title: Hu wt Mcm2-7 2

city: Durham

first: David

middle: M

last: MacAlpine

state: NC

address: Box 3813 DUMC

department: Pharmacology and Cancer Biology

institute: Duke University Medical Center

data_processing:
Genome assembly: For each sample sequenced reads were aligned to the S. cerevisiae S288C reference genome (SacCer2, SGD June 2008) (Kent et al., 2002) using MAQ (Li et al., 2008) allowing up to three mismatched bases. Reads with a mapping quality of >= 35 were used in downstream analysis.
Data normalization: Reads were binned across the genome, and RPKM (reads per kilobase per million mappable reads) was calculated for each bin.  For all of the BrdU ChIP-Seq experiments, bins of 5000 bp stepping every 1250 bp were used, and for all the Mcm ChIP-Seq experiments, bins of 1000 bp stepping every 250 bp were used. All in silico analyses were done in the R programming environment using the Bioconductor suite of packages (Gentleman et al., 2004; RDevelopmentCoreTeam, 2010). Experimental replicates were quantile normalized and combined by calculating the mean score within each bin.
Peak determination: For each bin along a chromosome, a probability was assigned according to that chromosome’s empirical cumulative distribution of RPKM. A threshold was determined, and bins with a probability greater than or equal to the cutoff were taken as peaks (the ranges of overlapping peaks were merged such that the resulting peaks represented the union of all enriched bins).  For BrdU ChIP-Seq in HU arrested cells, the thresholds used were as follows: WT strains p ≥ 0.95, Mrc1 p ≥ 0.75,  and Mcm2DENQ p ≥0.75. For ChIP-Seq experiments in G1 arrested cells, a threshold of p ≥ 0.96 was used. Replicates were combined by taking the intersection of peak calls.  When possible, peaks were assayed for concordance against analogous data previously reported (Crabbe et al., 2010).
Genome_build: SacCer2
Supplementary_files_format_and_content: .wig files represent RPKM across the genome; .bed files indicate regions of enrichment.

source_name: Yeast culture

extract_protocol: For G1 experiments, strains were arrested in α-factor for 3 hours at 23C then processed for ChIP.  For S-phase experiments, strain were similarly arrested with α-factor, then released into fresh media containing 400 µg/ml BrdU and 0.2 M HU until cell budding reached 75% (100-110 minutes at 23°C), harvested, and processed for ChIP-seq. Replica 1 of wild type was arrested in HU for 90 min, where 2DENQ and mrc1∆ were arrested in HU for 100 min; replica 2 of wild type, 2DENQ, and mrc1∆ were arrested in HU for 100 min; mcm2-1 and chaos3 were arrested in HU for 100 minutes. To assay Mcm-bound DNA, ChIP-seq DNA preparation was performed as previously described (Aparicio et al., 1997).  Formaldehyde was added to 50 ml of α-factor arrested cells to a final concentration of 1% and mixed for 15 minutes at room temperature.  Crosslinking was quenched by the addition of glycine to a final concentration of 125 mM and room temperature incubation for 5 minutes.  Cells were washed twice with 20 ml of ice-cold TBS (20 mM Tris-HCl, pH 7.6, and 150 mM NaCl) and the resulting cell pellet was frozen in liquid nitrogen and stored at -80C.  The cell pellet was thawed on ice, resuspended in 250 µl of 1X lysis buffer (50 mM HEPES/KOH, pH 7.5, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, and 0.1% Na-Deoxycholate) with fresh protease inhibitors (1 mM PMSF, 10 mM benzamidine, 0.1 mg/ml TPCK, 10 µg/ml aprotinin, 10 µg/ml leupeptin, 10 µg/ml pepstatin, and 0.5 mg/ml bacitracin), glass beads were added, and the sample vortexed (cycles of 30 seconds on ice and 30 seconds vortexing for a total of 30 min) . 250 µl of additional 1X lysis buffer was added and briefly mixed.  Using a hot 27-gauge needle, a hole was poked into the bottom of the tube, and the cell lysates were separated from the glass beads by centrifugation into a fresh tube).  The DNA in the lysate was then sheared using a Branson 250 model sonicator to yield an average DNA size of 700 bp.  6 µl of anti-Mcm2-7 antibody (UM174, Stephen P Bell, MIT) or 4 µl of anti-Mcm2 (sc6680, Santa Cruz,) was added to cell lysates and incubated at 4C for 2 hours.  30 µl of protein G beads pre-equilibrated in 1X PBS, 0.1% BSA (Gamma bind, GE Healthcare) was then added and incubated for an additional hour at 4°C.  Following incubation, beads were washed twice with 1 ml of lysis buffer with fresh PMSF; then once each with 1 ml of lysis buffer containing 500 mM NaCl once, 1 ml of TLNNE (10 mM Tris/HCl, pH 8.0, 0.25 M LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, and 1 mM EDTA), then 1 ml of TE.  Each wash was performed with 5 minutes of room temperature incubation with mixing.  To elute the DNA, 100     µl of elution buffer (50 mM Tris/HCl, pH 8.0, and 10 mM EDTA/1% SDS) was then added to the beads and incubated at 65°C for 15 min.  Beads were removed by centrifugation, and the supernatant was transferred to a fresh tube.  Beads were resuspended in 150 µl of TE containing 0.67% SDS and spun down again. The supernatants were pooled and incubated at 65°C overnight to reverse the proteinDNA crosslinks.  The next morning, 250 µl of TE, 5 µl of 20 mg/ml proteinase K, and 0.25 µl of 20 mg/ml glycogen were added and incubated at 37°C for 30 minutes.  After incubation, 55 µl of 4 M LiCl was added, and the DNA was phenol/chloroform extracted and precipitated with 10/24/11 6 ammonium acetate and ethanol. The dried DNA pellet was processed to construct the library for sequencing (see Materials and Methods). To assay BrdU incorporation, genomic DNA was prepared using standard procedures (Ryba et al., 2011), boiled, and immunoprecipitated with anti-BrdU antibodies (555627, BD Bioscience).  The resulting DNA pellet was subjected to sequencing library preparation.

value: Hu

value: wt


title: Hu mrc1∆ Mcm2-7 1

status: Public on Apr 20 2015

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae

tag: treatment

tag: genotype

tag: strain

tag: chip antibody


title: Hu mrc1∆ Mcm2-7 2


title: Hu mcm2DENQ Mcm2-7 1


title: Hu mcm2DENQ Mcm2-7 2


title: Hu mrc1∆ BrdU 2

value: BrdU


title: Hu wt BrdU 2


title: Hu wt BrdU 1


title: Hu mcm2DENQ BrdU 2


title: Hu mrc1∆ BrdU 1


title: WTf-d0-2

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

description:
Sample 3
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 3

library_source: transcriptomic

data_processing:
The sequencing company provided "clean reads" (i.e., low quality reads removed).
Basecalls performed using CASAVA version
ChIRP retrived DNA-Seq reads were aligned to the mm9 genome assembly using Bowtie version 1.0.0 with the default parameters
RNA-seq reads were aligned to the mm9 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Peaks of each sample were called using MACS v. 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include FPKM values for wild-type or Haunt KO Samples; ChIRP-seq: bedgraph files were generated using MACS v. 1.4.2, including peaks called by default parameters.

molecule: total RNA

organism: Mus musculus

source_name: JF4 mES cells

growth_protocol: Wild-type ESCs or Haunt KO ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

treatment_protocol: Cells were washed once with cold PBS, and then add TRIzol for RNA total RNA extraction

tag: cell line

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: WT

tag: time


title: WT-H3K4me3_RA

data_processing:
Basecalls performed using CASAVA version
ChIRP retrived DNA-Seq reads were aligned to the mm9 genome assembly using Bowtie version 1.0.0 with the default parameters
RNA-seq reads were aligned to the mm9 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Peaks of each sample were called using MACS v. 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for wild-type or Haunt KO Samples, bedgraph files were generated using MACS v. 1.4.2, including peaks called by default parameters.

source_name: 46C mES cells

growth_protocol:
Wild-type ESCs or Haunt KO ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol. Treat with 2mM RA and without LIF. Harvest cell at day 1 of RA treatment
Wild-type ESCs or Haunt KO ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
ChIP was done following previously protocol (Shen, 2008). Briefly, cell were crosslinked on plate with 0.9% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. Then Sonicated into average size 200-500 bp. 14000rpm for 15 min, supernatant were diluted by ChIP dilution buffer. 3 ug H3K4me3 (Abcam, ab8580) or H3K27me3 antibodies (Millipore, #07-449) were added, 4℃, end to end rotate overnight. 30 ul Protein AG UltraLink Resin (Thermo, 53133) were added,  4℃, end to end rotate for 3 times. after thoroughly wash, the DNA were eluted by elution buffer with protease K at 65℃.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrieved DNA was end repaired, and dA-tailed by respect module according to respect instruments. The DNA product then ligated with  adaptor with NEBNext Quick Ligation Module. The adaptor for the libary were sythersized from IDT with the first 7nt is "CAGATGT" as a barcode. After liagation, the DNA were amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.

treatment_protocol: Cells were washed once with cold PBS, then harvested by trypsin digestion.

tag: sample type

value: LIF withdrawal, 2uM RA, day1

tag: chirp probes

value: wild type

value: H3K4me3 (Abcam, ab8580)

tag: barcode

value: CAGATGT


title: WT-H3K4me3_D0

growth_protocol:
Wild-type ESCs or Haunt KO ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
Wild-type ESCs or Haunt KO ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
ChIP was done following previously protocol (Shen, 2008). Briefly, cell were crosslinked on plate with 0.9% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. Then Sonicated into average size 200-500 bp. 14000rpm for 15 min, supernatant were diluted by ChIP dilution buffer. 3 ug H3K4me3 (Abcam, ab8580) or H3K27me3 antibodies (Millipore, #07-449) were added, 4℃, end to end rotate overnight. 30 ul Protein AG UltraLink Resin (Thermo, 53133) were added,  4℃, end to end rotate for 3 times. after thoroughly wash, the DNA were eluted by elution buffer with protease K at 65℃.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrieved DNA was end repaired, and dA-tailed by respect module according to respect instruments. The DNA product then ligated with  adaptor with NEBNext Quick Ligation Module. The adaptor for the libary were sythersized from IDT with the first 7nt is "ACTGACT" as a barcode. After liagation, the DNA were amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.

