_Input_Rep1


title: Snyder_NHR-11_GFP_L4_ChIP_Rep1


title: Snyder_NHR-28_GFP_EMB_Input_Rep2


title: Snyder_NHR-11_GFP_L3_ChIP_Rep2


title: Snyder_NHR-11_GFP_L3_ChIP_Rep1


title: Snyder_NHR-11_GFP_L3_Input_Rep2


title: Snyder_NHR-2_GFP_EMB_ChIP_Rep2

value: OP99(official name :OP99 genotype :unc119(ed3);wgIs99(nhr-2::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-2::EGFP fusion protein is expressed in the correct nhr-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-2 transcription factor. made_by :Unknown )

value: mixed Male and Hermaphrodite population


title: Snyder_NHR-2_GFP_EMB_Input_Rep2


title: Snyder_NHR-2_GFP_EMB_Input_Rep1


title: Snyder_CEH-39_GFP_EMB_Input_Rep2

value: OP169(official name :OP169 genotype :unc119(ed3);wgIs169(ceh-39::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CEH-39::EGFP fusion protein is expressed in the correct ceh-39 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-39 transcription factor. made_by :Unknown )


title: Snyder_CEH-39_GFP_EMB_ChIP_Rep2


title: Snyder_CEH-39_GFP_EMB_Input_Rep1


title: Snyder_CEH-39_GFP_EMB_ChIP_Rep1


title: Snyder_CES-1_GFP_EMB_Input_Rep2

value: OP174(official name :OP174 genotype :unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by :S. Kim )


title: Snyder_CES-1_GFP_EMB_ChIP_Rep2

value: embryo

value: unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119)


title: Snyder_CES-1_GFP_EMB_ChIP_Rep1


title: Snyder_CES-1_GFP_EMB_Input_Rep1


title: Snyder_PAX-1_GFP_EMB_ChIP_Rep2

value: OP117(official name :OP117 genotype :unc119(ed3);wgIs117(pax-1::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PAX-1::EGFP fusion protein is expressed in the correct pax-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PAX-1 transcription factor. made_by :Unknown )


title: Snyder_PAX-1_GFP_EMB_Input_Rep1


title: Snyder_NHR-237_GFP_EMB_Input_Rep2

value: OP228(official name :OP228 genotype :unc119(ed3);wgIs228(nhr-237:TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-237::EGFP fusion protein is expressed in the correct nhr-237 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-237 transcription factor. made_by :Unknown )


title: Snyder_NHR-237_GFP_EMB_ChIP_Rep1


title: Snyder_nhr-237_GFP_L1_ChIP_Rep2

value: Hermaphrodite


title: Snyder_NHR-237_GFP_EMB_ChIP_Rep2


title: Snyder_PAX-1_GFP_EMB_ChIP_Rep1


title: Snyder_NHR-237_GFP_EMB_Input_Rep1


title: Snyder_nhr-237_GFP_L1_ChIP_Rep1


title: Snyder_nhr-237_GFP_L1_Input_Rep2


title: Snyder_nhr-237_GFP_L1_Input_Rep1


title: Snyder_nhr-237_GFP_L3_ChIP_Rep2


title: Snyder_nhr-237_GFP_L3_Input_Rep2


title: Snyder_NHR-11_GFP_L3_Input_Rep1


title: Snyder_NHR-2_GFP_EMB_ChIP_Rep1


title: Snyder_nhr-237_GFP_L3_ChIP_Rep1


title: Snyder_NHR-237_GFP_L2_ChIP_Rep2


title: Snyder_nhr-237_GFP_L3_Input_Rep1


title: Snyder_NHR-237_GFP_L2_ChIP_Rep1


title: Snyder_LSY-2_GFP_Starved_ChIP_Rep2

value: DevStageWorm:starved L1:MS:1(official name :starved L1 )

value: L1 larva

value: unc-119(ed3); wgIs367(lsy-2::TY1 EGFP FLAG; unc-119)


