title: Nanog ChIP in hES line HUES64 rep2

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

institute: Max Planck Institute of Psychiatry

data_processing:
BiSeq: raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
RNA-Seq: raw sequence reads were aligned using Tophat v2.0.6 and Bowtie version 0.12.7.
RNA-Seq: Reads were mapped to the human genome (hg19) using TopHat v2.0.6 (Trapnell et al., 2009)(http://tophat.cbcb.umd.edu) with the following options: “—library-type firststrand” and “—transcriptome-index” with a TopHat transcript index built from RefSeq. Transcript expression was estimated with an improved version of Cuffdiff 2 (Trapnell et al., 2013) (http://cufflinks.cbcb.umd.edu).  Cuffdiff was run with the following options: “—min-reps-for-js-test 2 –dispersion-method per-condition” against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html). The workflow used to analyze the data is described in detail in (Trapnell et al., 2012) (alternate protocol B).
ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using bwa version  0.5.7 (Li et al., 2009) with default parameter settings. Subsequently, an improved version of Cuffdiff 2 was used to conduct de novo transcript assembly and RNA expression quantification. Following assembly, transcripts were annotated using known RefSeq genes
For OCT4, SOX2, NANOG and FOXA2 aligned read files were processed with macs version 1.4 (Zhang et al., 2008) using the following parameters: -g 2.7e9 --tsize=36 --pvalue=1e-5 --keep-dup=1. HUES64 WCE (GSM772807) was used as input control.
Genome_build: hg19
Supplementary_files_format_and_content: NANOG_HUES64_p1e5_r2_peaks.bed is a BED format file which contains the peak locations.

source_name: hES HUES64

growth_protocol: Human embryonic stem cells were expanded on murine embryonic fibroblasts (Global Stem) in KO-DMEM (Life Technologies) containing 20% Knockout serum replace (Life Technologies) and FGF2 (10 ng/mL) (Millipore). Cultures were passaged by enzymatic dissociation using Collagenase IV (1mg/mL) (Life Technologies). Prior to differentiation, cells were plated on matrigel-coated plates (BD Biosciences) and cultured in mTeSR1 (Stem Cell Technologies) for 3 to 4 days. Endoderm differentiation was induced in Advanced RPMI (Invitrogen), 0.5% FBS (Hyclone), Activin A (100ng/mL) (R&D) and WNT3A (50 ng/mL) (R&D). HUES64- derived hepatoblasts (dHep) were induced by culturing day 5 endoderm in RPMI media containing B27(1X), FGF2 (10ng/mL)(Millipore) and BMP4(20ng/mL)(R&D) for five days, and collected after 10 days total of differentiation.

extract_protocol:
Cells collected by FACS were crosslinked in 1% formaldehyde for 15 minutes at room temperature, with constant agitation, followed by quenching with 125mM Glycine for 5 minutes at room temperature with constant agitation. Nuclei were isolated and chromatin was sheared using Branson sonifier until the majority of DNA was in the range of 200-700 base pairs. Chromatin was incubated with antibody overnight at 4°C, with constant agitation. Co-immunoprecipitation of antibody-protein complexes was completed using Protein A or Protein G Dynabeads for 1 hour 4°C, with constant agitation. ChIPs were completed using previously reported methods (Mikkelsen et al., 2010)
ChIP-Bisulfite Sequencing (adapted from Brinkman et al, 2012)  DNA was first subjected to end-repair in a 30-μl reaction containing 6 units T4 DNA polymerase, 2.5 units DNA Polymerase I (Large Klenow Fragment), 20 units T4 Polynucleotide Kinase (all New England Biolabs), dATP, dCTP, dGTP, and dTTP (0.125 mM each), and 1× T4 Ligase buffer with ATP for 30 min at 20°C. DNA was then adenylated in a 20-μl reaction containing 10 units Klenow Fragment (3′→5′ exo-) (New England Biolabs), 0.5 mM dATP and 1× NEB buffer 2 for 30 min at 37°C. DNA was then ligated to preannealed Illumina genomic DNA adapters containing 5-methylcytosine instead of cytosine (ATDBio) using T4 DNA ligase (New England Biolabs).   Adapter-ligated DNA fragments were subsequently purified by phenol extraction and ethanol precipitation and size-selected on gel. 50 ng sheared and dephosphorylated Escherichia coli K12 genomic DNA was added to adapter-ligated DNA as carrier during size-selection and bisulfite conversion. DNA was run on 2.5% Nusieve 3:1 Agarose (Lonza) gels. Lanes containing marker (50 bp ladder; New England Biolabs) were stained with SYBR Green (Invitrogen), and size regions to be excised were marked with toothpicks and adapter-ligated DNA fragments from 200–400 and 400–550 bp were excised. DNA was isolated from gel using the MinElute Gel Extraction kit (QIAGEN). The low and high libraries were kept separate in subsequent steps.  Adapter-ligated and size-selected DNA was subjected to two subsequent 5-h bisulfite treatments using the EpiTect Bisulfite kit (QIAGEN) following the manufacturer's protocol for DNA isolated from FFPE tissue samples. PCR amplification was done with 1.25 units Pfu Turbo Cx Hotstart DNA Polymerase (Stratagene), primer LPX 1.1 and 2.1 (0.3 μM each), dNTPs (0.25 mM each), 1× Turbo Cx buffer. Amplified libraries were purified with the MinElute PCR Purification kit (QIAGEN) and subsequently purified from gel essentially as described above; whole gels were stained with SYBR Green, and no carrier DNA was added. Final libraries were analyzed on analytical 4%–20% TBE Criterion precast gels (BioRad), and measured by Quant-iT dsDNA HS Assays (Invitrogen).   CHIP:Cells collected by FACS were crosslinked in 1% formaldehyde for 15 minutes at room temperature, with constant agitation, followed by quenching with 125mM Glycine for 5 minutes at room temperature with constant agitation. Nuclei were isolated and chromatin was sheared using Branson sonifier until the majority of DNA was in the range of 200-700 base pairs. Chromatin was incubated with antibody overnight at 4°C, with constant agitation.   Co-immunoprecipitation of antibody-protein complexes was completed using Protein A or Protein G Dynabeads for 1 hour 4°C, with constant agitation. ChIPs were completed using previously reported methods (Mikkelsen et al., 2010). Sequencing library production details can be found in the Supplemental Experimental Procedures. Sequencing libraries were submitted for sequencing on the Illumina Hiseq 2000.    Immunoprecipitated DNA was end repaired using the End-It DNA End-Repair Kit (Epicentre), extended using a Klenow fragment (3’-5’ exo)(NEB), and ligated to sequencing adapter oligos (Illumina). Each library was then PCR-amplified using PFU Ultra II Hotstart Master Mix (Agilent), and a size range of 300-600 was selected for sequencing.    RNA-Seq: Strand specific libraries were constructed as described in the main text using a strand specific method (Levin et al., 2010). Polyadenylated RNA was isolated using Oligo dT beads (Invitrogen) and fragmented to 200-600 base pairs, and then ligated to RNA adaptors using T4 RNA Ligase, (NEB), preserving strand of origin information. A primer that anneals to the RNA adaptor was used to facilitate cDNA synthesis, which was then followed by RNA degradation. The cDNA library was then ligated to a DNA adaptor, which was used for PCR enrichment of the library, with index sequences included in the primers used for amplification.

tag: chip antibody


title: POU5F1 ChIP in hES line HUES64

status: Public on May 01 2013

type: SRA

country: Germany

library_source: genomic

data_processing:
BiSeq: raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
RNA-Seq: raw sequence reads were aligned using Tophat v2.0.6 and Bowtie version 0.12.7.
RNA-Seq: Reads were mapped to the human genome (hg19) using TopHat v2.0.6 (Trapnell et al., 2009)(http://tophat.cbcb.umd.edu) with the following options: “—library-type firststrand” and “—transcriptome-index” with a TopHat transcript index built from RefSeq. Transcript expression was estimated with an improved version of Cuffdiff 2 (Trapnell et al., 2013) (http://cufflinks.cbcb.umd.edu).  Cuffdiff was run with the following options: “—min-reps-for-js-test 2 –dispersion-method per-condition” against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html). The workflow used to analyze the data is described in detail in (Trapnell et al., 2012) (alternate protocol B).
ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using bwa version  0.5.7 (Li et al., 2009) with default parameter settings. Subsequently, an improved version of Cuffdiff 2 was used to conduct de novo transcript assembly and RNA expression quantification. Following assembly, transcripts were annotated using known RefSeq genes
For OCT4, SOX2, NANOG and FOXA2 aligned read files were processed with macs version 1.4 (Zhang et al., 2008) using the following parameters: -g 2.7e9 --tsize=36 --pvalue=1e-5 --keep-dup=1. HUES64 WCE (GSM772807) was used as input control.
Genome_build: hg19
Supplementary_files_format_and_content: POU5F1_HUES64_p1e5_r1_peaks.bed is a BED format file which contains the peak locations.

molecule: genomic DNA

organism: Homo sapiens

tag: cell line


title: SOX2 ChIP in hES line HUES64 rep1

data_processing:
BiSeq: raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
RNA-Seq: raw sequence reads were aligned using Tophat v2.0.6 and Bowtie version 0.12.7.
RNA-Seq: Reads were mapped to the human genome (hg19) using TopHat v2.0.6 (Trapnell et al., 2009)(http://tophat.cbcb.umd.edu) with the following options: “—library-type firststrand” and “—transcriptome-index” with a TopHat transcript index built from RefSeq. Transcript expression was estimated with an improved version of Cuffdiff 2 (Trapnell et al., 2013) (http://cufflinks.cbcb.umd.edu).  Cuffdiff was run with the following options: “—min-reps-for-js-test 2 –dispersion-method per-condition” against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html). The workflow used to analyze the data is described in detail in (Trapnell et al., 2012) (alternate protocol B).
ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using bwa version  0.5.7 (Li et al., 2009) with default parameter settings. Subsequently, an improved version of Cuffdiff 2 was used to conduct de novo transcript assembly and RNA expression quantification. Following assembly, transcripts were annotated using known RefSeq genes
For OCT4, SOX2, NANOG and FOXA2 aligned read files were processed with macs version 1.4 (Zhang et al., 2008) using the following parameters: -g 2.7e9 --tsize=36 --pvalue=1e-5 --keep-dup=1. HUES64 WCE (GSM772807) was used as input control.
Genome_build: hg19
Supplementary_files_format_and_content: SOX2_HUES64_p1e5_r1_peaks.bed is a BED format file which contains the peak locations.


title: SOX2 ChIP in hES line HUES64 rep2

data_processing:
BiSeq: raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
RNA-Seq: raw sequence reads were aligned using Tophat v2.0.6 and Bowtie version 0.12.7.
RNA-Seq: Reads were mapped to the human genome (hg19) using TopHat v2.0.6 (Trapnell et al., 2009)(http://tophat.cbcb.umd.edu) with the following options: “—library-type firststrand” and “—transcriptome-index” with a TopHat transcript index built from RefSeq. Transcript expression was estimated with an improved version of Cuffdiff 2 (Trapnell et al., 2013) (http://cufflinks.cbcb.umd.edu).  Cuffdiff was run with the following options: “—min-reps-for-js-test 2 –dispersion-method per-condition” against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html). The workflow used to analyze the data is described in detail in (Trapnell et al., 2012) (alternate protocol B).
ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using bwa version  0.5.7 (Li et al., 2009) with default parameter settings. Subsequently, an improved version of Cuffdiff 2 was used to conduct de novo transcript assembly and RNA expression quantification. Following assembly, transcripts were annotated using known RefSeq genes
For OCT4, SOX2, NANOG and FOXA2 aligned read files were processed with macs version 1.4 (Zhang et al., 2008) using the following parameters: -g 2.7e9 --tsize=36 --pvalue=1e-5 --keep-dup=1. HUES64 WCE (GSM772807) was used as input control.
Genome_build: hg19
Supplementary_files_format_and_content: SOX2_HUES64_p1e5_r2_peaks.bed is a BED format file which contains the peak locations.


