title: HA-RpaA culture, anti-HA, peak binding (ZT 36 h)

city: Cambridge

first: Joseph

middle: Scott

last: Markson

state: MA

address: 52 Oxford St, Room 445

department: Molecular and Cellular Biology

institute: Harvard Univ / Howard Hughes Medical Institut

description: Sample 12

data_processing:
Read alignment: Bowtie, v 0.12.7, -v 3 -m 1 -p 16 -t --best
Peak finding: Aligned data were analyzed using a custom-coded, modified form of the PeakSeq algorithm (Rozowsky et al., 2009) that narrows the regions identified as peaks by requiring that each 50-bp window within a putative peak be enriched (p ≤ 0.05) relative to both the mock ChIP and the input DNA; also, the xset (extended single-end tags) tracks are smoothed with a moving window average over 10 bp prior to further processing. The fold enrichment for each final peak was calculated by finding the maximum ChIP-to-mock ratio within 50 bp of the location of the peak maximum in the raw ChIP-Seq signal (not in the enrichment ratio). Multiple hypothesis-corrected q-values were less than 10-78 (smallest q-value between the two replicates).
Peak reproducibility filter: For ChIP using the anti-RpaA antibody, we required peaks to be present in each of two biological replicates with enrichment ≥ 3-fold in replicate  1 and ≥ 2.22-fold in replicate 2, which had 26% lower enrichment overall.
Target transcript calling: To call targets of a given RpaA peak, we identified all transcripts with 5’ ends lying within 500 bp of the location of maximum ChIP-Seq signal. (For this analysis, we considered only annotated mRNA, tRNA, or rRNA transcripts and high-confidence non-coding transcripts (Vijayan et al., 2011).) Within that set of transcripts, we called as the target that transcript with its 5’ end nearest the ChIP-Seq signal maximum. To account for possible inaccuracies in the 5’ end identifications, we also assigned as targets any other transcripts with 5’ ends residing within 50 bp of the nominally closest transcript.
Genome_build: Main chromosome: NC_007604.1; plasmid pANL (plasmid 1), NC_004073.2; plasmid pANS (plasmid 2), NC_004990.1
Supplementary_files_format_and_content: .wig files were generated from the output of Bowtie using custom Matlab code.  Each sample is associated with one or two .wig files.  The first .wig file was constructed by extending the single-end reads to the median length of the insert (as described in Rozowsky et al Nature Biotechnology 2009), then smoothing with a moving average (filter width, 10 bp).  The second .wig file, if present, was constructed by dividing the extended reads of the ChIP sample by the PeakSeq-normalized extended ChIP reads for the background.  For Samples 1-7, the background was Sample 8 (anti-RpaA ChIP on the rpaA- strain).  For Samples 8 and 9, the backgrounds were the input DNA samples, i.e., Samples 18 and 19, respectively.  For Samples 10 and 11, the background was Sample 9 (anti-RpaA ChIP on the rpaA- strain).  For Sample 12, the background was the mock ChIP (anti-HA on the untagged wild-type strain), i.e., Sample 13.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: Strain EOC67, LL, ZT 36 h

growth_protocol: Cells were grown in a custom-made turbidostat described previously (Vijayan, V., et al. (2009). Proc Natl Acad Sci U S A 106, 22564-22568).  Cells were initially inoculated in the presence of antibiotics (5 µg/ml spectinomycin and 5 µg/ml chloramphenicol), and subsequently diluted with modified BG-11 only. Cells were exposed to surface flux of ~25 µmol photons m-2 s-1 white light, bubbled with 500 ml min-1 1% CO2 in air, maintained at 30º C, and stirred at 0.5-1 rotation per second. The initial OD750 (optical density at 750 nm) was 0.06 and was allowed to increase to 0.15, after which it was maintained at a constant level of 0.15.   Entrainment (see "treatment protocol") was begun after OD750 of 0.15 was reached.

extract_protocol:
Samples were thawed on ice and resuspended in 500-600 ul of ice-cold lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 1x Roche Complete EDTA-free Protease Inhibitor Cocktail). Cells were lysed by beadbeating at 4 °C in 2 ml screw-top tubes with 0.1 mm glass beads for 10 cycles of 30 seconds each separated by at least 30 sec of cooling on ice. Lysate was separated from the beads by piercing the bottom of each tube with a small-diameter needle, placing the tube into a clean 1.5 ml microcentrifuge tube, and centrifuging for several minutes at < 500 x g at 4 °C to transfer the lysate to the 1.5-ml tube. Chromatin was then sheared to a length of ~300 bp by sonication on ice in a Misonix sonicator 3000 for 9-11 cycles of 15 sec separated by at least 90 sec of cooling. Cell debris was removed by centrifuging twice at 14,000 x g for 15 min at 4 °C. Protein concentration in the lysates was determined by BCA assay using BSA as a standard.  Immunoprecipitation was then conducted as follows: For a given ChIP timecourse, equal mass quantities (typically 1-1.5 mg) of lysate from each timepoint were prepared in 500 ul of lysis buffer each. For anti-RpaA ChIP, equal amounts (typically 10-15 µg) of affinity-purified antibody was added to each tube; for anti-HA ChIP, 40 ul (bed volume) of anti-HA agarose beads (Pierce) were added to each tube. Samples were overnight in the dark at 4 °C with continuous rotation. The following morning, for anti-RpaA ChIP only, 50-70 µl of rProtein A Sepharose Fast Flow beads (GE Healthcare; 33% slurry in lysis buffer) was added to each sample, and the samples were then incubated for 2 h at 4 °C with rotation. For both anti-RpaA and anti-HA ChIP, beads were isolated by centrifugation for 1 min at 1000 x g at room temperature. Beads were then washed twice with 1 ml lysis buffer, once with 1 ml of buffer B (50 mM HEPES pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), once with 1 ml of wash buffer (10 mM TrisCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.1% sodium deoxycholate) and finally with 1 ml of TE pH 7.5 (10 mM TrisCl pH 7.5, 1 mM EDTA); each wash was conducted for 5 min at room temperature on a tube rotator followed by isolation of beads by centrifugation for 1 min at 1000 x g at room temperature. Protein-DNA complexes were then eluted with 250 µl elution buffer (50 mM TrisCl pH 8.0, 10 mM EDTA, 1% SDS) for 1 h at 65 °C. For both this eluate and a matched sample of lysate not subjected to immunoprecipitation (“input DNA”), crosslinks were reversed for 6-18 h at 65 °C. Next, 250 ul of TE was added to each sample to dilute the SDS, followed by addition of 100 µg of proteinase K and 80 µg of glycogen. Samples were incubated for 2 h at 37 °C. Samples were then supplemented with 55 µl of 4 M LiCl and extracted with 1 ml of phenol/chloroform/isoamyl alcohol. DNA in the aqueous phase was precipitated with ethanol and then washed once with 80% ethanol. Pellets were air-dried and then resuspended in 50 µl of TE containing 20 ng/µl of DNase-free RNase (Fermentas) and incubated for 1 h at 37 °C. Samples were then supplemented with 150 µl of TE and 22.2 µl of 3 M sodium acetate pH 5.2, extracted with phenol/chloroform/isoamyl alcohol, and precipitated with ethanol; alternatively, DNA was purified using a Qiagen PCR purification kit. DNA concentration in ChIP samples was estimated either by PicoGreen assay (Invitrogen) or by qPCR based on the abundance of the coding region of synpcc7942_0612, a region showing no enrichment for RpaA binding in ChIP-Seq experiments; for both methods, input DNA quantified by absorption spectrophotometry was used as a standard.
Except for Samples 9, 10, 11, 16, 17, and 19, libraries for Illumina sequencing of ChIP DNA were prepared following a protocol developed by Ethan Ford (http://ethanomics.files.wordpress.com/2012/09/chip_truseq.pdf), with modifications. 0.15-3 ng of ChIP DNA was used for each sample. DNA ends were blunted by treatment with 1.4 units of T4 DNA polymerase (NEB), 0.45 units of Klenow fragment (NEB), 4.5 units of T4 polynucleotide kinase (NEB), and 0.4 mM dNTPs (NEB) in 1x T4 DNA ligase buffer (NEB) in a total of 50 µl volume for 30 min at 20 °C. DNA was purified using 50 µl of AMPure XP beads (Beckman) and 50 µl of a solution containing 20% PEG8000 (Sigma) and 1.25 M NaCl. DNA was eluted in 16.5 ul of TE/10 (10 mM TrisCl pH 8.0, 0.1 mM EDTA). DNA was then A-tailed at the 3’ ends by treating the eluate with 2.5 units of Klenow fragment lacking 3’-5’ exonuclease activity (Klenow fragment 3’-->5’ exo-, NEB) and 0.2 mM dATP (GE Healthcare) in 1x NEB Buffer 2 in a total volume of 20 µl for 30 min at 37 °C. TruSeq adapters (Illumina or Eurofins MWG Operon) were ligated onto the A-tailed DNA by addition of 25 µl of 2X Quick Ligase Buffer (NEB), 0.5 µl of ~250 nM TruSeq adapter (1:30 dilution of Illumina stock), 3 µl of nuclease-free ddH2O, and 1.5 µl of Quick Ligase (NEB) followed by incubation for 20 min at 21 °C. The ligation reaction was stopped by addition of 5 µL of 0.5 M EDTA pH 8.0 (Ambion). Next, DNA was purified using 55 µl of AMPure XP beads without additional PEG or salt. DNA was eluted in 15.5 µl of TE/10. The Y-shaped adapters were then linearized with 5 cycles of PCR (initial denaturation of 30 sec at 98 °C followed by 5 cycles of [10 sec at 98 °C, 30 sec at 60 °C, 30 sec at 72 °C] followed by 5 min at 72 °C) using Phusion polymerase (Thermo) in HF Buffer and 1 µl of TruSeq primers (25 µM) in a total volume of 31 µL. Linearized DNA was purified using 30 µl of AMPure XP beads without additional PEG or salt. DNA was eluted in 30 µl of TE/10. Fragments between 300 and 500 bp were size-selected using agarose gel purification and the QIAquick gel extraction kit (Qiagen) or using a Pippin Prep (SAGE Science). Purified DNA was further amplified with 13-14 cycles of PCR, as above, in a total volume of 62.5 µl. Following PCR, DNA was purified using 51 µl of AMPure XP beads without additional PEG or salt. DNA was eluted in 12 µl of TE/10. Libraries were assessed using a DNA High Sensitivity chip on an Agilent Bioanalyzer 2100. Samples were sequenced on an Illumina HiSeq instrument or Genome Analyzer II (Illumina) by the core facility at the Harvard FAS Center for Systems Biology.  Reads were aligned to the S. elongatus genome using Bowtie (Langmead et al., 2009), counting only those aligning uniquely to one location with up to three mismatches.  For Samples 9, 10, 11, 16, 17, and 19, libraries were prepared by Libraries for Solexa sequencing were prepared using paired-end adapters and PCR primers from Illumina following the manufacturer’s protocol for ChIP-Seq sample preparation (part number 11257047 revision A) with modifications. All enzymes except for fast ligase were obtained from NEB instead of Illumina. First, 5 – 10 ng of ChIP or input DNA was blunted and phosphorylated with T4 DNA ligase, T4 DNA polymerase, and T4 polynucleotide kinase. 3’ dA overhangs were added using exo- Klenow fragment. Adapters (diluted 1:10 from the Illumina stock) were ligated for 15 min at room temperature using LigaFast DNA ligase (Promega). Adapter-ligated fragments were size-selected on 2% agarose/TAE gel containing 400 μg/ml ethidium bromide; a gel slice corresponding to the 200-300 bp region (based on 50 bp ladder, Promega) was excised. DNA was purified from the gel using the Qiagen gel extraction kit according to the manufacturer’s protocol, except that the gel slice was dissolved at room temperature. Adapter-ligated fragments were then amplified by PCR using PE Primers 1.0 and 2.0 (Illumina). The resulting libraries was purified with the Qiagen MinElute kit and eluted in 15 ul of buffer EB. The concentration and fragment length distribution of the libraries was then determined using the DNA 1000 Bioanalyzer assay (Agilent).

