title: H3K4me3

city: Edinburgh

first: Adrian

middle: P

last: Bird

state: Midlothian

address: Mayfield Road

department: WTCCB

institute: The University of Edinburgh

description: Chromatin IP against H3K4me3

data_processing: Alignment: Single-end sequence reads were mapped to the mouse genome (NCBIm37) using MAQ (http://maq.sourceforge.net/). Reads with a mapping score greater or equal to 30 where retained.

source_name: Whole Brain

growth_protocol: Whole brains were disected from C57black/6 mice.

extract_protocol: Protein-DNA complexes were immunoprecipitated with specific antibodies and the DNA was subsequently extracted.  Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating immunoprecipitated DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was extracted using MiniElute PCR clean up columns (Qiagen) and PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Brains were manually homogenised to a single cells suspension and crosslinked using 1% formaldehyde. Chromatin was sheared using a combination of Micrococcal nuclease and sonication.

value: Whole Brain

tag: age

value: 4 weeks

tag: chip antibody

value: H3K4me3 (AB8580 – Abcam)


title: RNAPII

status: Public on Apr 15 2010

type: SRA

country: United Kingdom

description: Chromatin IP against RNA polymerase II

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: strain

value: 9 weeks

value: RNA Polymerase II (Unmodified - AB817 - Abcam)


title: CFP1

description: Chromatin IP against CFP1

value: 7 weeks

value: CFP1 (Sc-25391 – Santa Cruz)


title: Bombyx_mori_RNA-Seq

city: Berkeley

first: Toshiro

last: Nishimura

state: CA

address: 211 Koshland Hall

department: Plant and Microbial Biology

country: USA

institute: University of California at Berkeley

description: RNA sequencing

library_source: transcriptomic

data_processing: RNA-seq datasets were aligned using Bowtie to both genomic and cDNA scaffolds, allowing up to two mismatches. Roughly five million reads were mapped for each organism . Each cDNA model was assigned a score equal to the number of mapped reads per 1000 bp of sequence. Genomic DNA alignments were used for visual display and to filter repeat datasets.

molecule: total RNA

organism: Bombyx mori

source_name: Whole larvae

extract_protocol: RNA-Seq library preparation: Total RNA samples were isolated using RNeasy mini kit (Qiagen #74106) or with TRIzol reagent (Invitrogen #15596-026) followed by a cleanup step using the RNeasy mini kit. DNase treatments were performed on columns for all samples. mRNA was purified from 10-50 µg of total RNA by two cycles of poly-A enrichment using the Oligotex kit (Qiagen #72022), followed by a rRNA removal step using the RiboMinus Eukaryote Kit for RNA-Seq (Invitrogen #A1083702). Precipitated mRNA samples were eluted with 9 µl of RNase free water and fragmented with 1 µl of 10X fragmentation buffer (Ambion, #AM8740) at 70oC. Reactions were stopped after 5 minutes by adding 1 µl Stop buffer and RNA was purified by ethanol precipitation. cDNA was synthesized from 100-300 ng of mRNA using Superscript III reverse transcriptase (Invitrogen #18080-051). Double-stranded DNA was synthesized as described (3). DNA was cleaned with a QIAquick PCR spin column (Qiagen, #28106), sequencing adapters were ligated according to the Illumina protocol and library was amplified by 18 cycles of PCR using Phusion DNA polymerase (NEB, #F-530). Bands around 300 bp were gel-purified and cloned for validation. Traditional sequencing confirmed that the libraries were properly constructed, showing high percentage of mRNA over rRNA. The libraries were sequenced at the UC Berkeley Genomic Sequencing Laboratory, generating single ends (SE) 36 base reads.


title: Oryza_sativa_RNA-Seq

description: RNA sequencing

organism: Oryza sativa

source_name: Shoots

growth_protocol: 14 days post germination, grown in MS media under 16/8 light/dark cycles at 25oC

value: japonica cultivar Nipponbare


title: Oryza_sativa_BS-Seq

description: Bisulfite sequencing

data_processing:
We used a mixture of paired ends (PE) and single ends (SE) Illumina sequencing datasets for bisulfite sequencing. PE datasets were aligned to genomic scaffolds exactly as described in PMID 19520962 (GEO Series GSE15922). For SE datasets, the 76 base reads were divided into the first 45 and the last 31 bases. Each half of the read was aligned independently using Bowtie (7), allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first. S. moellendorffii is highly polymorphic, so the two haplotypes were assembled by the Joint Genome Institute (ww.jgi.doe.gov) independently, creating a genomic scaffold twice the actual genome size. We discarded scaffolds with a high degree of homology to create a single pseudo-haplotype close to the actual genome size (Table 1) that we used as an alignment scaffold.
Alignment: We used Perl scripts to convert all the Cs in the ‘forward’ reads (and in the scaffold) to Ts, and all the Gs in the ‘reverse’ reads and scaffold to As, and aligned the converted reads to the converted  scaffold, allowing up to two mismatches per read.
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: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).

source_name: Mature leaves

growth_protocol: 2-3 month-old soil grown plants

extract_protocol: BS-Seq library preparation: We synthesized custom Illumina adapters in which cytosines were replaced by 5-methylcytosines, so that the adapters would survive bisulfite conversion.   About 1 microgram of genomic DNA was sheared by sonication to fragments of 100-500 bp, and the adapters were ligated following the Illumina protocol. The library was then treated twice with sodium bisulfite (which converts unmethylated Cs to Us) using the Qiagen EpiTect kit, and amplified by 18 cycles of PCR using PfuTurboCx DNA polymerase (Stratagene), a proofreading enzyme that tolerates uracil in the template strand. Bands around 300 bp were gel-purified and cloned for validation.


title: Bombyx_mori_BS-Seq

description: Bisulfite sequencing


title: Coprinopsis_cinerea_RNA-Seq

description: RNA sequencing

organism: Coprinopsis cinerea

source_name: Mycelium

value: Okayama 7


title: Physcomitrella_pattens_RNA-Seq

description: RNA sequencing

organism: Physcomitrium patens

source_name: Whole plants


title: Coprinopsis_cinerea_BS-Seq

description: Bisulfite sequencing

growth_protocol: Grown on YM agar plates (Difco #271210) at 24oC


title: Physcomitrella_pattens_BS-Seq

description: Bisulfite sequencing

growth_protocol: Grown on BCD agar plates


title: Phycomyces_blakesleeanus_RNA-Seq

description: RNA sequencing

organism: Phycomyces blakesleeanus

value: NRRL 1555


title: Uncinocarpus_reesi_BS-Seq

description: Bisulfite sequencing

organism: Uncinocarpus reesii

growth_protocol: Grown on YM agar plates at 24oC


title: Phycomyces_blakesleeanus_BS-Seq

description: Bisulfite sequencing

growth_protocol: Grown in liquid YM (Difco #271120) at 24oC


title: Tetraodon_nigroviridis_ChIP-Seq

description: ChIP Sequencing

data_processing: H2A.Z IP and input datasets were aligned to the T. nigroviridis genome using Bowtie. Potential duplicate reads - those that shared the same coordinate and strand - were discarded, yielding 2,377,525 IP reads and 2,258,233 input reads. Reads were counted with a 100 bp sliding window, and the IP counts were normalized by the input counts (log2(IP/IN)); IP or input counts of 0 were substituted with 0.5 to produce a more realistic log ratio. Outlying windows were removed by median smoothing (window size = 3) followed by triangular smoothing (Xn = 0.25X(n-1) + 0.5Xn + 0.25X(n+1)).

organism: Tetraodon nigroviridis

source_name: Whole adults

extract_protocol: H2A.Z immunoprecipitation: Whole T. nigroviridis (~1 g each) were frozen in liquid nitrogen. Tissue was homogenized, nuclei isolated and digested with Micrococcal nuclease, and soluble nucleosomes extracted exactly as previously described (4). H2A.Z-containing nucleosomes were precipitated using an antibody (Abcam #ab4174) that has been used successfully for H2A.Z chromatin immunoprecipitation (IP) (5, 6) exactly as described (4). DNA was purified from precipitated nucleosomes, as well as from nucleosomes incubated without the antibody (input control). Illumina libraries were constructed from the IP and input DNA samples and sequenced at the UC Berkeley Genomic Sequencing Laboratory, generating single ends (SE) 36 base reads.