title: Snyder_PAX-1_GFP_EMB_Input_Rep2


title: Snyder_NHR-237_GFP_L2_Input_Rep2


title: Snyder_LSY-2_GFP_Starved_Input_Rep2


title: Snyder_LSY-2_GFP_Starved_Input_Rep1


title: Snyder_LSY-2_GFP_Starved_ChIP_Rep1


title: Snyder_LSY-2_GFP_L1_Input_Rep2

value: OP367(official name :OP367 genotype :unc-119(ed3); wgIs367(lsy-2::TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by :Bob Waterston's lab from UW )

value: fed L1


title: Snyder_LSY-2_GFP_L1_Input_Rep1


title: Snyder_LSY-2_GFP_Embryo_ChIP_Rep2


title: Snyder_ELT-1_GFP_L3_ChIP_Rep2

value: OP354(official name :OP354 genotype :unc119(ed3);wgIs354(elt-1::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by :Bob Waterston's lab from UW )


title: Snyder_LSY-2_GFP_Embryo_Input_Rep2


title: Snyder_ELT-1_GFP_L3_Input_Rep2


title: Snyder_LSY-2_GFP_L1_ChIP_Rep1


title: Snyder_LSY-2_GFP_Embryo_Input_Rep1


title: Snyder_HAM-1_GFP_L4_Input_Rep3

value: OP102(official name :OP102 genotype :unc-119 (ed3); wgIs102 (ham-1::TY1 EGFP FLAG; unc-119(+)) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The HAM-1::EGFP fusion protein is expressed in the correct ham-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HAM-1 transcription factor. made_by :R Waterston )


title: Snyder_HAM-1_GFP_L4_ChIP_Rep3


title: Snyder_HAM-1_GFP_L4_ChIP_Rep2


title: Snyder_NHR-237_GFP_L2_Input_Rep1


title: Snyder_HAM-1_GFP_L4_ChIP_Rep1


title: Snyder_HAM-1_GFP_L4_Input_Rep1


title: Snyder_HAM-1_GFP_L4_Input_Rep2


title: STAT5A_P6

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

data_processing:
Basecalls performed using the CASAVA software.
Sequenced reads were aligned to the mm9 genome assembly using the Bowtie program (Langmead et al., Genome Biol., 2009).
Peaks were called using HOMER (http://biowhat.ucsd.edu/homer/) with the default setting.
Genome_build: MGSCv37
Supplementary_files_format_and_content: BED files.

source_name: Mammary gland tissues, p6, STAT5A ChIP

growth_protocol: Animals were handled and housed in accordance with the guidelines of NIH and all experiments were approved by the Animal Care and Use Committee of NIDDK.

extract_protocol: The ChIP DNA fragments were blunt-ended and ligated to the Illumina Indexed DNA adaptors using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (# E6240, New England BioLabs, Ipswich, MA), and sequenced using the Illumina HiSeq 2000.

treatment_protocol: Frozen-stored mammary tissues from p6 were broken into powder with mortar and pestle and then cross-linked with 1% formaldehyde for 10 min, and their nuclei were fractionated by sucrose density gradient centrifugation. Chromatin was fragmented to 200 to 300 bp by sonication. Antibodies against STAT5A (# sc-1081, Santa Cruz, CA) and histone H3K4me3 (# 17-614, Millipore, Temecula, CA) were used for ChIP.

tag: strain/background

value: wild type

value: mammary gland

value: day 6 of pregnancy

tag: chip antibody

value: STAT5A (Santa Cruz, sc-1081)


title: Input_P6

source_name: Mammary gland tissues, p6, input

tag: tissue


title: H3K4me3_P6

source_name: Mammary gland tissues, p6, H3K4me3 ChIP

value: H3K4me3 (Millipore, Temecula, 17-614)


title: Snyder_LSY-2_GFP_L1_ChIP_Rep2

tag: genotype


title: IgG control

status: Public on Jul 09 2013

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: Chromatin IP against IgG; This record is a duplicated record of GSM784045 (to ensure that its complete raw data can be readily retrieved from SRA).