treatment_protocol: Cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment prior to release into continuous light.  At designated times, approximately 18 OD750 nm units of culture were withdrawn from the turbidostat and crosslinked for 15 min with 1% formaldehyde followed by quenching for 5 min with 125 mM glycine. Cells were collected by centrifugation for 10 min at 6000 x g at 4 °C and then washed twice with 30 ml of ice-cold phosphate-buffered saline (PBS), centrifuging for 10 min at ~3000 x g at 4 °C after each wash. Samples were then resuspended in 1 ml ice-cold PBS and pelleted in a microcentrifuge tube for 3 min at 3,200 x g at 4 °C. The supernatant was discarded and the pellet was frozen in liquid nitrogen and stored at -80 °C.

tag: strain

tag: time in ll (zt)

value: anti-HA agarose beads (Pierce #26181)


title: 35942_MeDIPseq

status: Public on Dec 04 2013

type: SRA

city: London

first: Jordana

last: Bell

address: St Thomas' Hospital, Westminster Bridge Rd

department: Department of Twin Research and Genetic Epidemiology

country: United Kingdom

institute: King's College London

description: Unrelated individual 43

library_source: genomic

data_processing:
In the sample of 50 monozygotic (MZ) twins with paired-end MeDIP-seq data there were on average 50 million paired-end reads of length 50bp per individual. Alignment to hg18 was performed using Maq (v0.7.1). QC of the aligned data took into account base quality scores (no exclusions), read mapping scores (threshold maq q > 10), removal of duplicate PE reads, proper PE pairing criteria, and insert-size distribution checks. On average, 60% of reads passed alignment QC per individual. We used the post-QC PE reads to reconstruct MeDIP-fragments per individual. We quantified coverage of MeDIP-fragments per base-pair (bp) across the genome, and binned coverage into overlapping 1kb bins (overlap of 500bp). For each bin we calculated a normalized methylation score, the relative methylation quantification (RMQ) score, which was the sum of the MeDIP-fragment coverage of each bp in that bin, divided by the overall number of autosomal post-QC reads per individual. For pain-DMR analysis we only considered bins with RMQ variance > 0, where at least 10% of the sample had RMQ scores > 0.
In the sample of 50 unrelated individuals with single-end MeDIP-seq data there were on average 25 million single-end (SE) reads of length 50bp per individual. Sequence alignment to the human genome (hg18) was performed in Bwa (v0.5.9). Data were subject to quality control checks for base composition (no exclusions), read mapping quality (threshold bwa q > 10), and removal of duplicate reads. On average, 53% of reads passed alignment QC per individual. Post-QC single-SE reads were then extended by 175bp equilaterally to produce MeDIP-fragments of size 225bp. We quantified coverage of MeDIP-fragments per base-pair (bp) across the genome, and binned coverage per bp into overlapping 1kb bins (overlap of 500bp). For each bin we calculated the normalized methylation score (RMQ), , which was the sum of the MeDIP-fragment coverage of each bp in that bin, divided by the overall number of autosomal post-QC reads per individual. In the pain-DMR analyses we only considered bins with RMQ variance > 0, where at least 10% of the sample had RMQ scores > 0.
Genome_build: hg18
Supplementary_files_format_and_content: Each processed data file contains RMQ scores over a 1kb window for each individual in bed file format. The files consist of four tab-delimited columns: the chromosome, the start bp of the 1kb bin, the end bp of hte 1kb bin, and the RMQ score for that individual in that bin. The processed files can include genomic regions where the majority or all individuals had RMQ scores of 0, and these regions can be filtered out in the downstream analyses.

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
MeDIP-sequencing was performed and analyzed separately in the MZ twin and unrelated samples.
In the MZ twin sample 5 µg genomic DNA from each sample was sonicated on a Diagenode Bioruptor to produce a median fragment length of 180-230, and prepared for next generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps. Samples were quantified and size checked using a 2100 Bioanalyzer and DNA1000 chips (Agilent).  1 µg of each adapter-ligated sample was spiked with ~5x10-7pmoles methylated/unmethylated control DNA and subjected to methylated immunoprecipitation with 150 ng anti-5-methylcytidine using automation according to manufacturer’s reagents and protocols (Diagenode); 100ng was reserved as input for MeDIP quality control, which was conducted using qPCR with primers designed to amplify methylated / unmethylated control DNA.  MeDIP DNA was then purified (Zymo Reasearch) and amplified by 18 cycles adapter-mediated PCR.  PCR products were purified (QIAGEN) and run out on separate 2% low-melting point agarose gels. PCR fragments were excised and purified (QIAGEN).  The resulting libraries (300-350bp) were quality controlled using an Agilent 2100 Bioanalyzer and DNA1000 chips and qPCR. The samples were sequenced on Illumina GA2, using two lanes per sample, to produce on average 50 million paired-end reads of length 50bp.
In the unrelated samples 1.5µg of original genomic DNA was fragmented to DNA smear between 200bp to 500bp using a Bioruptor NGS (Diagenode) sonication system. End repair, <A> base addition and adaptor ligation steps were performed using Illumina’s Paired-End DNA Sample Prep kit following the manufacturer’s instructions.  Then, the methylated DNA fractions were immunoprecipitated using the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode, catalog number: mc-magme-048) with small adjustments. Briefly, 1.5µl of each two control templates (methylated and unmethylated DNA controls) with different sequences were mixed with adapter ligated DNA and heat denatured (95°C, 3min) in a final reaction volume of 90µl within the provided reagents of 24µl MagBuffer A and 6µl MagBuffer B. 7.5µl aliquot of the denatured genomic DNA was saved as input and another 75µl was immunoprecipitated with 5µl of prepared anti-5mC antibody and 20µl of prepared Magbeads. The DNA-antibody-magbeads mixture was incubated overnight at 4°C on a rotating wheel. The DNA-antibody-magbeads mixture was then washed twice using each of 150µl ice-cold MagWash Buffer-1 and washed once with 150µl of ice-cold MagWash Buffer-2. For each buffer, the washing reaction was incubated for 4min at 4°C on a rotating wheel. The input DNA and immunoprecipitated products were then in parallel treated with protease K and purified with ZYMO DNA Clean & Concentrator-5 (ZYMO). The efficiency and sensitivity of immunoprecipitation reaction were detected by qPCR using the enriched DNA and the unbound input DNA. MeDIP-seq library was constructed by PCR amplification with the enriched DNA as template. PCR reaction was performed in 50µl of reaction volume consisting of 20µl MeDIP enriched DNA, 5µl of 2.5mM dNTP, 2µl primers, 5µl of 10X pfx Amplification Buffer, 2µl of 50mM MgSO4, 15.2µl sterilized water and 0.8µl of Platinum pfx DNA polymerase (Invitrogen). The program of amplification was 94°C 2 min, 10 cycles of 94 °C 15s, 62°C 30s and 72°C 30 then prolong with 10min at 72°C. The products could be kept at 12°C. The PCR products were purified using Agencourt Ampure Beads (Beckman Counlter). After analyzing by the Bioanalyzer analysis system (Agilent, Santa Clara, USA) and quantified by the real time PCR, the prepared library was sequenced using Illumina HiSeq2000 with SE50 read length.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: individual

value: Unrelated individual 43

tag: age

tag: pain temperature

tag: medip antibody

value: anti-5-methylcytidine (Diagenode, Catalog# mc-magme-048)

tag: medip-seq id


title: WT culture, anti-HA, peak binding (ZT 32 h)

country: USA

description: Sample 13

source_name: Strain AMC408, LL, ZT 32 h

tag: chip antibody


title: 9_ganglion-number_19

city: Ramat Gan

first: Dror

last: Hibsh

address: Bar Ilan

department: Bioinformatics

country: Israel

institute: Bar Ilan University

description: 9_ganglion-number_19_GTGGCC_L004_R1_001.fastq

library_source: transcriptomic

data_processing:
FastQc for quality conroll
Trans ABySS for de novo transcriptome assembly with SE parameters
Trinity for de novo transcriptome assembly with inchworm method
RSEM for alignment and estimating counts
Tophat for alignment
cufflinks for estimate expression
Genome_build: n/a (de novo assembly)

molecule: total RNA

organism: Hirudo medicinalis

source_name: Ganglion 19

growth_protocol: All were obtained from a Hirudo Medicinalis colony grown in France at Ricarimpex Farm and maintained in our lab. Prior to use, all grew under the same environment (tanks populated with about 20 leeches, temp of 16Âºc).

extract_protocol:
Rneasy Lipid Tissue(Qiagen)
illumina hiseq preparation kit

tag: tissue

value: Ganglia chain

value: adult


title: 10_ganglion-number_10

description: 10_ganglion-number_10_CGTACG_L004_R1_001.fastq

source_name: Ganglion 10


title: 11_ganglion-number_10

description: 11_ganglion-number_10_GAGTGG_L004_R1_001.fastq


title: 35953_MeDIPseq

description: Unrelated individual 41

value: Unrelated individual 41


title: 12_ganglion-number_10

description: 12_ganglion-number_10_ATTCCT_L002_R1_001.fastq


title: 8_ganglion-number_10

description: 8_ganglion-number_10_ACAGTG_L008_R1_001.fastq


title: 35925_MeDIPseq

description: Unrelated individual 42

value: Unrelated individual 42


title: 7_ganglion-number_2

description: 7_ganglion-number_2_TGACCA_L002_R1_001.fastq

source_name: Ganglion 2


title: 36069_MeDIPseq

description: Unrelated individual 40

value: Unrelated individual 40


title: 5_ganglion-number_10

description: 5_ganglion-number_10_TAGCTT_L004_R1_001.fastq


title: 35910_MeDIPseq

description: Unrelated individual 39

value: Unrelated individual 39


title: 6_ganglion-number_19

description: 6_ganglion-number_19_GGCTAC_L008_R1_001.fastq


title: 36043_MeDIPseq

description: Unrelated individual 37

value: Unrelated individual 37


title: 4_ganglion-number_2

description: 4_ganglion-number_2_GATCAG_L008_R1_001.fastq


title: 35969_MeDIPseq

description: Unrelated individual 38

value: Unrelated individual 38


title: 2_ganglion-number_10

description: 2_ganglion-number_10_TTAGGC_L008_R1_001.fastq


title: 35952_MeDIPseq

description: Unrelated individual 36

value: Unrelated individual 36


title: 3_ganglion-number_19

description: 3_ganglion-number_19_ACTTGA_L008_R1_001.fastq


title: 35957_MeDIPseq

description: Unrelated individual 35

value: Unrelated individual 35


title: 35937_MeDIPseq

description: Unrelated individual 34

value: Unrelated individual 34


title: OX-Empty + IPTG, 3 hours

description:
Sample 17
Processed data file: RNAseq_ProcessedData.txt, column M (see supplementary file linked to Series record)

data_processing:
Read alignment: Bowtie, v 0.12.9, -v 3 -m 1 -p 16 -t --best --un
Gene expression quantification: alignment output from Bowtie was read into Matlab using custom code. To obtain gene expression values, we counted the number of coding-strand sequencing reads that had 5’ ends between the start and stop positions of the coding region of each gene
Gene expression normalization: To normalize gene expression values between samples, we utilized median normalization as described elsewhere (Anders and Huber, 2010). First, we calculated a pseudo-reference for each gene by determining the geometric mean of the expression counts for that gene across all samples, and calculated the ratio of the expression values with the appropriate pseudo-reference value. We determined the median value of these ratios within each sample and took this as a size factor that estimates the sequencing depth of each sample. To normalize, we divided all gene expression values within a sample by the appropriate size factor. Gene expression values were further normalized by dividing the gene expression values by the length of the appropriate open reading frame.
Genome_build: Main chromosome: NC_007604.1; plasmid pANL (plasmid 1), NC_004073.2; plasmid pANS (plasmid 2), NC_004990.1
Supplementary_files_format_and_content: Normalized gene expression values (see supplementary file linked to Series record).