tag: antibody


title: Chlorella_sp.NC64A_BS-Seq

description: Bisulfite sequencing

organism: Chlorella variabilis

growth_protocol: Cultured in ATCC Medium 5 shaking at 25oC 16/8 light cycle


title: Tetraodon_nigroviridis_RNA-Seq

description: RNA sequencing


title: Selaginella_moellendorffii_BS-Seq

description: Bisulfite sequencing

organism: Selaginella moellendorffii

source_name: Aerial tissues

growth_protocol: Soil grown


title: Selaginella_moellendorffii_RNA-Seq

description: RNA sequencing


title: Apis_mellifera_RNA-Seq

description: RNA sequencing

organism: Apis mellifera

source_name: Whole adult workers


title: Postia_placenta_RNA-Seq

description: RNA sequencing

organism: Rhodonia placenta


title: Tetraodon_nigroviridis_BS-Seq

description: Bisulfite sequencing


title: Apis_mellifera_BS-Seq

description: Bisulfite sequencing


title: Drosophila_melanogaster_BS-Seq

description: Bisulfite sequencing

organism: Drosophila melanogaster

source_name: Embryos

growth_protocol: 0-3 hours


title: Nematostella_vectensis_RNA-Seq

description: RNA sequencing

organism: Nematostella vectensis


title: Nematostella_vectensis_BS-Seq

description: Bisulfite sequencing


title: Postia_placenta_BS-Seq

description: Bisulfite sequencing


title: 120 hours

status: Public on Apr 14 2010

city: Cambridge

first: Cole

last: Trapnell

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: 2x76bp RNA Seq

data_processing:
Alignment: Fragments were mapped to build 37.1 of the mouse genome using TopHat version 1.0.13 (http://tophat.cbcb.umd.edu)
Assembly and differential analysis: Transcripts were assembled and quantitated using Cufflinks 0.8.0 (http://cufflinks.cbcb.umd.edu)

molecule: polyA RNA

source_name: Myoblast (120 hours post serum switch)

growth_protocol: Mouse skeletal muscle C2C12 cells were initially plated on 15 cm plates in DMEM with 20% fetal bovine serum.  At confluence, the cells were switched to low serum medium to initiate myogenic differentiation.  For extraction of total RNA, cells were first rinsed in PBS and then lysed in Trizol reagent (Invitrogen catalog # 15596-026) either during exponential growth in high serum medium, or at 60 hrs, 5 days and 7 days after medium shift.  Residual contaminating genomic DNA was removed from the total RNA fraction using Turbo DNA-free (Ambion catalog # AM1907M). mRNA was isolated from DNA-free total RNA using the Dynabeads mRNA Purification Kit (Invitrogen catalog # 610-06).

extract_protocol: Preparation of cDNA followed the procedure described in Mortazavi et al. 2008 Nature Methods, with minor modifications as described below.  RNA was fragmented to an average length of 200 nts by metal ion/heat catalyzed hydrolysis.  The hydrolysis was performed in a 25 uL volume at 94°C for 90 seconds.  The 5X hydrolyis buffer components are: 200 mM Tris acetate, pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate.  After removal of hydrolysis ions by G50 Sephadex filtration (USA Scientific catalog # 1415-1602), the fragmented mRNA was random primed with hexamers and reverse-transcribed using the Super Script II cDNA synthesis kit (Invitrogen catalog # 11917010).  After second strand synthesis, the cDNA went through end-repair and ligation reactions according to the Illumina ChIPSeq genomic DNA preparation kit protocol (Illumina catalog # IP102-1001), using the paired ends adapters and amplification primers (Illumina Catalog # PE102-1004).  The cDNA library was size-fractionated on a 2% TAE low melt agarose gel (Lonza catalog # 50080), with a 100 bp ladder (Roche catalog # 14703220) run in adjacent lanes.  Prior to loading on the gel, the ligated cDNA library was taken over a G50 Sephadex column to remove excess salts that interfere with loading the sample in the wells.  After post-staining the gel in ethidium bromide, a narrow slice (~2mm) of the cDNA lane centered at the 300 bp marker was cut.  The slice was extracted using the QiaEx II kit (Qiagen catalog # 20021), and the extract was filtered over a Microcon YM-100 microconcentrator (Millipore catalog # 42409) to remove DNA fragments shorter than 100 bps.  Filtration was performed by pipeting the extract into the upper chamber of a microconcentrator, and adding ultra pure water (Gibco catalog # 10977) to a volume of 500 uLs.  The filter was spun at 500 X g until only 50 uLs remained in the upper chamber (about 20 minutes per spin) and then the upper chamber volume was replenished to 500 uLs.  This procedure was repeated 6 times.  The filtered sample was then recovered from the filter chamber according to the manufacturer’s protocol.  One-sixth of the filtered sample volume was used as template for 15 cycles of amplification using the paired-end primers and amplification reagents supplied with the Illumina ChIPSeq genomic DNA prep kit.  The amplified product was then cleaned up over a Qiaquick PCR column (Qiagen catalog # 28104), and then the filtration procedure using the Microcon YM-30 microconcentrators described above was repeated, to remove both amplification primers and amplification products shorter than 100 bps.  A final pass over a G50 Sephadex column was performed, and the library was quantified using the Qubit fluorometer and PicoGreen quantification reagents (Invitrogen catalog # Q32853).  The library was then used to build clusters on the Illumina flow cell according to protocol.

tag: cell line

tag: time point

value: 120 hours


title: 60 hours

description: 2x76bp RNA Seq

source_name: Myoblast (60 hours post serum switch)

value: 60 hours


title: Lefterova_mac_CEBPb

city: philadelphia

first: Mitchell

middle: A.

last: Lazar

state: PA

address: 700 CRB, 415 Curie Blvd.

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

description: Chromatin IP against PPARgamma

data_processing: ChIP-seq peak calling. All transcription factor binding data were analyzed with GLITR using default parameters and an iteration number of 100. GLITR first filtered each data set such that each start coordinate was represented once. Then a Pseudo-ChIP data set that had the same number of tags as each filtered data set was generated. Pseudo-ChIP sequence tags were sampled from the input sequence tag data available at http://web.me.com/kaestnerlab1/GLITR/ and the remaining input sequence tags in this set were used as background for the GLITR sampling procedure. The following statistical cut-offs were used to generate the lists of high confidence binding intervals for transcription factors: False Discovery Rate (FDR) > 0.5% except for PU.1 (FDR > 0.1%); fold change over input>5; number of reads at the peak summit > 9. These criteria and filtering out of regions enriched in inputs were applied to minimize nonspecific effects from PCR bias or local chromatin structure. H3K9Ace enrichment was analyzed using Significance Tester for Accumulation of Reads (STAR, manuscript in preparation). Briefly, an algorithm was developed to determine regions with a locally significant accumulation of reads, while controlling for false positives. For each sample, a set of permutation controls was generated by randomizing the reads via a uniform distribution across the genome. For an error rate of alpha, a cutoff for peak height was chosen that gives a proportion of the (average) signal over the permuted controls to the signal in the ChIP sample of no more than alpha. This gives a cutoff for significant peak height that controls the proportion of false positives in the set of all calls, otherwise known as the FDR. Prior to the comparison with the permutation controls, regions previously identified as common input bias were filtered out. Calls were made using a window of length 500 bp with a displacement of 50 bp as appropriate for histone modifications and FDR < 5%.