value: ACTGACT


title: pKO-H3K4me3_D0

source_name: Haunt pKO mES cells

extract_protocol:
ChIP was done following previously protocol (Shen, 2008). Briefly, cell were crosslinked on plate with 0.9% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. Then Sonicated into average size 200-500 bp. 14000rpm for 15 min, supernatant were diluted by ChIP dilution buffer. 3 ug H3K4me3 (Abcam, ab8580) or H3K27me3 antibodies (Millipore, #07-449) were added, 4℃, end to end rotate overnight. 30 ul Protein AG UltraLink Resin (Thermo, 53133) were added,  4℃, end to end rotate for 3 times. after thoroughly wash, the DNA were eluted by elution buffer with protease K at 65℃.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrieved DNA was end repaired, and dA-tailed by respect module according to respect instruments. The DNA product then ligated with  adaptor with NEBNext Quick Ligation Module. The adaptor for the libary were sythersized from IDT with the first 7nt is "TGCTGAT" as a barcode. After liagation, the DNA were amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.

value: Haunt knock out in 46C cells

value: Haunt pKO

value: TGCTGAT


title: α-factor mcm2DENQ Mcm2-7

value: α-factor


title: WT-RA_DNA

extract_protocol:
ChIRP was done as described previously with the following modifications (Chu et al. 2011). First, 59 nt DNA probes were biotinylated through terminal transferase (New England Biolabs). Intensive crosslinking of cells was performed in the following sequence: two rounds of 3000J UV treatment on ice, 0.8% of formaldehyde (FMA) for 10 minutes, 2mM of DSP (Dithiobis [succinimidyl propionate]) for 30 minutes, and followed by 3.7% of FMA for 10 minutes at room temperature. Crosslinked cell pellets were lysed. Chromatin was fragmented into a range of 2 - 5 kb by sonication. Hybridization, washing and elution steps were performed as described previously, except that we included an additional stringent wash (0.1x SSC). After elution and reverse crosslinking, RNA was further extracted by TRIzol reagent (Life Technologies).
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrived RNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 210 seconds. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "TCACGTT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.

value: embryonic stem cells (RA, day1)

value: ChIRP probes targeting Haunt mRNA

value: TCACGTT


title: pKO-H3K4me3_RA

extract_protocol:
ChIP was done following previously protocol (Shen, 2008). Briefly, cell were crosslinked on plate with 0.9% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. Then Sonicated into average size 200-500 bp. 14000rpm for 15 min, supernatant were diluted by ChIP dilution buffer. 3 ug H3K4me3 (Abcam, ab8580) or H3K27me3 antibodies (Millipore, #07-449) were added, 4℃, end to end rotate overnight. 30 ul Protein AG UltraLink Resin (Thermo, 53133) were added,  4℃, end to end rotate for 3 times. after thoroughly wash, the DNA were eluted by elution buffer with protease K at 65℃.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrieved DNA was end repaired, and dA-tailed by respect module according to respect instruments. The DNA product then ligated with  adaptor with NEBNext Quick Ligation Module. The adaptor for the libary were sythersized from IDT with the first 7nt is "GTACCTT" as a barcode. After liagation, the DNA were amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.

value: GTACCTT


title: WT-H3K27me3_RA

extract_protocol:
ChIP was done following previously protocol (Shen, 2008). Briefly, cell were crosslinked on plate with 0.9% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. Then Sonicated into average size 200-500 bp. 14000rpm for 15 min, supernatant were diluted by ChIP dilution buffer. 3 ug H3K4me3 (Abcam, ab8580) or H3K27me3 antibodies (Millipore, #07-449) were added, 4℃, end to end rotate overnight. 30 ul Protein AG UltraLink Resin (Thermo, 53133) were added,  4℃, end to end rotate for 3 times. after thoroughly wash, the DNA were eluted by elution buffer with protease K at 65℃.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrieved DNA was end repaired, and dA-tailed by respect module according to respect instruments. The DNA product then ligated with  adaptor with NEBNext Quick Ligation Module. The adaptor for the libary were sythersized from IDT with the first 7nt is "TCACGTT" as a barcode. After liagation, the DNA were amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.


title: pKO-H3K27me3_RA

extract_protocol:
ChIP was done following previously protocol (Shen, 2008). Briefly, cell were crosslinked on plate with 0.9% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. Then Sonicated into average size 200-500 bp. 14000rpm for 15 min, supernatant were diluted by ChIP dilution buffer. 3 ug H3K4me3 (Abcam, ab8580) or H3K27me3 antibodies (Millipore, #07-449) were added, 4℃, end to end rotate overnight. 30 ul Protein AG UltraLink Resin (Thermo, 53133) were added,  4℃, end to end rotate for 3 times. after thoroughly wash, the DNA were eluted by elution buffer with protease K at 65℃.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrieved DNA was end repaired, and dA-tailed by respect module according to respect instruments. The DNA product then ligated with  adaptor with NEBNext Quick Ligation Module. The adaptor for the libary were sythersized from IDT with the first 7nt is "CTGAAGT" as a barcode. After liagation, the DNA were amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.

value: CTGAAGT


title: α-factor mcm2DENQ Mcm2p


title: WT_DNA

description:
Sample 24
barcode: GTACCTT
Sample 24

data_processing:
library strategy: ChIRP-seq
The sequencing company provided "clean reads" (i.e., low quality reads removed).
Basecalls performed using CASAVA version
ChIRP retrived DNA-Seq reads were aligned to the mm9 genome assembly using Bowtie version 1.0.0 with the default parameters
RNA-seq reads were aligned to the mm9 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Peaks of each sample were called using MACS v. 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include FPKM values for wild-type or Haunt KO Samples; ChIRP-seq: bedgraph files were generated using MACS v. 1.4.2, including peaks called by default parameters.

extract_protocol:
ChIRP was done as described previously with the following modifications (Chu et al. 2011). First, 59 nt DNA probes were biotinylated through terminal transferase (New England Biolabs). Intensive crosslinking of cells was performed in the following sequence: two rounds of 3000J UV treatment on ice, 0.8% of formaldehyde (FMA) for 10 minutes, 2mM of DSP (Dithiobis [succinimidyl propionate]) for 30 minutes, and followed by 3.7% of FMA for 10 minutes at room temperature. Crosslinked cell pellets were lysed. Chromatin was fragmented into a range of 2 - 5 kb by sonication. Hybridization, washing and elution steps were performed as described previously, except that we included an additional stringent wash (0.1x SSC). After elution and reverse crosslinking, then purified by MinElute PCR Purification Kit (QIAGEN).
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrieved DNA was end repaired, and dA-tailed by respect module according to respect instruments. The DNA product then ligated with  adaptor with NEBNext Quick Ligation Module. The adaptor for the libary were sythersized from IDT with the first 7nt is "GTACCTT" as a barcode. After liagation, the DNA were amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.


title: WT-H3K27me3_D0

extract_protocol:
ChIP was done following previously protocol (Shen, 2008). Briefly, cell were crosslinked on plate with 0.9% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. Then Sonicated into average size 200-500 bp. 14000rpm for 15 min, supernatant were diluted by ChIP dilution buffer. 3 ug H3K4me3 (Abcam, ab8580) or H3K27me3 antibodies (Millipore, #07-449) were added, 4℃, end to end rotate overnight. 30 ul Protein AG UltraLink Resin (Thermo, 53133) were added,  4℃, end to end rotate for 3 times. after thoroughly wash, the DNA were eluted by elution buffer with protease K at 65℃.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrieved DNA was end repaired, and dA-tailed by respect module according to respect instruments. The DNA product then ligated with  adaptor with NEBNext Quick Ligation Module. The adaptor for the libary were sythersized from IDT with the first 7nt is "AGCTCAT" as a barcode. After liagation, the DNA were amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.

value: AGCTCAT


title: pKO-H3K27me3_D0

extract_protocol:
ChIP was done following previously protocol (Shen, 2008). Briefly, cell were crosslinked on plate with 0.9% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. Then Sonicated into average size 200-500 bp. 14000rpm for 15 min, supernatant were diluted by ChIP dilution buffer. 3 ug H3K4me3 (Abcam, ab8580) or H3K27me3 antibodies (Millipore, #07-449) were added, 4℃, end to end rotate overnight. 30 ul Protein AG UltraLink Resin (Thermo, 53133) were added,  4℃, end to end rotate for 3 times. after thoroughly wash, the DNA were eluted by elution buffer with protease K at 65℃.
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrieved DNA was end repaired, and dA-tailed by respect module according to respect instruments. The DNA product then ligated with  adaptor with NEBNext Quick Ligation Module. The adaptor for the libary were sythersized from IDT with the first 7nt is "GATGTCT" as a barcode. After liagation, the DNA were amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.

value: embryonic stem cells

value: GATGTCT


title: WT_RNA

description:
Sample 22
barcode: TGCTGAT
Sample 22

extract_protocol:
ChIRP was done as described previously with the following modifications (Chu et al. 2011). First, 59 nt DNA probes were biotinylated through terminal transferase (New England Biolabs). Intensive crosslinking of cells was performed in the following sequence: two rounds of 3000J UV treatment on ice, 0.8% of formaldehyde (FMA) for 10 minutes, 2mM of DSP (Dithiobis [succinimidyl propionate]) for 30 minutes, and followed by 3.7% of FMA for 10 minutes at room temperature. Crosslinked cell pellets were lysed. Chromatin was fragmented into a range of 2 - 5 kb by sonication. Hybridization, washing and elution steps were performed as described previously, except that we included an additional stringent wash (0.1x SSC). After elution and reverse crosslinking, RNA was further extracted by TRIzol reagent (Life Technologies).
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrived RNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 210 seconds. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "TGCTGAT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.

value: WT


title: α-factor wt Mcm2p

value: wt


title: α-factor wt Mcm2-7


title: KO_DNA

description:
Sample 23
barcode: CAGATGT
Sample 23

source_name: Haunt P-exon2 KO mES cells

extract_protocol:
ChIRP was done as described previously with the following modifications (Chu et al. 2011). First, 59 nt DNA probes were biotinylated through terminal transferase (New England Biolabs). Intensive crosslinking of cells was performed in the following sequence: two rounds of 3000J UV treatment on ice, 0.8% of formaldehyde (FMA) for 10 minutes, 2mM of DSP (Dithiobis [succinimidyl propionate]) for 30 minutes, and followed by 3.7% of FMA for 10 minutes at room temperature. Crosslinked cell pellets were lysed. Chromatin was fragmented into a range of 2 - 5 kb by sonication. Hybridization, washing and elution steps were performed as described previously, except that we included an additional stringent wash (0.1x SSC). After elution and reverse crosslinking, then purified by MinElute PCR Purification Kit (QIAGEN).
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrieved DNA was end repaired, and dA-tailed by respect module according to respect instruments. The DNA product then ligated with  adaptor with NEBNext Quick Ligation Module. The adaptor for the libary were sythersized from IDT with the first 7nt is "CAGATGT" as a barcode. After liagation, the DNA were amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.