source_name: Strain EOC339, LL, 3 hours + IPTG

growth_protocol: Cells were initially inoculated in tissue culture flasks in 200 mL of BG-11M supplemented with 10 mM HEPES-KOH pH 8.0 in the presence of 2 ug/mL spectinomycin and 5 ug/mL chloramphenicol (EOC 113) or 2 ug/mL gentamycin, 5 ug/mL chloramphenicol, and 7.5 ug/mL kanamycin (EOC339, EOC345, and EOC346). Cultures were grown with bubbling of 1% CO2 in air at 30°C while illuminated with 100 μE  m-2 s-1 (μmoles photons m-2 s-1) of cool fluorescent light. After initial inoculation, cells were diluted in 800 mL of BG-11M with HEPES in the absence of antibiotics with bubbling.

extract_protocol:
Total RNA was prepared from extracted cells using the hot phenol/SDS method as described previously (Vijayan, V., et al. (2009). Proc Natl Acad Sci U S A 106, 22564-22568).
Ribosomal RNA was depleted from 6 μg of total RNA using the MICROBExpress Bacterial mRNA enrichment kit (Applied Biosystems) according to manufacturer’s instructions. Strand-specific RNA-sequencing libraries were prepared from 375 ng of rRNA-depleted RNA using the TruSeq Stranded mRNA Sample Prep Kit (Illumina). Samples were multiplexed and sequenced on an Illumina HiSeq machine by the core facility at the Harvard FAS Center for Systems Biology.

treatment_protocol: Cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment prior to release into continuous light. Just prior to the beginning of sampling, cells were diluted to an OD750 of 0.3. This OD was kept relatively constant throughout the experiment by periodic dilution with warm BG-11M + 10 mM HEPES pH 8.0. 24 hours after release into constant light, approximately 55 mL of cells were collected via filtration onto a .45 μm 87 mm nitrocellulose filter and quickly flash frozen in a 50 mL conical tube with liquid nitrogen. Immediately after withdrawing cells, IPTG was added to a final concentration of 100 μM, where appropriate. Cultures to which IPTG was added were subsequently diluted with BG-11M + 10 mM HEPES pH 8.0 + 100 μM when dilution was required. Sampling was carried out at the designated times as described above. Cells were stored at -80 °C until RNA was extracted.

tag: time since iptg addition

value: 3 hours


title: OX-Empty + IPTG, 12 hours

description:
Sample 18
Processed data file: RNAseq_ProcessedData.txt, column N (see supplementary file linked to Series record)

source_name: Strain EOC339, LL, 12 hours + IPTG

value: 12 hours


title: 35763_MeDIPseq

description: Unrelated individual 32

value: Unrelated individual 32


title: 35863_MeDIPseq

description: Unrelated individual 33

value: Unrelated individual 33


title: OX-Empty + IPTG, 0 hours

description:
Sample 16
Processed data file: RNAseq_ProcessedData.txt, column L (see supplementary file linked to Series record)

source_name: Strain EOC339, LL, 0 hours + IPTG

value: 0 hours


title: 182_MeDIPseq

description: Family 1 monozygotic twin 1

value: Family 1, monozygotic twin 1

value: anti-5-methylcytidine (Diagenode, Catalog# mc-magme-048)


title: OX-D53E - IPTG, 12 hours

description:
Sample 15
Processed data file: RNAseq_ProcessedData.txt, column K (see supplementary file linked to Series record)

source_name: Strain EOC346, LL, 12 hours - IPTG


title: OX-D53E - IPTG, 0 hours

description:
Sample 13
Processed data file: RNAseq_ProcessedData.txt, column I (see supplementary file linked to Series record)

source_name: Strain EOC346, LL, 0 hours - IPTG


title: 35961_MeDIPseq

description: Unrelated individual 30

value: Unrelated individual 30


title: 35854_MeDIPseq

description: Unrelated individual 29

value: Unrelated individual 29


title: 35856_MeDIPseq

description: Unrelated individual 27

value: Unrelated individual 27


title: OX-D53E - IPTG, 3 hours

description:
Sample 14
Processed data file: RNAseq_ProcessedData.txt, column J (see supplementary file linked to Series record)

source_name: Strain EOC346, LL, 3 hours - IPTG


title: 35976_MeDIPseq

description: Unrelated individual 28

value: Unrelated individual 28


title: OX-D53E + IPTG, 6 hours

description:
Sample 11
Processed data file: RNAseq_ProcessedData.txt, column G (see supplementary file linked to Series record)

source_name: Strain EOC346, LL, 6 hours + IPTG

value: 6 hours


title: OX-D53E + IPTG, 12 hours

description:
Sample 12
Processed data file: RNAseq_ProcessedData.txt, column H (see supplementary file linked to Series record)

source_name: Strain EOC346, LL, 12 hours + IPTG


title: 36041_MeDIPseq

description: Unrelated individual 26

value: Unrelated individual 26


title: OX-D53E + IPTG, 3 hours

description:
Sample 10
Processed data file: RNAseq_ProcessedData.txt, column F (see supplementary file linked to Series record)

source_name: Strain EOC346, LL, 3 hours + IPTG


title: OX-D53E + IPTG, 0.5 hours

description:
Sample 8
Processed data file: RNAseq_ProcessedData.txt, column D (see supplementary file linked to Series record)

source_name: Strain EOC346, LL, 0.5 hours + IPTG

value: 0.5 hours


title: S. cerevisiae Ribo-seq Rep 1

city: Pittsburgh

first: Charles

middle: Joel

last: McManus

state: Pennsylvania

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

description: NCBI Biosample; SAMN02302496

data_processing:
Base-calling was performed with Illumina Casava version 1.8.
Sequences were trimmed to remove ligated adapters using cutadapt v1.2.1
All sequences were aligned to both species genomes using bowtie v 0.12.8 --best.
Allignments were compared to identify reads mapping specifically on one allele using a custom perl script.
Allele-specific reads were mapped to genes using coverageBed from bedtools v 2.17.0
Normalized abundance table for gene expression was created using a custom perl script.  This program normalized both for ORF length (which differs between species), and for total read number in each sample.
BedGraph browser tracks were produced using genomeCoverageBed from bedTools v 2.17.0
Genome_build: S. paradoxus - CBS432 from www.saccharomycessensustricto.org
Genome_build: S. cerevisiae - S288C sacCer3.
Supplementary_files_format_and_content: bed files contain updated annotations of orthologous genes in the two species. bedGraph files contain coverage data for each sequencing library.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Strains were all grown in YEP+D medium at 30C to OD600 = 0.6-0.9

extract_protocol:
Polysome extracts were prepared as previously described (Ingolia, N. T. (2010). Chapter 6 - Genome-Wide Translational Profiling by Ribosome Footprinting. Guide to Yeast Genetics: Functional Genomics, Proteomics, and Other Systems Analysis (2nd ed., Vol. 470, pp. 119–142). Elsevier Inc. doi:10.1016/S0076-6879(10)70006-9).
Libraries were constructed as previously described (Ingolia, N. T., Lareau, L. F., & Weissman, J. S. (2011). Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes. Cell, 147(4), 789–802. doi:10.1016/j.cell.2011.10.002).
Illumina TruSeq compatible; single-end sense strand-specific.

treatment_protocol: Cycloheximide 5' prior to extraction.

tag: developmental stage

value: diploid


title: OX-D53E + IPTG, 2 hours

description:
Sample 9
Processed data file: RNAseq_ProcessedData.txt, column E (see supplementary file linked to Series record)

source_name: Strain EOC346, LL, 2 hours + IPTG

value: 2 hours


title: 1_ganglion-number_2

description: 1_ganglion-number_2_ATCACG_L004_R1_001.fastq

value: Ganglia chain

value: adult


title: OX-D53E + IPTG, 0 hours

description:
Sample 7
Processed data file: RNAseq_ProcessedData.txt, column C (see supplementary file linked to Series record)

source_name: Strain EOC346, LL, 0 hours + IPTG


title: 36039_MeDIPseq

description: Unrelated individual 25

source_name: Whole blood

value: Unrelated individual 25


title: 35870_MeDIPseq

description: Unrelated individual 31

value: Unrelated individual 31


title: S. cerevisiae RNA-seq Rep 2

description: NCBI Biosample; SAMN02302493


title: 35882_MeDIPseq

description: Unrelated individual 23

value: Unrelated individual 23


title: WT culture, ZT 44 hours

description:
Sample 6
Processed data file: RNAseq_ProcessedData.txt, column T (see supplementary file linked to Series record)

source_name: Strain EOC113, LL, ZT 44 hours

value: 44 hours


title: S. cerevisiae RNA-seq Rep 1

description: NCBI Biosample; SAMN02302492


title: 35972_MeDIPseq

description: Unrelated individual 21

value: Unrelated individual 21


title: WT culture, ZT 36 hours

description:
Sample 4
Processed data file: RNAseq_ProcessedData.txt, column R (see supplementary file linked to Series record)

source_name: Strain EOC113, LL, ZT 36 hours

value: 36 hours


title: WT culture, ZT 40 hours

description:
Sample 5
Processed data file: RNAseq_ProcessedData.txt, column S (see supplementary file linked to Series record)

source_name: Strain EOC113, LL, ZT 40 hours

value: 40 hours


title: WT culture, ZT 32 hours

description:
Sample 3
Processed data file: RNAseq_ProcessedData.txt, column Q (see supplementary file linked to Series record)

source_name: Strain EOC113, LL, ZT 32 hours

value: 32 hours


title: WT culture, ZT 28 hours

description:
Sample 2
Processed data file: RNAseq_ProcessedData.txt, column P (see supplementary file linked to Series record)

source_name: Strain EOC113, LL, ZT 28 hours

value: 28 hours


title: 35885_MeDIPseq

description: Unrelated individual 19

value: Unrelated individual 19

value: anti-5-methylcytidine (Diagenode, Catalog# mc-magme-048)


title: 35973_MeDIPseq

description: Unrelated individual 20

value: Unrelated individual 20


title: 35887_MeDIPseq

description: Unrelated individual 17

value: Unrelated individual 17


title: 35928_MeDIPseq

description: Unrelated individual 16

value: Unrelated individual 16


title: ΔrpaA culture, input DNA for ZT 24 - 44 h pool, replicate 2

description: Sample 19

source_name: Strain EOC66, LL, pool of ZT 24, 28, 32, 36, 40 and 44 h

value: no antibody (input DNA)


title: S. cerevisiae Ribo-seq Rep 2

description: NCBI Biosample; SAMN02302497

value: diploid


title: 35760_MeDIPseq

description: Unrelated individual 15

value: Unrelated individual 15


title: ΔrpaA culture, input DNA for ZT 24 - 44 h pool, replicate 1

description: Sample 18


title: WT culture, input DNA at peak binding (ZT 44 h), replicate 1

description: Sample 15

source_name: Strain AMC408, LL, ZT 44 h


title: WT culture, ZT 24 hours

description:
Sample 1
Processed data file: RNAseq_ProcessedData.txt, column O (see supplementary file linked to Series record)

source_name: Strain EOC113, LL, ZT 24 hours

value: 24 hours


title: 35936_MeDIPseq

description: Unrelated individual 24

value: Unrelated individual 24


title: 35879_MeDIPseq

description: Unrelated individual 22

value: Unrelated individual 22


title: 35914_MeDIPseq

description: Unrelated individual 14

value: Unrelated individual 14


title: ΔrpaA culture, anti-RpaA, pool of ZT 24 - 44 h, replicate 1

description: Sample 8

value: affinity-purified anti-RpaA


title: 35929_MeDIPseq

description: Unrelated individual 12

value: Unrelated individual 12


title: WT culture, input DNA at peak binding (ZT 32 h), replicate 2

description: Sample 16

source_name: Strain AMC408, LL, ZT 32 h


title: WT culture, input DNA at peak binding (ZT 44 h), replicate 2

description: Sample 17


title: 35917_MeDIPseq

description: Unrelated individual 13

value: Unrelated individual 13


title: WT culture, anti-RpaA, ZT 48 h, replicate 1

description: Sample 7

source_name: Strain AMC408, LL, ZT 48 h


title: WT culture, anti-RpaA, trough binding (ZT 44 h), replicate 2

description: Sample 11


title: 35890_MeDIPseq

description: Unrelated individual 11

value: Unrelated individual 11


title: WT culture, anti-RpaA, peak binding (ZT 32 h), replicate 2

description: Sample 10


title: 35908_MeDIPseq

description: Unrelated individual 10

value: Unrelated individual 10


title: 35905_MeDIPseq

description: Unrelated individual 18

value: Unrelated individual 18


title: WT culture, anti-RpaA, ZT 44 h, replicate 1

description: Sample 6


title: WT culture, anti-RpaA, ZT 40 h, replicate 1

description: Sample 5

source_name: Strain AMC408, LL, ZT 40 h


title: 35896_MeDIPseq

description: Unrelated individual 9

value: Unrelated individual 9

value: anti-5-methylcytidine (Diagenode, Catalog# mc-magme-048)


title: Mixed parental ribosome protected fragments replicate 2 lane 1

city: Stanford

first: Carlo

middle: G.