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 (July 2007) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome_build: mm9

source_name: liver tissue

growth_protocol: Male and female CD-1 mice (Charles River Laboratories), 7-8 weeks old, were killed and their livers extracted.

extract_protocol: Multiplexed samples were prepared for Illumina sequencing using standard Illumina methods.

treatment_protocol: Mouse livers were excised from individual male and female mice killed at either a peak of STAT5 binding activity, or during the interpulse interval, when STAT5 activity is either low (females) or essentially undetectable (males).  Sonicated, cross-linked liver nuclear chromatin was then used to identify STAT5 binding sites by ChIP-Seq.

tag: gender

value: male

tag: age

value: 7-8 weeks old

value: normal rabbit IgG

tag: chip antibody vendor

value: Santa Cruz Biotechnology, Inc

tag: chip antibody cat./batch #


title: Total mononucleosomes

city: Seattle

first: Sangsoon

last: Woo

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description:
SC0016_61YDGAAXX_7_TCATTC
Strain yFR212 is in a W303 background where the HTZ1 gene is tagged with 3 Myc epitopes in its 3' end (C-terminal of the Htz1 protein).
MNase-Seq

data_processing:
BWA was used for alignment.
samtools was used for converting fastq format to BAM format.
Data were called and filtered using R (development version).
R/Bioconductor package PING version 2.0.0 was used for peak-calling. We did run PING for PE and SE options. The option is shown in the Processed data file names : "_PE/SE_".
Genome_build: sacCer2
Supplementary_files_format_and_content: Tab-delimited text files. The processed data files are outputs of the PING software, which was developed to identify nucleosomes positions. The output includes the information for each identified nucleosome: chromosome, the coordinate of center of the nucleosome, estimated parameter (indication of uncertainty), enrichment score, range of the identified nucleosome region, and rank based on the enrichment score.

organism: Saccharomyces cerevisiae

source_name: Yeast cells, total mononucleosomes

growth_protocol: Two hundred mL of yeast cells were grown in YPD to an OD600 of 0.8, crosslinked for 15 minutes with 1% formaldehyde and quenched for 5 minutes with 125mM glycine. The culture was split into four 50mL Falcon tubes, centrifuged for 5 minutes at 3,000rpm, resuspended in H2O and pooled into two Falcon tubes. Cells were centrifuged again and each dry yeast pellets was individually snap frozen in liquid nitrogen and stored at -80˚C.