title: FOXA2 ChIP followed by bisulfite sequencing in in vitro derived endoderm rep1

data_processing:
BiSeq: raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
RNA-Seq: raw sequence reads were aligned using Tophat v2.0.6 and Bowtie version 0.12.7.
RNA-Seq: Reads were mapped to the human genome (hg19) using TopHat v2.0.6 (Trapnell et al., 2009)(http://tophat.cbcb.umd.edu) with the following options: “—library-type firststrand” and “—transcriptome-index” with a TopHat transcript index built from RefSeq. Transcript expression was estimated with an improved version of Cuffdiff 2 (Trapnell et al., 2013) (http://cufflinks.cbcb.umd.edu).  Cuffdiff was run with the following options: “—min-reps-for-js-test 2 –dispersion-method per-condition” against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html). The workflow used to analyze the data is described in detail in (Trapnell et al., 2012) (alternate protocol B).
ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using bwa version  0.5.7 (Li et al., 2009) with default parameter settings. Subsequently, an improved version of Cuffdiff 2 was used to conduct de novo transcript assembly and RNA expression quantification. Following assembly, transcripts were annotated using known RefSeq genes
For OCT4, SOX2, NANOG and FOXA2 aligned read files were processed with macs version 1.4 (Zhang et al., 2008) using the following parameters: -g 2.7e9 --tsize=36 --pvalue=1e-5 --keep-dup=1. HUES64 WCE (GSM772807) was used as input control.
Genome_build: hg19
Supplementary_files_format_and_content: BiSeq_cpgMethylation_BioSam_1326_Cell_Type_498_290608.BiSeq.bed is a bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column.

source_name: in vitro derived endoderm

tag: tissue

value: HUES64 derived day 5 endoderm


title: FOXA2 ChIP followed by bisulfite sequencing in in vitro derived endoderm rep2

data_processing:
BiSeq: raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
RNA-Seq: raw sequence reads were aligned using Tophat v2.0.6 and Bowtie version 0.12.7.
RNA-Seq: Reads were mapped to the human genome (hg19) using TopHat v2.0.6 (Trapnell et al., 2009)(http://tophat.cbcb.umd.edu) with the following options: “—library-type firststrand” and “—transcriptome-index” with a TopHat transcript index built from RefSeq. Transcript expression was estimated with an improved version of Cuffdiff 2 (Trapnell et al., 2013) (http://cufflinks.cbcb.umd.edu).  Cuffdiff was run with the following options: “—min-reps-for-js-test 2 –dispersion-method per-condition” against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html). The workflow used to analyze the data is described in detail in (Trapnell et al., 2012) (alternate protocol B).
ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using bwa version  0.5.7 (Li et al., 2009) with default parameter settings. Subsequently, an improved version of Cuffdiff 2 was used to conduct de novo transcript assembly and RNA expression quantification. Following assembly, transcripts were annotated using known RefSeq genes
For OCT4, SOX2, NANOG and FOXA2 aligned read files were processed with macs version 1.4 (Zhang et al., 2008) using the following parameters: -g 2.7e9 --tsize=36 --pvalue=1e-5 --keep-dup=1. HUES64 WCE (GSM772807) was used as input control.
Genome_build: hg19
Supplementary_files_format_and_content: BiSeq_cpgMethylation_BioSam_1327_Cell_Type_498_290601.BiSeq.bed is a bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column.


title: FOXA2 ChIP in in vitro derived endoderm rep1

data_processing:
BiSeq: raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
RNA-Seq: raw sequence reads were aligned using Tophat v2.0.6 and Bowtie version 0.12.7.
RNA-Seq: Reads were mapped to the human genome (hg19) using TopHat v2.0.6 (Trapnell et al., 2009)(http://tophat.cbcb.umd.edu) with the following options: “—library-type firststrand” and “—transcriptome-index” with a TopHat transcript index built from RefSeq. Transcript expression was estimated with an improved version of Cuffdiff 2 (Trapnell et al., 2013) (http://cufflinks.cbcb.umd.edu).  Cuffdiff was run with the following options: “—min-reps-for-js-test 2 –dispersion-method per-condition” against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html). The workflow used to analyze the data is described in detail in (Trapnell et al., 2012) (alternate protocol B).
ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using bwa version  0.5.7 (Li et al., 2009) with default parameter settings. Subsequently, an improved version of Cuffdiff 2 was used to conduct de novo transcript assembly and RNA expression quantification. Following assembly, transcripts were annotated using known RefSeq genes
For OCT4, SOX2, NANOG and FOXA2 aligned read files were processed with macs version 1.4 (Zhang et al., 2008) using the following parameters: -g 2.7e9 --tsize=36 --pvalue=1e-5 --keep-dup=1. HUES64 WCE (GSM772807) was used as input control.
Genome_build: hg19
Supplementary_files_format_and_content: FOXA2_BS_ChIP_dEN_p1e5_1326_peaks.bed is a BED format file which contains the peak locations.


title: FOXA2 ChIP in in vitro derived endoderm rep2

data_processing:
BiSeq: raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
RNA-Seq: raw sequence reads were aligned using Tophat v2.0.6 and Bowtie version 0.12.7.
RNA-Seq: Reads were mapped to the human genome (hg19) using TopHat v2.0.6 (Trapnell et al., 2009)(http://tophat.cbcb.umd.edu) with the following options: “—library-type firststrand” and “—transcriptome-index” with a TopHat transcript index built from RefSeq. Transcript expression was estimated with an improved version of Cuffdiff 2 (Trapnell et al., 2013) (http://cufflinks.cbcb.umd.edu).  Cuffdiff was run with the following options: “—min-reps-for-js-test 2 –dispersion-method per-condition” against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html). The workflow used to analyze the data is described in detail in (Trapnell et al., 2012) (alternate protocol B).
ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using bwa version  0.5.7 (Li et al., 2009) with default parameter settings. Subsequently, an improved version of Cuffdiff 2 was used to conduct de novo transcript assembly and RNA expression quantification. Following assembly, transcripts were annotated using known RefSeq genes
For OCT4, SOX2, NANOG and FOXA2 aligned read files were processed with macs version 1.4 (Zhang et al., 2008) using the following parameters: -g 2.7e9 --tsize=36 --pvalue=1e-5 --keep-dup=1. HUES64 WCE (GSM772807) was used as input control.
Genome_build: hg19
Supplementary_files_format_and_content: FOXA2_BS_ChIP_dEN_p1e5_1327_peaks.bed is a BED format file which contains the peak locations.


title: CEBPbeta ChIP-seq in Liver

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

country: USA

institute: U.S. Environmental Protection Agency

data_processing:
Mapping was performed using the Illumina Eland pipeline and the mm8 reference genome.
Mapped reads were filtered to discard ambiguously aligned reads and reads mapping with greater than 2 mismatches. When multiple reads in a biological replicate mapped to an identical genomic position (redundant reads), only one such read was used for further processing.
CREB Peak Calling: For each condition (fasted, re-fed), non-redundant reads from all five biological replicates were pooled into a single read set, and initial peak-calling was performed with HOMER v3.0 (5% FDR), using a large pool of previous experimental inputs as the background control. To identify peaks that are not dependent on any single replicate, additional read subsets were created by pooling every possible combination of four replicates from each condition (fasted or re-fed), and peak-calling was repeated with the same parameters. Initial peak-calls from the 5-replicate pool were discarded if they failed to be called in any of the 4-replicate pools. Peaks passing this "Single-Sample Independence" test were further filtered by removing all peaks with height less than 0.35 reads per million, which was an empirical cut-off determined by validation of randomly selected peaks.
Genome_build: MGSCv36
Supplementary_files_format_and_content: BedGraph: Stack height profiles of each ChIP-seq biological replicate are provided in BedGraph format. Non-redundant reads were extended to 108bp fragments before computing stack height profiles.

organism: Mus musculus

source_name: mouse whole liver

growth_protocol: All mice used in this study were 8-12 week-old male C57BL/6J mice.

extract_protocol:
Chromatin extraction: Mouse livers were minced finely in cold phosphate-buffered saline (PBS) and cross-linked in 1% formaldehyde for 10 min while rotating. Cross-linking was quenched by adding glycine to a final concentration of 0.125 M for 5 min while rotating. The tissue was rinsed in cold PBS and homogenized with a Dounce homogenizer in cold cell lysis buffer (10 mM Tris–Cl, pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) and protease inhibitors. Cells were incubated at 4°C for 5 min to release nuclei. Nuclei were centrifuged at 13 000 g for 5 min to form a pellet. The pellet was resuspended in nuclear lysis buffer [1% sodium dodecyl sulfate (SDS), 5 mM EDTA, 50 mM Tris–Cl, pH 8.1) and protease inhibitors and sonicated using the Diagenode Bioruptor for 10 min on high, using 30 s intervals. Debris were removed by centrifugation at 13 000 g for 10 min, and the supernatant was collected and snap frozen in liquid nitrogen. A 10 μl aliquot was reversed by the addition of NaCl to a final concentration of 192 mM, overnight incubation at 65°C, and purification using a PCR purification kit (Qiagen, CA, USA). The chromatin concentration was determined using a NanoDrop 3.1.0 nucleic acid assay (Agilent Technologies, Santa Clara, CA, USA).
Chromatin Immunoprecipitation: Ten micrograms of chromatin per sample was precleared by adding 90 μl of protein A/G-agarose in 1 ml of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 167 mM NaCl, 16.7 mM Tris–Cl, pH 8.1) and rotating the sample for 1 h at 4°C. Protein A/G-agarose was sedimented by centrifugation at 3000 g for 30 s. Two micrograms of antibody was added to the supernatant and incubated overnight at 4°C. Protein A/G-agarose was blocked overnight at 4°C with 1 mg/ml bovine serum albumin in ChIP dilution buffer, added to the chromatin, and rotated for 1 h at 4°C. Following three consecutive washes of 5 min each with TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris–Cl, pH 8.1, 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris–Cl, pH 8.1, 500 mM NaCl) and ChIP buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris–Cl, pH 8.1), chromatin was eluted by adding 100 μl of freshly made ChIP elution buffer (1% SDS, 0.1 M NHCO3) to the pellet and rotating the sample for 10 min. Elution was repeated with an additional 100 μl of ChIP elution buffer, and the eluates were combined. Cross-linking was reversed by the addition of NaCl to a final concentration of 192 mM and overnight incubation at 65°C.
Immunoprecipitated DNA was modified for sequencing following the manufacturer’s protocol (Illumina). Briefly, DNA samples were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK, then a single 3′-end “A” base was added using Klenow exo (3′ to 5′ exo minus). Adapters provided by Illumina were then ligated to the ends of the modified DNA before size selection of ~200bp fragments via PAGE extraction. The isolated DNA was then amplified by 18 cycles of PCR as described. PCR products were column purified with the QIAquick PCR Purification Kit (Qiagen) and assayed for quantity and quality with the Agilent 2100 Bioanalyzer (Agilent Technologies), then diluted to a concentration of 10nM. All sequencing was performed on an Illumina GAIIx, some libraries were sequenced twice to achieve sufficient read counts.

treatment_protocol: Fasted mice had food removed from their cages for 24h prior to liver harvest. Re-fed mice had food removed from their cages for 24h, and then were given access to food for 2h prior to liver harvest. Ad-lib fed mice were given unrestricted access to food.