source_name: primary macrophage

growth_protocol: Macrophages were obtained from male C57Bl6 mice (Jackson Laboratory) via peritoneal lavage 3 days post intraperitoneal injection with 1 ml of sterile 3% thioglycollate. Cells were harvested after 24 h of adherence purification in culture. 3T3-L1 preadipocytes were obtained from American Type Culture Collection and differentiated to adipocytes according to standard protocol. All cells were cultured in high-glucose DMEM  supplemented with 10% fetal bovine serum  and 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: ChIP samples were amplified using the ChIP-Seq Sample Prep Kit (Illumina) according to manufacturer's instructions. For macrophages, cells from at least 4 animals were pooled per sequencing run to minimize the effects of biological variability. Two sequencing runs were performed for the macrophage PPAR  ChIP and the data were concatenated; one sequencing run was performed for all other transcription factors and histone modifications. Sequence reads of 36 bp were obtained using the Solexa Analysis Pipeline, and mapped to the mouse genome (mm8) using ELAND allowing up to two mismatches.  Only reads with a unique best match were included in further analysis.

treatment_protocol: ChIP was performed as described using cross-linked 3T3-L1 nuclear lysates or macrophage whole-cell lysates. The following antibodies were used: anti-PPAR  (sc-7196, Santa Cruz or 81b8, Cell Signaling Technologies), anti-RXR (sc-774, Santa Cruz), anti-H3K9Ace (ab4441, Abcam), anti-H3K9Me2 (ab1220, Abcam), anti-H3K27Me3 (07-449, Millipore), anti-PU.1 (sc-352x, Santa Cruz), anti-C/EBP  (sc-61, Santa Cruz), and anti-C/EBP  (sc-150x, Santa Cruz). For the ChIP-chip experiments, the anti-H3K9Ace (06-942, Upstate) and anti-histone 3(H3) (ab1791) antibodies were used.

tag: cell type

value: C/EBPbeta


title: Lefterova_mac_H3K9Ace

description: Chromatin IP against PPARgamma


title: Uncinocarpus_reesi_RNA-Seq

description: RNA sequencing


title: -24 hours

description: 2x76bp RNA Seq

source_name: Myoblast (exponential)

value: -24 hours


title: Lefterova_mac_PU.1

description: Chromatin IP against PPARgamma


title: Lefterova_mac_PPARg

description: Chromatin IP against PPARgamma

value: PPARgamma


title: HeLa_TotalRNAseq_Rep1

city: Bethesda

first: Andrew

middle: J

last: Oler

state: MD

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

description: RNA-Seq for Total RNA

data_processing:
Alignment: Reads were aligned to Hg18/ NCBI 36.1/ H_sapiens_Mar_2006 using the Illumina Pipeline's ELAND extended aligner.
Peak: Reads were filtered against satellite repeats and enriched regions relative to input were identified using the USeq analysis package (http://useq.sourceforge.net, Nix et al BMC Bioinfo Dec 5:9(1):523 (2008)).

organism: Homo sapiens

source_name: HeLa S3 cell line

growth_protocol: Cells were cultured in DMEM, 10% FBS, 10 mM glutamine in plastic tissue-culture-treated dishes.  Cells were harvested at ~80% confluence and if used for ChIP, cells were crosslinked in 1% (v/v) formaldehyde for 30 min.

extract_protocol: For ChIP, Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to standard Illumina protocols. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: HeLa S3


title: HeLa_TFIIICChIPseq_Rep1

description: ChIP-Seq for TFIIIC

tag: antigen


title: CAR_sample

status: Public on Apr 13 2010

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

data_processing: The Solexa sequencing reads were mapped to a repeat-masked human genome (hg18) using ELAND. The alignment was performed using standard parameters, where a 32 base-pair seed was used for alignment, allowing maximum of two mismatches in the seed.

molecule: nuclear RNA

source_name: Fibroblast CARs

extract_protocol: Approximately 10 million cells were resuspended in nuclei isolation buffer [0.5 M sucrose, 0.5% TritonX-100 in TES (15mM Tris-HCl pH7.4, 60mM KCl, 2mM EDTA, 1mM DTT)], kept on ice for 10 minutes, and then homogenized by 15 strokes with a dounce homogenizer. The volume was made up to 3mL with nuclei isolation buffer and centrifuged at 4000 rpm for 15 minutes. After washing the nuclei once with TES, the nuclei were resuspended in 300 mL of TES containing 3mM CaCl2, and treated with one unit of MNase in 500 mL reaction volume at 37oC for one minute. The reaction was stopped by adding EDTA to a final concentration 50 mM. The nuclei were centrifuged at 8000 rpm for 2 minutes at 4oC to collect the supernatant (supernatant1), and were further resuspended in 0.2 mM EDTA to disrupt the nuclei and obtain the soluble chromatin (supernatant 2). Supernatants 1 and 2 were mixed and loaded on a 5-30% sucrose gradient, prepared in TES, and centrifuged overnight at 28000 rpm at 4oC. One millilitre fractions from the sucrose gradient were collected. A sample of each fraction (200 mL) was taken for isolation of DNA and the remainder was used for preparation of RNA, using Trizol (Invitrogen). DNA was loaded on a 1% agarose gel to check for the separation of chromatin fragments according to length. The RNA isolated from the gradient fractions was treated extensively with DNase I to remove the contaminating DNA, and a part of the DNase-treated chromatin-bound RNA was used for reverse transcription reaction to make cDNA using Super Script II reverse transcriptase (Invitrogen). We performed a PCR reaction on the cDNA with b-Actin primers to check whether the chromatin-bound RNA is devoid of free RNAs. Based on this initial quality-control step, we pooled the cDNA prepared from the different chromatin-bound RNA fractions. The pooled cDNA was converted into double-stranded cDNA using Universal Riboclone cDNA Sunthesis System (Promega, C4361) following the manufacturer´s protocol. A sequencing library was prepared from cDNA according to the manufacturer’s manual except that the sample was not fragmented, as most of the dsDNA fragments prepared from chromatin-purified RNA were within the range of 100 to 150 bp. Briefly, the DNA was end-repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase (PNK), followed by purification on a QIAquick PCR purification column (Qiagen). An A-base was ligated to the blunt ends of the DNA fragments using the Klenow DNA polymerase and the sample was purified using a MinElute PCR purification column (Qiagen). Adapters for sequencing were ligated to the DNA fragments and the library was size selected on an agarose gel. A 150-200bp fragment was excised from the gel, purified using a QIAGEN gel extraction column and amplified for 14 or 18 cycles of PCR, followed by purification using a QIAquick or MinElute PCR Purification column.

value: fibroblast

tag: rna type

value: chromatin-associated RNA (CAR)


title: Jurkat_Pol3ChIPseq_Rep1

description: ChIP-Seq for Pol III

source_name: Jurkat E6-1 cell line

value: Jurkat E6-1

value: RPC32 (Pol III)

value: sc-21754 (Santa Cruz Biotech.)


title: HeLa_InputChIPseq_Rep1

description: ChIP-Seq Input Control


title: 168 hours

description: 2x76bp RNA Seq

source_name: Myoblast (168 hours post serum switch)

value: 168 hours


title: HeLa_Pol3ChIPseq_Rep2

description: ChIP-Seq for Pol III


title: HeLa_Brf2ChIPseq_Rep1

description: ChIP-Seq for BRF2

value: ab17011 (abcam)


title: HEK293T_Pol3ChIPseq_Rep1

description: ChIP-Seq for Pol III

source_name: HEK293T cell line


title: HeLa_Brf1ChIPseq_Rep1

description: ChIP-Seq for BRF1

value: anti-RPB90 (R. Roeder)


title: Lefterova_ad_PPARg

description: Chromatin IP against PPARgamma


title: HeLa_Pol3ChIPseq_Rep1

description: ChIP-Seq for Pol III


title: Lefterova_ad_H3K9Ace

description: Chromatin IP against PPARgamma


title: HumanForeskinFibroblast_Pol3ChIPseq_Rep1

description: ChIP-Seq for Pol III

source_name: Human foreskin fibroblast hTERT cell line


title: Human ES MspI rep2

status: Public on Apr 12 2010

city: Bronx

first: John

last: Greally

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

description: MspI reference for HELP-tagging

data_processing: Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions 1.3-1.4).  Initial data processing was performed using the default read length of 36 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).  The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg18 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.  To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.