last: Artieri

state: California

address: Herrin Labs Rm. 309

department: Biology

institute: Stanford University

description: Ribosome protected RNA fragments isolated from S. cerevisiae and S. paradoxus using the riboprofiling method

data_processing:
Bases were called using Illumina CASAVA version 1.8.2  and only reads passing the software's quality filter were retained.
S. cerevisiae and S. paradoxus genome assemblies, annotations, and orthology assignments were obtained from (Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT. 2011. The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) 1:11-25.). For all analyses, we focused only on the nuclear genome. From the list of genes orthologous between S. cerevisiae and S. paradoxus, we identified those that in both species a) began with an ATG and terminated in a canonical stop codon (TAA, TAG, TGA), b) had a sequence length that was divisible by three, c) lacked in-frame stop codons, d) lacked any âNâ nucleotides in their genomic sequence, e) were annotated as either possessing or lacking introns in both species, and f) possessed at least 100 uniquely mappable nucleotides. Furthermore, we required that the lengths of both orthologs be within 50% of one another and excluded genes that were annotated as having a different number of introns in the Scannell et al. (2011) S. cerevisiae annotation than in the Saccharomyces Genome Database (SGD) annotation available as of 14 August 2012. The Scannell et al. (2011) annotation provides spliced, processed mRNA sequences for each annotated gene, however the positions of introns are not indicated in the genomic annotation files. These were obtained by using BLAT (Kent WJ. 2002. BLAT--the BLAST-like alignment tool. Genome Res 12: 656-664.) to map each speciesâ mRNA to its respective genome. Intron flanking segments of 84 of the 105 intron containing mRNAs mapped uniquely and were retained for analysis. Finally we eliminated orthologs for LYS2 (Scer_2.299) as its knockout in the S. cerevisiae parental strain was used as a selectable marker as well as CTR3 (Scer_12.598) as it is interrupted by a Ty2 transposon in BY strains of S. cerevisiae. Our final analysis set contained 4,640 orthologs between the two parental species.    Reads from both mRNA and Ribofootprint fractions were mapped to the S. cerevisiae and S. paradoxus genome assemblies of Scannell et al. (2011) in a strand-specific manner using the iterative method described in Ingolia (Ingolia NT. 2010. Genome-Wide Translational Profiling by Ribosome Footprinting. In Methods in Enzymology Vol. 470 [eds. J Weissman, C Guthrie, GR Fink], pp. 119â142. Academic Press, Waltham, Massachusetts.) in order to enrich for ribosome protected fragments and account for spurious adenine (A) bases added to the 3' ends of reads by the oligo-dT mediated reverse transcription. We first excluded any reads that, when trimmed to 23 bases from the 5' end, mapped to the complete rDNA sequence of S. cerevisiae allowing 3 mismatches and a maximum of 20 mapping locations using Bowtie version 0.12 (Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.). Remaining reads from the parental mRNA samples were mapped to their respective genomes allowing no multimappers, and a single mismatch. Mapping reads were filtered such that no more than 30 bp (31 bp if the 3' most base ended with an A), and no less than 27 bp (28 if the 3' most base was an A) from the 5' end of the read mapped uniquely. These were used to reannotate the genome assemblies by identifying nucleotides that were overlapped by at least 10 reads differing at a specific nucleotide with the reference genomes at a frequency >= to 0.8, and that did not introduce nonsense mutations in annotated genes (the absence of true nonsense mutations was confirmed in the five cases where substitutions were detected by the presence of abundant Ribo fraction read coverage 3' of the putative stop codon). This identified 239 and 605 differences between our data and the S. cerevisiae and S. paradoxus assemblies, respectively. Replicate reads from both fractions were then mapped to a concatenation of the updated assemblies, as above, but allowing no mismatches.    S. cerevisiae and S. paradoxus show sufficient divergence at the nucleotide level (~5%) that the 27-30 nt RNA fragments produced by the riboprofiling protocol mapped uniquely to most genomic regions (~87% when accounting for non-unique regions both within and between the two genomes). Therefore, all analyses of coverage were restricted to locations where all possible reads spanning the nucleotide of interest would map uniquely. Non-unique mapping nucleotides were identified by truncating each of the speciesâ genomes into overlapping 27 bp fragments in single-base increments along each chromosome. These fragments were then mapped back to the concatenation of the two species genomes using Bowtie allowing no mismatches and retaining all reads mapping to more than a single location (multi-mapping reads). Any position in the concatenated genomes that was represented in a multi-mapping 27 bp segment was removed from further analysis. Furthermore, we removed all nucleotides within 27 bp of a splice junction as junction-spanning reads were likely to be underrepresented in our short read lengths. Mapping reads were assigned to genomic locations (CDS, 5' and 3' UTRs, or introns) based on the position of their 5' most base (Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218â223.): CDS, 16 bases upstream of the first nucleotide and 16 bases upstream of the last nucleotide; 5' UTR, first base of the UTR to 17 bases upstream of the stop codon; 3' UTR, 13 bases upstream of the first nucleotide to 15 bases upstream of the last nucleotide; intron, first base of the intron to 8 nucleotides before the last base. Note that our positions differ slightly from those of Ingolia et al. (2009).
Supplementary_files_format_and_content: provided in the 'readme.txt'

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

growth_protocol: All samples and replicates were derived from single-colonies grown for at least 16 hours in 750 ml of YPD medium at 30Â°C and collected during log phase (OD600 0.5 - 0.7).

extract_protocol: Ribosome profiling next-generation sequencing (NGS) libraries were prepared as detailed in [Ingolia NT. 2010. Genome-Wide Translational Profiling by Ribosome Footprinting. In Methods in Enzymology Vol. 470 (eds. J Weissman, C Guthrie, GR Fink), pp. 119-142. Academic Press, Waltham, Massachusetts] with the following modifications: Cryo-grinding of lysates was performed in a Retsch Mixer-Mill MM 301 (Retsch Technology GmbH) at maximum frequency for two 1.5 minute cycles with immersion in liquid N2 before grinding, in between cycles, and following grinding. After purification of the cryo-ground lysate, RNA abundance was determined from the A260 measured using a Nanodrop 2000c (Thermo Scientific) and 1000 µg of RNA was subjected to density gradient centrifugation for monosome isolation. Gradients were fractionated and fractions corresponding to the 80S monosome were collected using a Biocomp Instruments Gradient Station attached to a Foxy Jr Fraction Collector (Teledyne Isco). Total RNA was isolated from the purified lysate using the Epicenter MasterPure Yeast RNA Purification Kit beginning with 500 µg of lysate RNA diluted to 125µl using polysome lysate buffer. Following circularization, the libraries were subjected to an rRNA subtraction step as described in [Brar GA, et al. 2012. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science 335: 552-557].

value: S. cerevisiae BY4176 & S. paradoxus CBS432

tag: growth conditions

value: YPD medium, 30C

tag: growth strage

value: log phase

tag: ploidy

value: haploid/diploid


title: 35932_MeDIPseq

description: Unrelated individual 8

value: Unrelated individual 8


title: Mixed parental ribosome protected fragments replicate 2 lane 2


title: WT culture, anti-RpaA, ZT 36 h, replicate 1

description: Sample 4

source_name: Strain AMC408, LL, ZT 36 h


title: WT culture, anti-RpaA, ZT 32 h, replicate 1

description: Sample 3


title: WT culture, input DNA at peak binding (ZT 32 h), replicate 1

description: Sample 14

value: no antibody (input DNA)


title: 35868_MeDIPseq

description: Unrelated individual 6

value: Unrelated individual 6


title: WT culture, anti-RpaA, ZT 28 h, replicate 1

description: Sample 2

source_name: Strain AMC408, LL, ZT 28 h


title: Mixed parental ribosome protected fragments replicate 1


title: Mixed parental selected mRNA fragments

description: Poly-A selected mRNA fragments isolated from haploid S. cerevisiae and S. paradoxus using the riboprofiling method

source_name: Mixed parental selected mRNA fragments


title: 35893_MeDIPseq

description: Unrelated individual 5

value: Unrelated individual 5


title: ΔrpaA culture, anti-RpaA, pool of ZT 24 - 44 h, replicate 2

description: Sample 9


title: 35769_MeDIPseq

description: Unrelated individual 7

value: Unrelated individual 7


title: 35839_MeDIPseq

description: Unrelated individual 4

value: Unrelated individual 4


title: S. paradoxus Ribo-seq Rep 2

description: NCBI Biosample; SAMN02302499

organism: Saccharomyces paradoxus

source_name: Saccharomyces paradoxus

value: diploid


title: 35922_MeDIPseq

description: Unrelated individual 3

value: Unrelated individual 3


title: S. paradoxus RNA-seq Rep 2

description: NCBI Biosample; SAMN02302495


title: WT culture, anti-RpaA, ZT 24 h, replicate 1

description: Sample 1

source_name: Strain AMC408, LL, ZT 24 h

value: affinity-purified anti-RpaA


title: S. paradoxus Ribo-seq Rep 1

description: NCBI Biosample; SAMN02302498


title: Hybrid Ribo-seq Rep 2

description: NCBI Biosample; SAMN02302505

source_name: Saccharomyces cerevisiae x Saccharomyces paradoxus


title: S. paradoxus RNA-seq Rep 1

description: NCBI Biosample; SAMN02302494


title: 35872_MeDIPseq

description: Unrelated individual 1

source_name: Whole blood

value: Unrelated individual 1


title: Asexual stage parasites 1

status: Public on Dec 03 2013

city: Rockville

first: Ewen

middle: F

last: Kirkness

state: Maryland

address: 9704 Medical Center  Drive

institute: JCVI

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to Plasmodium falciparum Pf3D7 whole genome using CLC Genomics Workbench with default parameters.
RPKM values were calculated with the CLC Genomics Workbench expression experiments.
Supplementary_files_format_and_content: Files with RPKM values for each Sample.