value: Haunt P-exon2 KO


title: KO_RNA

description:
Sample 21
barcode: ACTGACT
Sample 21

extract_protocol:
ChIRP was done as described previously with the following modifications (Chu et al. 2011). First, 59 nt DNA probes were biotinylated through terminal transferase (New England Biolabs). Intensive crosslinking of cells was performed in the following sequence: two rounds of 3000J UV treatment on ice, 0.8% of formaldehyde (FMA) for 10 minutes, 2mM of DSP (Dithiobis [succinimidyl propionate]) for 30 minutes, and followed by 3.7% of FMA for 10 minutes at room temperature. Crosslinked cell pellets were lysed. Chromatin was fragmented into a range of 2 - 5 kb by sonication. Hybridization, washing and elution steps were performed as described previously, except that we included an additional stringent wash (0.1x SSC). After elution and reverse crosslinking, RNA was further extracted by TRIzol reagent (Life Technologies).
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrived RNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 210 seconds. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "ACTGACT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Illumina instrument following the manufacturer's protocols.


title: Hu wt Mcm2-7 1

value: Hu


title: Tremella fuciformis strain Tr21

city: Fuzhou

first: Baogui

last: Xie

state: Fujian

address: Shangdian Road

department: Mycological Research Center

country: China

institute: mrcfafu

description:
3'-tag digital gene expression (DGE)
dikaryon

data_processing:
Illumina Cluster Station and Illumina HiSeq™ 2000 instrument used for basecalling.
Raw sequences have 3' adaptor fragments as well as a few low-quality sequences and several types of impurities. Raw sequences are transformed into Clean Tags after certain steps of data-processing.
A virtual libraries containing all the possible CATG+17 bases length sequences of the reference gene sequences.All clean tags were mapped to the reference sequences and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). ('t Hoen, Ariyurek, et al. 2008; Morrissy, Morin, et al. 2009).
Supplementary_files_format_and_content: tab-delimited text files include tag sequences,tag number and TPM values for each strain.

organism: Tremella fuciformis

source_name: Mushroom

growth_protocol: Yeast-like cells were cultivated in 2% potato dextrose broth (PDB) at 20 degree into their exponential growth phase.

extract_protocol:
Total RNA was extracted from cells using pBIOZOL Plant Total RNA Extraction Reagent, according to the manufacturer’s protocol (BioFlux). The isolated RNA was treated with RNeasy plant mini kit to remove potential genomic DNA contamination, according to the manufacturer’s protocol (QIAGEN, Germany). RNA integrity and concentration were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). RNA (6 μg) from each of the three strains was submitted to BGI-Shenzhen (Shenzhen, China) for library construction and sequencing.
Sequence tag preparation was carried out using the Illumina Gene Expression Sample Prep Kit according to the manufacturer’s protocol.

tag: tissue

value: yeast


title: CS-B 6-4PP XR-seq, rep2

status: Public on Apr 19 2015

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

description:
Excised oligomer released in Nucleotide Excision Repair (XR-seq).
Processed data files:
CSB64_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw
CSB64_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw

data_processing:
Library strategy: XR-seq
Base calling using Casava v1.8.2. Demultiplexing performed allowing 1 mismatch in the index.
Flanking adapter sequences were removed from the reads using trimmomatic (Bolger et al. 2014).
Reads were aligned to the hg19 human genome using Bowtie (Langmead et al. 2009) with the command options -q --nomaqround --phred33-quals -m 4 -n 2 -e 70 -l 20 --best –S
Aligned reads for each biological replicate were split into "PLUS" and "MINUS" strands, transformed to bed format, and sorted to remove duplicate reads.
Aligned reads from both replicates were merged, wiggle base counts files of 25bp fixed step windows were created from the bed files. The count data was normalized for total sequencing depth on each chromosome. Wiggle files were transferred to bigWig format for viewing on the UCSC browser.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: For XR-seq performed for either CPD or (6-4)PP repair, in NHF1, XP-C and CS-B cells, there are bigWig files of normalized 25bp fixedStep count data for the merged data of both biological replicates, split into plus and minus strands.

organism: Homo sapiens

growth_protocol: XP-C and CS-B mutant cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum at 37 °C in a 5% CO2 humidified chamber. The NHF1 cells were maintained under the same conditions with the addition of 2 mM glutamine.

extract_protocol:
Cell pellets from one 150mm tissue culture dish were resuspended in 400 µl of ice cold Buffer A (25 mM Hepes pH 7.9, 100 mM KCl, 12 mM MgCl2, 0.5 mM EDTA, 2 mM DTT, 12.5% glycerol, 0.5% NP-40) and incubated for 10 min on ice. Resuspended cells were transferred to an ice-cold Dounce homogenizer/tissue grinder and lysed on ice with 15 strokes using a tight plunger. The chromatin fraction was then pelleted by centrifugation for 30 min at 16, 873 x g at 4oC.
The supernatants were collected, 2 µg anti-p89 (XPB, Santa Cruz, cat sc293, lot L1514), 1 µg anti-p62 (Santa Cruz, cat sc292, lot F2113) and 200 µg RNase A (Sigma R4642) were added. The reactions were rotated for 3-5 hrs at 4oC and then incubated overnight with 15 µL of recombinant protein A/G PLUS-agarose (Santa Cruz sc2003). After washing three times with 1 ml of buffer A and once with 1ml of buffer B (25 mM Hepes pH 7.9, 100 mM KCl, 12 mM MgCl2, 0.5 mM EDTA, 2 mM DTT, 12.5% glycerol, 1% NP-40), DNA was eluted from immunoprecipitates with 100 µl of buffer C (10 mM Tris-Cl pH 7.5, 1 mM EDTA, and 1% SDS) at 65oC for 15 min. The eluted DNA was then isolated by phenol/chloroform extraction followed by ethanol precipitation. DNA pellets were resuspended in 45 µl water, and then incubated with 5 µL of RNaseA/T1 mixture (Thermo EN0551) for 1 hr at 37oC. After phenol-chloroform extraction, purification through G50 filtration columns (GE Healthcare) and ethanol precipitation, the DNA was then used for ligation.
To add double-stranded adaptors to both ends, purified excised oligomers were incubated with 40 pmol 5' adaptor and 100 pmol 3' adaptor in 10 µL 2x Hybridization Buffer (20mM Tris-HCl pH7.5, 200mM NaCl, 0.2mM EDTA) at 60oC for 10min, then 16oC for 5min in a thermal cycler. To perform ligation, 4 µL 5x ligase buffer, 1 µL T4 DNA ligase HC (Life 15224-041), 1 µL 50% PEG8000 (NEB) and 4 µL H2O were added to each reaction. The reactions were incubated at 16oC overnight. After phenol-chloroform extraction and ethanol precipitation, ligation products were subjected to immunoprecipitation with anti-CPD (Kamiya, cat MC-062, lot 11569062) or anti-(6-4)PP (Cosmo, cat NM-DND-002, lot TM-P-03) antibodies. For NHF1 and CS-B samples, the ligation products were first immunoprecipitated with anti-CPD then the supernatant were subjected to immunoprecipitation with anti-(6-4)PP. For XP-C samples, the order was reversed: first IP with anti-(6-4)PP then the flowthrough IP with anti-CPD. Purified DNA were repaired by (6-4)PP photolyase or CPD photolyase. DNA containing (6-4)PP or CPD were incubated with 1.25pmol E.coli (6-4)PP photolyase or 20pmol D. melanogaster CPD photolyase in 50 µL PLR buffer for 2hr on ice and irradiated with 18mW/cm2 of 366 nm light. 1% of unrepaired or repaired samples were used for quality check. After phenol-chloroform extraction and ethanol precipitation, repaired DNA were PCR amplified by Kapa Hifi HotStart ReadyMix with RP1 and RPIn (n means different index sequences, compatible with Illumina TrueSeq Small RNA Kit.) The PCR products were extracted with phenol-chloroform, precipitated with ethanol and subjected to electrophoresis in a 10% native polyacrylamide gel in 1xTBE. Gel slices corresponding to 130- to 155-nt fragments were excised. The DNA was eluted for 6 hrs in 0.3 M NaCl at room temperature, precipitated with ethanol and resuspended in buffer EB (10mM Tris-HCl pH8.5).

treatment_protocol: UV irradiation was performed as described previously (Gaddameedhi et al. 2010). Briefly, cells were grown to ~80% confluence before UV irradiation. Culture medium was removed, and then cells were placed under a GE germicidal lamp emitting primarily 254-nm UV light (1J/m2/s) connected with a digital timer for 20s (20J/m2 in total). Following irradiation, fresh culture medium was added to the cells, which were further incubated for the indicated time. Cells were washed with ice-cold PBS, harvested with a cell scraper in PBS and collected by centrifugation at 2500rpm for 4min.