source_name: human embryonic stem cell

growth_protocol: H1 human embryonic stem cells (hESCs, NIH code WA01 from Wicell Research Institute, Madison WI) were cultured on matrigel (BD Biosciences, San Diego), at 37 °C, 5% O2 and 5% CO2.  Amplified hESC pluripotency was assessed by flow cytometry with SSEA4, CD24 and Oct4 markers.  To extract DNA, the cells were suspended in 10 ml of a solution of 10 mM Tris-HCl (pH 8.0), 0.1 M EDTA and 1 ml of 10% SDS to which 10 μl of RNase A (20 mg/ml) was added.  After incubation for 1 hour at 37 oC, 50 μl of proteinase K (20 mg/ml) was added and the solution was gently mixed and incubated in a 50 oC water bath overnight.  To purify the lysate, it was extracted three times using saturated phenol, then twice with chloroform, and dialyzed for 16 hours at 4 oC against three changes of 0.2x SSC.  Following dialysis, the DNA was concentrated by coating the dialysis bags in polyethylene glycol (molecular weight 20,000).  The purity and final concentration of the purified DNA was checked by spectrometry (Nanodrop, Wilmington, DE).

extract_protocol: Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  Five micrograms of genomic DNA were digested with HpaII and MspI in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA or 1 μg of MspI-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).

value: H1 (WA01) human embryonic stem (ES) cell line


title: Human ES HpaII

description: HpaII test for HELP-tagging


title: Human ES MspI rep1

description: MspI reference for HELP-tagging


title: Human ES MspI rep3

description: MspI reference for HELP-tagging


title: HeLa_CappedRNAseq_Rep1

description: RNA-Seq for Capped RNA


title: Head_Dmoj_Male_rep1 (GA II)

status: Public on Apr 11 2010

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: Collected from Catalina Island, California during March 2002. Lat: 33o 20'31" N; Long: 118o 20'11" W. Inbred eight generations through single brother-sister pairs by Laura Reed (2003-2004). Unknown subsequent inbred generations prior to acquisition in Oliver lab. This is the same strain used for the genome project (Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218).

data_processing: Reads that passed default parameters of the Illumina quality filter were mapped with Bowtie 0.11.3. The reference sequence used to built an index for mapping was flybase r1.3. for D. mojavensis. Reference index was created using the bowtie-build function with default parameters. Reads were then mapped using -v 2 -m 1 in Bowtie v. 0.11.3

organism: Drosophila mojavensis

source_name: head tissue

growth_protocol: D. mojavensis (Drosophila Species Stock Center (DSSC) 15081-1352.22) were grown at 22°C, 60% relative humidity in standard plastic vials containing banana-opuntia media. All media was purchased from the Tucson Stock Center, Tucson, Arizona (recipes:: http://flyfood.arl.arizona.edu/opuntia.php3). There were no lights inside of incubators and room lighting (standard fluorescent bulbs) was on at all times. Newly eclosed flies of both females and males were housed together in vials at normal density (60-100 flies) and aged for 7 days. On day 7, flies were anesthetized with CO2 and then females and males were sorted and placed into separate vials. Flies in same sex vials were aged an additional 24 hours then flash frozen on dry ice in 50 ml Falcon tubes and stored at -80°C until dissection.

extract_protocol: Fly heads were immersed in 250 µl of TRIzol and thoroughly homogenized using a 1.5 ml RNAase free pestle (Kimble-Chase, Vineland, New Jersey) fitted to a Pellet Pestle Motor (Sigma-Aldrich, St. Louis, Missouri). After initial homogenization, 550 µl of TRIzol was added and the solution was further homogenized by hand. Chloroform (160 µl) was added to the homogenate and then the sample was centrifuged at 12,000 g for 15 minutes at 4°C. The aqueous layer was removed, precipitated with isopropyl alcohol and glycogen (8 µg), then centrifuged for 10 minutes at 4°C to pellet the RNA. The supernatant was removed and the RNA pellet was washed with fresh 75% ethanol. The pellet was dried briefly and then dissolved in 50 µl DEPC treated H2O. mRNA was enriched from total RNA by poly A+ selection using a QIAGEN Oligotex mRNA kit (Valencia, California) following manufacture instructions. mRNA was eluted from small spin columns twice with hot 30 µl buffer OEB. mRNA quality and quantity was determined by Bioanalyzer (Agilent, Santa Clara, California) and 260/280 ratio from Nanodrop ND-1000 UV spectrophotometer.  We fragmented mRNA using alkaline hydrolysis. First, 9 µl of 100 ng of mRNA and 1 µl of 10X fragmentation buffer (Ambion, Austin, Texas.) was incubated at 70°C for 5 minutes to fragment mRNA. One microliter of Stop Buffer (Ambion, Austin, Texas) was added and samples were placed on ice. Fragments were precipitated with 1 µl 3 M NaOAC (pH 5.2), 2 µl glycogen (5 µg/µl , Ambion, Austin, Texas), and 30 µl 100% EtOH and then incubated for 30 minutes at -80 °C. Fragmented RNA was pelleted at 14000 rpm with a microcentrifuge at 4°C. The pellet was washed with 70% EtOH, air dried and resuspended with 10.5 µl RNase free H2O. Fragmented mRNA was reverse transcribed to create cDNA. One microliter of random hexamer primers (3µg/µl, Invitrogen, Carlsbad, California) was placed with 10.5 µl of fragmented mRNA, then samples were incubated at 65°C for 5 minutes and placed on ice. Four microliters 5X first strand buffer, 2 µl 100 mM DTT, 1 µl dNTP, and 0.5 µl RNaseOUT were added to the mRNA and samples were incubated at 25°C for 2 minutes. One microliter of SuperScript II (200 U/µl, Invitrogen, Carlsbad, California) was added and samples were incubated under the following conditions: 25°C-10 minutes, 42°C-50 minutes, 70°C-15 minutes. Samples were then placed on ice. Second strand cDNA was synthesized by adding 61µl H2O to the first strand mix, 10 µl 10X second strand buffer (500 mM Tris-HCl pH 7.8, 50 mM MgCl2, 10 mM DTT), and 3 µl dNTP (10 mM), mixed, incubated on ice for 5 minutes, then 1 µl RNaseH (2U/µl, Invitrogen, Carlsbad, California) and 5 µl DNA Pol I (10 U/µl, Invitrogen, Carlsbad, California) were added. Samples were incubated at 16°C for 2.5 hours and DNA products purified using a QIAquick spin column and following manufacture directions and eluted with 30 µl. cDNA fragment libraries were prepared for sequencing. The ends of cDNA fragments were repaired using 30 µl of DNA, 45 µl H2O, 10 µl T4 DNA ligase buffer with 10 mM ATP, 4 µl dNTP mix (10 mM), 5 µl T4 DNA polymerase (3 U/µl), 1 µl Klenow DNA polymerase (5U/µl), and 5 µl T4 PNK(10 U/µl). Samples were incubated for 30 minutes at 20°C, purified with QIAquick PCR spin columns, and eluted with 32 µl of Buffer EB. A single "A" base was added to the ends of cDNA by using 5 µl Klenow buffer, 10 µl dATP (1 mM) and 3 µl Klenow 3' to 5' exonuclease (5 U/µl). Samples were incubated at 37°C for 30 minutes, purified with a QIAquick MiniElute column, and eluted with 19µl of EB solution. Adaptor oligonucleotdies were ligated to A overhang fragments as follows. Overhang fragments were combined with 25 µl DNA ligase buffer, 1 µl adaptor olio mix, and 5 µl DNA ligase (1U/µl). Samples were incubated at room temperature for 15 minutes, purified with a QIAquick MiniElute column, and eluted with 10 µl of buffer EB. cDNA templates were sized selected by gel purification then amplified by PCR using oligo-specific primers. Samples were loaded into a 2% agarose gel with 1X TAE buffer and run for 50 minutes with a 100 bp ladder. The gel was stained with ethidium bromide and bands were visualized under UV fluorescence. For each sample, a gel slice was cut at the 200 (+/- 25) bp region, purified with a QIAquick gel extraction kit, and eluted with 30 µl buffer EB. Purified cDNA was amplified in a 50 µl reaction using 25 µl Phusion Mix (Phusion polymerase, dNTPs, and buffer), 1 µl primer 1.1, 1 µl primer 2.1, and 23 µl template along with the following cycling conditions: initial denaturation 98°C-30 sec, cycle denaturation 98°C-10 sec, anneal 65°C-30 sec, and extend 72°C -30 sec with 15X cycles and a final extension of 72°C for 5 minutes followed by a hold at 4°C. The amplified product was purified using a QIAquick column and eluted with 30 µl buffer EB.