organism: Plasmodium falciparum NF54

source_name: Blood

extract_protocol:
Total RNA was extracted and depleted of rRNA (Ribo-zero; Epicentre)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: asexual blood stage


title: 35865_MeDIPseq

description: Unrelated individual 2

value: Unrelated individual 2


title: Asexual stage parasites 2


title: Cultured sporozoites 2

source_name: Mosquito salivary glands

value: sporozoites grown axenically for 3 days


title: Cultured sporozoites 1


title: ARRY/PX-866-4:CCSP/TGFalpha mice on Doxycycline 8 weeks

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm9 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited rpkm values with genes in rows and samples in columns

organism: Mus musculus

source_name: Lung

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB/N

tag: cell group

value: MAPK/PI3K inhibitors

tag: treatment

value: Treated

tag: day


title: ARRY/PX-866-2:CCSP/TGFalpha mice on Doxycycline 8 weeks

tag: strain


title: Sporozoites 1

value: sporozoites from salivaly gland


title: ARRY/PX-866-3:CCSP/TGFalpha mice on Doxycycline 8 weeks


title: Hybrid RNA-seq Rep 2

description: NCBI Biosample; SAMN02302503


title: ARRY/PX-866-1:CCSP/TGFalpha mice on Doxycycline 8 weeks


title: PX-866-4:CCSP/TGFalpha mice on Doxycycline 8 weeks

value: PI3K inhibitor


title: PX-866-1:CCSP/TGFalpha mice on Doxycycline 8 weeks


title: ARRY-4:CCSP/TGFalpha mice on Doxycycline 8 weeks

value: MAPK inhibitor


title: ARRY-3:CCSP/TGFalpha mice on Doxycycline 8 weeks


title: PX-866-3:CCSP/TGFalpha mice on Doxycycline 8 weeks


title: Hybrid Ribo-seq Rep 1

description: NCBI Biosample; SAMN02302504


title: Fibrosis-3:CCSP/TGFalpha mice on Doxycycline 8 weeks

value: Fibrosis control

value: Ctrl


title: Sporozoites 2


title: ARRY-1:CCSP/TGFalpha mice on Doxycycline 8 weeks


title: Hybrid RNA-seq Rep 1

description: NCBI Biosample; SAMN02302502


title: Fibrosis-2:CCSP/TGFalpha mice on Doxycycline 8 weeks


title: Normal-2:CCSP/- mice on Doxycycline 8 weeks

value: Normal control


title: Normal-4:CCSP/- mice on Doxycycline 8 weeks


title: Fibrosis-4:CCSP/TGFalpha mice on Doxycycline 8 weeks


title: Fibrosis-1:CCSP/TGFalpha mice on Doxycycline 8 weeks


title: Normal-3:CCSP/- mice on Doxycycline 8 weeks


title: Normal-1:CCSP/- mice on Doxycycline 8 weeks


title: DDAH1TG HDM Rep 1

description:
TH1
HDM-treated DDAH1-transgenic mice, rep1.

data_processing:
Bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8.
Fastq sequences were aligned to mm10 using Tophat.
Number of read counts was calculated for each Entrez gene.
Differential expression analysis was performed using Deseq.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file containing genes (Entrez Gene IDs) with raw counts for each Sample.

source_name: Lung tissue, DDAH1-transgenic, HDM

extract_protocol:
Total RNA was extracted with the RNeasy MinElute kit  (Qiagen) according to the manufacturer's specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The mice were intratracheally challenged with 100 micrograms of HDM in 50 microliters of PBS or 50 microliters of PBS alone 3 times per week for 3 weeks. Lung tissues were harvested 24 hours after the last challenge.

tag: strain/background

tag: genotype/variation

value: lung

value: house dust mite (HDM)


title: DDAH1TG PBS Rep 2

description:
TP2
PBS-treated DDAH1-transgenic mice, rep2.

source_name: Lung tissue, DDAH1-transgenic, PBS

value: PBS


title: WT PBS Rep 2

description:
WP2
PBS-treated wild-type mice, rep2.

source_name: Lung tissue, WT, PBS

value: wild-type


title: WT PBS Rep 1

description:
WP1
PBS-treated wild-type mice, rep1.


title: WT HDM Rep 2

description:
WH2
HDM-treated wild-type mice, rep2.

source_name: Lung tissue, WT, HDM


title: Rv0431 Mtb-infected, rep 3

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequence reads were aligned to RefSeq transcripts (mm9) using BWA with default parameters.
RPKMs were calculated as described in Mortazavi et al., 2008 (PMID 18516045).
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text file containing RPKM values for each RefSeq transcript.

source_name: Macrophages, infected with Rv0431 mutant Mtb

extract_protocol:
Cells were lysed with Trizol, and RNA was extracted with a kit from Qiagen.
cDNA libraries were synthesized following the protocol of Illumina Inc. (San Diego) and sequenced on an Illumina GA2x SR40.

treatment_protocol: Uninfected, or infected with WT or rv0431 mutant Mycobacterium tuberculosis (Mtb).

tag: cell type

value: macrophages

value: infected with rv0431 mutant Mycobacterium tuberculosis


title: Rv0431 Mtb-infected, rep 2


title: WT Mtb-infected, rep 1

source_name: Macrophages, infected with WT Mtb

value: infected with wild-type Mycobacterium tuberculosis


title: WT Mtb-infected, rep 3


title: Uninfected, rep 1

source_name: Macrophages, uninfected


title: Rv0431 Mtb-infected, rep 1


title: Uninfected, rep 2


title: qHFSC_input DNA

first: Wen-Hui

last: Lien

address: 1230 York Ave Box#300

department: Mammalian cell biology and development

institute: The Rockefeller Unoversity

description: input DNA

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program. Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification using software MACS.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm
wig files created using IGVtools with 25bp windows
Genome_build: mm9
Supplementary_files_format_and_content: wig files; enrichment values in 25bp windows

source_name: Mouse back skins

growth_protocol: HFSCs were FACS-purifed from the telogen back skins of indicated ages of mice

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of 150-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No treatment

tag: gender

value: female

tag: age

value: telogen back skin

tag: sorting markers

value: integrin α6 and CD34

value: Telogen quiescent hair follicle stem cells (HFSCs)


title: Th1_WCE

city: Liverpool

first: Aditi

last: Kanhere

address: Institute of Systems, Molecular and Integrative Biology

institute: University of Liverpool

description: Whole Cell Extract

data_processing:
Initial processing was performed with the CASAVA pipeline. Reads were aligned to the Mouse NCBI37/mm9 reference genome with ELAND, background corrected using whole cell extract data, and converted to tags per million total reads. Significant peaks were identified with MACS using a p-value threshold of 10-6.
Genome_build: mm9
Supplementary_files_format_and_content: bed: alignment (bed format)
Supplementary_files_format_and_content: peaks.txt: MACS peaks (pvalue cut-off <= 1e-6)
Supplementary_files_format_and_content: bw: bigwig

source_name: T cells

growth_protocol: CD4+ T cells from spleens and lymph nodes of 4-10 week-old mice were purified by CD4 positive selection (Miltenyi Biotec) followed by sorting of naïve CD4+CD25-CD62LhighCD44low cells using FACSAria II (BD Biosciences). Cells were activated by plate-bound anti-CD3 and anti-CD28 (both 10 μg/ml; clones 145-2C11 and 37.51 respectively; BioXCell). Th1 conditions comprised recombinant human IL-2 (20 ng/ml; R&D Systems) and mouse IL-12 (20 ng/ml; eBioscience, San Diego, CA, USA), and anti-IL-4 (10 μg/ml; BioXCell).

extract_protocol: Polarized Th1 cells from WT and T-bet-/- mice were activated for 4 hours with PMA (50 ng/ml) and ionomycin (1 μg/ml), crosslinked with 11% formaldehyde, lysed and sonicated at 24W for 10 x 30 second pulses using a Misonix Sonicator 3000. The resulting whole cell extract was incubated overnight at 4oC with Dynal Protein G beads preincubated with 10ul of purified rabbit anti-T-bet polyclonal antiserum (9856). Beads were washed and bound complexes eluted and crosslinks reversed by heating at 65oC. IP and input DNA were then purified by treatment with RNAseA, proteinase K and phenol:chloroform extraction. Libraries were constructed from IP and input DNA by standard Illumina protocols, except that DNA in the range 150-350bp was gel-purified after PCR-amplification. The library was quantified using an Agilent bioanalyzer and subjected to 35bp single-end read sequencing with an Illumina Genome Analyzer IIx.

tag: antibody

value: T-cell

tag: cell number

tag: genotype

value: wild type


title: DDAH1TG HDM Rep 2

description:
TH2
HDM-treated DDAH1-transgenic mice, rep2.

tag: tissue


title: Th1_Tbet -/-

description: Chromatin IP against Tbet -/- Th1 cells

source_name: Tbet -/- Th1 cells

value: T-bet (Lab produced (Szabo et al., Nature 2000))


title: PHA-4 ChIP repA

city: Houston

first: Jiaofang

last: Shao

state: Texas

address: 6431 Fannin St

department: Department of Biochemistry and Molecular Biology

institute: McGovern Medical School, University of Texas Health Science Center

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the WS232 genome assembly using bowtie2 version 2.0.0-beta7 with the default parameters
Only uniquely mapped reads were remained for peak calling
peaks were called using MACS2 version 2.0.10 with the following setting: bw=200
Genome_build: WS232
Supplementary_files_format_and_content: bedGraph files were generated using MACS2; Scores represent normalized signal intensity.

organism: Caenorhabditis elegans

source_name: embryonic stage

growth_protocol: Synchronized L1 transgenic animals expressing NHR-25::GFP or PHA-4::GFP were fed on OP50 E. coli on agar plates for six hours and cross-linked with 2% formaldehyde for half an hour as described with modifications. The larvae were collected and crosslinked with 2% formaldehyde at room temperature for 30 minutes with gentle rotation. Glycine was added to a final concentration of 0.125 M for 5 minutes and the pellet was washed twice with 1 × PBS. The packed larvae pellet (equivalent to ~500,000 larvae) was resuspended in 0.4 ml nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS) with proteinase inhibitor cocktail (Roche) for 10 minutes at 4 °C. The chromatin was then sheared in a 15-ml conical tube at 4 °C via a Diagenode Bioruptor (Diagenode, Denville, NJ) at the setting “H” for 2 cycles of 15 minutes (30s “ON”; 30s “OFF” for each cycle). The supernatant was collected and diluted with 9 parts of dilution buffer (50 mM Tris-HCl pH 8.0, 0.166 M NaCl, 1.1 % Triton X-100, 0.11 % sodium deoxycholate), supplemented with proteinase inhibitor cocktail (Roche).

extract_protocol:
The fixed worms were sheared with sonication and the cell lysate were used for ChIP with anti-GFP antibody
The libraries were constructed following Illumina standard protocol. Briefly, DNA was end-repaired (End-it DNA END-Repair kit, Epicentre) and the adenines were added to the 3’ ends by Klenow exo- (NEB). The barcoded adapters were ligated to the A-tailed fragments by T4 DNA ligase (NEB). The ligation products were purified by Agencourt AMPure XP system (Beckman Coulter, Inc) and PCR-amplified in a thermocycler for 16 cycles with KAPA HiFi hotstart mix (KAPA Biosystems) and PCR primers. Amplified libraries were size-selected on a 2% agarose gel and purified with MinElute columns (QIAGEN). The libraries were then sequenced on an Illumina Genome Analyzer IIx (Illumina, Hayward, CA) by the High-Throughput Genomics Unit (University of Washington) according to a standard protocol.

tag: Stage

value: Fed L1

value: anti-GFP (polyclonal goat IgG; produced in Hyman lab)


title: PHA-4 ChIP input repA


title: NHR-25 ChIP input repA


title: ARRY-2:CCSP/TGFalpha mice on Doxycycline 8 weeks

value: FVB/N

value: MAPK inhibitor

value: Treated


title: NHR-25 ChIP repA


title: WT HDM Rep 1

description:
WH1
HDM-treated wild-type mice, rep1.

value: lung

value: house dust mite (HDM)


title: NHR-25 ChIP repB


title: DDAH1TG PBS Rep 1

description:
TP1
PBS-treated DDAH1-transgenic mice, rep1.