extract_protocol:
Cells were centrifuged again and the dry yeast pellets were snap frozen in liquid nitrogen and stored at -80C. One cell pellet was kept as a backup and the other one was thawed and resuspended in 20 mL of buffer Z (1M Sorbitol, 50mM Tris pH 7.4) before adding 14 μL of β-mercaptoEtOH and 0.5 mL of zymolase solution (1mg/mL, freshly prepared in buffer Z). Cells were shaken for 40 minutes at 30˚C and centrifuged 10 minutes at 1,500 rpm. The supernatant was aspired and discarded while the pellet was resuspended in 1.25 mL of NP buffer (50mM NaCl, 10mM Tris pH7.4, 5mM MgCl2, 1mM CaCl2, 0.075% NP40, 0.5mM spermidine, 1mM β-mercaptoEtOH). After this one, one of two different protocols was applied.
Three hundred μL aliquots (five) were treated with different amounts of MNase for 20 minutes at 37  C and reactions were stop by adding 6μL of 500mM EDTA.
For total nucleosomes, one 150 μL from each reaction was treated with 38 μL of 5xTE/SDS (50mM Tris pH8, 5mM EDTA, 5% SDS) overnight at 65˚C to reverse the crosslink. The remaining of the extract was kept as a backup at -20˚C. The next day, 210 μL of RNase mix (205 μL TE, 3 μL RNaseA, 2 μL glycogen) was added, followed by an incubation of two hours at 37˚C. 8 μL of proteinase K (from 20mg/mL stock) was added and incubation was pursued for an additional two hours at 37˚C. DNA was purified by phenol:chloroform extraction, EtOH precipitated and resuspended in 50 μL of 10mM Tris pH 8.0. Inspection on agarose gel revealed some residual RNA so an additional RNaseA treatment, followed by phenol:chloroform extraction and EtOH precipitation was performed. Aliquots were inspected on 2% agarose gel and the sample contains mainly monononucleosomes.
The library was prepared by following the paired-end library protocol (Illumina Inc., USA). Briefly, the DNA was subject to end-repair, and phosphorylation by T4 DNA polymerase, Klenow DNA Polymerase, and T4 polynucleotide kinase respectively in a single reaction, and then 3' A overhangs generation by Klenow fragment (3' to 5' exo minus), and ligated to Illumina PE adapters, which contain 5' T overhangs. The adapter-ligated products were purified on QIAquick spin columns (Qiagen), then PCR-amplified with Phusion DNA Polymerase in 10-15 cycles using Illumina's PE primer set (Illumina). PCR product of desired size range was purified using a 8% PAGE, and the DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay and Nanodrop 7500 spectrophotometer (Nanodrop, USA) and diluted to 10nM. The final concentration was double checked and determined by Quant-iT dsDNA HS Assay Kit using Qubit fluorometer (Invitrogen). Clusters were generated on the Illumina cluster station and sequence was run on an Illumina Genome Analyzer IIx following the manufacturer's instructions.

tag: background

tag: genotype/variation


title: H2A.Z mononucleosomes

description:
SC0017_61YDGAAXX_8_TCATTC
Strain yFR212 is in a W303 background where the HTZ1 gene is tagged with 3 Myc epitopes in its 3' end (C-terminal of the Htz1 protein).
MNase-Seq, ChIP-Seq