treatment_protocol: Frozen whole flies were placed on 10.8 x 10.8 cm ceramic plates frozen on dry ice. Forceps were used to dissect 400-500 heads/sex for subsequent RNA extraction.

tag: sex

value: male

value: Drosophila Species Stock Center (DSSC) 15081-1352.22.


title: Head_Dmoj_Male_rep1 (GA I)


title: Head_Dmoj_Female_rep1 (GA II)

value: female


title: Dmel2_RNAseq

status: Public on Apr 10 2010

city: Heidelberg

first: Michael

last: Boutros

address: Im Neuenheimer Feld 580

department: Signaling and Functional Genomics

country: Germany

institute: German Cancer Research Center (DKFZ)

description: paired-end sequencing

data_processing: Paired-end reads were obtained with Illumina's software pipeline v. 1.4.0. All reads were trimmed to 45 bps and aligned to the Drosophila melanogaster genome v. 5 using Tophat (Trapnel,C et al; PMID 19289445; v. 1.0.13; using -r 90 --solexa1.3-quals parameters). FKPM values for each gene were calculated with cufflinks (Trapnell,C et al; in press; v. 0.12.1.0) based on the Drosophila melanogaser gene annotation v.5.13 obtained from Ensembl.

source_name: D.Mel-2 cell line

growth_protocol: D.Mel-2 cells (Invitrogen, Carlsbad, CA) were grown in Express Five SFM (Invitrogen, Carlsbad, CA) supplemented with 20 mM Glutamax I, 100 U/ml penicillin, 100 microgram/ml streptomycin

extract_protocol: Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), followed by Rneasy cleanup (Qiagen, Hilden, Germany) including on-column DNAse digest. mRNA was isolated with the MicroPoly(A)Purist kit (Ambion, Austin, TX). The library was prepared according to Illumina's mRNA Sequencing Sample Preparation Guide (1004898 Rev. C). Mean insert size: 104 bp, standard deviation: 30 bp.


title: Head_Dmoj_Female_rep1 (GA I)


title: Mmu_wildtype_embryos_bisulfite

status: Public on Apr 09 2010

city: Los Angeles

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

description:
Bisulfite conversion of unmethylated cytosines
all sequences are Cycles 1..5: BS-Seq FW=tctgt, BS-Seq RC=tccat

data_processing:
Illumina Genome Analyzer 200 tiles/lane (sample 1), Illumina Genome Analyzer II 100 tiles/lane (samples 2/3/4/7/9), Illumina Genome Analyzer 300 tiles/lane (samples 5/6/8/10/11/13/14), Illumina Genome Analyzer 330 tiles/lane (sample 12)
Illumina_native (_sig2, _seq, _prb):  All samples are single end by Solexa pipeline 0.2.2.4/OS X with all physical cycles given to the pipeline, except samples 2/3/4 are by Solexa pipeline 1.3rc5/OS X and samples 7/9 are by Solexa pipeline 1.3rc5/Linux.  All lanes are single end 36 cycles, except lanes for samples 7/9 are single end 55 cycles.  Autocalibration on each flow cell was from all tiles and cycles of lane 4 on the same flow cell, which was one of four genomic libraries (#1 for flow cells 070625_SLXA-EAS20_5701 / 071030_HWI-EAS172_14517, #2 for 090306_HWI-EAS399_S014_3126D / 090616_HWI-EAS399_S022_30155, #3 for 080604_HWI-EAS172_20DYB, and #4 for the remaining six) with high representation of A/C/G/T.

extract_protocol: BS-Seq DNA library construction and high-throughput sequencing by Illumina/Solexa Genome Analyzer were performed according to published protocols (Cokus et al., Nature 451, 215-219), except that a total number of six PCR cycles were removed from the library generation procedure. NEBNext DNA sample preparation kit (New England BioLabs) and CpGenome DNA Modification Kit (Chemicon) were used during library construction.

tag: genotype

value: wild type

tag: sample type

value: Embryos


title: Mmu_uhrf1_EScells_bisulfite

source_name: ES cells

value: ES cells


title: Mmu_wildtype_EScells_bisulfite


title: N2

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description: Small RNA sequence data

data_processing: 3' adapter sequences were trimmed and inserts longer than 18 nt were mapped to the C. elegans genome (ce4).

organism: Caenorhabditis elegans

source_name: small RNA from N2 wild-type adults

extract_protocol: RNA was isolated using Trizol reagent and small RNA from 18-30 nucleotides were purified from gel. For cDNA synthesis, the RNA molecules in this fraction were first poly A-tailed using poly(A)polymerase followed by ligation of synthetic RNA adapter to the 5' phosphate of the miRNAs. First strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLVRNase H- reverse transcriptase. cDNA was PCR-amplified with adapter-specific primers and used in Illumina sequencing.


title: Ath_vim1vim2vim3_flowers_bisulfite

organism: Arabidopsis thaliana

source_name: Flowers

value: vim1 vim2 vim3

value: Flowers


title: Ath_met1_flowers_bisulfite


title: Cymbidium Ringspot Virus (CymRSV)-derived siRNAs

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

institute: University of East Anglia

description: CymRSV-derived small RNAs from early systemic leaves of Nicotiana benthamiana.

data_processing: Removed adaptors. Sequences without adapters were discarded. Small RNA sequences were mapped to the CymRSV genome (GenBank: X15511.1).

organism:
Nicotiana benthamiana
Cymbidium ringspot virus

source_name: Early systemic leaves of CymRSV-infected Nicotiana benthamiana

growth_protocol: 3 weeks old Nicotiana benthamiana plants grown in soil under normal growth conditions were used for virus infection. After infection with CymRSV, plants were grown in fitotrons under a 14 h light (50 E µm-2s-1) and 10 h dark regime at 21°C

extract_protocol: Total RNA was extracted from early systemic leaves of Nicotiana benthamiana infected with CymRSV. The homogenized plant materials were resuspended in 600 \u03bcL of extraction buffer (0.1 M glycine-NaOH, pH 9.0, 100 mM NaCl, 10 mM EDTA, 2% SDS, and 1% sodium lauroylsarcosine) and mixed with an equal volume of phenol. The aqueous phase was treated with equal volumes of phenol and chloroform, precipitated with ethanol, and resuspended in sterile water and used in subsequent reactions.

value: early systemic leaves

tag: treatment

value: CymRSV infection


title: P19 silencing suppressor mutant Cymbidium Ringspot Virus (Cym19stop)-derived siRNAs

description: Cym19stop-derived small RNAs from systemic leaves of Nicotiana benthamiana.

source_name: Early systemic leaves of Cym19stop-infected Nicotiana benthamiana

growth_protocol: 3 weeks old Nicotiana benthamiana plants grown in soil under normal growth conditions were used for virus infection. After infection with Cym19stop, plants were grown in fitotrons under a 14 h light (50 E µm-2s-1) and 10 h dark regime at 21°C

extract_protocol: Total RNA was extracted from early systemic leaves of Nicotiana benthamiana infected with Cym19stop. The homogenized plant materials were resuspended in 600 \u03bcL of extraction buffer (0.1 M glycine-NaOH, pH 9.0, 100 mM NaCl, 10 mM EDTA, 2% SDS, and 1% sodium lauroylsarcosine) and mixed with an equal volume of phenol. The aqueous phase was treated with equal volumes of phenol and chloroform, precipitated with ethanol, and resuspended in sterile water and used in subsequent reactions.