value: PBS


title: PX-866-2:CCSP/TGFalpha mice on Doxycycline 8 weeks

value: PI3K inhibitor


title: HBx_MIRA

city: Seoul

first: Sun-Min

last: LEE

address: Shinchon-dong Seodeamun-gu

department: Biochemistry

country: South Korea

institute: Yonsei University

description:
MBD2B,MBD3L affinity purified
Genomic DNA samples from three mice

data_processing:
mRNA libraries were sequenced on Illumina genome analyzer and MIRA libraries were sequenced on Illumina HiSeq 2500
Sequenced reads of 51 bp that passed quality control filters(ASCII Qscore Offset 33) were used
Sequence tags were mapped to the mouse genome (UCSC mm9 database based on NCBI Build 37 assembly) using the Bowtie2
We extended the 51-bp reads toward the 3’ end to cover DNA fragments bound by the MBD proteins (200 bp)
We counted overlapping sequence tags at 50-bp resolution.
We then calculated RPKM (reads per million base pairs mapped per kb) at 50-bp resolution
The reads from mRNA-seq were aligned to mm9 using TopHat
Genome_build: mm9

source_name: liver

extract_protocol:
Genomic DNA from 25-mg liver tissue samples was purified with a DNeasyR Blood & Tissue Kit. Total RNA from 3 livers collected from 3-month-old mice was extracted using Qiagen RNeasy mini kits.
We generated cDNA libraries for sequencing using a Illumina mRNA sample prep kit (Hayward, CA). And TruSeq® DNA sample prep kit were used for generation of MIRA libraries.

value: 3 months after birth

value: HBx TG mouse


title: WT Mtb-infected, rep 2

value: macrophages

value: infected with wild-type Mycobacterium tuberculosis


title: RN2_JQ1_0h

status: Public on Dec 02 2013

city: Cold Spring Harbor

first: Christopher

middle: R

last: Vakoc

address: 1 Bungtown Rd

institute: Cold Spring Harbor Lab

data_processing:
For NSR and illumine RNA-seq, The obtained reads from illumina HiSEq 2000. were trimmed into 28 base reads corresponding to 9th to 36th position from the 5′ ends of the reads. The trimmed reads were mapped to the mouse genome (mm9) using Bowtie with no mismatch. Gene expression was analyzed by using Cufflinks software (http://cufflinks.cbcb.umd.edu/).
For JQ1 RNA-seq time course experiment, illumina sequences were split into separate files based on sample barcodes.  For each read pair one read consists of primer and a 7 base sequence identifying the sample.  Both reads are examined, the sample ID is found on one read and the other read is mapped to the mouse mm9 reference genome, from the UCSC Genome Browser ftp site, using Tophat2.  Read counts per gene are computed by counting reads that overlap the mm9 refseq gene annotations downloaded from the UCSC Genome Browser ftp site.  These counts are normalized by dividing by the total number of reads counted for all genes.  For each series of time points for each gene a best continuous piecewise linear fit is computed.  The intent is to model the response of each gene by a latency period of no response followed by a response reaching a new stable level after a period of time.  The form of this curve is three linear segments with the first and last segments slope zero and the middle segment connecting the two end segments.  The curves are defined by the pair of endpoints of the middle segment.  All pairs of points are tested to find the pair of points minimizing the sum of the squared difference to the data. Rapidly down regulated genes were identified based on two criteria: a three-fold decrease in mRNA level at 6 hours together with a good fit to two-step linear model of consistent decreases over consecutive time points.
Genome_build: mm9
Supplementary_files_format_and_content: txt

source_name: MLL-AF9/NrasG12D murine cell line

growth_protocol: Murine AML cell line was cultured in RPMI1640 supplement with 10% FBS and penicillin/streptomycin

extract_protocol:
Total RNA was prepared using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. 1 ug of total RNA was subjected to “not-so-random” (NSR) primer-based RNA-seq library preparation according to protocols described previously (Armour et al. 2009). For the polyA+ tail RNA-seq, the library was made following the instructions of illumina Truseq RNA sample prep kit v2.
For JQ1 RNA-seq timecourse, the RNA-seq evaluation was performed using a custom method. Briefly, amplified cDNA (>2ng) was used to construct Illumina sequencing libraries following the Illumina’s Ultra Low Input mRNA-Seq Guide.  The amplified cDNA was fragmented into 200bp using Covaris acoustic shearing instrument.  The resulting fragments were end-repaired, single A base added, followed by ligation with PE adaptor and amplification by 15 cycles of PCR.  The resulting libraries are expected to show a peak at around 300bp on Bioanalyzer (Agilent).  In order to enrich the reads containing variental tag and sample barcode, we using Dynabeads® mRNA Purification Kit for mRNA Purification (Invitrogen Cat. No. 610-06).  The libraries were heat at 95C for 2min before mixing with polyT magnetic beads.  Then, we incubated the beads at 47C for overnight and run 6-8 cycles of PCR from the elution the next day.   As a result, approximately 50% of the sequencing raw reads will contain variental tags and sample barcodes.

treatment_protocol: For measuring the basal transcripts level, RNA of mouse murine AML RN2 cell were isolated by using TRIzol. For detecting the rapid downregulated genes in response to JQ1, BET bromodomian inhibitor, we treated RN2 cell with 250nM JQ1, BET bromodomain inhibitor, and isolate RNA at indicated time point during 48h time course. \

tag: cell line

tag: barcode

value: TGTAACC

value: JQ1 treatment for 0h


title: illumina_RN2

value: no treatment


title: Th1_Tbet

description: Chromatin IP against T-bet in Th1 cells

source_name: Th1 cells

value: T-bet (Lab produced (Szabo et al., Nature 2000))

value: wild type


title: RN2_JQ1_0.5h

value: TAGGAGC

value: JQ1 treatment for 0.5h


title: RN2_JQ1_1h

value: GCACAGG

value: JQ1 treatment for 1h


title: 3P-seqs in kidney  with miR-22 knockout

first: Jin-Wu

last: Nam

address: 222 Wangsimni Seongdong-gu

institute: Hanyang University

data_processing:
Basecalls performed using CASAVA version 1.7
Reads are reverse-complemented first and mapped reads with at least one untemplated adenylate residue using Bowtie with option (bowtie -p 4 -q --phred33-quals -5 3 -l 25 -n 1 -e 240 --best --strata -m 1).
We considered as a cluster those 3P-tags ending 31 nucleotides within the most frequently implicated cleavage position, which was then regarded as a candidate poly(A) cleavage site.
To control for PCR amplification bias, we only used those clusters with at least two identifiably independent reads in our downstream analysis (e.g. tags with different ends, different number 3’-terminal adenylates, and/or from two different libraries).
Genome_build: mm9
Supplementary_files_format_and_content: bed files including 3P-seq clusters

source_name: Kidney

extract_protocol:
RNA from wild type and miR-22D (Gurha et al., 2012) mouse tissues was isolated by adding a steel bead and 1 mL TRI Reagent to tissues and then vortexing for two minutes in a TissueLyser II (Qiagen) at 30 Hz, twice. The homogenate was centrifuged for 8 min at 12,000xg and the supernatant was purified according to manufacturer’s protocol with an additional phenol/chloroform extraction after phase separation.
3P-Seq libraries were prepared from 75 μg of isolated RNA (mouse tissues, mESC, NIH3T3) as described previously (Jan et al., 2011) with modifications (see Supplemental Information).

tag: data type

value: 3P-seq fastq

value: Kidney

value: miR-22 knockout

tag: genetic background


title: 3P-seqs in wat  with miR-22 knockout

source_name: White adipose tissue (WAT)

value: White adipose tissue (WAT)


title: NSR_RN2

tag: treatment


title: 3P-seqs in heart with miR-22 knockout

source_name: Heart

value: Heart


title: 3P-seqs in muscle with miR-22 knockout

source_name: Muscle

value: Muscle


title: Normal_MIRA

tag: strain

value: 3 months after birth


title: 3P-seqs in kidney wild type

value: willd type


title: 3P-seqs in wat wild type


title: NHR-25 ChIP input repB

value: Fed L1

value: anti-GFP (polyclonal goat IgG; produced in Hyman lab)


title: 3P-seqs in liver wild type

source_name: Liver

value: Liver


title: 3P-seqs in lung wild type

source_name: Lung

value: Lung


title: 3P-seqs in muscle wild type


title: 3P-seqs in heart wild type


title: ChIP_Brg1_RN2_DMSO

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all ChIP-Seq samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 1 -n 2 --best --sam. Seed length (-l) was set to read length for each dataset.
Genome_build: mm8
Supplementary_files_format_and_content: Supplementary_files_format_and_content: WIG files: For all ChIP-Seq samples, wiggle files were produced by MACS 1.4 with --space=50.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. 1x10^8 cells were sonicated at 21 watts in 20 second pulses for 3 min of sonication time. The chromatin extracts containing DNA fragments with an average size of 500 bp were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
All protocols for Illumina/Solexa sequence preparation, sequencing and quality control are provided by Illumina (http://www.illumina.com/pages.ilmn?ID=203).

treatment_protocol: Cells were treated with DMSO or nothing before crosslining. In brief, cells were crosslinked using 1% formaldehyde for 20 min at room temperature.

value: MLL-AF9/NrasG12D AML cell line

value: DMSO

tag: chip antibody

value: anti-Brg1 (Abcam, ab4081)


title: WCE_RN2_DMSO


title: ChIP_Brd4_RN2_DMSO


title: ChIP_H3K27ac_RN2


title: ChIP_H3K4me3_RN2

value: anti-H3K4me3 (Abcam, ab8580)


title: WCE_RN2


title: Sample 10_P14 effector CTLs IL-2 + IL-12 +CpG #1

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

description: Sample 10; B10ST10_CATGGC

data_processing:
Cutadapt [http://code.google.com/p/cutadapt/] was used to remove adapter sequences.
Bowtie was used to map all the reads longer than 15 nucleotides to the mm9 genome without allowing mismatches. If a read had multiple mappable positions, then one was selected randomly.
MicroRNA annotations were extracted from the miRBase (mus musculus) database. The number of reads falling into each miRNA locus was quantified using BEDTools. To count a read as a miRNA read we required that it had the correct strand information and resided completely within the annotated miRNA region.
Read counts were normalized based on the total number of million mapped reads and the average miRNA length (0.022 kilobases) and expressed as RPKM values.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

source_name: P14 effector CTLs IL-2 + IL-12 +CpG

growth_protocol: Stimulation of purified CD8+ T cells from control (samples 1,2,4,5) or Dicer knockout (samples 3,6) with antiCD3 plus anti-CD28, followed by culture in 100U/ml IL-2 for 6 days; Stimulation of P14 transgenic CD8+ T cells with gp33 (samples 9,11) or gp33 plus CpG (samples 10,12) followed by culture in 100U/ml IL-2 (samples 9,11) or IL-2 plus IL-12 (samples 10,12); Sorting of KLRG1+CD127- and KLRG1-CD127+ cells from spleens of mice 8 days after LCMV-Arm infection.