source_name: Yeast cells, H2A.Z mononucleosomes

extract_protocol:
Cells were centrifuged again and the dry yeast pellets were snap frozen in liquid nitrogen and stored at -80C. One cell pellet was kept as a backup and the other one was thawed and resuspended in 20 mL of buffer Z (1M Sorbitol, 50mM Tris pH 7.4) before adding 14 μL of β-mercaptoEtOH and 0.5 mL of zymolase solution (1mg/mL, freshly prepared in buffer Z). Cells were shaken for 40 minutes at 30˚C and centrifuged 10 minutes at 1,500 rpm. The supernatant was aspired and discarded while the pellet was resuspended in 1.25 mL of NP buffer (50mM NaCl, 10mM Tris pH7.4, 5mM MgCl2, 1mM CaCl2, 0.075% NP40, 0.5mM spermidine, 1mM β-mercaptoEtOH). After this one, one of two different protocols was applied.
Three hundred μLaliquots (five) were treated with different amounts of MNase for 20 minutes at 37  C and reactions were stop by adding 6μL of 500mM EDTA.
For H2A.Z nucleosomes, 40 μL of 500mM HEPES pH7.5, 22,4 μL of NaCl 5M, 16 μL of 5% Na-deoxycholate, 80 μL of 10% TritonX-100 and a protein inhibitor cocktail were added to the extracts. H2A.Z was immunoprecipitated overnight at 4˚C with agitation using 50 uL magnetic beads (Dynal) coupled to 2 μg of anti-Myc antibody 3E10 (prepared in-house) with rotation (note that the yeast strain used has a 3xMyc-tagged HTZ1 gene). The beads were then processed as described before (PMID 19378172), inspected on agarose gel as described above and the sample contains mainly H2A.Z mononucleosomes.
ChIP samples were prepared from yeast cells. Briefly, cells were cross-linked with 1% formaldehyde for 10 min at room temperature, the reaction was quenched by 0.125 M glycine, and the cells were washed in PBS and harvested in the presence of protease inhibitors. ChIP was performed as described in Robertson et al. 2008. Briefly, chromatin DNA was fragmented and chromatin was pre-cleared with 40µl of blocked Protein A/G sepharose beads (Amersham, USA) at 4oC for 2 hrs, supernatants were removed from the beads following centrifugation, and transferred to fresh tubes. Sepharose beads were used for ChIPs and each immunoprecipitation was carried out with pre-cleared chromatin and 5 μg of antibody (anti-Myc 9E10) and incubated at 4oC for 1 hr. To each immunoprecipitation reaction, 20 µl of Protein A/G beads were added and incubated by rotating at 4oC overnight. Beads were recovered by centrifugation and washed twice with ChIP wash buffer (20 mM Tris-HCl [pH 8.0], 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl) and once with ChIP final wash buffer (20 mM Tris-HCl [pH 8.0], 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl). DNA-antibody complexes were eluted using 100uL Elution Buffer (100 mM NaHCO3, 1% SDS), and 5 µg of DNase-free RNase (Roche, Canada) was added and incubated at 68°C for 2 hours with shaking on a thermomixer to reverse the crosslink. The beads were pelleted by centrifugation and the supernatant was collected. Elution was repeated with the addition of 100 µl of Elution Buffer and incubation at 68oC for 5 min with shaking on a thermomixer. After pooling the two elutions, DNA was recovered from the eluate using the QIAquick PCR Purification kit (Qiagen, Germany). ChIP DNA was run and size separated by PAGE (8%). The 100-300bp DNA fraction was excised and eluted from the gel slice overnight at 4°C in 300 μl of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation.
The library was prepared by following the paired-end library protocol (Illumina Inc., USA). Briefly, the DNA was subject to end-repair, and phosphorylation by T4 DNA polymerase, Klenow DNA Polymerase, and T4 polynucleotide kinase respectively in a single reaction, and then 3' A overhangs generation by Klenow fragment (3' to 5' exo minus), and ligated to Illumina PE adapters, which contain 5' T overhangs. The adapter-ligated products were purified on QIAquick spin columns (Qiagen), then PCR-amplified with Phusion DNA Polymerase in 10-15 cycles using Illumina's PE primer set (Illumina). PCR product of desired size range was purified using a 8% PAGE, and the DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay and Nanodrop 7500 spectrophotometer (Nanodrop, USA) and diluted to 10nM. The final concentration was double checked and determined by Quant-iT dsDNA HS Assay Kit using Qubit fluorometer (Invitrogen). Clusters were generated on the Illumina cluster station and sequence was run on an Illumina Genome Analyzer IIx following the manufacturer's instructions.

value: anti-Myc 9E10


title: Snyder_LSY-2_GFP_Embryo_ChIP_Rep1

value: embryo

value: mixed Male and Hermaphrodite population


title: Snyder_ELT-1_GFP_L3_ChIP_Rep1

value: Hermaphrodite


title: Snyder_ELT-1_GFP_L3_Input_Rep1


title: NT2 DRIP-seq 2 rep 1

city: Davis

first: Yoong Wearn

last: Lim

state: CA

address: One Shields Avenue

department: Molecular and Cellular Biology

institute: University of California, Davis

description: gDNA digested with BamHI, NcoI, ApaLI, NheI and PvuII

data_processing:
Library strategy: DRIP-seq
Fastq reads were aligned to hg19 using BWA version 0.6.1
Peak calling was performed using MACS 1.4.2
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated by MACS

source_name: NT2 DRIP-seq 2 rep 1

extract_protocol:
Genomic DNA was extracted from NT2 cells and was either fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI (DRIP-seq 1) or BamHI, NcoI, ApaLI, NheI and PvuII (DRIP-seq 2). Monoclonal S9.6 antibody was used to enrich for RNA/DNA hybrids.
Sequencing library was constructed using standard Illumina protocol.