value: Cym19stop infection


title: Cin_wildtype_animals_bisulfite

organism: Ciona intestinalis

source_name: Animals

value: Half Moon Bay

value: Animals

value: whole organism


title: Human Normal Liver Tissue Sample 3

city: Hangzhou

first: Meng

last: Xia

address: 866 Yuhangtang Road

country: China

institute: Institute of Immunology, Zhejiang University School of Medicine

description: 18-30 nt small RNA

data_processing: Image files generated by the sequencer were processed to produce digital-quality data. The subsequent procedures performed with Solexa were summarizing data production, evaluating sequencing quality, calculating length distribution of small RNA reads and filtrating reads contaminated by rRNA, tRNA, mRNA, snRNA, and snoRNA. Finally, clean reads were compared with a miRBase database (release 13.0) and the copy numbers of each unique sequence were calculated. Sequencing data alignment were mainly analyzed using SOAP (Short Oligonucleotide Alignment Program) (http://soap.genomics.org.cn) algorithm.

source_name: Human Normal Liver Tissue

growth_protocol: Liver tissue samples were obtained from patients during operation. All samples were collected with the informed consent of the patients and the experiments were approved by the ethics committee of Second Military Medical University, Shanghai, China.

extract_protocol: Briefly, after PAGE purification of small RNA molecules under 30 bases and ligation of a pair of Solexa adaptors to their 5' and 3' ends, the small RNA molecules were amplified using the adaptor primers for 12 cycles and the fragments around 90 bp (small RNA+adaptors) were isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's Solexa Sequencer according to the manufacturer's instructions.

treatment_protocol: Surgically removed tissues were quickly frozen in liquid nitrogen until analysis. Total RNA, containing miRNA, was extracted using miRNeasy Mini Kit (Qiagen 217004, Germany) and passed the RNA quality control for Solexa sequencing.

value: liver

tag: tumor stage

value: Normal liver

tag: clinical characteristics

value: Distal normal liver tissue of liver hemangioma


title: P19 silencing suppressor mutant Cymbidium Ringspot Virus (Cym19stop)-derived de- and re-phosphorylated siRNAs

description: Cym19stop-derived small RNAs from systemic leaves of Nicotiana benthamiana. The eluted sRNA fraction was de-phosphorylated with Shrimp Alkaline Phosphatase and re-phosphorylated with T4 Polynucleotide Kinase. The resulting sRNAs were used in subsequent reactions.


title: Ath_wildtype_flowers_bisulfite


title: Dazao strain p50_biological_Replicate2 DGE analysis

city: Kunming

first: Hui

last: Xiang

state: Yunnan Province

address: 32 East Jiaochang Road

institute: Kunming Insititute of Zoology

data_processing: Gene annotation information was downloaded from the SilkDB (ftp://silkworm.swu.edu.cn/pub/Glean_genes/silkworm_glean.gff.gz). Because annotated genes were mainly predicted using prediction software, only ORF positions were available. We created putative full-length cDNA sequences for each gene by adding 1kb downstream sequences of ORF to coding sequences. Then all possible CATG + 17nt tag sequences were created from putative full-length cDNAs and used as reference tag database. Unique tag sequences and their numbers were extracted from our raw DGE tags and these tags were aligned against the reference tag database using SOAP 4. Only perfect matches were kept for further analysis, and no mismatches were allowed. Expression level of one gene was represented by the total number of tags which uniquely aligned to this gene.

organism: Bombyx mori

source_name: the silkgland of female larva of fifth instar of silkworm P50 strain

extract_protocol: Each silk gland of 5th instar larvae of two individuals (called Biological Replicate 1 and 2, respectively) of the silkworm (Bombyx mori) strain Dazao was ground into powder in liquid nitrogen. Total RNAs extract were extracted using RNeasy Mini Kit (Qiagen). DGE-tag libraries were constructed using DGE-Tag Profiling NlaIII Sample Prep Kit (Illumina). Libraries were sequenced using the Illumina Genetic Analyzer (GA2) according to the manufacturer’s instruction.

value: silkworm Dazao strain P50

tag: gender

value: fifth instar larva

value: the silkgland


title: HBV(+) Side Tissue Sample 1

description: 18-30 nt small RNA

source_name: HBV(+) Side Tissue

value: HBV-related HCC Side Tissue

value: Side liver tissue of primary HBV-related HCC


title: Severe Chronic Hepatitis B Liver Tissue

description: 18-30 nt small RNA

source_name: Severe Chronic Hepatitis B Liver Tissue

value: Severe Chronic Hepatitis B

value: Distal liver tissue of liver hemangioma in severe chronic hepatitis B liver


title: HBV(+) Distal Tissue Sample 1

description: 18-30 nt small RNA

source_name: HBV(+) Distal Tissue

value: HBV-related HCC Distal Tissue

value: Distal liver tissue of primary HBV-related HCC


title: HBV-infected Liver Tissue

description: 18-30 nt small RNA

source_name: HBV-infected Liver Tissue

value: HBV-infected Liver

value: Distal liver tissue of liver hemangioma in HBV infected liver


title: Cymbidium Ringspot Virus (CymRSV)-derived de-phosphorylated and re-phosphorylated siRNAs

description: CymRSV-derived small RNAs from early systemic leaves of Nicotiana benthamiana. The eluted sRNA fraction was de-phosphorylated with Shrimp Alkaline Phosphatase and re-phosphorylated with T4 Polynucleotide Kinase. The resulting sRNAs were used in subsequent reactions.

value: early systemic leaves

value: CymRSV infection


title: HBV(+) HCC Tissue Sample 2

description: 18-30 nt small RNA

source_name: HBV(+) HCC Tissue

value: HBC-related HCC Tissue

value: Primary HBV-related HCC


title: HBV(+) HCC Tissue Sample 1

description: 18-30 nt small RNA

value: liver


title: Human Normal Liver Tissue Sample 2

description: 18-30 nt small RNA

value: Normal liver

value: Distal normal liver tissue of liver hemangioma


title: Cre_wildtype_vegetativeCells_bisulfite

organism: Chlamydomonas reinhardtii

source_name: Vegetative cells

value: wild type

value: Vegetative cells


title: Human Normal Liver Tissue Sample 1

description: 18-30 nt small RNA


title: HBV(+) Adjacent Tissue Sample 1

description: 18-30 nt small RNA

source_name: HBV(+) Adjacent Tissue

value: HBV-related HCC Adjacent Tissue

value: Adjacent liver tissue of primary HBV-related HCC


title: Dre_uhrf1_embryos_bisulfite

organism: Danio rerio

source_name: Embryos

value: ZFIN ZDB-GENO-070209-94 incross

value: Embryos


title: Dre_wildtype_embryos_bisulfite


title: Dazao strain p50_biological_Replicate1 DGE analysis

description: DGE-tag libraries were constructed using DGE-Tag Profiling NlaIII Sample Prep Kit (Illumina). Libraries were sequenced using the Illumina Genetic Analyzer (GA2) according to the manufacturer’s instruction.

value: silkworm Dazao strain

value: female

tag: age

value: fifth instar larva

value: the silkgland


title: Osa_wildtype_leaves_bisulfite

organism: Oryza sativa

source_name: Leaves

value: Nipponbare

value: Leaves


title: Ptr_wildtype_leaves_bisulfite

organism: Populus trichocarpa


title: Head_Dmel_Male (GA I)

status: Public on Apr 08 2010

data_processing: Reads that passed default parameters of the Illumina quality filter were mapped with Bowtie 0.11.3. The reference sequence used to built an index for mapping was the dm3 from the UCSC Genome Browser which corresponds to the April 2006 Drosophila melanogaster draft assembly from the Berkeley Drosophila Genome Project (Release 5). The reference index was created using the bowtie-build function with default parameters. Reads were mapped using -v 2 -m 1 in Bowtie v. 0.11.3.