extract_protocol:
mirVana miRNA isolation kit or Qiagen miRNeasy isolation kit
TruSeq small RNA (Illumina)

tag: strain background

tag: genotype/variation

value: P14 TCRa-/-

value: In vitro generated CTLs

tag: differentiation time

value: 6 days


title: Sample 12_P14 effector CTLs IL-2 + IL-12 +CpG #2

description: Sample 12; B12ST12_CCAACA

tag: cell type


title: Sample 11_P14 effector CTLs IL-2 only #2

description: Sample 11; B11ST11_CATTTT

source_name: P14 effector CTLs IL-2 only


title: Sample 8_KLRG1-CD127+ (memory precursors)

description: Sample 8; B8ST8_CACTCA

source_name: KLRG1-CD127+ (memory precursors)

value: infected with LCMV-Armstrong

value: ex vivo sorted CD8+ memory precursors

value: 8 days (in vivo)


title: 3P-seqs in liver with miR-22 knockout

value: 3P-seq fastq

value: miR-22 knockout


title: Sample 7_KLRG1+CD127- (effectors)

description: Sample 7; B7ST7_CACGAT

source_name: KLRG1+CD127- (effectors)

value: ex vivo sorted effector CTLs


title: Sample 4_P14 Dicer+/+ Cre-RV (Ctrl)

description: Sample 4; B4ST4_CAAAAG

source_name: P14 Dicer+/+ Cre-RV (Ctrl)

value: P14 Dicer+/+


title: Sample 6_P14 Dicerfl/fl Cre-RV (KO)

description: Sample 6; B6ST6_CACCGG

source_name: P14 Dicerfl/fl Cre-RV (KO)

value: P14 Dicerfl/fl


title: Sample 2_P14 Dicerfl/fl Mock transduced (Ctrl)

description: Sample 2; B2ST2_ATGAGC

source_name: P14 Dicerfl/fl Mock transduced (Ctrl)


title: Sample 5_P14 Dicerfl/fl Mock transduced (Ctrl)

description: Sample 5; B5ST5_CAACTA


title: Sample 1_P14 Dicerfl/+ Cre-RV (Ctrl)

description: Sample 1; B1ST1_ACTGAT

source_name: P14 Dicerfl/+ Cre-RV (Ctrl)

value: P14 Dicerfl/+


title: HDAC3-dIEC input

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

description: pooled inputs from HDAC3-dIEC (1-3)

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 0.12.7 using option of --best -v 2 --strata -m 1
Genome_build: mm9

source_name: intestinal epithelial cells

extract_protocol:
10  μg of chromatin was  incubated with anti-H3K9Ac antibody. Protein A sepharose beads were used to obtain the ChIP product. Chromatin was reverse crosslinked at 65℃ 16hours, and DNA was purified by phenol/chloroform extraction.
Intestinal epithelial cells from the large intestine were fixed in 1% PFA for 10 min and quenched with glycine. Cells were lysed and extracts were sonicated using a Bioruptor (Diagenode) and appropriate sonication was confirmed using an Agilent bioanalyzer.
ChIP and input DNA libraries for each genotype were prepared for sequencing according to the multiplex amplification protocol from Illumina.

value: large intestine

value: IEC


title: H3K9ac in HDAC3-FF-3

description: genomic DNA from  H3K9Ac ChIP

value: rabbit anti-H3K9ac (Millipore; 06-942)


title: HDAC3-FF input

description: pooled inputs from HDAC3-FF (1-3)


title: H3K9ac in HDAC3-dIEC-2

description: genomic DNA from  H3K9Ac ChIP


title: H3K9ac in HDAC3-dIEC-1

description: genomic DNA from  H3K9Ac ChIP


title: H3K9ac in HDAC3-FF-2

description: genomic DNA from  H3K9Ac ChIP


title: Sample 9_P14 effector CTLs IL-2 only #1

description: Sample 9; B9ST9_CAGGCG


title: Sample 3_P14 Dicer fl/fl Cre-RV (KO)

description: Sample 3; B3ST3_ATTCCT

source_name: P14 Dicer fl/fl Cre-RV (KO)


title: H3K4me2_gastrula

city: Vienna

first: Michaela

last: Schwaiger

address: Althanstr. 14

country: Austria

institute: University of Vienna

data_processing:
Reads were mapped to the genome using BWA with default settings and those with a quality score < 30 were discarded.
Peakfinding on each p300 and RNA Polymerase II dataset was performed using the peakzilla software, using Input reads as control. Peaks with > 2-fold enrichment over control and a score > 3 (p300) or > 5 (Pol2) were considered significant for each replicate, if they overlapped more than 2-fold enriched peaks in the other replicate. Finally, the significant peaks of the two replicates were merged.
For chromatin modifications, the bam files were converted to bed files and reads were counted in 200bp windows aross the whole Nematostella genome using bedtools.
The RNAseq reads were aligned to our gene models using tophat with default settings. FPKM values were calculated using cuffdiff v1.3.0. All RNA-seq experiments for each developmental stage were combined for calculating the stage specific FPKM values.
Genome_build: Nemvec1
Supplementary_files_format_and_content: ChIP-Seq: bed, chromatin: read counts in 200bp windows across the genome, p300 and RNA Pol2: genomic location of significant peaks

organism: Nematostella vectensis

source_name: gastrulae (24h)

growth_protocol: Nematostella vectensis was grown in 1/3rd artificial seawater and fed with brine shrip larvae.

extract_protocol:
After removal from jelly, eggs were fixed in 2% formaldehyde for 12 minutes at room temperature. Cross-linking was stopped by adding 125mM glycine followed by rotation for 10 min at 4 degrees.  After washing with cold PBS and HEG Buffer (50mM HEPES pH7.5, 1mM EDTA, 20% Glycerol), embryos were snap-frozen and stored at -80 degrees. Embryos were homogenized in Nuclei Buffer 1 (50mM HEPES pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X-100, 1mM DTT) and centrifuged at 500g for 3 minutes, after which the pellet containing debris was discarded. After another centrifugation at 2000g for 10 minutes the pellet contained nuclei, which were washed with Nuclei Buffer 2 (50mM HEPES pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X-100) and finally resuspended in Lysis Buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 0.1% DOC, 01% Triton X-100, 0.1% SDS). After shearing the chromatin to 100-200bp using a Covaris Instrument and removing the non-soluble material, we blocked the chromatin with pre-blocked (1mg/ml tRNA, 1mg/ml BSA) protein A beads CL-4B (GE Healthcare 71-7090-00 AE). At this point we removed a small aliquot of chromatin for Input DNA and incubated the remaining chromatin with the desired antibodies, rotating at 4 degrees over night. We then added pre-blocked protein A beads to bind the antibodies and washed the beads twice with Lysis Buffer, twice with DOC Buffer (10mM Tris pH8, 0.25M LiCl, 0.5% NP-40, 0.5% DOC, 1mM EDTA), and once with TE Buffer. Chromatin was eluted from the beads with Elution Buffer (1%SDS, 0.1M NaHCO3) and de-crosslinked. RNA was isolated using Trizol.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or HiSeq machine following the manufacturer's protocols. Strand-specific RNA-seq libraries were prepared using dUTP incorporation during the 2nd strand synthesis.

tag: developmental stage

value: gastrulae (24h)

tag: chip antibody source

value: Diagenode

tag: chip antibody order/lot number

tag: fragmentation

value: sonication

tag: library method

value: ChIP-Seq

tag: read length


title: H3K4me2_planula

source_name: planulae (4 days)

value: planulae (4 days)


title: H3K4me2_adultfemale

source_name: adult female polyps

value: adult polyps

tag: gender

value: female


title: H3K4me3_adultfemale


title: Input_adultfemale


title: H3K4me1_planula

value: Abcam


title: H3K4me1_gastrula


title: Input_gastrula_36


title: H3K4me3_planula


title: Mock transfection to HEK293, replicate 1

description:
PolyA-selected RNAs
HEK293.exp.qn

data_processing:
Basecalls performed using CASAVA version 1.7
All RNA-seq data were mapped to the human reference genome (hg19) using Bowtie version 0.12.8 (Trapnell et al., 2009), allowing at most five genomic matches but choosing the best one (-n 1 -e 240 -m 5 --best --strata).
To measure expression level, we estimated both reads per kilobases per million reads (RPKM) values and reads per million reads (RPM) values based on RefSeq annotation (Aug-22-2011 version).
Quantile normalization was performed to reduce technical global bias of expressions between replicates and between wild type and transfected cells.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for pUC19_1, pUC19_2, miR-124_1, miR-124_2, miR-155_1, and miR-155_2

source_name: HEK293 cells

extract_protocol:
After 24 hours, cells were harvested, and RNA was extracted using TRI-reagent (Life Technologies).
After RNA isolation, poly(A)+ RNA was selected using oligo(dT) beads (Invitrogen). RNA-seq libraries were prepared by either a ligation-based approach, as previously described (Guo et al., 2010), or a dUTP-based approach (Bioo Scientific), according the manufacturer’s directions.

treatment_protocol: Cells were transfected with Lipofectamine 2000 (Invitrogen) and 100 nM miRNA duplex or pUC19, as described by the manufacturer.

tag: transfection

tag: cell line

value: HEK293 cells

value: RNA-seq fastq


title: miR-155 transfection to HEK293, replicate 2

description:
PolyA-selected RNAs
HEK293.exp.qn

tag: data type


title: H3K36me3_planula


title: H3K36me3_gastrula


title: 3P-seqs in lung  with miR-22 knockout

value: 3P-seq fastq

tag: tissue

value: Lung

tag: genotype

value: miR-22 knockout

tag: genetic background


title: H3K9ac in HDAC3-dIEC-3

description: genomic DNA from  H3K9Ac ChIP

tag: strain

tag: antibody


title: Mock transfection to HEK293, replicate 2

description:
PolyA-selected RNAs
HEK293.exp.qn


title: miR-155 transfection to HEK293, replicate 1

description:
PolyA-selected RNAs
HEK293.exp.qn


title: H3K36me3_adultfemale

tag: chip antibody


title: H3K27ac_planula


title: H3K9ac in HDAC3-FF-1

description: genomic DNA from  H3K9Ac ChIP

tag: cell type


title: miR-124 transfection to HEK293, replicate 2

description:
PolyA-selected RNAs
HEK293.exp.qn


title: H3K27ac_adultfemale

tag: developmental stage

value: adult


title: Input_planula_36


title: Input_gastrula


title: miR-124 transfection to HEK293, replicate 1

description:
PolyA-selected RNAs
HEK293.exp.qn


title: Mock transfection to HeLa, replicate 2

description:
PolyA-selected RNAs
HeLa.exp.qn

source_name: HeLa cells

value: HeLa cells


title: H3K4me3_gastrula

tag: chip antibody source


title: Input sequencing in bud-stage embryo rep 1

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: Input

data_processing:
Basecalls performed using CASAVA version 1.4
Alignment: sequencing reads were aligned to the zebrafish genome (version danRer6) using Bowtie version 0.12.7 with options "-q --best --strata -m 1 -p 4 --chunkmbs 1024", and only uniquely mapping reads were retained for further analysis.
Peak-calling: Binding events were detected using GPS as previously described (Guo et al. 2010). In GPS, the scaling ratio between IP and control channels was estimated using the median ratio of all 10Kbp windows along the genome. The GPS binding model was initialized to the default and iteratively updated over up to 3 training rounds, and the shape deviation threshold for final peaks was set to -0.2. In this study, we require that reported peaks contain a ChIP-seq enrichment level that is significantly greater than 1.5 times the control channel read count over the same region with p-value <0.001 as tested using a Binomial test.
Domain-calling: Histone mark domains were detected using a 200bp sliding window (offset = 100bp) along the genome, merging neighboring windows that individually contain significantly more signal reads than expected by a global Poisson background model  (p<10^-9) and significantly more signal reads than expected by local Poisson background models parameterized by the input samples (p<10^-9).
Genome_build: danRer6
Supplementary_files_format_and_content: BED: Cdx4 and Sall4 peaks.bed files are conversions of GPS output files to BED format, centered on the GPS binding event location and extended to 100bp width. Chromatin enriched domains are also output in BED format.
Supplementary_files_format_and_content: BIGWIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts. WIG files were converted to bigWig using wigToBigWig (UCSC)

organism: Danio rerio

source_name: Bud stage embryo

growth_protocol: Zebrafish were maintained and raised under standard conditions.