tag: strain

value: liver

tag: condition

value: Ad-lib fed

tag: time of day

tag: target

value: CEBPB

tag: antibody

value: C/EBP β Antibody (Santa Cruz Biotech, catalog# sc-150)


title: CREB ChIP-seq in Re-fed Liver (Rep3)

description:
CREB_Refed_Liver_3
CREB_peaks_refed_final.bed

data_processing:
Mapping was performed using the Illumina Eland pipeline and the mm8 reference genome.
Mapped reads were filtered to discard ambiguously aligned reads and reads mapping with greater than 2 mismatches. When multiple reads in a biological replicate mapped to an identical genomic position (redundant reads), only one such read was used for further processing.
CREB Peak Calling: For each condition (fasted, re-fed), non-redundant reads from all five biological replicates were pooled into a single read set, and initial peak-calling was performed with HOMER v3.0 (5% FDR), using a large pool of previous experimental inputs as the background control. To identify peaks that are not dependent on any single replicate, additional read subsets were created by pooling every possible combination of four replicates from each condition (fasted or re-fed), and peak-calling was repeated with the same parameters. Initial peak-calls from the 5-replicate pool were discarded if they failed to be called in any of the 4-replicate pools. Peaks passing this "Single-Sample Independence" test were further filtered by removing all peaks with height less than 0.35 reads per million, which was an empirical cut-off determined by validation of randomly selected peaks.
Genome_build: MGSCv36
Supplementary_files_format_and_content: BedGraph: Stack height profiles of each ChIP-seq biological replicate are provided in BedGraph format. Non-redundant reads were extended to 108bp fragments before computing stack height profiles.
Supplementary_files_format_and_content: BED: CREB peak calls are provided in BED format for each condition, with peak height normalized to reads per million in the score column.

value: Fasted 24h, Re-fed 2h

value: CREB

value: CREB-1 Antibody (Santa Cruz Biotech, catalog# sc-186)


title: Nanog ChIP in hES line HUES64 rep1

data_processing:
BiSeq: raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
RNA-Seq: raw sequence reads were aligned using Tophat v2.0.6 and Bowtie version 0.12.7.
RNA-Seq: Reads were mapped to the human genome (hg19) using TopHat v2.0.6 (Trapnell et al., 2009)(http://tophat.cbcb.umd.edu) with the following options: “—library-type firststrand” and “—transcriptome-index” with a TopHat transcript index built from RefSeq. Transcript expression was estimated with an improved version of Cuffdiff 2 (Trapnell et al., 2013) (http://cufflinks.cbcb.umd.edu).  Cuffdiff was run with the following options: “—min-reps-for-js-test 2 –dispersion-method per-condition” against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html). The workflow used to analyze the data is described in detail in (Trapnell et al., 2012) (alternate protocol B).
ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using bwa version  0.5.7 (Li et al., 2009) with default parameter settings. Subsequently, an improved version of Cuffdiff 2 was used to conduct de novo transcript assembly and RNA expression quantification. Following assembly, transcripts were annotated using known RefSeq genes
For OCT4, SOX2, NANOG and FOXA2 aligned read files were processed with macs version 1.4 (Zhang et al., 2008) using the following parameters: -g 2.7e9 --tsize=36 --pvalue=1e-5 --keep-dup=1. HUES64 WCE (GSM772807) was used as input control.
Genome_build: hg19
Supplementary_files_format_and_content: NANOG_HUES64_p1e5_r1_peaks.bed is a BED format file which contains the peak locations.


title: GR ChIP-seq in Liver

value: Mix of GR Antibody (Santa Cruz Biotech, catalog# sc-1004) and Glucocorticoid Receptor Antibody (Thermo Scientific, catalog# PA1-511A)


title: CREB ChIP-seq in Re-fed Liver (Rep4)

description:
CREB_Refed_Liver_4
CREB_peaks_refed_final.bed


title: Hepatoblast derived from HUES64 RNA-Seq reps1and2

library_source: transcriptomic

data_processing:
BiSeq: raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
RNA-Seq: raw sequence reads were aligned using Tophat v2.0.6 and Bowtie version 0.12.7.
RNA-Seq: Reads were mapped to the human genome (hg19) using TopHat v2.0.6 (Trapnell et al., 2009)(http://tophat.cbcb.umd.edu) with the following options: “—library-type firststrand” and “—transcriptome-index” with a TopHat transcript index built from RefSeq. Transcript expression was estimated with an improved version of Cuffdiff 2 (Trapnell et al., 2013) (http://cufflinks.cbcb.umd.edu).  Cuffdiff was run with the following options: “—min-reps-for-js-test 2 –dispersion-method per-condition” against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html). The workflow used to analyze the data is described in detail in (Trapnell et al., 2012) (alternate protocol B).
ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using bwa version  0.5.7 (Li et al., 2009) with default parameter settings. Subsequently, an improved version of Cuffdiff 2 was used to conduct de novo transcript assembly and RNA expression quantification. Following assembly, transcripts were annotated using known RefSeq genes
For OCT4, SOX2, NANOG and FOXA2 aligned read files were processed with macs version 1.4 (Zhang et al., 2008) using the following parameters: -g 2.7e9 --tsize=36 --pvalue=1e-5 --keep-dup=1. HUES64 WCE (GSM772807) was used as input control.
Genome_build: hg19
Supplementary_files_format_and_content: Hepatoblast_genes_fpkm_tracking.gtf file contains transcript coordinates, FPKM counts and detection p-values.

molecule: polyA RNA

source_name: in vitro derived hepatoblast

tag: cell type

value: HUES64 derived hepatoblast


title: siRbm3_37-1_RNA-seq

city: Shanghai

first: Yuting

last: Liu

department: Functional Genomics

country: China

institute: PICB

data_processing:
For PAR-CLIP, all PAR-CLIP sequencing data were analyzed with a computational analysis pipeline (Lebedeva, S. et al. 2011 Mol Cell 43, 340-52).Illumina PAR-CLIP cDNA sequencing reads were aligned to the mouse genome assembly (mm9) allowing for up to one mismatch, insertion or deletion. Only uniquely mapped reads were retained. We identified the clusters of aligned reads continuously covering genomic regions based on the condition that a sequence cluster requires at least one T-to-C conversion. The number of T-to-C mismatches served as a crosslink score, and the position with the highest frequency of T-to-C conversion was referred to as the preferred crosslinking position. We also assigned a quality score based on the number and positions of distinct reads contributing to the cluster. As the reads should originate from protein-bound transcripts we regarded clusters aligning antisense to the annotated direction of transcription as false positives. We were thus able to select cutoffs on both scores such as to keep the estimated false positive rate below 5%. After filtering by these cutoffs we expect each remaining cluster to harbor at least one binding site.
For RNA-seq, all obtained reads were mapped to the mm9 genome sequence with TopHat (v1.1.2) with options -p 6 -a 5 -g 1 --segment-length 30, then use Cufflink (v1.3.0) to estimate the isoform FPKM-levels with options -p 6 using the aligned reads and the RefSeq gene models. Theprocessed data (_cufflink.txt) files contain FPKM values.
Genome_build: mm9
Supplementary_files_format_and_content: bed and txt

molecule: total RNA

source_name: Mouse embryonic fibroblasts

growth_protocol: The MEFs were cultured in DMEM medium with 10% FBS at 37°C

extract_protocol: For RNA-seq, Polyadenylated RNA from the mock cells at 37°C or 32°C with two replicates, siCirbp-1, siCirbp-2, siRbm3-1 and siRbm3-2 MEFs at 37°C were sequenced on Illumina GAII using 76 bp single-end kits according to the manufacturers instructions.

treatment_protocol: For PAR-CLIP, the MEFs were incubated with 4-thiouridine (4SU) for 16 h before crosslinking. For RNA-seq, no treatment.

value: Mouse embryonic fibroblasts

tag: technology

value: Transcriptome RNA-seq

tag: treatment

value: siRbm3 transfected at 37C


title: siCirbp_37-1_RNA-seq

value: siCirbp transfected at 37C


title: CREB ChIP-seq in Re-fed Liver (Rep1)

description:
CREB_Refed_Liver_1
CREB_peaks_refed_final.bed


title: CREB ChIP-seq in Re-fed Liver (Rep2)

description:
CREB_Refed_Liver_2
CREB_peaks_refed_final.bed


title: Mock_32-1_RNA-seq

value: mock transfected at 32C


title: Mock_37-2_RNA-seq

value: mock transfected at 37C


title: CREB ChIP-seq in Fasted Liver (Rep5)

description:
CREB_Fasted_Liver_5
CREB_peaks_fasted_final.bed

value: Fasted 24h


title: siRbm3_37-2_RNA-seq


title: CREB ChIP-seq in Fasted Liver (Rep4)

description:
CREB_Fasted_Liver_4
CREB_peaks_fasted_final.bed


title: Mock_32-2_RNA-seq


title: CREB ChIP-seq in Fasted Liver (Rep2)

description:
CREB_Fasted_Liver_2
CREB_peaks_fasted_final.bed


title: CREB ChIP-seq in Fasted Liver (Rep3)

description:
CREB_Fasted_Liver_3
CREB_peaks_fasted_final.bed


title: CREB ChIP-seq in Fasted Liver (Rep1)

description:
CREB_Fasted_Liver_1
CREB_peaks_fasted_final.bed


title: H3K36me3_untreated

city: Lebanon

first: xiaoyang

last: zhang

address: 1 Medical Center Driver

institute: Dartmouth Medical School

data_processing: Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.

source_name: Breast Cancer Cell Line

growth_protocol: MCF7 cells were maintained in DMEM (Invitrogen) supplemented with 10% FBS, MCF7-LTED cells were developed by being maintained in Phenol-red free DMEM media for more than one year.

extract_protocol: Library preparation for next-generation sequencing was performed according to manufacturer’s instruction starting with 5 ng of material (Illumina Inc.).

treatment_protocol: For MCF7 cells, 10-8M E2 treatment 45mins; No treatment was applied to LTED cells. Antibody was used as 4ug/ChIP.

value: Untreated

tag: vendor

value: Abcam

tag: catalog#


title: siCirbp_37-2_RNA-seq


title: Cirbp_PAR-CLIP

extract_protocol: For PARCLIP, the experiment was performed as in Hafner et. al 2010 Cell, but with an antibody against Flag (Sigma) in MEFs. The MEFs that are stably expressing the FLAG epitope-tagged protein of interest were grown in medium supplemented with 100µM 4SU for 16h prior to harvest.

value: anti-Flag (Sigma)

value: PAR-CLIP


title: CREB ChIP-seq in Re-fed Liver (Rep5)

description:
CREB_Refed_Liver_5
CREB_peaks_refed_final.bed

value: liver


title: Mock_37-1_RNA-seq


title: Rbm3_PAR-CLIP


title: Oryza Sativa L Endosperm Cultivar Kitaake KNA

city: Berkeley

first: Toshiro

last: Nishimura

state: CA

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

description:
small RNA
Oryza Sativa L Endosperm 7 DAF Cultivar Kitaake

data_processing:
Alignment of BS-seq reads: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted  Nipponbare and Kitaake scaffolds using the aligner Bowtie, allowing up to two mismatches per read. Reads that aligned to either Nipponbare or Kitaake with fewer mismatches were assigned to that ecotype.
Alignment of small RNA-seq reads: We used Perl and Python scripts to trim adapter sequences in the reads, sorted reads according to size, and aligned the size-sorted reads to the Nipponbare and Kitaake scaffolds using the aligner Bowtie, allowing up to one mismatch per read. Reads that aligned to either Nipponbare or Kitaake with fewer mismatches were assigned to that ecotype.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: For BS-seq data, we used a Perl script to calculate fractional methylation (#C/(#C+#T)) within 50 bp windows of the genome for each sequence context (CG, CHG, CHH). For small RNA-seq data, we used a Perl script to calculate the number of reads mapping within 50 bp windows of the genome.
Genome_build: Oryza sativa L. cv Nipponbare rice reference genome (MSU 6.1)
Supplementary_files_format_and_content: All files are in GFF format. BS-seq files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows. Small RNA-seq files have 24 nt abundance calculated in 50 bp windows.