value: Coriell GM16095 (CS1ANps3g2)

tag: cell line source

value: Cockayne Syndrome patient (CS-B mutant)

value: skin fibroblast cell line

tag: uv exposure

tag: time between uv exposure and harvesting

tag: type of uv-induced dna damage

value: (6-4) pyrimidine-pyrimidone photoproduct ((6-4)PP)


title: XP-C 6-4PP XR-seq, rep1

description:
Excised oligomer released in Nucleotide Excision Repair (XR-seq).
Processed data files:
XPC64_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw
XPC64_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw

value: Coriell GM15983 (XP4PA-SV-EB)

value: Xeroderma Pigmentosum patient (XP-C mutant)


title: XP-C 6-4PP XR-seq, rep2


title: CS-B 6-4PP XR-seq, rep1


title: XP-C CPD XR-seq, rep1

description:
Excised oligomer released in Nucleotide Excision Repair (XR-seq).
Processed data files:
XPCCPD_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw
XPCCPD_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw

source_name: XP-C, CPD

value: cyclobutane pyrimidine dimer (CPD)


title: NHF1 6-4PP XR-seq, rep2

description:
Source of NHF1 cell line: W.K. Kaufmann, UNC, Chapel Hill (Heffernan et al. 2002).
Excised oligomer released in Nucleotide Excision Repair (XR-seq).
Processed data files:
PP641h_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw
PP641h_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw

value: normal newborn

value: foreskin fibroblast cell line


title: NHF1 6-4PP XR-seq, rep1


title: Hu mcm2DENQ BrdU 1

extract_protocol: For G1 experiments, strains were arrested in α-factor for 3 hours at 23C then processed for ChIP.  For S-phase experiments, strain were similarly arrested with α-factor, then released into fresh media containing 400 µg/ml BrdU and 0.2 M HU until cell budding reached 75% (100-110 minutes at 23°C), harvested, and processed for ChIP-seq. Replica 1 of wild type was arrested in HU for 90 min, where 2DENQ and mrc1∆ were arrested in HU for 100 min; replica 2 of wild type, 2DENQ, and mrc1∆ were arrested in HU for 100 min; mcm2-1 and chaos3 were arrested in HU for 100 minutes. To assay Mcm-bound DNA, ChIP-seq DNA preparation was performed as previously described (Aparicio et al., 1997).  Formaldehyde was added to 50 ml of α-factor arrested cells to a final concentration of 1% and mixed for 15 minutes at room temperature.  Crosslinking was quenched by the addition of glycine to a final concentration of 125 mM and room temperature incubation for 5 minutes.  Cells were washed twice with 20 ml of ice-cold TBS (20 mM Tris-HCl, pH 7.6, and 150 mM NaCl) and the resulting cell pellet was frozen in liquid nitrogen and stored at -80C.  The cell pellet was thawed on ice, resuspended in 250 µl of 1X lysis buffer (50 mM HEPES/KOH, pH 7.5, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, and 0.1% Na-Deoxycholate) with fresh protease inhibitors (1 mM PMSF, 10 mM benzamidine, 0.1 mg/ml TPCK, 10 µg/ml aprotinin, 10 µg/ml leupeptin, 10 µg/ml pepstatin, and 0.5 mg/ml bacitracin), glass beads were added, and the sample vortexed (cycles of 30 seconds on ice and 30 seconds vortexing for a total of 30 min) . 250 µl of additional 1X lysis buffer was added and briefly mixed.  Using a hot 27-gauge needle, a hole was poked into the bottom of the tube, and the cell lysates were separated from the glass beads by centrifugation into a fresh tube).  The DNA in the lysate was then sheared using a Branson 250 model sonicator to yield an average DNA size of 700 bp.  6 µl of anti-Mcm2-7 antibody (UM174, Stephen P Bell, MIT) or 4 µl of anti-Mcm2 (sc6680, Santa Cruz,) was added to cell lysates and incubated at 4C for 2 hours.  30 µl of protein G beads pre-equilibrated in 1X PBS, 0.1% BSA (Gamma bind, GE Healthcare) was then added and incubated for an additional hour at 4°C.  Following incubation, beads were washed twice with 1 ml of lysis buffer with fresh PMSF; then once each with 1 ml of lysis buffer containing 500 mM NaCl once, 1 ml of TLNNE (10 mM Tris/HCl, pH 8.0, 0.25 M LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, and 1 mM EDTA), then 1 ml of TE.  Each wash was performed with 5 minutes of room temperature incubation with mixing.  To elute the DNA, 100     µl of elution buffer (50 mM Tris/HCl, pH 8.0, and 10 mM EDTA/1% SDS) was then added to the beads and incubated at 65°C for 15 min.  Beads were removed by centrifugation, and the supernatant was transferred to a fresh tube.  Beads were resuspended in 150 µl of TE containing 0.67% SDS and spun down again. The supernatants were pooled and incubated at 65°C overnight to reverse the proteinDNA crosslinks.  The next morning, 250 µl of TE, 5 µl of 20 mg/ml proteinase K, and 0.25 µl of 20 mg/ml glycogen were added and incubated at 37°C for 30 minutes.  After incubation, 55 µl of 4 M LiCl was added, and the DNA was phenol/chloroform extracted and precipitated with 10/24/11 6 ammonium acetate and ethanol. The dried DNA pellet was processed to construct the library for sequencing (see Materials and Methods). To assay BrdU incorporation, genomic DNA was prepared using standard procedures (Ryba et al., 2011), boiled, and immunoprecipitated with anti-BrdU antibodies (555627, BD Bioscience).  The resulting DNA pellet was subjected to sequencing library preparation.

value: BrdU


title: WT-D0_DNA

extract_protocol:
ChIRP was done as described previously with the following modifications (Chu et al. 2011). First, 59 nt DNA probes were biotinylated through terminal transferase (New England Biolabs). Intensive crosslinking of cells was performed in the following sequence: two rounds of 3000J UV treatment on ice, 0.8% of formaldehyde (FMA) for 10 minutes, 2mM of DSP (Dithiobis [succinimidyl propionate]) for 30 minutes, and followed by 3.7% of FMA for 10 minutes at room temperature. Crosslinked cell pellets were lysed. Chromatin was fragmented into a range of 2 - 5 kb by sonication. Hybridization, washing and elution steps were performed as described previously, except that we included an additional stringent wash (0.1x SSC). After elution and reverse crosslinking, RNA was further extracted by TRIzol reagent (Life Technologies).
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrived RNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 210 seconds. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "AGCTCAT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer. ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions.

value: embryonic stem cells

value: ChIRP probes targeting Haunt mRNA

value: AGCTCAT


title: XP-C CPD XR-seq, rep2


title: NHF1 CPD XR-seq, rep1

description:
Source of NHF1 cell line: W.K. Kaufmann, UNC, Chapel Hill (Heffernan et al. 2002).
Excised oligomer released in Nucleotide Excision Repair (XR-seq).
Processed data files:
CPD1h_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw
CPD1h_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw

source_name: NHF1, CPD


title: NHF1 CPD XR-seq, rep2


title: 1059-1

status: Public on Apr 18 2015

city: Houston

first: Randall

middle: J

last: Olsen

state: TX

address: 6565 Fannin Street; MS:B250

department: Pathology and Genomic Medicine

institute: Houston Methodist Research Institute

description:
group A streptococcus
MgaH273A

data_processing:
Reads obtained per sample  were mapped to the MGAS15252 genome using the CLC-Biosystems WorkBench, version 7 (CLC Bio).
Expression values were obtained as RPKM (reads per kilobase of exon model per million mapped reads) and normalized using Quantile normalization
Differential expression was computed using a Baggerly’s test on proportions and P-values correction for multiple testing was performed using Bonferroni correction.
genome build: ASM25090v1
Supplementary_files_format_and_content: Excel data sheet containing comparisions between all six strains.

organism: Streptococcus pyogenes MGAS15252

source_name: bacteria grown in THY broth

growth_protocol: GAS was grown routinely on Todd–Hewitt broth containing 0.2% yeast extract (THY; DIFCO) at 37˚C with 5% CO2.

extract_protocol:
RNA isolation and purification were performed using an RNeasy mini kit (Qiagen) and treated with DNAse using the TURBO DNA-free kit (Ambion). Purified RNA was evaluated for quality and concentration with an Agilent 2100 Bioanalyzer and fluorometric quantitation (Qubit RNA assay kit, Life Technologies). The ribosomal RNA was then removed using a Ribo-Zero treatment kit (Epicenter) and further purified using the Min-Elute RNA purificiation kit (Qiagen).
Adaptor tagged libraries were synthesized  using the ScriptSeq V2 RNA-Seq library preparation kit (Epicentre).  The directional cDNA library was prepared and indexed at single end using reverse primers (Epicentre) and amplified by 15 cycles of PCR.


title: 1059-2

description:
group A streptococcus
MgaH273A


title: 1029-3

description:
group A streptococcus
MgaH273D


title: 1013-2

description:
group A streptococcus
MgaH207D


title: 1029-2

description:
group A streptococcus
MgaH273D


title: 1011-3

description:
group A streptococcus
mga deletion strain


title: 1011-2


title: 1013-3

description:
group A streptococcus
MgaH207D


title: 1029-1

description:
group A streptococcus
MgaH273D


title: 1059-3

description:
group A streptococcus
MgaH273A


title: 1011-1


title: 1012-1

description:
group A streptococcus
MgaH207A


title: 1013-1

description:
group A streptococcus
MgaH207D


title: 1010-3

description:
group A streptococcus
wild-type GAS


title: WT, pre-fragmented, Replicate 1

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

data_processing:
Unique Molecular Index (UMI) trimmed and duplicates removed using Umitools
Alignment to SacCer1 using Bowtie
Calculation of 5' end coverage and conversion to bedGraph format using bedtools
Genome_build: SacCer1
Supplementary_files_format_and_content: Genome Coverage of 5' end of reads in bedGraph format

molecule: polyA RNA

source_name: WT, pre-fragmented

growth_protocol: Yeast cells were grown overnight in YEPD at 30ºC, then diluted back to OD600 0.15 and grown to mid-log phase before treatment

extract_protocol:
Total RNA was obtained via hot-phenol extraction, then treated with TURBO DNase (Ambion).  oligo-dT beads (Life Technologies) were used to enrich for polyA RNA
RNAs with 5OH termini were ligated to a DNA/RNA hybrid oligo linker containing a 5' desthiobiotin, 8 nucleotide unique molecular index (UMI), and a 3'-phosphate using purified E. coli RtcB. Samples were electrophoresed on denaturing gel and excised. Samples were reverse transcribed with Protoscript II RT (NEB) and a degenerate primer, then purified with RNAClean XP Beads (Beckman-Coulter). DNA Polymerase I (Enzymatics), E Coli Ligase (Enzymatics), and RNAse H (NEB) were used to perform second strand synthesis.  Following purification with AMPure XP beads (Beckman-Coulter), samples were purified with Streptavidin Dynabeads (Invitrogen).  Samples were PCR amplified using barcoded Illumina Truseq primers and purified with SPRIselect beads (Beckman-Coulter).  Samples were quantitated with Qubit before sequence submission.