extract_protocol:
For each ChIP experiment, ~2000 embryos were carefully staged. 500 embryos were then collected, transferred into PBS containing 20mM Na-butyrate, protease inhibitors (Sigma). Embryos were then transferred to 5ml syringe fitted with 21G needle. After leaving ~500ul buffer above the embryos, embryos were forced through the needle by pushing the pistons to dissociate the embryos. The resulting lysed extract was collected in 2ml eppendorf tubes, and crosslinked by adding formaldehyde solution to final concentration of 1.1%. Crosslinking was conducted for 15 minutes at room temperature while samples were mixed using nutator. After crosslinking, glycine was added to 0.125M to quench the formaldehyde, and incubated on ice for 5 minutes. Tubes were then centrifuged at 470g for 10 minutes at 4C to sediment the cells. The cells were then washed twice with 500ul ice-cold PBS/Na-butyrate/protease inhibitor solution, and flash-frozen and kept at -80C until the ChIP experiment.
ChIP-seq libraries prepared using standard Illumina protocols

treatment_protocol: Wild-type (Tu) embryos were collected at the 1-cell stage, and were kept uninjected, or injected with mRNA for further experiments.

value: whole embryo

value: Tu

value: Input


title: miR-155 transfection to HeLa, replicate 2

description:
PolyA-selected RNAs
HeLa.exp.qn


title: ChIP-seq myc-tagged Sall4 in bud-stage embryo

description: Chromatin IP against myc-tagged Sall4

value: Anti-Myc (Abcam ab9132)


title: Mock transfection to HeLa, replicate 1

description:
PolyA-selected RNAs
HeLa.exp.qn


title: ChIP-seq myc-tagged Cdx4 in bud-stage embryo

description: Chromatin IP against myc-tagged Cdx4


title: miR-124 transfection to HeLa, replicate 1

description:
PolyA-selected RNAs
HeLa.exp.qn


title: miR-124 transfection to HeLa, replicate 2

description:
PolyA-selected RNAs
HeLa.exp.qn


title: 3P-seqs in IMR90 cells

data_processing:
Basecalls performed using CASAVA version 1.7
Reads are reverse-complemented first and mapped reads with at least one untemplated adenylate residue using Bowtie with option (bowtie -p 4 -q --phred33-quals -5 3 -l 25 -n 1 -e 240 --best --strata -m 1).
We considered as a cluster those 3P-tags ending 31 nucleotides within the most frequently implicated cleavage position, which was then regarded as a candidate poly(A) cleavage site.
To control for PCR amplification bias, we only used those clusters with at least two identifiably independent reads in our downstream analysis (e.g. tags with different ends, different number 3’-terminal adenylates, and/or from two different libraries).
Genome_build: hg19
Supplementary_files_format_and_content: bed files including 3P-seq clusters

source_name: IMR90 cells

extract_protocol:
RNA from cell lines was isolated by adding a steel bead and 1 mL TRI Reagent to tissues and then vortexing for two minutes in a TissueLyser II (Qiagen) at 30 Hz, twice. The homogenate was centrifuged for 8 min at 12,000xg and the supernatant was purified according to manufacturer’s protocol with an additional phenol/chloroform extraction after phase separation.
3P-Seq libraries were prepared from 75 μg of isolated RNA (HeLa, HEK293, Huh7, IMR90 cells) as described previously (Jan et al., 2011) with modifications (see Supplemental Information).

value: IMR90 cells


title: 3P-seqs in Huh7 cells

source_name: Huh7 cells

value: Huh7 cells


title: HUG1N IgG Control

city: Boston

first: Ramesh

last: Shivdasani

state: Massachusetts

address: Dana Bldg, Room 720, 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Sample 4
processed data file: HUG1N.peaks.bed

data_processing:
Basecalls performed using CASAVA.
Reads aligned with Bowtie, default parameters with ambiguous reads dropped
Peaks called with MACS 1.4.*
AGS calls: MACS version 1.4.2 20111207, ARGUMENTS LIST:, name = macs_output, format = AUTO, effective genome size = 2.77e+09, band width = 300, model fold = 10,30, pvalue cutoff = 1.00e-05, Large dataset will be scaled towards smaller dataset., Range for calculating regional lambda is: 1000 bps and 10000 bps, tag size is determined as 50 bps, total tags in treatment: 115925467, tags after filtering in treatment: 38124475, maximum duplicate tags at the same position in treatment = 1, Redundant rate in treatment: 0.67, total tags in control: 79027562, tags after filtering in control: 58738470, maximum duplicate tags at the same position in control = 1, Redundant rate in control: 0.26, d = 62
HUG1N calls: MACS version 1.4.0beta, ARGUMENTS LIST:, name = GATA6_SCruz_HUG1N_hg18_over_IgG_HUG1N_hg18_pe-5, format = AUTO, effective genome size = 2.70e+09, band width = 300, model fold = 10,30, pvalue cutoff = 1.00e-05, Range for calculating regional lambda is: 1000 bps and 10000 bps, tag size is determined as 39 bps, total tags in treatment: 10813282, tags after filtering in treatment: 9895257, maximum duplicate tags at the same position in treatment = 1, Redundant rate in treatment: 0.08, total tags in control: 6579354, tags after filtering in control: 6230975, maximum duplicate tags at the same position in control = 1, Redundant rate in control: 0.05, d = 58
Genome_build: hg18
Supplementary_files_format_and_content: bed file

growth_protocol: AGS cells were grown in 10cm plate in DMEM media, HUG1N cells were grown in suspension in RPMI media

extract_protocol:
Cells were lysed in SDS lysis buffer. Cells were crosslinked at 50% confluency with 1% formaldehyde.
Libraries were made using the NEB kit following the instructions of the manufacturer.

value: gastric carcinoma


title: RN2_JQ1_48h

source_name: MLL-AF9/NrasG12D murine cell line

tag: barcode

value: CTTATGG

tag: treatment

value: JQ1 treatment for 48h


title: RN2_JQ1_40h

value: GACGTGG

value: JQ1 treatment for 40h


title: 3P-seqs in HeLa cells


title: AGS IgG Control

description:
Sample 2
processed data file: AGS.peaks.bed

value: AGS


title: RN2_JQ1_44h

value: CGTGACC

value: JQ1 treatment for 44h


title: H3K27ac_gastrula

value: gastrulae (24h)

value: Abcam

tag: chip antibody order/lot number

tag: fragmentation

value: sonication

tag: library method

value: ChIP-Seq


title: RN2_JQ1_36h

value: AAGATCG

value: JQ1 treatment for 36h


title: AGS GATA6

description:
Sample 1
processed data file: AGS.peaks.bed

tag: chip antibody vendor

value: Cell Signaling

tag: chip antibody cat. #


title: RN2_JQ1_32h

tag: cell line

value: CTTCTGC

value: JQ1 treatment for 32h


title: RN2_JQ1_28h

value: CCTGACG

value: JQ1 treatment for 28h


title: RN2_JQ1_24h

value: ACTCTGG

value: JQ1 treatment for 24h


title: 3P-seqs in 3T3

tag: data type

value: 3P-seq fastq


title: RN2_JQ1_18h

value: TAGGAGC

value: JQ1 treatment for 18h


title: RN2_JQ1_15h

value: TGTAACC

value: JQ1 treatment for 15h


title: RN2_JQ1_21h

value: GCACAGG

value: JQ1 treatment for 21h


title: TSS_Rluc_1

data_processing:
Mapping of 4C data was performed using 4Cseqpipe, as described in (van de Werken et al. 2012). 4Cseqpipe analyzes 4C-seq experiments by including packages that allow sequence extraction, mapping, normalization, and plotting of cis-contact profiles around viewpoints. Custom restriction site tracks were built using the -build_re_db option of 4Cseqpipe for the mm8 mouse genomic version (UCSC) with HindIII and DpnII as first and second restriction cutters, respectively. A total of 3618110 PE 100x100 reads (2014321 rep1 + 1603789 rep2) were obtained for the MycTSS viewpoint experiments, and 3649354 PE 100x100 reads (2059310 rep1 + 1590044 rep2) for Enh3. Paired-end 2 reads from the first biological replicates were used for analysis in the 4Cseq pipeline as these contain the HindIII restriction site fragment. PE 2 reads were trimmed to a size of 53bp which include the 4C HindIII amplification primer in the beginning of the read (GCTTCCTTGCCTAAGACAAGCTT, 23bp) followed by 30bp of interacting sequence. These processed reads were mapped to the custom mm8 tracks with the in-built 4Cseqpipe mapper. Near-cis domainograms were generated for the whole chr15 for both viewpoints using the median stat_type and plotting the 80th quantile of the distribution of normalized contact intensities for 10Kb windows in MycTSS_4C and in Enh3_4C. These values were put into wig files for visualization using the UCSC genome browser mm8 version, where data range of the vertical axis was set to the ~7% and 8% of the maximal normalization value for MycTSS_4C and Enh3_4C, respectively, to deal with the fact that the majority of data are very close to the viewpoint.
2,958,300 PE 100x100 reads were obtained for Myc TSS shBrg1 (1465526 rep1 + 579006 rep2) and 4,860,980 (2430490 rep1 + 1400170 rep2) for Myc TSS Rluc viewpoints. For calculating the mean value of the 4C-seq data, P1+P2 (paired-end read 1 + 2) reads from replicate 1 of Brg1 and Rluc were mapped against the mm8 mouse genome using bowtie with max two mismatches and binned into 1kb windows for the whole sequence of chromosome 15. Total number of mapped reads were then normalized using rep1 TSS RN2 viewpoint read number as reference. Sliding windows of 10kb were made for chromosome 15. For each 10kb sliding window, the highest 1kb bin value in the window was substituted for the second highest value to avoid outlier bias for mean calculation.
Genome_build: mouse mm8
Supplementary_files_format_and_content: wig

extract_protocol:
Isolated nuclei were digested for 4 hrs with 200U HindIII at 37°C, followed by overnight incubation with 400U HindIII, and a final 4hr incubation with 200U HindIII. Then, samples were ligated overnight in 7ml using 50U T4 DNA ligase (at 16°C. Ligation circles were phenol-chloroform extracted and ethanol precipitated with glycogen as a carrier. These were further digested with 50U of DpnII  overnight at 37°C, followed by heat inactivation for 25 min at 65°C, and ligation in 14ml with 100U T4 DNA ligase at 16°C. These trimmed circles (4C template) were phenol-chloroform extracted and ethanol precipitated with glycogen as a carrier.
4C-seq library construction (Splinter et al. Nat Methods. 2012)

treatment_protocol: Murine AML cell lines RN2 cell line or shRNA transduced RN2 cell lines are used for 4C-seq experiments. Before crosslinking, RN2 cells transduced with indicated constructs were treated with 1ug/ml doxycycline to induce shRNA expression for 48h. TRMPV_Rluc is negative control shRNA targeting Renilla luciferase. In brief, cells were crosslinked using 1% formaldehyde for 20 min at room temperature.

value: Rluc control shRNA induction for 48h


title: RN2_JQ1_10h

value: CGTGACC

value: JQ1 treatment for 10h


title: miR-155 transfection to HeLa, replicate 1

description:
PolyA-selected RNAs
HeLa.exp.qn

tag: transfection

value: HeLa cells

value: RNA-seq fastq


title: 3P-seqs in HEK293 cells

value: HEK293 cells


title: HUG1N GATA6

description:
Sample 3
processed data file: HUG1N.peaks.bed

value: gastric carcinoma

value: Cell Signaling


title: TSS_BRG1_1

value: Brg1 shRNA induction for 48h


title: RN2_JQ1_8h

value: AAGATCG

value: JQ1 treatment for 8h


title: RN2_JQ1_4h

value: GACGTGG

value: JQ1 treatment for 4h


title: RN2_JQ1_6h

value: CTTCTGC

value: JQ1 treatment for 6h


title: RN2_JQ1_3h

value: CCTGACG

value: JQ1 treatment for 3h


title: Enh_RN2_2


title: Enh_RN2_1


title: TSS_RN2_2