organism: Oryza sativa

growth_protocol: For root and shoot samples, Nipponbare rice seedlings were grown in sterile flask culture with Gamborg’s B-5 medium with sucrose (Caisson Laboratories) for 21 days with 24 hours of light and constant shaking. Seed samples were obtained at 7 to 8 DAF from rice plants grown under greenhouse conditions at the University of California, Davis.

extract_protocol:
DNA and RNA was extracted from snap-frozen tissues using CTAB and TRIzol reagent (Invitrogen), respectively.
For bisulfite sequencing, about 1µg of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen) as outlined in the manufacturer’s instructions. One quarter of the bisulfite-converted libraries was PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 μl of 10X Extaq reaction buffer, 25 μM dNTPs, 1 μl Primer 1.1, 1 μl Primer 2.1 (50 μl final). PCR reactions were carried out as follows: 95 ̊C 3 min, then 12-14 cycles of 95 ̊C 30 sec, 65 ̊C 30 sec and 72 ̊C 60 sec. For small RNA libraries, 10 µg of total RNA was loaded on a 15% polyacrylamide, 7M urea gel, and small RNA in the 17-30 nt size range were excised. The 3' miRNA cloning linker 1 (IDT) was ligated to the gel-excised small RNA using truncated T4 RNA ligase 2 (NEB), and ligation products were purified on a 15% polyacrylamide, 7M urea gel. The 5' Illumina RNA linker (5'-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU-3') was added using T4 RNA ligase (NEB) and ligation products were again purified on a 15% polyacrylamide, 7M urea gel. Purified ligated small RNAs were reverse transcribed using SuperScriptIII (Invitrogen) and PCR-amplified with Phusion High-Fidelity DNA Polymerase (NEB) for 25 cycles (Forward primer: 5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACG-3', Reverse primer: 5'-CAAGCAGAAGACGGCATACGATTGATGGTGCCTACAG-3'). Sequencing was performed on the Illumina HiSeq 2000 (crossed F1 embryo and endosperm) and GA-II (self-fertilized embryo, endosperm, seedling root and seedline shoot) platforms. Small RNA reads are either 36 or 50 bp long, while BS-seq reads are 100 bp long.
Bisulfite sequencing and small RNA sequencing with Illumina technology

treatment_protocol: No specific treatments were applied, other than controlled growth conditions for seedling tissue, and emasculation and artificial pollination of rice flowers to obtain F1 seeds.

tag: genetic background

value: Kitaake

value: enodsperm


title: Oryza Sativa L Embryo Cultivar Kitaake KEA

description:
small RNA
Oryza Sativa L Embryo 7 DAF Cultivar Kitaake

source_name: Oryza Sativa L Embryo Cultivar Kitaake

value: embryo


title: Oryza Sativa L Endosperm Cultivar Nipponbare NNA

description:
small RNA
Oryza Sativa L Endosperm 7 DAF Cultivar Nipponbare

value: Nipponbare


title: Oryza Sativa L Embryo Cultivar Nipponbare NEA

description:
small RNA
Oryza Sativa L Embryo 7 DAF Cultivar Nipponbare


title: Oryza Sativa L Shoot Cultivar Nipponbare RSF

description:
small RNA
Oryza Sativa L Shoot 1; 3 weeks Cultivar Nipponbare

value: shoot


title: Oryza Sativa L Root Cultivar Nipponbare RRG

description:
small RNA
Oryza Sativa L Root 2; 3 weeks Cultivar Nipponbare

source_name: Oryza Sativa L Root Cultivar Nipponbare

value: root


title: Oryza Sativa L Root Cultivar Nipponbare RRF

description:
small RNA
Oryza Sativa L Root 1; 3 weeks Cultivar Nipponbare


title: Oryza Sativa L Endosperm F1 Cultivar Kitaake x Cultivar Nipponbare KNNS1

description:
small RNA
Oryza Sativa L Endosperm 7 DAF F1 Cultivar Kitaake x Cultivar Nipponbare


title: Oryza Sativa L Endosperm F1 Cultivar Kitaake x Cultivar Nipponbare NKNB2

description:
Genomic DNA
Oryza Sativa L Endosperm 7 DAF F1 Cultivar Kitaake x Cultivar Nipponbare


title: Oryza Sativa L Embryo F1 Cultivar Kitaake x Cultivar Nipponbare NKEB2

description:
Genomic DNA
Oryza Sativa L Embryo 7 DAF F1 Cultivar Kitaake x Cultivar Nipponbare


title: Oryza Sativa L Endosperm F1 Cultivar Kitaake x Cultivar Nipponbare NKNS2


title: Oryza Sativa L Embryo F1 Cultivar Kitaake x Cultivar Nipponbare KNES1

description:
small RNA
Oryza Sativa L Embryo 7 DAF F1 Cultivar Kitaake x Cultivar Nipponbare


title: Oryza Sativa L Shoot Cultivar Nipponbare RSG

description:
small RNA
Oryza Sativa L Shoot 2; 3 weeks Cultivar Nipponbare


title: Oryza Sativa L Endosperm F1 Cultivar Kitaake x Cultivar Nipponbare KNNB1


title: CTCFbiotag/Mus musculus:activated B/mZF1/rep_c

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing: ***Short read processing and alignment***: Fastq files were generated from the Illumina Real Time Analysis output using CASAVA with default settings. The 36 nt or 50 nt reads were then aligned to the mm9 genome with 'bowtie --sam --all --strata --best -m1 -n2 -l50'. The result of this alignment strategy is to only include reads that have a unique alignment in the top stratum of alignments where the stratum is defined by the number of mismatches.  Up to two mismatches over the whole read length were allowed.  ***Density tracks (wiggle format) for visualization***: Density tracks were generated using custom software based on the samtools library that counted the number of reads per 100 nt window across the genome and normalized to window size and library size to obtain densities in units of reads per million per kb (RPKM).  A redundancy of up to 5 reads was allowed in the density tracks. Tracks were smoothed in the UCSC browser for display.

source_name: murine primary activated B cells

extract_protocol: Cells (10-20 x 10^6 cells) were crosslinked for 10min at 37C with 1% (vol/vol) formaldehyde, followed by quenching with 0.125 M glycine (final concentration). Crosslinked cell samples were then sonicated with a Covaris sonicator to obtain DNA fragments 200-300 bp in length. Biotinylated samples were incubated with 40ul of Dynabeads M-280 Streptavidin Beads (Invitrogen) overnight at 4C in RIPA buffer (10 mM Tris, pH 7.6, 1 mM EDTA, 0.1% (wt/vol) SDS, 0.1% (wt/vol) sodium deoxycholate and 1% (vol/vol) Triton X-100). Beads were washed twice with Wash buffer1 (2% (vol/vol) SDS), once with Wash buffer2 (0.1% (vol/vol) deoxycholate, 1% (vol/vol), once with Wash buffer3 (250 mM LiCl, 0.5% (vol/vol) NP-40, 0.5% (vol/vol) deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and then twice with TE buffer (10 mM Tris-HCl (pH 7.5) and 1 mM EDTA). ChIP DNA was then extracted for 4h at 65C in Tris-EDTA buffer with 0.3% (wt/vol) SDS and proteinase K (1 mg/ml). Library preparation followed standard protocols

treatment_protocol: B lymphocytes were isolated from spleens of wild-type C57BL6 male mice by immunomagnetic depletion using CD43 MACS beads (Miltenyi Biotec). Purified cells were cultured at 0.3x10^6 cells per ml in B cell media (Advanced RPMI 1640, 10% FCS, 1x antibiotic-antimycotic, 1% glutamine, 50uM 2-beta-mercaptoethanol, and 10mM Hepes). Cells were pre-activated overnight in the presence of 0.5 ug/ml of antiCD180 (RP105) antibody (RP/14, BD Pharmingen). At 0, 8, and 24h cells were transduced with Vector1 (pMy-CTCFbiotag-T2A-mOrange) and Vector2 (pMy-BirA-T2A-eGFP) by centrifugation for 90min at 2500rpm, at 32C. B cell media was supplemented with 50 ug/ml of LPS (Escherichia coli 0111:B4; Sigma-Aldrich), 2.5 ng/ml of IL-4 (Invitrogen), and 0.5 ug/ml of antiCD180. At 32h cells were diluted to 0.1x10^6 cells per ml. 72h after 1st infection, B cells were harvested and GFP/mOrange double positives were cell sorted using a BD FACSAria III (Becton, Dickinson and Company). The percentage of double positive cells was 30-40%.

tag: experiment type

value: ChIP-Seq

value: Streptavidin beads

tag: chip antibody manufacturer

value: Invitrogen

tag: chip antibody catalog #

tag: activation protocol

tag: precipitated ctcf genotype


title: CTCF/Mus musculus:activated B/wt/rep_b

data_processing: ***Short read processing and alignment***: Fastq files were generated from the Illumina Real Time Analysis output using CASAVA with default settings. The 36 nt or 50 nt reads were then aligned to the mm9 genome (for Mus musculus C57BL/6 samples) or a motified mm9 genome that incorporated all Mus spretus SNVs (for Mus spretus samples) with 'bowtie --sam -all --strata -best -m1 -n2 -l50'. The result of this alignment strategy is to only include reads that have a unique alignment in the top stratum of alignments where the stratum is defined by the number of mismatches.  Up to two mismatches over the whole read length were allowed.  This approach allows visualization of both sample sets using mm9 genome coordinates (in for example the UCSC browser). ***Density tracks (wiggle format) for visualization***: Density tracks were generated using custom software based on the samtools library that counted the number of reads per 100 nt window across the genome and normalized to window size and library size to obtain densities in units of reads per million per kb (RPKM).  A redundancy of up to 5 reads was allowed in the density tracks. Tracks were smoothed in the UCSC browser for display.

extract_protocol: Cells (10-20 x 10^6 cells) were crosslinked for 10min at 37C with 1% (vol/vol) formaldehyde, followed by quenching with 0.125 M glycine (final concentration). Crosslinked cell samples were then sonicated with a Covaris sonicator to obtain DNA fragments 200-300 bp in length. Samples were incubated with 5ug of anti-CTCF antibody (07-729, Millipore) overnight at 4C in RIPA buffer (10 mM Tris, pH 7.6, 1 mM EDTA, 0.1% (wt/vol) SDS, 0.1% (wt/vol) sodium deoxycholate and 1% (vol/vol) Triton X-100). Beads were washed twice with RIPA buffer, twice with RIPA buffer/300 mM NaCl, once with Wash buffer3 (250 mM LiCl, 0.5% (vol/vol) NP-40, 0.5% (vol/vol) deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and then once with TE (10 mM Tris-HCl (pH 7.5) and 1 mM EDTA) + 0.2% Triton and once with TE. ChIP DNA was then extracted for 4h at 65C in Tris-EDTA buffer with 0.3% (wt/vol) SDS and proteinase K (1 mg/ml). Library preparation follwed standard protocols.

treatment_protocol: B lymphocytes were isolated from spleens of wild-type C57BL6 or Spretus mice by immunomagnetic depletion using CD43 MACS beads (Miltenyi Biotec). Purified cells were cultured at 0.3x10^6 cells per ml in B cell media (Advanced RPMI 1640, 10% FCS, 1x antibiotic-antimycotic, 1% glutamine, 50uM 2-beta-mercaptoethanol, and 10 mM Hepes). B cell media was supplemented with 50 ug/ml of LPS (Escherichia coli 0111:B4; Sigma-Aldrich), 2.5 ng/ml of IL-4 (Invitrogen), and 0.5 ug/ml of antiCD180 for 72h.