source_name: head tissue

growth_protocol: Drosophila melanogaster (OregonR) were grown at 22°C, 60% relative humidity in standard plastic vials containing cornmeal media. All media was purchased from the Tucson Stock Center, Tucson, Arizona (recipes: http://flyfood.arl.arizona.edu/recipes.php3). There were no lights inside of incubators and room lighting (standard fluorescent bulbs) was on at all times. Newly eclosed flies of both females and males were housed together in vials at normal density (60-100 flies) and aged for 7 days. On day 7, flies were anesthetized with CO2 and then females and males were sorted and placed into separate vials. Flies in same sex vials were aged an additional 24 hours then flash frozen on dry ice in 50 ml Falcon tubes and stored at -80°C until dissection.

extract_protocol:
Fly heads were immersed in 250 µl of TRIzol and thoroughly homogenized using a 1.5 ml RNAase free pestle (Kimble-Chase, Vineland, New Jersey) fitted to a Pellet Pestle Motor (Sigma-Aldrich, St. Louis, Missouri). After initial homogenization, 550 µl of TRIzol was added and the solution was further homogenized by hand. Chloroform (160 µl) was added to the homogenate and then the sample was centrifuged at 12,000 g for 15 minutes at 4°C. The aqueous layer was removed, precipitated with isopropyl alcohol and glycogen (8 µg), then centrifuged for 10 minutes at 4°C to pellet the RNA. The supernatant was removed and the RNA pellet was washed with fresh 75% ethanol. The pellet was dried briefly and then dissolved in 50 µl DEPC treated H2O. mRNA was enriched from total RNA by poly A+ selection using a QIAGEN Oligotex mRNA kit (Valencia, California) following manufacture instructions. mRNA was eluted from small spin columns twice with hot 30 µl buffer OEB. mRNA quality and quantity was determined by Bioanalyzer (Agilent, Santa Clara, California) and 260/280 ratio from Nanodrop ND-1000 UV spectrophotometer.
We fragmented mRNA using alkaline hydrolysis. First, 9 µl of 100 ng of mRNA and 1 µl of 10X fragmentation buffer (Ambion, Austin, Texas.) was incubated at 70°C for 5 minutes to fragment mRNA. One microliter of Stop Buffer (Ambion, Austin, Texas) was added and samples were placed on ice. Fragments were precipitated with 1 µl 3 M NaOAC (pH 5.2), 2 µl glycogen (5 µg/µl , Ambion, Austin, Texas), and 30 µl 100% EtOH and then incubated for 30 minutes at -80 °C. Fragmented RNA was pelleted at 14000 rpm with a microcentrifuge at 4°C. The pellet was washed with 70% EtOH, air dried and resuspended with 10.5 µl RNase free H2O. Fragmented mRNA was reverse transcribed to create cDNA. One microliter of random hexamer primers (3µg/µl, Invitrogen, Carlsbad, California) was placed with 10.5 µl of fragmented mRNA, then samples were incubated at 65°C for 5 minutes and placed on ice. Four microliters 5X first strand buffer, 2 µl 100 mM DTT, 1 µl dNTP, and 0.5 µl RNaseOUT were added to the mRNA and samples were incubated at 25°C for 2 minutes. One microliter of SuperScript II (200 U/µl, Invitrogen, Carlsbad, California) was added and samples were incubated under the following conditions: 25°C-10 minutes, 42°C-50 minutes, 70°C-15 minutes. Samples were then placed on ice. Second strand cDNA was synthesized by adding 61µl H2O to the first strand mix, 10 µl 10X second strand buffer (500 mM Tris-HCl pH 7.8, 50 mM MgCl2, 10 mM DTT), and 3 µl dNTP (10 mM), mixed, incubated on ice for 5 minutes, then 1 µl RNaseH (2U/µl, Invitrogen, Carlsbad, California) and 5 µl DNA Pol I (10 U/µl, Invitrogen, Carlsbad, California) were added. Samples were incubated at 16°C for 2.5 hours and DNA products purified using a QIAquick spin column and following manufacture directions and eluted with 30 µl. cDNA fragment libraries were prepared for sequencing. The ends of cDNA fragments were repaired using 30 µl of DNA, 45 µl H2O, 10 µl T4 DNA ligase buffer with 10 mM ATP, 4 µl dNTP mix (10 mM), 5 µl T4 DNA polymerase (3 U/µl), 1 µl Klenow DNA polymerase (5U/µl), and 5 µl T4 PNK(10 U/µl). Samples were incubated for 30 minutes at 20°C, purified with QIAquick PCR spin columns, and eluted with 32 µl of Buffer EB. A single “A” base was added to the ends of cDNA by using 5 µl Klenow buffer, 10 µl dATP (1 mM) and 3 µl Klenow 3’ to 5’ exonuclease (5 U/µl). Samples were incubated at 37°C for 30 minutes, purified with a QIAquick MiniElute column, and eluted with 19µl of EB solution. Adaptor oligonucleotdies were ligated to A overhang fragments as follows. Overhang fragments were combined with 25 µl DNA ligase buffer, 1 µl adaptor olio mix, and 5 µl DNA ligase (1U/µl). Samples were incubated at room temperature for 15 minutes, purified with a QIAquick MiniElute column, and eluted with 10 µl of buffer EB. cDNA templates were sized selected by gel purification then amplified by PCR using oligo-specific primers. Samples were loaded into a 2% agarose gel with 1X TAE buffer and run for 50 minutes with a 100 bp ladder. The gel was stained with ethidium bromide and bands were visualized under UV fluorescence. For each sample, a gel slice was cut at the 200 (+/- 25) bp region, purified with a QIAquick gel extraction kit, and eluted with 30 µl buffer EB. Purified cDNA was amplified in a 50 µl reaction using 25 µl Phusion Mix (Phusion polymerase, dNTPs, and buffer), 1 µl primer 1.1, 1 µl primer 2.1, and 23 µl template along with the following cycling conditions: initial denaturation 98°C-30 sec, cycle denaturation 98°C-10 sec, anneal 65°C-30 sec, and extend 72°C -30 sec with 15X cycles and a final extension of 72°C for 5 minutes followed by a hold at 4°C. The amplified product was purified using a QIAquick column and eluted with 30 µl buffer EB.

value: OregonR


title: Ath_wildtype_shoots_bisulfite

source_name: Shoots

value: Shoots


title: Head_Dmel_Male (GA II)

value: head


title: Head_Dmel_Female (GA II)


title: Brain MAQC Human s_8_2

city: Stanford

first: Kin Fai

last: Au

address: 390 Serra Mall, Stanford University

department: Statistics

institute: Stanford University

description:
RNA_Seq.
Brain MAQC Human s_x_y:
In the sequencing experiment, there are 8 lanes in one run. The data uploaded to GEO were from three lanes of one run. That is, x=3,6 or 8 are the indexes of the lanes, which do not have any biological significance. y=1 or 2 represents the paired data. In a pair of data, y=1 represents the reads on 5' end while y=2 represents the ones on 3' end.
The average insert size is about 200bp. But we do not have any estimate of standard deviation.

data_processing:
The processed files are the mapping results of the reads on human genome(hg18) by SeqMap. Up to 2 mismatches are allowed.