treatment_protocol: At mid-log phase (OD600 ~0.6), cells were treated with Tunicamycin (Sigma) 2.5ug/uL or DMSO control

value: MATalpha his3-delta1 leu2-delta0 lys2-delta0 ura3-delta0

value: Fragmentation Reagent (Ambion)


title: 1010-2

description:
group A streptococcus
wild-type GAS


title: xrn1∆, Tunicamycin treatment, SAP treatment, Replicate 2

source_name: xrn1-delta Tunicamycin treatment, SAP treatment

value: MATalpha his3-delta1 leu2-delta0 lys2-delta0 ura3-delta0 xrn1::hygMX

value: Tunicamycin 2.5ug/uL, recombinant Shrimp Alkaline Phosphatase (Affymetrix)


title: 1010-1

description:
group A streptococcus
wild-type GAS


title: WT, Tunicamycin treatment, SAP treatment, Replicate 1


title: xrn1∆, DMSO control, SAP treatment, Replicate 1

source_name: xrn1-delta DMSO control, SAP treatment

value: DMSO, recombinant Shrimp Alkaline Phosphatase (Affymetrix)


title: xrn1∆, Tunicamycin treatment, SAP treatment, Replicate 1


title: WT, Tunicamycin treatment, SAP treatment, Replicate 2


title: xrn1∆, DMSO control, SAP treatment, Replicate 2


title: WT, DMSO control, SAP treatment, Replicate 1

source_name: WT, DMSO control, SAP treatment


title: WT, DMSO control, SAP treatment, Replicate 2


title: MEF_KO_RNA_dox_rep2

city: Kansas City

first: Scott

middle: T

last: Younger

state: MO

address: 2401 Gillham Road

institute: Children's Mercy Kansas City

data_processing:
RNA-Seq Read Alignment: TopHat 2.0 with default options using UCSC known genes from hg19 or mm9 as reference transcriptome
RNA-Seq Differential Expression: Cuffdiff 2.1 with default options using UCSC known genes from hg19 or mm9 as reference transcriptome
ChIP-Seq Read Alignment: Bowtie 2.0 with default options using hg19 or mm9 as reference genome
ChIP-Seq general peak calling: Scripture using hg19 or mm9 as reference genome
ChIP-Seq significant peak calling: Cuffdiff 2.0 using Scripture output as peak reference
Genome_build: hg19 / mm9
Supplementary_files_format_and_content: TXT files are expression matrices with FPKM values for each sample / BED files are p53 ChIP-Seq peak coordinates

source_name: Mouse embryonic fibroblasts

extract_protocol:
RNA: TriZol / ChIP: Immunopurification of DNA followed by phenol:chloroform extraction
Illumina TruSeq

value: 0.2 ug/ml Doxorubicin 6 hours


title: 1012-2

description:
group A streptococcus
MgaH207A


title: 1012-3

description:
group A streptococcus
MgaH207A


title: xrn1∆, Tunicamycin treatmentl, Replicate 2

source_name: xrn1-delta Tunicamycin treatmentl

value: Tunicamycin (Sigma) 2.5ug/uL


title: MEF_KO_RNA_unt_rep2


title: MEF_KO_RNA_unt_rep1


title: MEF_KO_RNA_dox_rep1


title: xrn1∆, DMSO control, Replicate 2

source_name: xrn1-delta DMSO control

value: DMSO


title: xrn1∆, Tunicamycin treatment, Replicate 1

source_name: xrn1-delta Tunicamycin treatment


title: WT, Tunicamycin treatment, Replicate 1

source_name: WT, Tunicamycin treatment


title: MEF_WT_RNA_unt_rep2


title: GM00011_ChIP_p53

source_name: Fetal skin fibroblasts

value: 0.2 ug/ml Doxorubicin 12 hours


title: MEF_WT_RNA_dox_rep2


title: MEF_WT_RNA_unt_rep3


title: WT, DMSO control, Replicate 2

source_name: WT, DMSO control


title: WT, Tunicamycin treatment, Replicate 2


title: MEF_WT_RNA_dox_rep1


title: WT, DMSO control, Replicate 1


title: GM00011_ChIP_input

value: input


title: MEF_WT_RNA_unt_rep1


title: GM06170_ChIP_p53


title: MEF_ChIP_p53


title: MEF_ChIP_input


title: GM00011_RNA_dox_rep2


title: GM06170_ChIP_input


title: GM00011_RNA_dox_rep1


title: GM00011_RNA_unt_rep2


title: GM00011_RNA_unt_rep1


title: GM06170_RNA_dox_rep2


title: GM06170_RNA_dox_rep1


title: MEF_WT_RNA_dox_rep3


title: GM06170_RNA_unt_rep2


title: xrn1∆, DMSO control, Replicate 1


title: GM06170_RNA_unt_rep1


title: ChIP RXR 24h

status: Public on Apr 17 2015

city: Villeurbanne

first: Philippe

last: Veber

address: 16 rue Raphael Dubois

country: France

institute: CNRS

description:
chIP-RXR-24h
Processed data files: RAR_RXR_regions.bed, RAR_RXR_regions.xlsx

data_processing:
ChIP-seq read alignment: bowtie version 0.12.9, -n 3 -e 70 -m 1
Peak calling: MACS version 1.4.2, --pvalue 1e-3
RNA-seq read alignment: Tophat version 2.0.7, default.
RNA-seq read assignment to genes: htseq-count, default.
Differential gene expression detection: DESeq
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: RAR_RXR_regions.bed: BED, binding regions for RAR/RXR obtained via the protocol described in the associated paper.
Supplementary_files_format_and_content: RAR_RXR_regions.xlsx: Excel spreadsheet, binding regions for RAR/RXR obtained via the protocol described in the associated paper with binding intensities from all ChIP-seq samples.
Supplementary_files_format_and_content: Gene_expression.xlsx: Excel spreadsheet, gene expression values for all RNA-seq samples.
Supplementary_files_format_and_content: mRNA_*.counts.gz: Tab-separated text file, for mRNA-seq samples, number of reads falling in each gene of the Ensembl annotation (v63), as obtained with HTseq-count.

source_name: F9 cells, RA, 24h, RXR ChIP

growth_protocol: Mouse embryonic carcinoma F9 cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) containing 4.5% glucose, L-glutamine, and sodium pyruvate supplemented with 5% fetal bovine serum, 0.1 mg/ml streptomycin and 100 U/ml penicillin and cultured at 37°C in a humidified 5% CO2 atmosphere. 3.5 x 10^5 cells were seeded in gelatine-coated 100 mm tissue culture plates (0.1%) 16 hours prior to drug treatment.

extract_protocol:
ChIP-seq: Cells were cross-linked by a two-step procedure, with 2mM disuccinimidyl glutarate for 30 minutes at room temperature and then with 1% formaldehyde for 10 min at 37°C. The ChIP lysis buffer composition was 50mM Tris-HCl pH 8, 10mM EDTA, 1% SDS and 1X Protease Inhibitor Cocktail w/o EDTA. After lysis, chromatin extract were sonicated to reduce the length of DNA fragments to 200-400 bp using a Diagenode Bioruptor.
ChIP-seq library: ChIP-seq libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Sequencing was performed on Illumina Genome Analyzer IIx (IGBMC) single-end 36bp.

treatment_protocol: All-trans retinoic acid (ATRA) was dissolved in 100% DMSO at a concentration of 1 x 10-2 M, and diluted in cell culture medium to a final concentration of 1 x 10-7 M. Control samples were treated with 0.001 % DMSO.

value: embryonal carcinoma cell line

value: all-trans retinoic acid

tag: time after ra stimulation

value: anti-panRXR (Santa Cruz, Sc-553)


title: ChIP RXR 48h

description:
chIP-RXR-48h
Processed data files: RAR_RXR_regions.bed, RAR_RXR_regions.xlsx

source_name: F9 cells, RA, 48h, RXR ChIP

tag: treatment


title: ChIP RAR 2h

description:
chIP-RAR-2h
Processed data files: RAR_RXR_regions.bed, RAR_RXR_regions.xlsx

source_name: F9 cells, RA, 2h, RAR ChIP

value: anti-panRAR (Santa Cruz, Sc-773)


title: mRNA DMSO 24h

description:
mRNA-DMSO-24h
mRNA
Processed data file: Gene_expression.xlsx

source_name: F9 cells, DMSO, 24h

extract_protocol:
RNA-seq: Total RNA was extracted with TRIzol (Invitrogen) according to supplier recommendations, and treated with DNase I. The concentrations of all the RNA samples were measured using the NanoDrop (Thermo Scientific) and their integrity was determined using an Agilent 2100 Bioanalyzer. RNA-seq libraries were made from samples with a RNA Integrity Number (RIN) of at least 8.0.
RNA-seq library preparation kit: RNA-seq libraries were prepared using the True Seq V2 (Illumina) according to supplier's recommendations. Sequencing was performed on Illumina Genome Analyzer IIx (IGBMC), single-end 72bp or Illumina HiSeq 2000 (ProfileXpert), single-end 50bp.


title: ChIP RXR 2h

description:
chIP-RXR-2h
Processed data files: RAR_RXR_regions.bed, RAR_RXR_regions.xlsx

source_name: F9 cells, RA, 2h, RXR ChIP


title: mRNA 12h, rep 1

description:
mRNA-12h-1
mRNA
Processed data file: Gene_expression.xlsx

source_name: F9 cells, RA, 12h


title: mRNA 24h, rep 1

description:
mRNA-24h-1
mRNA
Processed data file: Gene_expression.xlsx

source_name: F9 cells, RA, 24h


title: mRNA DMSO 48h

description:
mRNA-DMSO-48h
mRNA
Processed data file: Gene_expression.xlsx

source_name: F9 cells, DMSO, 48h


title: ChIP RAR 0h

description:
chIP-RAR-0h
Processed data files: RAR_RXR_regions.bed, RAR_RXR_regions.xlsx

source_name: F9 cells, RA, 0h, RAR ChIP


title: ChIP RAR 48h

description:
chIP-RAR-48h
Processed data files: RAR_RXR_regions.bed, RAR_RXR_regions.xlsx

source_name: F9 cells, RA, 48h, RAR ChIP


title: mRNA 0h, rep 1

description:
mRNA-0h-1
mRNA
Processed data file: Gene_expression.xlsx

source_name: F9 cells, RA, 0h


title: ChIP RAR 24h

description:
chIP-RAR-24h
Processed data files: RAR_RXR_regions.bed, RAR_RXR_regions.xlsx

source_name: F9 cells, RA, 24h, RAR ChIP


title: mRNA 48h, rep 1

description:
mRNA-48h-1
mRNA
Processed data file: Gene_expression.xlsx

source_name: F9 cells, RA, 48h


title: mRNA 6h, rep 1

description:
mRNA-6h-1
mRNA
Processed data file: Gene_expression.xlsx

source_name: F9 cells, RA, 6h


title: WCE 0h

description:
WCE-0h
WCE-Seq
Processed data files: RAR_RXR_regions.bed, RAR_RXR_regions.xlsx

source_name: F9 cells, RA, 0h, total chromatin


title: bursa_K27_L72_inf_10_2

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

data_processing:
Sequence reads were aligned to the chicken genome version galGal3 using bowtie version 0.12.7 (Langmead et al. 2009). Default alignment policies of bowtie were enforced: a valid alignment could have a maximum of two mismatches and if a read aligned equally well to multiple places in the genome, one was chosen at random. If multiple r\eads mapped to the same genomic location, only one was kept to avoid amplification bias.
Peak-calling was carried out using the WaveSeq algorithm (Mitra et al. 2012). We used recommended values for parameters: for H3K4me3 data, the mother function was ‘morlet’ and gap size was 2 (400 bp), while for H3K27me3, the mother function was ‘mexican hat’ and gap size was 10. For increased sensitivity for the broad H3K27me3 mark, the p-value threshold was lowered to 0.4.
Genome_build: galGal3
Supplementary_files_format_and_content: bedGraph files were generated using WaveSeqR package (http://r-forge.r-project.org/projects/waveseqr/). Redundant reads were removed and interval size was 200 bp. Scores represent total read count within corresponding genomic interval.
Supplementary_files_format_and_content: Peak files were generated using WaveSeqR. Each row represents one peak with the following information in six columns: chromosome, start, end, read count, p-value, adjusted p-value.