tag: chip antibody

value: CTCF

value: Millipore

value: wt


title: CTCFbiotag/Mus musculus:activated B/mZF1/rep_a


title: CTCFbiotag/Mus musculus:activated B/wt/rep_c


title: CTCFbiotag/Mus musculus:activated B/mZF9/rep_c


title: CTCFbiotag/Mus musculus:activated B/mZF9/rep_b


title: CTCF/Mus musculus:activated B/wt/rep_c


title: CTCFbiotag/Mus musculus:activated B/mZF1/rep_b


title: CTCFbiotag/Mus musculus:activated B/mZF9/rep_a


title: CTCFbiotag/Mus musculus:activated B/mZF6/rep_c


title: CTCFbiotag/Mus musculus:activated B/mZF7/rep_c


title: CTCFbiotag/Mus musculus:activated B/wt/rep_b


title: CTCFbiotag/Mus musculus:activated B/mZF6/rep_b


title: CTCFbiotag/Mus musculus:activated B/mZF7/rep_b


title: CTCFbiotag/Mus musculus:activated B/mZF5/rep_c


title: CTCFbiotag/Mus musculus:activated B/mZF5/rep_d


title: CTCFbiotag/Mus musculus:activated B/mZF4/rep_d


title: CTCFbiotag/Mus musculus:activated B/mZF4/rep_c


title: CTCF/Mus musculus:activated B/wt/rep_d


title: Oryza Sativa L Embryo F1 Cultivar Kitaake x Cultivar Nipponbare NKES2

tag: tissue


title: CTCFbiotag/Mus musculus:activated B/mZF3/rep_d


title: Oryza Sativa L Embryo F1 Cultivar Kitaake x Cultivar Nipponbare KNEB1


title: CTCFbiotag/Mus musculus:activated B/mZF3/rep_c


title: CTCFbiotag/Mus musculus:activated B/mZF3/rep_b


title: CTCFbiotag/Mus musculus:activated B/mZF2/rep_c


title: CTCFbiotag/Mus musculus:activated B/mZF2/rep_b


title: CTCFbiotag/Mus musculus:activated B/mZF2/rep_a


title: CTCFbiotag/Mus musculus:activated B/mZF7/rep_a


title: CTCFbiotag/Mus musculus:activated B/mZF11/rep_c


title: CTCFbiotag/Mus musculus:activated B/mZF6/rep_a


title: CTCFbiotag/Mus musculus:activated B/mZF8/rep_a


title: CTCFbiotag/Mus musculus:activated B/R339W/rep_b


title: CTCFbiotag/Mus musculus:activated B/mZF11/rep_b


title: CTCFbiotag/Mus musculus:activated B/R339W/rep_a


title: CTCFbiotag/Mus musculus:activated B/mZF10/rep_c


title: CTCFbiotag/Mus musculus:activated B/mZF10/rep_a


title: CTCFbiotag/Mus musculus:activated B/mZF10/rep_b


title: CTCFbiotag/Mus musculus:activated B/mZF11/rep_a


title: CTCFbiotag/Mus musculus:activated B/R339W/rep_c


title: CTCFbiotag/Mus musculus:activated B/mZF8/rep_b


title: Single cell #4

city: Cologne

first: Kemal

last: Akman

address: Carl-von-Linné-Weg 10

department: Plant Breeding Research

institute: Max Planck Institute Cologne

description:
H4
Reduced Representation BS-Seq (RRBS)

data_processing:
Library strategy: RRBS-Seq
Basecalls were performed using CASAVA version 1.4
BS-Seq reads were preprocessed for better alignment quality using FASTX-toolkit 0.0.13, trimgalore 0.2.2 and cutadapt 1.0
BS-Seq reads were aligned to the mm10 genome using Bowtie2 2.0.0 and Bismark 0.7.6
CpG-Methylation calling was done using Bismark 0.7.6
CpG sites were grouped into regions of 1000 nt's with a minimum coverage of 10 CG sites using R 2.13 with custom scripts
Methylation status and differential methylation between single-cells and reference H1 were assessed using bayesian estimation for a beta-binomial model using R 2.13
Methylating epimutations were called on regions showing low methylation in the reference L1 but high methylation in a single-cell sample using R 2.13
Demethylating epimutations were called on regions showing high methylation in the reference L1 but low methylation in a single-cell sample using R 2.13
Genome_build: mm10
Supplementary_files_format_and_content: GFF listing all regions with methylation and demethylating epimutation were generated using R 2.13
Supplementary_files_format_and_content: GFF scores represent the CG methylation level of each region with epimutations

source_name: Mouse liver single cell

growth_protocol: C57BL/6 mice were obtained from the National Institute of Aging (NIA) and liver cells were collected and sequenced without growth

extract_protocol:
Single hepatocytes were collected using hand-held capillaries under an inverted microscope
Library construction for RRBS sequencing was done as described by Meissner 2005 (PubMed: PMC1258174), but with MseI as digest vector and add adding 2 ng salmon DNA (samples H1,H2) or 2 ng tRNA cDNA (samples H3,H4) as buffer DNA to stabilize single-cell samples.

treatment_protocol: Liver tissue was perfused with collagenase

tag: strain


title: CTCFbiotag/Mus musculus:activated B/mZF5/rep_a


title: Single cell #1

description:
H1
Reduced Representation BS-Seq (RRBS)


title: Reference cell pool

description:
L1
Reduced Representation BS-Seq (RRBS)

source_name: Mouse liver reference cell pool


title: CTCFbiotag/Mus musculus:activated B/mZF4/rep_a


title: WT TAC 17 LV mRNA Seq

city: Taipei

first: Kai-Chien

last: Yang

address: No.1, Sec. 1, Jen-Ai Rd, 1150R

department: Graduate Institute and Department of Pharmacology

country: Taiwan

institute: National Taiwan University

data_processing:
(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.
(for mRNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the mouse genome (mm9) with Bowtie, allowing up to two mismatches. Sequence reads aligned to the mouse genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.
Yang et al_miRNASeq.txt (mm9)
Yang et al_mRNASeq.txt (mm9)

source_name: WT TAC 17 LV RNA

growth_protocol: Adult WT or caPI3Kalpha animals

extract_protocol: Small RNA libraries were prepared using TrueSeq Small RNA Sample Prep Kits (Illumina) in accordance with the manufacturer’s instructions. Briefly, 3’ and 5’ adapters were sequentially ligated to small RNAs (from 1 µg total RNA), followed by a reverse transcription reaction to create single stranded cDNAs, which were then amplified (by PCR) and barcoded using a common primer and a primer containing unique six-base index sequence. The amplified libraries were size-selected/gel-purified and quantified using Qubit dsDNA HS Assay kit (Life Technologies). Six to eight barcoded libraies were pooled in equimolar (10 nmol/L) amounts and diluted to 8 pmol/L for cluster formation on a single flow cell lane, followed by single-end sequencing on an Illumina HiSeq 2000 sequencer. Messenger RNA (mRNA) libraries were prepared using TrueSeq RNA Sample Prep Kits (Illumina) in accordance with the manufacturer’s recommendations. In brief, 3µg of total LV RNA was twice oligo(dT) selected using poly-T oligo-attached magnetic beads. The poly-A(+) RNA was then eluted, fragmented and reverse transcribed into first strand cDNA using random hexamers, followed by second-strand cDNA synthesis. Double-stranded cDNAs were end-repaired and adenylated (singly) at the 3’ ends. Barcoded adapters containing unique six-base index sequences and T-overhangs were ligated to the cDNA samples prepared from each of the individual mouse LV samples. Individual cDNA libraries were PCR amplified and purified; six barcoded libraries were pooled in equimolar (10 nmol/L) amounts and diluted to 4 pmol/L for cluster formation on a single flow cell lane, followed by single-end sequencing on an Illumina HiSeq 2000 sequencer.

treatment_protocol: LV collected from animals 7 days after sham or TAC operation

tag: genotype

value: WT

value: FVB

value: heart left ventricle

value: TAC


title: PI3Kalpha TAC 211 LV mRNA Seq

source_name: PI3Kalpha TAC 211 LV RNA

value: PI3Kalpha mutant


title: PI3Kalpha TAC 11 LV mRNA Seq

source_name: PI3Kalpha TAC 11 LV RNA


title: PI3Kalpha Sham 8 LV mRNA Seq

source_name: PI3Kalpha Sham 8 LV RNA

value: Sham


title: PI3Kalpha Sham 5 LV mRNA Seq

source_name: PI3Kalpha Sham 5 LV RNA


title: CTCFbiotag/Mus musculus:activated B/mZF8/rep_c


title: WT TAC 1 LV mRNA Seq

source_name: WT TAC 1 LV RNA


title: WT Sham 7 LV mRNA Seq

source_name: WT Sham 7 LV RNA


title: WT Sham 15 LV mRNA Seq

source_name: WT Sham 13 LV RNA


title: WT Sham 13 LV mRNA Seq


title: Single cell #2

description:
H2
Reduced Representation BS-Seq (RRBS)

value: liver


title: PI3Kalpha TAC 211 LV miRNA Seq


title: PI3Kalpha TAC 11 LV miRNA Seq


title: Single cell #3

description:
H3
Reduced Representation BS-Seq (RRBS)


title: PI3Kalpha TAC 9 LV miRNA Seq

source_name: PI3Kalpha TAC 9 LV RNA


title: PI3Kalpha Sham 14 LV miRNA Seq

source_name: PI3Kalpha Sham 14 LV RNA


title: PI3Kalpha Sham 8 LV miRNA Seq


title: WT Sham 6 LV mRNA Seq

source_name: WT Sham 6 LV RNA


title: PI3Kalpha TAC 8 LV miRNA Seq

source_name: PI3Kalpha TAC 8 LV RNA


title: WT TAC 19 LV miRNA Seq

source_name: WT TAC 19 LV RNA


title: WT TAC 2 LV miRNA Seq

source_name: WT TAC 2 LV RNA


title: WT Sham 15 LV miRNA Seq

source_name: WT Sham 15 LV RNA


title: WT TAC 17 LV miRNA Seq


title: WT TAC 1 LV miRNA Seq


title: WT TAC 20 LV miRNA Seq

source_name: WT TAC 20 LV RNA


title: PI3Kalpha Sham 5 LV miRNA Seq


title: WT Sham 7 LV miRNA Seq


title: WT Sham 13 LV miRNA Seq


title: WT TAC 19 LV mRNA Seq


title: WT Sham 6 LV miRNA Seq


title: CTCF/Mus spretus:activated B/wt/rep_c

organism: Mus spretus

source_name: murine primary activated B cells


title: CTCF/Mus spretus:activated B/wt/rep_a


title: CTCF/Mus spretus:activated B/wt/rep_b


title: Sample 2 Replicate 1

city: Boston

first: Katherine

last: Hill

state: MA

address: 330 Brookline Avenue, DA-679

department: Medicine

institute: Beth Israel Deaconess Medical Center

description: Lane 3

data_processing:
The leading 21 bases were trimmed from the 36-bp reads based on the quality score and the length of mature miRNAs. The trimmed reads were mapped to miRNA precursor sequences in miRBase 16.0 to achieve more sensitive expression profiles using the software miRExpress. No differences between the reads and the miRNA precursor sequences were allowed, which indicates exact matches only. The number of reads mapped to a miRNA sequence was taken to represent the expression level of that particular miRNA.
miRNA-seq quantification.txt; genome build: miRBase 16.0

source_name: liposarcoma

extract_protocol: Total RNA samples were prepared for smRNA sequencing using Illumina’s Small RNA v1.5 Sample Preparation Guide. Total RNA input ranged from 5-10μg and first underwent 3’ and 5’ adaptor ligation followed by reverse transcription and 12 cycles of amplification on a Bio-Rad iCycler. cDNA constructs were then purified using a 6% Novex TBE PAGE gel on Invitrogen’s XCell SureLock Novex Mini-Cell System. Band sizes ranging from 80-100bp were cut from the gel and purified. cDNA constructs were eluted from the gel and purified by ethanol precipitation according to Illumina’s protocol. Libraries were analyzed on Agilent’s 2100 Bioanalyzer with a High Sensitivity DNA Chip specific for next generation sequencing. Final libraries were immobilized onto a single read Illumina flowcell at a concentration of 12pM and underwent cluster amplification on Illumina’s Cluster Station using their DGE Small RNA Cluster Generation Kit. The amplified flowcell was then sequenced on Illumina’s GAIIx with 36 cycles of sequencing.