tag: cell line


title: NT2 input 1

description: gDNA digested with HindIII, EcoRI, BsrGI, XbaI and SspI

source_name: NT2 input 1


title: NT2 DRIP-seq 1

source_name: NT2 DRIP-seq 1


title: NT2 DRIP-seq 2 rep 2

source_name: NT2 DRIP-seq 2 rep 2


title: Asynchronous GM06990 Biological BubbleSeq

city: Charlottesville

first: Stefan

last: Bekiranov

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry & Molecular Genetics

institute: University of Virginia

description:
Replication Initiating genomic DNA
CEPH/UTAH PEDIGREE 1331, CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 9; CYP2C9, HUMAN VARIATION PANEL - EUROPEAN CAUCASIAN PANEL OF 8, HUMAN VARIATION PANEL - EUROPEAN CAUCASIAN PANEL OF 16, HUMAN VARIATION PANEL - EUROPEAN CAUCASIAN PANEL OF 24, SNP500 PANE

data_processing:
Illumina Casava1.7 software used for basecalling.
Bubble-seq reads for Samples 1, 2 and 3 were aligned to the hg18 genome assembly using BWA version 0.5.7 and individual enriched read wig files were generated. Reads for the three samples were merged togther and an enriched read wig file was generated for the combined dataset as well. Read depths (RD) were calculated over all EcoRI intervals in the genome - statistically enriched regions, also termed bubbles were determined by fitting to a negative binomial distribution.
RNA-seq reads for Samples 4 and 5 were merged and aligned to the hg18 genome assembly using Bowtie version 0.12.5.0. Parameters used were min-intron-length 30, and a reference transcript annotation file (wgEncodeGencodeManualV3.gtf). RNA-Seq read alignments were converted to SAM format by TopHat version 1.0.13. Cufflinks version 0.8.3 was then used to assemble transcripts from the aligned reads in SAM format, and estimate their relative abundances based on the same reference transcript annotation file.
Genome_build: hg18
Supplementary_files_format_and_content: Wig files of read depths of bubbles, FPKM measurements for genes and transcripts as determined by cufflinks 0.8.3

source_name: lymphoblastoid cell line

growth_protocol: The lymphoblastoid cell line, GM06990, was obtained from Coriell Institute for Medical Research and propagated in RPMI 1640 supplemented with 50ug/ml Gentamicin and 15% serum (Fetal Clone II, Hyclone).  Cells were maintained in culture for no longer than 3 weeks, passaged every 2-3 days and maintained at a cell density of 3-8X105 cells per ml.

extract_protocol: Each RNA-seq library was prepared from poly A+ RNA, which was isolated from 108 asynchronously growing cells.  Each bubble trap library was prepared from DNA that was isolated from 10 preparations of 109 cells (1010 cells per library). The construction and subsequent single-end sequencing of these libraries using an Illumina Gene Analyzer IIx was performed as outlined by the manufacturer.

treatment_protocol: Cells were harvested 36-48h after passage and at a density of 5-6X105 cells / ml.  Total RNA was isolated as outlined (Chomczynski and Sacchi (1987) Anal Biochem 162(1):156-9) followed by poly A+ RNA (Kingston (1992), Current protocols in Molecular Biology. Supplement 21).  Actively initiating replicative DNA (bubbles) was isolated exactly as described (Mesner et al (2009a), Methods Mol. Biol. 521: 121-137; Mesner and Hamlin (2009b), Methods Mol. Biol. 521: 315-328)

tag: sample type

value: Replication Initiating genomic DNA


title: Asynchronous GM06990 RNASeq1

description:
Poly A selected RNA
CEPH/UTAH PEDIGREE 1331, CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 9; CYP2C9, HUMAN VARIATION PANEL - EUROPEAN CAUCASIAN PANEL OF 8, HUMAN VARIATION PANEL - EUROPEAN CAUCASIAN PANEL OF 16, HUMAN VARIATION PANEL - EUROPEAN CAUCASIAN PANEL OF 24, SNP500 PANE

value: Poly A selected RNA


title: Asynchronous GM06990 Technical BubbleSeq1


title: Asynchronous GM06990 Technical BubbleSeq2


title: pooled total RNA subjected to "short" running  conditions for two dimensional gel electrophoresis