organism: Gallus gallus

source_name: bursa tissue

growth_protocol: Two specific-pathogen-free inbred lines of White Leghorn either resistant (L63) or susceptible (L72) to MD were hatched, reared and maintained in Avian Disease and Oncology Laboratory (ADOL, Michigan, USDA).

extract_protocol:
About 30 mg bursa samples were digested with micrococcal nuclease to obtain mononucleosomes.
MNase digestion was followed by end-repair with PNK and Klenow enzymes (NBE, Ipswich, MA, USA) and ChIP with the specific antibody (H3K4me3: Millipore, Cat. #17-614; H3K27me3: Abcam, Cat. # ab6002). This was followed by addition of 3’ adenine, Illumina adaptor ligation, PCR amplification (17 cycles) and size-selection (~ 150 bp), cluster generation and sequencing on the Illumina Hi-Seq 2000.

treatment_protocol: Eight chickens from each line were injected intra-abdominally with a partially attenuated very virulent plus strain of MDV (648A passage 40) at 14 days after hatch with a viral dosage of 500 plaque-forming units (PFU). Another eight chickens were not infected as age-matched controls. Infected and control chickens (n=4) from both lines were terminated at 5 or 10dpi to collect bursa tissues. All procedures followed the standard animal ethics and use guidelines of ADOL.

tag: histone mark

tag: chicken line

tag: days post infection

tag: condition

value: infected


title: bursa_K27_L72_non_10_1

value: control


title: bursa_K27_L72_non_10_2


title: bursa_K27_L72_inf_10_1


title: HFD Liver treated with vehicle replicate 2

city: La Jolla

first: Ruth

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
Read alignment and junction mapping was accomplished using TopHat2 v2.0.4 using a 25 bp 5’ segment seed for initial mapping followed by differential gene expression analysis using Cuffdiff v2.0.2 to map reads to the reference genome annotation.
BEDTools was used to generate bedGraphs from the bam files generated from TopHat2.
Bigwig files were generated from bedGraphs using the bedGraph to bigwig command from UCSC.
Genome_build: NCBI mouse build 37.2
Supplementary_files_format_and_content: Bigwig files for UCSC browser viewing

source_name: mouse liver

extract_protocol: Standard Illumina RNA library construction with multiplexing

treatment_protocol: Wild-type male mice were maintained on a HFD for 3 months, starting at 2 months of age, and treated with amlexanox or vehicle control by oral gavage, liver samples were collected 4 hours latter

tag: strain

value: wild type

tag: gender

value: male

tag: age

value: 5 months

tag: growth protocol

value: High-fat Diet

value: Vehicle

tag: barcode info

value: ACAGTG


title: HFD Liver treated with Amlexanox replicate 2

tag: genotype/variation

value: Amlexanox


title: bursa_K27_L72_non_5_1


title: HFD Liver treated with vehicle replicate 3

value: GCCAAT


title: HFD Liver treated with Amlexanox replicate 1

value: CGATGT


title: bursa_K27_L72_non_5_2


title: HFD Liver treated with Amlexanox replicate 3


title: HFD Liver treated with vehicle replicate 1


title: bursa_K27_L72_inf_5_2


title: ChIP RXR 0h

description:
chIP-RXR-0h
Processed data files: RAR_RXR_regions.bed, RAR_RXR_regions.xlsx

source_name: F9 cells, RA, 0h, RXR ChIP

tag: cell line

tag: cell type

tag: chip antibody


title: bursa_K27_L63_non_10_2


title: mRNA 0h, rep 3

description:
mRNA-0h-3
mRNA
Processed data file: Gene_expression.xlsx


title: bursa_K27_L72_inf_5_1


title: bursa_K27_L63_non_10_1


title: mRNA 0h, rep 2

description:
mRNA-0h-2
mRNA
Processed data file: Gene_expression.xlsx


title: mRNA 12h, rep 2

description:
mRNA-12h-2
mRNA
Processed data file: Gene_expression.xlsx


title: mRNA 6h, rep 2

description:
mRNA-6h-2
mRNA
Processed data file: Gene_expression.xlsx


title: bursa_K27_L63_inf_10_2


title: mRNA 24h, rep 2

description:
mRNA-24h-2
mRNA
Processed data file: Gene_expression.xlsx


title: Trans_Day4_Rep4

city: Seattle

first: Gwenn

middle: M M

last: Hennon

state: WA

address: 616 NE Northlake

department: Oceanography

institute: University of Washington

data_processing:
convert to fastq: raw SOLiD files were converted to fastq files using solid2fastq version v0.5_dev_0.4.18-6-gb20983c from the SEAStAR package
trimming step: Reads were quality controlled (using a cut-off of p =0.99 and minimum length =30); software trimfastq version v0.5_dev_0.4.18-6-gb20983c from SEAStAR package
alignment step: trimmed reads were aligned to T. pseudonana gene models using the Burrows-Wheeler Alignment tool (bwa: version 0.5.9-r26-dev)
counting step: reads were counted for each gene model using ref_select (version v0.5_dev_0.4.18-6-gb20983c from the SEAStAR package)
removal of antisense reads: kept reads that were reverse aligned to the gene models using gawk (version 4.0.1) due to library prep which created antisense amplified mRNA
Spearman correlation: Read counts from all transcriptomes were first normalized by the trimmed mean of M-values method (TMM: R package, edgeR version 3.6.8), then each gene was normalized to its own average expression level at low CO2  (< 312 μatm for transition samples and < 350 μatm for steady-state samples) and log2 transformed. The normalized gene expression data was tested for correlation to CO2 using the Spearman rank correlation test (cor.test, R stats version 3.1.1).
Gene clustering analysis: A dataset of 98 microarray and RNAseq samples representing ten experiments (Mock et al. 2008, Carvalho et al. 2011, Thamatrakoln et al.2012, Shrestha et al. 2012, Ashworth et al. 2013, Bender et al. 2014) was used to identify co-expressed gene clusters. All RNA-seq data were TMM normalized, and log2 ratios vs. triplicate control samples were combined with microarray log2 ratios. To estimate the co-expression of transcripts, Pearson pairwise correlation distances were computed across all samples following normalization such that all within-sample standard deviations were equal to one. Hierarchical clustering of these distances using Ward’s method (fastcluster, http://danifold.net/fastcluster.html) identified a hierarchy of co-expressed genes, from which 400 co-expressed groups were selected using arbitrary cut height.
Genome_build: Joint Genome Institute: thaps3 extended models
Supplementary_files_format_and_content: tab delimited files with columns of sample IDs and rows of read counts mapping to gene identifiers (JGI Thaps3 ID)

organism: Thalassiosira pseudonana

source_name: whole cell

growth_protocol: nitrate limited chemostats were used to maintain cells at 70% of their max growth rate (1.5 day-1)

extract_protocol:
ToTALLY RNA kit (Life Technologies)
Messenger RNA was selectively amplified using MessageAmp II aRNA Amplification kit (Life Technologies) and used to prepare SOLiD barcoded libraries (SOLiD Total RNA-seq kit, Life Technologies).  Libraries were sequenced on a SOLiD 5500XL sequencer in two paired-end runs: one containing steady-state barcoded libraries and one containing transition barcoded libraries.

treatment_protocol: CO2 concentrations were maintained by bubbling the media upstream of the chemostats and was measured in the chemostat bottles on the day of sampling

tag: growth condition

value: transition

tag: co2 level or day of experiment

tag: co2 concentration (uatm)


title: bursa_K27_L63_non_5_2


title: bursa_K27_L63_inf_10_1


title: bursa_K27_L63_non_5_1


title: Trans_Day2_Rep4


title: bursa_K27_L63_inf_5_2


title: Trans_Day3_Rep4


title: bursa_K27_L63_inf_5_1


title: bursa_K4_L72_non_10_2


title: mRNA 48h, rep 2

description:
mRNA-48h-2
mRNA
Processed data file: Gene_expression.xlsx

tag: treatment

tag: time after ra stimulation


title: Trans_Day1_Rep4


title: Trans_Day4_Rep3


title: bursa_K4_L72_inf_10_1

tag: histone mark

tag: chicken line


title: bursa_K4_L72_inf_10_2

tag: days post infection

tag: condition


title: bursa_K4_L72_non_5_2


title: Trans_Day3_Rep3


title: Trans_Day1_Rep3


title: mRNA 0h, rep 4

description:
mRNA-0h-4
mRNA
Processed data file: Gene_expression.xlsx


title: Trans_Day4_Rep2


title: Trans_Day3_Rep2


title: bursa_K4_L63_non_10_2


title: bursa_K4_L72_non_5_1


title: Trans_Day2_Rep2


title: bursa_K4_L72_inf_5_1


title: Trans_Day3_Rep1


title: Trans_Day4_Rep1


title: bursa_K4_L72_inf_5_2


title: bursa_K4_L63_inf_10_2


title: Trans_Day2_Rep3


title: High_CO2_Rep4

value: steady-state

value: High


title: Trans_Day1_Rep1


title: bursa_K4_L72_non_10_1


title: bursa_K4_L63_non_5_1


title: bursa_K4_L63_non_5_2


title: bursa_K4_L63_inf_5_1


title: Med_CO2_Rep4

value: Med


title: High_CO2_Rep1


title: bursa_K4_L63_inf_10_1


title: High_CO2_Rep3


title: Med_CO2_Rep2


title: Med_CO2_Rep3


title: High_CO2_Rep2


title: bursa_K4_L63_inf_5_2


title: Low_CO2_Rep4

value: Low


title: Trans_Day1_Rep2


title: bursa_K4_L63_non_10_1


title: Trans_Day2_Rep1


title: Low_CO2_Rep3


title: Low_CO2_Rep2


title: Br_12h

city: Shenzhen

first: Yabing

last: Zhu

state: Guangdong

address: Main Building,Beishan Industrial Zone,Beishan Road,Yantian District

institute: BGI-tech

data_processing:
Base-calling performed using Illunima HiSeq 2000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Larimichthys crocea whole genes using SOAPaligner v2.21 with parameters -m 0 -x 1000 -s 40 -l 32 -v 5 -r 2 -p 5
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nature Methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Gene models derived with Glean pipeline (unpublished)
Genome_build: L_crocea_1.0
Supplementary_files_format_and_content: bedGraph and rpkm files