tag: condition

value: liposarcoma


title: Sample 1 Replicate 1

description: Lane 1

source_name: leiomyosarcoma

value: leiomyosarcoma


title: Sample 1 Replicate 2

description: Lane 2


title: PBX1_LETD

data_processing:
Reads were generated by the ELAND Illumina pipeline with a GAII
Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome_build: hg19
Supplementary_files_format_and_content: Bedfile generated using MACS 1.4

source_name: Long-term estrogen deprived breast cancer cell line

growth_protocol: MCF7-LTED cells were developed by being maintained in Phenol-red free DMEM media for more than one year.

treatment_protocol: No treatment was applied to LTED cells

tag: cell line

tag: antibody

value: PBX1 monoclonal antibody (M01)

tag: vendor/catalog#

value: Untreated


title: nLac.fastq.gz

city: Waltham

last: Marr

state: Massachusetts

address: 415 South St

department: Biology

institute: Brandeis University

description: nascent transcript

data_processing:
fastx_clipper from fastx_toolkit-0.0.13.2 to remove the 3' adapter sequence with paramaters "-M 9 -n -l 20"
take the reverse complement sequences after 3' adapter is removed
Genome_build: Drosophila melanogaster, BDGP R5/dm3 (http://www.ncbi.nlm.nih.gov/assembly/GCA_000001215.2/)
Supplementary_files_format_and_content: tab delimited text format; 1st column: sequence (after trimming adapters and reverse-complement), 2nd column: frequency

organism: Drosophila melanogaster

source_name: S2_mock control

growth_protocol: Drosophila melanogaster Schneider line 2 (S2) cells were maintained at 25C in Schneider‘s Medium containing 10% FBS, 100 units/mL penicillin, and 0.1 mg/ml streptomycin.

extract_protocol:
6x10^7 cells were pelleted (1500xg) and washed once with cold 1xPBS. Nascent RNA was harvested using the NUN RNA isolation protocol as described in Khodor YL, et al. (2011) with the following addition: after lysis and dounce homogenization in buffer AT (15 mM HEPES-KOH at pH 7.6, 10 mM KCl, 5 mM MgOAc, 3 mM CaCl2, 300 mM sucrose, 0.1% Triton X-100, 1 mM DTT, 1× SigmaFAST), nuclei were pelleted at 1000xg for 5 minutes and resuspended in 1 mL of fresh buffer AT prior to layering on Buffer B (15 mM HEPES-KOH at pH 7.6, 10 mM KCl, 5 mM MgOAc, 3 mM CaCl2, 1 M sucrose, 1 mM DTT, 1× SigmaFAST). RNA was purified from pellets in 1 mL of TriReagent.
Ribosomal RNA was depleted from 6 µg of nascent RNA as follows: 950 pmoles of a mixture of biotinylated oligos targeting ribosomal RNA (Table S3) were bound to 0.6 ml of Magnesphere Beads (Promega). Beads were washed 4 times with 0.5x SSC containing 10 mM EDTA. Oligo-bound beads were combined with nascent RNA in 2xSSC/10 mM EDTA and heated at 68C for 10 minutes followed by incubation at 25C for 15 minutesand held on ice for 2 hours with periodic mixing. Ribosomal-depleted RNA was collected. Beads were washed once with 0.5xSSC/10 mM EDTA. Ribosomal-depleted RNA from the supernatant and wash were combined and precipitated with alcohol.

treatment_protocol: RNAi was performed as described, for 1 hour in serum-free media before addition of Chelex-100 treated complete media. Cells were incubated with dsRNA for 3.5 days. S2 cells were treated with 40 ug/ml of dsRNA against TAF1 or mock treated for 1 hour in the absence of serum.

value: 24hr embryo

tag: cell type

value: Schneider line 2 (S2) cells

tag: treated with

value: dsRNA directed against E. coli LacI (Control)


title: MspJI digesting sequencing repeat 2 in arabidopsis thaliana

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

data_processing:
The library products were sequenced using the Illumina HiSeq 2000
Firstly, Low-quality reads that contained more than 30% ‘N’s or over 10% of the sequence with low quality value (quality value <20) per read were omitted from data analysis. Then the sequencing adapters were trimmed off from clean reads.
The raw reads were mapped to the reference sequence TAIR9 using SOAPaligner soap2.20(http://soap.genomics.org.cn/index.html) with default parameters. The digested sites were detected from uniquely mapped reads and CNNR sites methylation was determined by a perl script. The regular matching seeking algorithm in perl was used to identify the CNNR sites within the mapped reads, and the cytosines in notarized CNNR sites obtained by MspJI-seq were determined as the methylated cytosines.  The WGBS seq data (aerial_tissues_BS_seq_CNNR.gff) generated from GSM399600 Supplementary files (GSM399600_aerial_tissues_BS_seq_alignment_batch-*.gff.gz) was utilized to do comparative study with our MspJI-seq data  including sensitivity and specificity analysis.
Genome_build: TAIR9
Supplementary_files_format_and_content: ara_rep*_MspJI_site.txt file format: 1.Chromosome; 2.Coordinate for single 'c'; 3.the strand of the single 'c'; 4.tags; 5.consensus sequences type for single 'c'; 6.the real sequence context; 7.three bases sequence context. See 'README.txt' for more information.

organism: Arabidopsis thaliana

source_name: arabidopsis leaf

growth_protocol: arabidopsis thaliana (ecotype columbia) grow in 28℃ ,2000 lx light for 45 days.

extract_protocol: 1.5µg genomic DNA was digested at 37°C for 16h by 12U MspJI enzyme (NEB) in the presence of 0.8µM double-stranded DNA activator (Invitrogen) in a 30µl volume. The digestion system was optimized for the Arabidopsis genome from the original NEB protocol. By running the digested DNA in a 15% native polyacrylamide gel electrophoresis (PAGE), a narrow-band containing all the visible fragments around 28-35bp was excised in reference of 10bp DNA ladder (NEB). DNA was isolated by Crush and Soak Method(Sambrook J: Gel Electrophoresis of DNA and Pulsed-Field Agarose. In Molecular cloning. Volume 2. 3 rd edition. New York: Cold Spring Harbor Laboratory Press; 2001) and purified by ethanol precipitation. Recovered DNA was used to construct sequencing library according to the Illumina Pair-End protocol including procedures of DNA end-repair, ‘A’ base addition, adapters ligation and PCR amplification. Phenol: chloroform extraction and ethanol precipitation were used to purify the products of each process. PCR reaction was fulfilled by JumpStart™ Taq DNA Polymerase (Sigma) for 6 cycles, and its products at length of 148-155bp were recovered from a 2% agarose gel electrophoresis in reference of 50bp DNA ladder (NEB), and purified according to QIAquick gel extraction kit (Qiagen). The obtained Library was analyzed by Bioanalyzer analysis system (Agilent, Santa Clara, USA) before sequencing with Illumina HiSeq2000.

treatment_protocol: arabidopsis leaves were cutted down and cleaned by ddH2O, then they were soaked in ethylalcohol for 1-2 minutes and dried by absorbent paper before extract preparation.

tag: ecotype

value: columbia

value: leaves

tag: age

value: 45 days


title: 050112lac.fastq.gz

description: nascent transcript


title: T1 B

city: Nottingham

first: David

last: Archer

address: University Park

department: School of Biology

country: United Kingdom

institute: Nottingham University

data_processing:
Sequencing was performed on a SOLiD 5500xl ABi sequencer according to the manufacturer’s instructions to generate 50bp/35bp paired-end reads in colour space. Reads were mapped to the genome sequence assembly of the A. niger ATCC 1015 strain as it is the most closely related sequenced strain to the N402 strain used in this study. In order to ensure the most comprehensive gene model possible, genes that are predicted in the CBS 513.88 genome, but absent in the ATCC 1015 model due to differences in prediction algorithms used, were mapped to the A. niger JGIv3 Genome sequence using GMAP and Exonerate. GMAP: all selected Ensembl gene cDNA sequences were aligned to the genome (default settings). Exonerate: all selected Ensembl gene PROTEIN sequences were aligned to the genome with exonerate2protein (default settings). All GMAP alignment results were accepted first. Those not mapped by GMAP, but mapped by exonerate were then integrated into the annotation. SOLiD reads were mapped and read counts per gene were determined using the LifeScope 2.5.1 Whole Transcriptome Pipeline (LifeTechnologies). Reads were initially filtered against sequencing adaptors and barcodes and a collection of published A. niger rRNA sequences prior to read mapping. LifeScope provided all read alignment positions of each paired-read mapped against the complete genome sequence and exon spanning junctions using the GTF gene annotation information. Read alignment results were recorded in BAM format for further downstream analysis. Read counts per gene were determined from primary read alignments with a mapping quality of 20 or more (MAPQ20).These counts were then used to calculate normalized expression values (RPKM) (Reads Per Kilobase of gene model per Million mapped reads) for each gene as well as being the input for determining significant differential gene expression. Antisense transcription was detected by comparing gene counts generated by Htseq-count (http://www-huber.embl.de/users/anders/HTSeq) using F3.Bam files as input and opting to ignore or include strand-specificity in the calculations.
Genome_build: combined genome model based on CBS.588.13 and ATCC 1015
Supplementary_files_format_and_content: tab-delimited text files include read counts and RPKM values for each sample

organism: Aspergillus niger

source_name: conidia germinated for 1h

growth_protocol: A. niger strain N402, a cpsA1 derivative of A. niger N400 (Bos et al. 1988) was grown on Aspergillus complete medium (ACM) (containing per litre: NaNO3 6g, KCl, 0.52 g; MgSO4.7H2O, 0.52 g; KH2PO4, 1.52 g; Na2B4O7.10H2O, 0.008 mg; CuSO4.5H2O, 0.16 mg; FePO4.H2O, 0.16 mg; MnSO4.4H2O, 0.16 mg; NaMoO4.2H2O, 0.16 mg; ZnSO4, 1.6 mg, Bacto casamino acids, 1g, yeast extract, 1g, Bacto peptone, 2g, glucose, 10g, vitamins: p-aminobenzoic acid, 4mg, thiamine HCl, 0.5mg, D-biotin, 0.02mg, nicotinic acid, 1mg,  pyridoxine hydrochloride, 2.5mg, choline chloride, 0.014g, riboflavin, 1mg, agar 20g where applicable  ) for 6 days at 28oC to develop mature conidia. Conidia were harvested by washing the agar slopes with a 0.01% (w/v) Tween 80 solution. The conidial suspension was filtered through sterile synthetic wool and conidia were counted using a haemocytometer. Conidia (104/ml) were germinated in liquid ACM media for 1 hour at 28˚C, in 2L conical flasks containing 1000 ml of medium, shaken at 150rpm.  Germinated conidia were recovered by filtration into 0.5 ml RNA extraction buffer (0.6M NaCl, 0.2M sodium acetate, 0.1M EDTA, 4% w/v SDS) and snap frozen in liquid nitrogen. Frozen dormant or germinated conidia were mixed with 0.5ml glass beads and disintegrated in a Sartorius dismembranator (4 min, 2000rpm).