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: total pooled RNA was run on a 7.5% acrylamide, 8.3M urea gel in 1X TBE at 40 mA until the bromophenol blue had migrated 12 cm. This lane was cut out of the gel and recast across the top of a 15% gel. This second gel was run at 30 mA until the bromophenol blue had migrated 28 cm.

data_processing:
barcode trimming: first three bases at the five prime end of every read were removed
alignment: trimmed reads were uniquely aligned to the S. pombe reference genome using bowtie-0.12.3 with the following parameters: -v0 -m1
peak calling: samtools was used to generate a pileup file from the aligned file from the previous step. In-house perl scripts were used to infer non-zero read regions as "peaks" from the pileup file
peak classification: in-house perl scripts were used to probabilisitcally infer and classify splicing events from peaks, as described in (Supplemental Methods in  www.pnas.org/lookup/suppl/doi:10.1073/pnas.1218353110/-/DCSupplemental)
branch point detection:  in-house perl scripts were used to infer branch points for introns from certain reads, as described in (Supplemental Methods in  www.pnas.org/lookup/suppl/doi:10.1073/pnas.1218353110/-/DCSupplemental)
Genome_build: S. pombe reference genome pombe_040211.fasta, available from www.pombase.org
Supplementary_files_format_and_content: peak raw read counts for previously-annotated introns from the "short" sample
Supplementary_files_format_and_content: peak raw read counts for novel introns from the "short" sample
Supplementary_files_format_and_content: peak raw read counts for exon-skipping events from the "short" and "long" samples
Supplementary_files_format_and_content: branch point sequence, location and read count for introns from the "short" sample

organism: Schizosaccharomyces pombe

source_name: circular RNA portion of total cellular RNA pooled from 41 growth/treatment conditions

growth_protocol: Over 41 different growth and treatment conditions were used for all samples. See Table S1 in www.pnas.org/lookup/suppl/doi:10.1073/pnas.1218353110/-/DCSupplemental

extract_protocol:
Hot phenol extraction of total RNA, followed by pooling of RNA from all 41 growth conditions, then two dimensional acrylamide gel electrophoresis and excision of arc corresponding to circular RNA (see Supplemental Methods in  www.pnas.org/lookup/suppl/doi:10.1073/pnas.1218353110/-/DCSupplemental)
Same as that of Quail et al. Nature Methods 2008 (PMID: 19034268), with slight modifications (see Supplemental Methods in  www.pnas.org/lookup/suppl/doi:10.1073/pnas.1218353110/-/DCSupplemental)


title: fun30D

status: Public on Jul 08 2013

city: Augusta

first: Wei-Hua

last: Wu

state: GA

address: 1462 Laney Walker Blvd

department: Neurology

institute: IMMAG/MCG/GRU

data_processing:
Sequence reads were aligned using Bowtie 0.12.7.
Nucleosomes were mapped using a TemplateFilter algorithm (Weiner A et al, Genome Research 20: 90-100, 2010)
Nucleosome occupancies were normalized by the total reads numbers, followed by quantile normalization
Genome_build: S. cerevisiae 2003 (Bowtie CYGD default)
Supplementary_files_format_and_content: Text files have the locations and normalized occupancies of nucleosomes

growth_protocol: Wild type and mutant yeast cells were grow in YPD medium at 30°C and harvested at ~ O.D. 0.5.  Cells were fixed with 1% paraformaldehyde at room temperature for 30 minutes.

extract_protocol:
Crude yeast nuclei was extracted and digested with micrococcal nuclease at 37°C for 10 minutes.  Mononucleosomal DNA was gel purified.
Library was constructed as previously described (Barski A et al, Cell 129: 823-837, 2007)

value: fun30D mutant