organism: Larimichthys crocea

source_name: Brain, 12h hypoxia

growth_protocol: Grow to body weight at 90-100 g from mariculture farm

extract_protocol:
Total polyA RNA was extracted using Trizol and Invitrogen
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: brain


title: Br_24h

source_name: Brain, 24h hypoxia


title: Br_3h

source_name: Brain, 3h hypoxia


title: Br_6h

source_name: Brain, 6h hypoxia


title: Br_1h

source_name: Brain, 1h hypoxia


title: Br_48h

source_name: Brain, 48h hypoxia


title: RybB

status: Public on Apr 16 2015

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

data_processing:
Basecalls performed using MCS Version 2.4.1.3
Reads were aligned to the Escherichia coli K12 genome assembly using Bowtie for Illumina (Galaxy Project)
Read counts were normalized by coverage according to Oshlack et al., 2010
Genome_build: Escherichia coli K12
Supplementary_files_format_and_content: tab-delimited text file include normalized reads for each sample and MS2-RybB/RybB ratio

organism: Escherichia coli K-12

source_name: Bacterium

growth_protocol: The bacterial strains were grown in 100mL of LB medium to an OD600nm of 0.5

extract_protocol:
Cells were resuspended in 2 mL of buffer A and lysed using a French Press (430 psi, three times). Lysate was then cleared by centrifugation. The soluble fraction was subjected to affinity chromatography. The column was prepared by adding 75 µL of amylose resin (New England Biolabs) to Bio-Spin disposable chromatography columns (Bio-Rad). The column was washed with 3 mL of buffer A. Next, 100 pmol of MS2-MPB protein was immobilized on the amylose resin, and the column was washed with 2 mL of buffer A. The cleared lysate was then loaded onto the column, which was washed with 5 mL of buffer A. RNA was eluted from the column with 1 mL of buffer A containing 15 mM maltose. Eluted RNA was extracted with phenol-chloroform, followed by ethanol (3 vol) precipitation of the aqueous phase in the presence of 20 mg of glycogen. RNA samples were treated with TURBO DNA-free (DNase treatment) and precipitated again.
cDNA libraries were prepared with ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre)

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2-RybB/RybB during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.

tag: strain

value: MG1655 rne131 delta-rybB

tag: growth phase

value: exponential phase (OD600nm=0.5)


title: MS2-ITSmetZWV

data_processing:
Basecalls performed using MCS Version 2.4.1.3
Reads were aligned to the Escherichia coli K12 genome assembly using Bowtie for Illumina (Galaxy Project)
Read counts were normalized by coverage according to Oshlack et al., 2010
Genome_build: Escherichia coli K12
Supplementary_files_format_and_content: tab-delimited text file include normalized reads for each sample and MS2-ITSmetZWV/ITSmetZWV ratio

growth_protocol: For ITSmetZW and ITSmetWV, cells were harvested in exponential (OD600nm=0.5; 50 mL LB medium) and in stationary phase (OD600nm=1; 50 mL LB medium).

extract_protocol:
Cells were resuspended in 3 mL of buffer A and lysed using a French Press (430 psi, four times). Lysate was then cleared by centrifugation. The soluble fraction was subjected to affinity chromatography. The column was prepared by adding 100 µL of amylose resin (New England Biolabs) to Bio-Spin disposable chromatography columns (Bio-Rad). The column was washed with 3 mL of buffer A. Next, 200 pmol of MS2-MPB protein was immobilized on the amylose resin, and the column was washed with 2 mL of buffer A. The cleared lysate was then loaded onto the column, which was washed with 8 mL of buffer A. RNA was eluted from the column with 1 mL of buffer A containing 15 mM maltose. Eluted RNA was extracted with phenol-chloroform, followed by ethanol (3 vol) precipitation of the aqueous phase in the presence of 20 mg of glycogen. RNA samples were treated with TURBO DNA-free (DNase treatment) and precipitated again.
cDNA librairies were prepared with ScriptMinerTM Small RNA-Seq Library Preparation Kit to target small RNA fragments (Epicentre).

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2-ITSmetZWV/ITSmetZWV during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.

value: exponential and stationary phases


title: ITSmetZWV


title: 2 ck

city: Shanghai

first: Yu

last: Sang

address: 280 S. Chongqing Rd

department: Microbiology and Immunology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Firstly, remove the low sequence to get the clean reads.
Then mapped to the gene sequence of Salmonella enterica serovar Typhimurium 14028S with bowtie2 software.
Count the gene reads number from each sample respectively, convert to RPM (ref: Mortazavi, A., et al., Nat Methods, 2008)
Calculate expression abundance difference of each gene in two groups of samples
genome build: NCBI Reference Sequence: NC_016856.1
Supplementary_files_format_and_content: txt files include processed file (remove joint, merge the same sequence), sequence arranged for two columns: SEQ and COUNT

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

growth_protocol: The overnight culture was diluted in 5 ml pH 7.7 E medium supplemented with 0.4% glucose (EG medium), followed by incubation at 37℃ with shaking. When OD600 reached to 0.4, the culture was centrifuged at 2,500 g for 4 min, washed with pH 3.0 EG medium once, and then resuspended in 5 ml pH 3.0 EG medium. Control culture was similarly treated instead with pH 7.7 EG medium.

extract_protocol:
RNA was isolated by using TRIzol (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The two cultures were further incubated for 15 min, and harvested for RNA isolation.

value: log stage

tag: genotype

value: wild type


title: L3_wt_2

city: East Lansing

first: Cheng

last: Peng

state: MI

address: 603 Wilson Rd

institute: Michigan State University

description:
replicate: 2
multiplex barcode: ACTTGA

data_processing:
The sequencing adapters were removed using the following parameters in Trimmomatic version 0.30 (Bolger et al., 2014): ILLUMINACLIP: TruSeq3-SE, SLIDINGWINDOW: 4:15, and MINLEN:35.
Processed reads were filtered by fastq_quality_filter in the FASTX-toolkit version 0.0.13.2 (http://hannonlab.cshl.edu/fastx_toolkit/index.html), satisfying the criterion that > 85% bases must have Q-score ≥ 20.
The processed and filtered reads were mapped to the A. thaliana reference genome (TAIR10) using TopHat version 1.4.1 (Trapnell et al., 2009), sorted by SAMtools version 0.1.19 (Li et al., 2009), and analyzed with Cuffdiff version 2.1.1 (Trapnell et al., 2013).
The read counts were calculated by HTSeq-count using union mode and TAIR10 annotation.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample, calculated by HTSeqCount (union mode)

organism: Arabidopsis thaliana

source_name: rosette leaves, 8h light/16h dark for 72h

growth_protocol: Plants grown on soil under 8h light/16h dark for 5 weeks

extract_protocol:
Total RNA from 9th to 12th rosette leaves was extracted using RNeasy plant mini kit (Qiagen) and on-column digestion performed with RNase-free DNase Set (Qiagen). RNA quality was assessed using the Agilent 2100 Bioanalyzer with the RNA 6000 Pico Chip (Agilent Technologies).
Library construction was conducted using the Illumina Tru-Seq Stranded kit, following the manufacturer’s protocols.

treatment_protocol: Treated in prolonged darkness for 0, 6, 24, 48 or 72h, or kept in 8h light/16h dark for 72h

tag: age

value: 5 weeks in 8h light/16h dark


title: 1 acid


title: L3_wt_1

description:
replicate: 1
multiplex barcode: ACTTGA


title: W23708/7998_6-28-10_L8.D701

city: Foster City

first: Li

last: Li

address: 333 Lakeside Drive

institute: Gilead Sciences

description: Processed data: rsem_gcounts_matrix.txt

data_processing:
Clipping adapters and low-quality bases.
RSEM and BWA.
Genome_build: Marmota monax transcriptome assembly
Supplementary_files_format_and_content: rsem_gcounts_matrix.txt: Tab-delimited text file with raw gene level counts from RSEM output.
Supplementary_files_format_and_content: Trinity.annot.fa: FASTA file with assembled sequences.

organism: Marmota monax

source_name: Liver, GS-9620, 78 days

extract_protocol:
Total RNA was extracted from liver biopsies.
cDNA libraries were constructed using the TruSeq Stranded Total RNA-RiboZero Gold Sample Prep Kit (Illumina, San Diego, CA).

treatment_protocol: Woodchucks chronically infected with woodchuck hepatitis virus (WHV) were treated with placebo or GS9620 (5mg/kg QW).