extract_protocol:
Total RNA was extracted using the Plant/Fungi total RNA Purification Kit (Norgen Biotek, Canada) including the on-column DNAase treatment step.
SOLiD whole transcriptome libraries were made as outlined in the SOLiD Total RNA-Seq kit protocol (Applied Biosystems).  Libraries were quantified by qPCR using a KAPA library quantification kit for Applied Biosystems SOLiD platform and pooled in equimolar amounts.  Pooled libraries were gel-purified using 2% size-select E-gels to 200-300 bp (Invitrogen). Emulsion PCR and bead-based enrichment was carried out using the SOLiD EZ bead system.

tag: developmental stage

value: conidia germinated for 1h


title: T1 A


title: nTAF.fastq.gz

description: nascent transcript

source_name: S2_taf1 depleted

value: dsRNA directed against TAF1


title: T0 A

source_name: dormant conidia

value: dormant conidia


title: 050112taf1.fastq.gz

description: nascent transcript


title: male blood after exercise BF2P

city: Seoul

first: HYEONGMIN

last: KIM

address: Seoul National Univ., Daehak-dong, Gwanak-gu,

department: College of Agriculture Sciences

country: South Korea

institute: Seoul National University

data_processing:
Sequences reads were mapped to the EquCab2 reference genome using BWA. Briefly, the reference genome was indexed using “bwa index –a bwtsw”, fastq-formatted reads were aligned using “bwa aln”, and sored, merged BAM files were generated using “bwa sampe” followed by reference genome sorting with “picard-tools”. And, statistics on apparently miscalled bases are gathered from the initial BAM files, conditional on specified covariates, excluding sites likely to be polymorphic. As covariates we used the raw quality scores, the machine cycle number (read position), and the dinucleotide context.  Then, reads around indels identified from the initial BAM files are realigned using “picard-tools”.
fragments per kilobase of exon per million fragments mapped (FPKM) value for expression level of gene and isoform were calculated using Cufflinks (v. 1.3.0)
Genome_build: EquCab2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Equus caballus

source_name: blood

extract_protocol: Total RNAs from muscle and blood were prepared using TRIzol (Invitrogen) and a RNeasy RNA Purification Kit with DNase treatment (Qiagen), according to the instruction manual.  One microliter of cleaned total RNA was consumed to check RNA quality using BioAnalyzer 2011 with an RNA chip (RIN > 7 and 28S:18S ratio > 1.0). Messenger RNA sequencing libraries were generated using an mRNA Seq Sample Prep Kit following the manufacturer’s manual (Illumina). 5 ug of poly(A) mRNA was isolated from the total RNA using oligo-dT beads. The mRNA was then fragmented and randomly primed for reverse transcription, followed by the second-strand synthesis to create double-stranded cDNA fragments. The double-stranded short cDNA fragments were purified with a QiaQuick PCR extraction kit (Qiagen) and resuspended in an EB buffer. Each end of cDNA was repaired with a combination of fill-in reactions and blunted by exonuclease. The addition of A-base was applied to the blunt end DNA followed by sequencing adaptor ligation. The required fragments were purified by agarose gel electrophoresis and a QIAquick Gel Extraction Kit (Qiagen), and enriched by PCR amplification.

tag: sampling position

value: carotid artery

tag: subject

tag: treatment

value: after exercise

value: blood

tag: Sex

value: male

tag: birth date


title: female blood after exercise BS2P

tag: tissue

value: female


title: male blood after exercise BF3P


title: DREF_Mitosis_ChIPseq_1

city: Atlanta

first: Gurudatta

last: Baraka Vishwanathan

state: GA

address: 1510 clifton road ne

department: Biology Department

institute: Emory University

description:
DREF_Mitosis_ChIPseq_1
*these were ChIP-seq experiments, and not paired for data analysis

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS1.4.0alpha2) algorithm using equal numbers of unique reads for input and ChIP samples and a p-value cutoff of 1e-10.
The paired-end files were treated independently, thus, the raw files have been brokered/processed as single-end.

growth_protocol: Kc cells were maintained in HyClone CCM3 Serum-free media.

extract_protocol: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200–1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody at 4oC.  Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC.  After washing and eluting from beads the crosslinking was reversed and DNA was isolated. To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’  - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.

tag: chip antibody

value: DREF Rabbit polyclonal

value: Embryonic Cell


title: DREF_Mitosis_ChIPseq_2

description:
DREF_Mitosis_ChIPseq_2
*these were ChIP-seq experiments, and not paired for data analysis


title: DREF_TOTAL_ChIPseq_1

description:
DREF_TOTAL_ChIPseq_1
*these were ChIP-seq experiments, and not paired for data analysis


title: DREF_TOTAL_ChIPseq_2

description:
DREF_TOTAL_ChIPseq_2
*these were ChIP-seq experiments, and not paired for data analysis


title: female blood after exercise BS3P


title: male blood after exercise BS1P


title: Sample 2 Replicate 2

description: Lane 5

value: liposarcoma


title: female blood before exercise BS3B

value: before exercise


title: female blood before exercise BS2B


title: male blood before exercise BS1B


title: male blood before exercise BF2B


title: male blood before exercise BF3B


title: E. coli + TAP

city: Leeds

last: Romero A.

state: West Yorkshire

address: Woodhouse lane

institute: University of Leeds

description:
Escherichia coli K12 strain BW25113
Wild-type reference strain.
Enriched for mRNA.
RNA-seq (differential)

data_processing:
The sample sources of individual reads were determined by the barcoding. The barcodes for the minus and plus TAP treatments were ACTTGA and CGATGT, respectively, for the E. coli RNA, and CAGATC and ATCACG, respectively, for the S. coelicolor RNA.
RNA sequences from each of the two differential analyses were processed and mapped to the corresponding genomes as a service provided by vertis Biotechnologie AG, Germany (www.vertis-biotech.com). This involved trimming adaptor sequence and masking for low-quality sequence.
For each of the 4 libraries (2 bacterial samples x 2 treatments), we counted the number of times each nucleotide position was the first in a sequence read using a simple script (unpubl. resource). The forward and reverse strands were then processed separately.
Genome_build: The reference genomes used for E. coli K12 strain BW25113 and S. coelicolor A3(2) strain M145 were U00096.2 and AL645882, respectively.
Supplementary_files_format_and_content: BedGraphs of the reads before and after TAP treatment for each of the samples. Separate files are provided for the forward and reverse strands.

organism: Escherichia coli BW25113

source_name: E. coli batch culture with TAP

growth_protocol: Escherichia coli K12 strain BW25113 (Datsenko & Wanner 2000. PNAS 97: 6640) was cultivated in 100 mL of LB broth ( Miller 1972. In: Experiments in molecular genetics. Cold Spring Harbor Laboratory, NY) in a 250 mL Erlenmeyer flask at 37°C with shaking (250 rpm) to an O.D.600nm of 0.6. S. coelicolor A3(2) strain M145 (Kieser et al. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich.) was incubated in YEME broth (Kieser et al. 2000) at 30°C with shaking until the mycelia became pigmented.

extract_protocol:
RNA was isolated from the pellet of E. coli cells using a well-established, published protocol (Kime et al. 2008. In RNA Turnover in Bacteria, Archaea and Organelles, Vol 447 (ed. LE Maquat, CM Arraiano), pp. 215). The cell pellet of S. coelicolor was resuspended in Kirby mix (Kieser et al. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich.), 100 µL per 1 O.D.600nm unit, and transferred to Lysing Matrix B tubes containing fine silica beads (MP Biomedical). Tubes were then placed in a high-speed benchtop homogenizer (Fastprep-24, MP Biomedical; set at 6.5 M/s). Cells were lysed by three cycles of homogenisation for 1 min with cooling between each cycle in an ice-water bath for 1 min. The lysates were extracted using an equal volume of acidic phenol: chloroform: isoamyl alcohol (50: 50: 1) and then chloroform: isoamyl alcohol (49: 1). Nucleic acid in the aqueous phase was precipitated by adding NaCl to 150 mM and 2.5 x volumes of 100% [v/v] ethanol, chilling at -20°C for 1 h, and then harvested by centrifugation (13,000 x g for 30 min at 4°C) . The nucleic acid pellet was washed twice with 700 µL of 70% [v/v] ethanol, air dried for 5 min and resuspended in RNase-free water. Contaminating DNA was removed from both E. coli and S. coelicolor by incubating with DNase as described by the vendor (Ambion) and extracted with phenol: chloroform as described above. The concentration and integrity of RNA samples were determined using a NanoDropTM 1000 spectrophotometer (Thermo Fisher Scientific) and agarose gel electrophoresis (Kime et al. 2008), respectively. Samples were enriched for mRNA using MICROBExpress-Bacteria beads, as described by the manufacturer (Ambion).
Libraries were constructed by vertis Biotechnologie AG, Germany (www.vertis-biotech.com) as a service that included treating an aliquot of each RNA sample with TAP. The 5'-sequencing adaptor was ligated to transcripts prior to fragmentation, thereby allowing the 5' ends of both long and short transcripts to be detected. Each of the 4 libraries was constructed using a different barcode.

treatment_protocol: At the appropriate phase of growth, a one-eighth volume of stop solution (95% [v/v] ethanol; 5% [v/v] phenol) was added to a culture to inhibit cell metabolism (Kime et al. 2008. In RNA Turnover in Bacteria, Archaea and Organelles, Vol 447 (ed. LE Maquat, CM Arraiano), pp. 215), and the cells were harvested by centrifugation. When necessary, cell pellets were stored frozen at -80C.

tag: strain

tag: genotype

value: wild-type

value: tobacco acid pyrophosphatase (TAP)


title: E. coli - TAP

source_name: E. coli batch culture without TAP


title: female muscle after exercise MS3P

source_name: muscle

value: right leg

value: muscle


title: MspJI digesting sequencing repeat 1 in arabidopsis thaliana

value: columbia

value: leaves

value: 45 days


title: T0 B

value: dormant conidia


title: male muscle after exercise MS1P


title: male muscle after exercise MF2P


title: female muscle after exercise MS2P


title: male muscle after exercise MF3P


title: female muscle before exercise MS3B


title: male muscle after exercise MF1P


title: male blood after exercise BF1P

value: carotid artery


title: female muscle before exercise MS2B


title: male muscle before exercise MS1B


title: A mixed tissues of bud, leaf, petiole, stems and flower from Cleome hassleriana

first: Zhijun

last: Zheng

address: #11 Building 2/F│Beishan Industrial Zone│Yantian District

institute: BGI

description: mixed tissue from Cleome hassleriana

data_processing:
filter reads with many Ns or with adapter or with small  size using in-house script
filter reads which were generated by PCR duplication with in-house software
map reads to the Cleome hassleriana genome using Tophat (v 1.3.3) with parameters set to be "--max-intron-length 50000  -m 1 -r 20 --mate-std-dev 20  --closure-search  --coverage-search --microexon-search"
convert *bam files generated by Tophat to bedGraph format
Genome_build: Genome build is pending [Bioproject ID is PRJNA175231].
Supplementary_files_format_and_content: bedGraph

organism: Tarenaya hassleriana

source_name: mixed tissues

growth_protocol: Samples were kept at natural environment

extract_protocol:
RNA was purified using TRIzol from the five fresh tissues included  the bud, leaf, petiole, stems and flowers of Cleome.
Standard 200bp library protocol provide by Illumina.
200bp index library.