tag: disease state

tag: treatment group

tag: developmental stage

value: adult

value: liver

tag: time (day)

tag: animal id


title: V02926/7969_12-17-10_L3

description: Processed data: rsem_gcounts_matrix.txt

source_name: Liver, GS-9620, 250 days

value: chronically infected with woodchuck hepatitis virus (WHV)


title: W23708/7989_9-27-10_L6.D706

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/7989_6-28-10_L6.D705

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/7969_6-28-10_L4.D710

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/7950_6-28-10_L3.D705

description: Processed data: rsem_gcounts_matrix.txt


title: L3_ivd_2

description:
replicate: 2
multiplex barcode: TTAGGC


title: L3_ivd_1

description:
replicate: 1
multiplex barcode: TTAGGC


title: W23708/7998_6-7-10_L8.D712

description: Processed data: rsem_gcounts_matrix.txt

source_name: Liver, GS-9620, 57 days


title: L3_hml_2

description:
replicate: 2
multiplex barcode: ATCACG


title: W23708/7994_6-7-10_L7.D709

description: Processed data: rsem_gcounts_matrix.txt


title: D6h_wt_2

description:
replicate: 2
multiplex barcode: ATTCCT

source_name: rosette leaves, prolonged darkness for 6h


title: Br_0h

source_name: Brain, 0h hypoxia


title: W23708/7998_12-17-10_L8.D702

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/7994_12-17-10_L7.D710

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/7950_12-17-10_L3.D706

description: Processed data: rsem_gcounts_matrix.txt


title: V02966/7969_6-9-10_L5

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/7950_6-7-10_L2.D704

description: Processed data: rsem_gcounts_matrix.txt


title: D6h_wt_1

description:
replicate: 1
multiplex barcode: GTGAAA


title: D6h_ivd_2

description:
replicate: 2
multiplex barcode: ACTGAT


title: MS2-RybB


title: D6h_hml_2

description:
replicate: 2
multiplex barcode: GAGTGG


title: D6h_ivd_1

description:
replicate: 1
multiplex barcode: GTCCGC


title: W23708/79941_5-4-10_L6.D708

description: Processed data: rsem_gcounts_matrix.txt

source_name: Liver, GS-9620, 23 days


title: Low_CO2_Rep1

tag: growth condition

tag: co2 level or day of experiment

tag: co2 concentration (uatm)


title: W23708/7989_6-7-10_L5.D704

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/7978_5-4-10_L5.D701

description: Processed data: rsem_gcounts_matrix.txt


title: D3_wt_2

description:
replicate: 2
multiplex barcode: CGTACG

source_name: rosette leaves, prolonged darkness for 72h


title: V02926/7989_5-4-10_L4

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/7950_5-4-10_L2.D703

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/7969_5-4-10_L3.D708

description: Processed data: rsem_gcounts_matrix.txt


title: V02966/7933_5-4-10_L4

description: Processed data: rsem_gcounts_matrix.txt


title: D3_wt_1

description:
replicate: 1
multiplex barcode: ATGTCA


title: L3_hml_1

description:
replicate: 1
multiplex barcode: ATCACG


title: D3_ivd_2

description:
replicate: 2
multiplex barcode: GTTTCG


title: W23708/7998_4-5-10_L7.D711

description: Processed data: rsem_gcounts_matrix.txt

source_name: Liver, GS-9620, -14 days


title: D3_ivd_1

description:
replicate: 1
multiplex barcode: AGTTCC


title: D3_hml_2

description:
replicate: 2
multiplex barcode: GTGGCC


title: W23708/7978_4-6-10_L4.D712

description: Processed data: rsem_gcounts_matrix.txt


title: D3_hml_1

description:
replicate: 1
multiplex barcode: AGTCAA


title: W23708/7969_4-5-10_L3.D707

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/7950_4-5-10_L2.D702

description: Processed data: rsem_gcounts_matrix.txt


title: D2_wt_2

description:
replicate: 2
multiplex barcode: GGCTAC

source_name: rosette leaves, prolonged darkness for 48h


title: D6h_hml_1

description:
replicate: 1
multiplex barcode: CCGTCC


title: V02966/7933_4-5-10_L3

description: Processed data: rsem_gcounts_matrix.txt


title: Med_CO2_Rep1

source_name: whole cell


title: H23539/GGPL_7995_12-17-10_L8.D711

description: Processed data: rsem_gcounts_matrix.txt

source_name: Liver, placebo, 250 days

value: placebo


title: D2_hml_2

description:
replicate: 2
multiplex barcode: GATCAG


title: D2_ivd_2

description:
replicate: 2
multiplex barcode: TAGCTT


title: H23539/GGPL_7993_12-17-10_L7.D706

description: Processed data: rsem_gcounts_matrix.txt


title: D2_hml_1

description:
replicate: 1
multiplex barcode: GCCAAT


title: H23539/GGPL_7972_12-17-10_L6.D701

description: Processed data: rsem_gcounts_matrix.txt


title: D2_ivd_1

description:
replicate: 1
multiplex barcode: CTTGTA


title: V02966/GGPL_7968_9-27-10_L2

description: Processed data: rsem_gcounts_matrix.txt


title: D1_ivd_2

description:
replicate: 2
multiplex barcode: TTAGGC

source_name: rosette leaves, prolonged darkness for 24h


title: D1_wt_2

description:
replicate: 2
multiplex barcode: ACTTGA


title: D1_wt_1

description:
replicate: 1
multiplex barcode: ACAGTG


title: H23539/GGPL_7957_12-17-10_L4.D703

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/GGPL_7896_10-21-10_L3.D710

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/GGPL_7875_12-17-10_L2.D705

description: Processed data: rsem_gcounts_matrix.txt


title: D1_ivd_1

description:
replicate: 1
multiplex barcode: TGACCA


title: H23539/7995_8-9-10_L8.D710

description: Processed data: rsem_gcounts_matrix.txt

source_name: Liver, placebo, 120 days


title: W23708/7989_4-6-10_L5.D702

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/7994_4-6-10_L6.D707

description: Processed data: rsem_gcounts_matrix.txt


title: D1_hml_2

description:
replicate: 2
multiplex barcode: ATCACG


title: D1_hml_1

description:
replicate: 1
multiplex barcode: CGATGT


title: H23539/7993_8-9-10_L7.D705

description: Processed data: rsem_gcounts_matrix.txt


title: D2_wt_1

description:
replicate: 1
multiplex barcode: CAGATC


title: W23708/8-9-10_7972_L1.D712

description: Processed data: rsem_gcounts_matrix.txt


title: 0h_wt_2

description:
replicate: 2
multiplex barcode: GGCTAC

source_name: rosette leaves, prolonged darkness for 0h


title: 0h_wt_1

description:
replicate: 1
multiplex barcode: GGCTAC


title: H23539/8-9-10_7968_L5.D707

description: Processed data: rsem_gcounts_matrix.txt


title: 0h_ivd_2

description:
replicate: 2
multiplex barcode: TAGCTT


title: H23539/7896_8-9-10_L3.D709

description: Processed data: rsem_gcounts_matrix.txt


title: 0h_ivd_1

description:
replicate: 1
multiplex barcode: TAGCTT


title: H23539/8-9-10_7957_L4.D702

description: Processed data: rsem_gcounts_matrix.txt


title: 0h_hml_2

description:
replicate: 2
multiplex barcode: GATCAG


title: H23539/7993_6-21-10_L6.D704

description: Processed data: rsem_gcounts_matrix.txt

source_name: Liver, placebo, 71 days


title: 0h_hml_1

description:
replicate: 1
multiplex barcode: GATCAG


title: H23539/6-21-10_7968_L5.D706

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/6-21-10_7972_L1.D711

description: Processed data: rsem_gcounts_matrix.txt


title: V03084/6-21-10_7957_L1

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/7995_6-21-10_L8.D709

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/7993_5-24-10_L6.D703

description: Processed data: rsem_gcounts_matrix.txt

source_name: Liver, placebo, 43 days


title: H23539/6-21-10_7875_L1.D703

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/6-21-10_7896_L2.D708

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/5-24-10_7968_L5.D705

description: Processed data: rsem_gcounts_matrix.txt


title: V02966/5-24-2010_7957_L1

description: Processed data: rsem_gcounts_matrix.txt


title: W23708/5-24-10_7972_L1.D710

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/7995_5-24-10_L7.D708

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/5-24-10_7875_L1.D702

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/7995_4-6-10_L7.D707

description: Processed data: rsem_gcounts_matrix.txt

source_name: Liver, placebo, -14 days


title: H23539/4-6-10_7993_L6.D702

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/5-24-10_7896_L2.D707

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/4-5-10_7957_L3.D711

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/4-5-10_7896_L2.D706

description: Processed data: rsem_gcounts_matrix.txt


title: H23539/4-5-10_7875_L1.D701

description: Processed data: rsem_gcounts_matrix.txt


title: shWtx.2460

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
geneExpressionMatrix.xlsx: Helicos Digital Gene Expression pipeline. Pubmed ID 19581875
repetitiveElementExpressionMatrix.xlsx: Helicos Basic pipeline for alignment to the genome followed by PASA method of coverage computation (Kim, Wittner, Amzallag, et al., in preparation) followed by summing coverage in regions and dividing by average read length
Genome_build: mm9
Supplementary_files_format_and_content: geneExpressionMatrix.xlsx: Transcript abundances as determined by smsDGE described in Pubmed ID 19581875 (i.e., the RMC column of the output of the Helicos Digital Gene Expression pipeline run using the Mouse.Txome reference file). Columns correspond to samples and rows correspond to genes.
Supplementary_files_format_and_content: repetitiveElementExpressionMatrix.xlsx: Estimate of number of reads originating from all genomic locations annotated by a certain repetitive element class. Columns correspond to samples and rows correspond to a repClass/repRamily/repName as defined by the mm9 table rmsk from UCSC's table browser. ID_REFs are annotated in repetitiveElementPlatform.xlsx.

source_name: embryonic stem cells

growth_protocol: Mouse embryonic stem cells ES-D3 were obtained from ATCC. ES-D3 cells were grown on γ-irradiated feeder layer in DMEM supplemented with 15% FBS, 10 ng/ml Leukemia Inhibitory Factor (LIF, Millipore), 1x MEM Non-Essential Amino Acids (Gibco), 0.1 mM β-Mercaptoethanol, 2 mM L-glutamine, and 50 units/mL penicillin/streptomycin. Feeder cells were depleted by trypsinization and replating on a plate for 30 min before extracting RNA.

extract_protocol:
RNA extraction and single molecular sequencing was described previously in PubMed ID 22763454
Qiagen RNeasy MinElute kit followed by Helicos single molecule sequencing: PubMed ID 18388294, 20133332

treatment_protocol: Lentiviral shRNA infection followed by puromyacin selection

tag: shRNA target

value: Wtx

tag: shRNA target sequence

tag: cell line


title: shWtx.2461


title: shTrim28.2856


title: H23539/7875_8-9-2010_L1.D704

description: Processed data: rsem_gcounts_matrix.txt


title: shTrim28.2065