tag: type

value: landrace

value: mixed tissues [bud, leaf, petiole, stems, flower]


title: male muscle before exercise MF1B

value: male


title: S. coelicolor - TAP

description:
Streptomyces coelicolor A3(2) strain M145
Wild-type reference strain.
Enriched for mRNA.
RNA-seq (differential)

organism: Streptomyces coelicolor A3(2)

source_name: S. coelicolor batch culture without TAP


title: Protruding-mouth, 72hpf

status: Public on Apr 30 2013

first: Hongxing

address: 3888 Chenhua Rd, Songjiang District

institute: Shanghai Chenshan Botanical Garden

description: ~2000 individuals

data_processing:
Primary processing by SOLiD 3.0 online software
The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope (v1.2) obtained from Life Techlogies.
Reads per kilobase of transcript per million mapped reads (RPKM) were calculated using an in-house developed perl script, which is available upon request.
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for gene models from the genome annotation ((release Ensembl 62) of the Zv9 assembly

organism: Danio rerio

source_name: Zebrafish embryos at the Protruding-mouth stage

growth_protocol: Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C, and were staged according to their morphological features and hours (h) or days (d) post-fertilization as described previously (Kimmel et al. 1995)

extract_protocol:
Total RNA was extracted from each stage of (about 2000) embryos or larvae using Trizol (Invitrogen,Carlsbad, CA, USA) methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis, and the concentration was measured with NanoDrop 2000 (Thermo Scientific，Waltham, MA,USA).The aliquots were stored at -80 oC.
A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA-seq libraries. First, the total RNA was estimated on an Agilent 2100 Bioanalyzer (Agilent Technologies,Waldbronn,Germany). Second, The ribosomal RNA-removal steps were replaced by two rounds of polyA purification, with the first round using the PolyATtract® mRNA Isolation Systems (Promega, Madison, WI, USA) and the second round using the Poly(A)Purist™ Kit (Ambion, Austin, TX, USA). About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A, subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE-Urea Gel (Invitrogen, Carlsbad, CA, USA) and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11-15 cycles of PCR amplification, with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.

treatment_protocol: Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.

value: AB

value: Protruding-mouth, 72hpf

value: embryo


title: larva, 1-week

description: ~2000 individuals

source_name: Zebrafish 1-week old larvae

value: larva, 1-week

value: larva


title: Prim-25, 36hpf

description: ~2000 individuals

source_name: Zebrafish embryos at the Prim-25 stage

value: Prim-25, 36hpf


title: S. coelicolor + TAP

source_name: S. coelicolor batch culture with TAP

value: wild-type

value: tobacco acid pyrophosphatase (TAP)


title: 15-somite, 16.5-17.5hpf

description: ~2000 individuals

source_name: Zebrafish embryos at the 15-somite stage


title: male muscle before exercise MF3B

value: right leg

value: before exercise

value: muscle


title: 50%-epiboly, 5.25hpf

description: ~2000 individuals

source_name: Zebrafish embryos at the 50%-epiboly stage

value: 50%-epiboly, 5.25hpf


title: male blood before exercise BF1B

value: blood


title: oblong-sphere, 3.6-4hpf

description: ~2000 individuals

source_name: Zebrafish embryos at the oblong-sphere stage

value: oblong-sphere, 3.6-4hpf


title: 64-cell, 2 hpf

description: ~2000 individuals

source_name: Zebrafish embryos at the 64-cell stage

value: 64-cell, 2 hpf


title: Long-pec, 48hpf

description: ~2000 individuals

source_name: Zebrafish embryos at the Long-pec stage

value: Long-pec, 48hpf


title: no BARTS Dox

city: Madison

first: Bill

last: Sugden

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin-Madison

description: total RNA after RISC-IP

data_processing:
Basecalls performed using CASAVA 1.7.0
Sequence analysis was conducted using CLC Genomics Workbench Version 4.9; reads were mapped to hg18 human genome build
Unique exon reads for each gene were then used to create expression values for each gene with the following formula: Expression Value = (unique exon reads)(10^9)/(exon length)(total unique exon reads)
A table was constructed consisting of genes with the respective associated expression values for each condition.
Genome_build: hg18
Supplementary_files_format_and_content: genes and associated enrichment values (each sample in separate sheet)

source_name: Burkitt's Lymphoma Cells

growth_protocol: Sav-BL S1-1 cells were grown in RPMI 1640 (Gibco) supplemented with 10% fetal bovine serum (R10F) and 200 U/mL penicillin and 200 µg/mL streptomycin at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol:
1×10^8 cells were washed with PBS and lysed with 500 µl of PLB buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 0.5% NP-40, 5 mM MgCl2, 200 U/ml RNase inhibitor (Ambion), 1 mM DTT, proteinase inhibitor cocktail) at 4°C for 30 min. Following centrifugation, the lysate was incubated with either anti-GST or anti-human Ago2 (11A9) antibodies (Provided by Dr. Gunter Meister [24]) conjugated dynabeads (Invitrogen) in 500 µl of NET-2 buffer (20 mM EDTA, pH 8.0, 1 mM DTT, and 200 U/ml RNase inhibitor in NT-2 buffer (150 mM Tris-HCl, pH 7.0, 100 mM Tris-HCl, pH 8.0, 750 mM NaCl, 0.25% NP-40, 5 mM MgCl2)) at 4°C for overnight. The protein-dynabead complexes were washed 6 times with NT-2 buffer, once with NTmS buffer (150 mM Tris-HCl, pH 7.0, 100 mM Tris-HCl, pH 8.0, 0.25% NP-40, 5 mM MgCl2) and resuspended with 1× Turbo DNase buffer and 2 U of Turbo DNase (Ambion) at 37°C for 30 min. The activity of DNase was eliminated with 15 mM of EDTA followed by addition of same volume of proteinase K buffer (2.4 mg/ml of proteinase K and 2% SDS in NT-2 buffer) at 55°C for 30 min. The RNA was extracted with acid-phenol/chloroform (pH 4.5) once, chloroform once and precipitated and resuspended in RNAse-free water.
Libraries were generated using Illumina’s mRNA Seq kit (lot#5701543) Rev. D according to manufacturer's protocol.  Briefly, Poly-A selection was used on Sample 1 to reduce ribosomal RNA, Samples 2-4 were fragmented.  Samples were precipitated at -80°C, followed by first strand & second strand cDNA synthesis.  After end repair and adenylation of 3' ends, adapters were ligated to cDNA molecules.  Following ligation, cDNA was purified using E-gel Size Select 2% agarose gels.  Enrichment of purified cDNA was done via LMPCR (15 cycles) followed by purification using ZymoResearch DNA Clean & Concentrator columns (20ul elution volume). Libraries were validated on Agilent 1000 DNA chip and Kapa qPCR quantification.

treatment_protocol: Cells were cultured in media supplemented with either ethanol control or with 10 ng/mL doxycycline.  Doxycycline treated cells express dnEBNA1

tag: cell line

value: Sav S1-1

tag: ectopic barts

value: no

value: yes

value: Doxycycline


title: miRNAseq for day E9.5 TGCs

city: Cambridge

first: Jessica

last: Von Stetina

address: 9 Cambridge Center

institute: Whitehead Institute

data_processing:
For miRNA-seq, after adapter trimming, Illumina reads were aligned to mature miRNAs (miRBase Release 16) using Novoalign (http://www.novocraft.com/), and reads per miRNA were calculated.
Genome_build: mm9

source_name: mouse day E9.5 implantation sites

extract_protocol: TGC tissues were lysed by homogenization in TRIzol reagent and RNA was prepared as indicated in the manufacture's protocol. TGCs miRNA sequencing samples were processed using an Illumina miRNA kit following manufacture's instructions.

tag: cell type

value: polyploid trophoblast giant cells


title: no BARTs EtOH

description: total RNA after RISC-IP

value: Ethanol (vehicle)


title: BARTs EtOH

description: total RNA after RISC-IP


title: BARTs Dox

description: total RNA after RISC-IP


title: Day E9.5 TGCs-RNAseq

data_processing:
RNA-seq images acquired were processed by the bundled Illumina image extraction pipeline v1.6 and aligned to Mus musculus NCBI build mm9 using tophat.
Gene-level quantification was performed by cufflinks using Ensembl gene models.
Genome_build: mm9

extract_protocol: Tissues were lysed by homogenization in TRIzol reagent and RNA was prepared as indicated in the manufacture's protocol. Ten micro grams of RNA were processed with an Illumina mRNA kit to generate cDNA libraries for mRNA-sequencing according to manufacture's instructions.Thirty-six base sequencing was performed on an Illumina Genome Analyzer II (GAII) sequencer, according to Illumina’s standard protocols.


title: Pec-fin, 60hpf

description: ~2000 individuals

source_name: Zebrafish embryos at the Pec-fin stage

value: AB

value: Pec-fin, 60hpf

value: embryo


title: PND_21_2

status: Public on Apr 29 2013

city: Jokioinen

first: Anu

last: Sironen

address: Myllytie 1

department: Biotechnology and Food Research

country: Finland

institute: Agrifood Research Finland

data_processing:
Sequence reads were obtained and mapped to the  Mus musculus (mm9) genome using SOLiD Lifescope v2.1 software with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: .tab files report Counts and RPKM values.

source_name: testis

extract_protocol: Total RNA was extracted from the mouse testis at post natal days 7, 14, 17, 21 and 28 with RNeasy Midi kit (Qiagen). The libraries were constructed following the SOLiD™ Total RNA-Seq Kit's (Whole Transcriptome library) protocol, Applied Biosystems Part Number 4452437 Rev A, 01/2010

tag: time

value: PND 21

value: testis


title: PND_17_2

value: PND 17


title: male muscle before exercise MF2B

value: right leg

value: before exercise

value: muscle

value: male


title: PND_17_1


title: Ribo_primerset3

city: la jolla

first: vipul

last: bhargava

state: California

address: 9500 gilman drive

institute: ucsd

data_processing:
Illumina Casava1.4 - SFM, SB, AA3, AA15, AA15_2,AA100,SFM_2
Illumina Casava1.7 - Ribo_primerset2, Ribo_primerset3
Illumina Casava1.8 - all rest of the samples
Sequence reads obtained from Illumina Genome Analyzer Iix were trimmed of first 2 and last 2 bases and mapped to mus musculus REFSEQ database using in-house mapping code allowing upto 2 mismatches
Sequence reads obtained from Illumina HiSEQ2000 were trimmed of first 14 bps (except for 10pg_TR2, 1pg_TR1 and 1pg_TR2) and next 32 bps were used for mapping with mus musculus REFSEQ database using in-house mapping code allowing upto 2 mismatches
Sequence reads obtained from Illumina HiSEQ2000 were trimmed of first 7 bps for 10pg_TR2, 1pg_TR1 and 1pg_TR2 and next 32 bps were used for mapping with mus musculus REFSEQ database using in-house mapping code allowing upto 2 mismatches
Genome_build: mus musculus REFSEQ database of RNA
Supplementary_files_format_and_content: tab-delimited text files include REFSEQ gene id and Unique Reads

source_name: embryoid body

growth_protocol: Differentiating ESCs were grown in serum free conditions.

extract_protocol: Day 4 embroid bodies treated with either Activin A or SB-431542 compound were harvest and total RNA was extracted for each sample. Later mRNA was isolated from each sample and single stranded cDNA was prepared. Sequencing libraries were generated by using our DP-seq strategy which involved generation of the amplicon library from defined heptamer primers based amplification. Std. RNA-seq libraries were prepared as described by Mortazavi et al. (2008). SMARTseq libraries were prepared as described by Ramsköld et al. 2012. 13 cycles of uniform cDNA amplifications were performed and the amplified libraries were verified on high sensitivity Bioanalyzer.

treatment_protocol: At day2 of differentiation, embryoid bodies were dispersed and treated with either Activin A or SB-431542 compound for two days.

value: day 4 of differentiation

value: addition of Activin A (3ng/mL), mRNA~500pg; Library prepared using Primer set3 for suppression of ribosomal transcript.


title: PND_21_1