Contents of processed data files (fastq.out):
The first column is the combination of the data file name and the read index, which are separated by dash.
The second column is the sequence of the raw data.
The third column is the numbers of the mapping hits that allow no mismatch, 1 mismatch and 2 mismatch, respectively.
The forth column are the mapping hits that describe the chromosomal positions.

source_name: Human brain tissue

extract_protocol: mRNA is purified from total RNA with oligo-dT magnetic beads. cDNA is synthesized with random primer priming. ds-cDNA is sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

value: mixed human brain


title: Head_Dmel_Female (GA I)


title: HBV(-) HCV(-) Adjacent Tissue Sample

description: 18-30 nt small RNA

source_name: HBV(-) HCV(-) Adjacent Tissue

value: liver

value: HBV(-) HCV(-) Adjacent Tissue

value: Adjacent liver tissue of primary HBV(-) HCV(-) HCC


title: HBV(-) HCV(-) HCC  Tissue Sample

description: 18-30 nt small RNA

source_name: HBV(-) HCV(-) HCC  Tissue

value: HBV(-) HCV(-) HCC  Tissue

value: Primary HBV(-) HCV(-) HCC


title: Brain MAQC Human s_8_1


title: Brain MAQC Human s_6_2


title: RDE1

description: Small RNA sequence data

source_name: small RNA from rde-1 mutants (allele pk3301)

extract_protocol: RNA was isolated using Trizol reagent and small RNA from 18-30 nucleotides were purified from gel.  For cDNA synthesis, the RNA molecules in this fraction were first poly A-tailed using poly(A)polymerase followed by ligation of synthetic RNA adapter to the 5' phosphate of the miRNAs. First strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLVRNase H- reverse transcriptase. cDNA was PCR-amplified with adapter-specific primers and used in Illumina sequencing.


title: Brain MAQC Human s_3_2


title: Brain MAQC Human s_6_1


title: Brain MAQC Human s_3_1


title: HBV(+) Adjacent Tissue Sample 2

description: 18-30 nt small RNA

value: HBV-related HCC Adjacent Tissue

value: Adjacent liver tissue of primary HBV-related HCC


title: KLF1_ChIPSeq, 3.0

city: The University of Queensland, St Lucia, Brisbane

middle: C

last: Perkins

state: QLD

address: Institute for Molecular Bioscience

department: Institute for Molecular Bioscience

country: Australia

institute: The University of Queensland

description: ChIP against KLF1.

data_processing:
Alignment: Sequencing reads were mapped to the mm9 mouse genome using the mapreads algorithm (Applied Biosystems). In order to maximize the number of mappable reads, we removed the final 5 nucleotides for unmapped reads in a recursive strategy until the reads reached 25 nucleotides in length.

Peaks: We employed the same method used by Chen et al. (2008, Cell 133, 1106-1117) in order to declare a set of KLF1-bound regions for downstream analysis. When generating the tag intensity profile used in peak declaration, we added a count of 1 to each position up to 100bp 3' from the start of each tag.  To be declared a peak, a genomic position must pass both a tag intensity threshold and a fold-change threshold.  We applied a false discovery rate (FDR) threshold of 1%, which resulted in a tag intensity profile threshold of 9. We applied negative control tag library fold-change threshold of 5.0 at the centre of each declared peak, yielding the final set of 945 declared peaks.

organism: Mus musculus

source_name: E14.5 fetal liver, ChIP

growth_protocol: 4 x Klf3 -/- fetal livers were collected at E14.5 from timed mated female mice, homogenized using a 23G needle, then strained through a 40 micron cell strainer and pooled.

extract_protocol: The SOLiD System 2.0 workflow for Lower Input/Lower Complexity DNA fragment library preparation (Applied Biosystems) was followed to prepare libraries containing 80-130bp of ChIP DNA (or Input DNA) flanked by the appropriate adaptors. A detailed description of the method is provided in the Supplemental Experimental Procedures of the publication.

value: erythroid

tag: developmental stage

value: fetal

value: Balb/c Klf3 -/-

tag: passages

value: primary tissue

value: rabbit polyclonal to KLF1


title: KLF1_Input, 3.0

description: Input DNA negative control for ChIP against KLF1.

source_name: E14.5 fetal liver, input

tag: tissue

tag: strain

value: female


title: KLF1_Input, 2.0

tag: antibody


title: Expression_RJF-Muscle_YJ

status: Public on Apr 02 2010

city: beijing

first: qinghe

last: li

address: no2, yuanmingyuan west road

institute: China Agricultural university

description: RNA sequencing

data_processing: The sequences obtained by RNA-seq were mapped onto the refSeq database. Unmapped and redundantly mapped sequences were removed from the dataset. Sequences uniquely mapped to refseq genes were used for subsequent analysis. All libraries were normalized to 1M sequences according to clean sequences (sequences without undefined nucleotides and excluding sequences that were sequenced only once or contained adaptor sequences).

organism: Gallus gallus

source_name: muscle

extract_protocol: The mRNAs were isolated and reverse transcribed into double-stranded cDNA on magnetic beads which were covered with oligo d(T), the cDNA was digested with NlaIII and ligated to Illumina specific adapter containing a recognition site of MmeI. Following Mme1 digestion, a second Illumina adapter, containing a 2 bp degenerate 3’ overhang was ligated. Then tags that were close to the 3’ terminus of the mRNA were enriched by an 15 cycles PCR. The PCR products were run on a 6% TBE-PAGE gel and the ~85bp DNA band was excised and purified for cluster generation and sequencing analysis.

treatment_protocol: Two 7-day-old chickens were utilized in this experiment, one red jungle fowl and one avian broiler. The chickens were fed with the same diet and sacrificed according to local standards of animal welfare issues. Liver and muscle tissues taken from each animal were flash frozen in liquid nitrogen and then stored at -80°C.

tag: breed

value: red junglefowl


title: Expression_RJF-Liver_YG

description: RNA sequencing

source_name: liver


title: Ame_wildtype_immatureMale_bisulfite

organism: Apis mellifera

source_name: Immature male

value: wild type

value: Immature male

value: whole organism


title: Expression_AA-Muscle_AJ

description: RNA sequencing

value: avian broiler


title: KLF1_ChIPSeq, 2.0

description: ChIP against KLF1.

value: liver

tag: cell type


title: PolII_Nterm_shcMyc_ChIP_Seq

first: Charles

last: Lin

address: 9 Cambridge Center

department: Biology

institute: Massachusetts Institute of Technology

description: Chromatin IP against total Pol II in cells infected and selected with c-Myc shRNA

data_processing: Images acquired from the Illumina/Solexa sequencer were processed through the bundled Solexa image extraction pipeline which identified polony positions, performed base-calling and generated QC statistics. Sequences were aligned using ELAND software to NCBI Build 36 (UCSC mm8) of the mouse genome (WIG files linked to GSE20530). Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple reads mapped to the same genomic position, a maximum of two reads mapping to the same position were used.  Sequence reads from multiple flow cells for each IP target were combined. Each read was extended 100bp, towards the interior of the sequenced fragment, based on the strand of the alignment. Across the genome, in 25 bp bins, the number of ChIP-Seq reads within a 1kb window surrounding each bin (+/- 500bp) was tabulated. The 25bp genomic bins that contained statistically significant ChIP-Seq enrichment were identified by comparison to a Poissonian background model. Assuming background reads are spread randomly throughout the genome, the probability of observing a given number of reads in a 1kb window can be modeled as a Poisson process in which the expectation can be estimated as the number of mapped reads multiplied by the number of bins (40) into which each read maps, divided by the total number of bins available (we estimated 70%). Enriched bins within 1kb of one another were combined into regions. The complete set of RefSeq genes was downloaded from the UCSC table browser (http://genome.ucsc.edu/cgi-bin/hgTables?command=start) on December 20, 2008. Gene with enriched regions within 5kb of their transcription start site were called bound.     The Poissonian background model assumes a random distribution of background reads, however we have observed significant deviations from this expectation. Some of these non-random events can be detected as sites of apparent enrichment in negative control DNA samples and can create many false positives in ChIP-Seq experiments. To remove these regions, we compared genomic bins and regions that meet the statistical threshold for enrichment to a set of reads obtained from Solexa sequencing of DNA from whole cell extract (WCE) in mES cells (WCE sample from Cole et al. 2008). We required that enriched bins and enriched regions have five-fold greater ChIP-Seq density in the specific IP sample, compared with the control sample, normalized to the total number of reads in each dataset. This served to filter out genomic regions that are biased to having a greater than expected background density of ChIP-Seq reads.

source_name: V6.5 mES cells

growth_protocol: V6.5 cells were grown under standard mES cell conditions as described previously (Boyer et al., 2005).  Briefly, cells were grown on 0.2% gelatinized tissue culture plates in ESC media; DMEM-KO supplemented with 15% fetal bovine serum, 1000 U/mL LIF, 100 uM nonessential amino acids, 2 mM L-glutamine, 100 U/mL penicillin, 100 ug/mL streptomycin and 8 nL/mL of 2-mercaptoethanol

extract_protocol: ChIP was done following the Agilent Mammalian ChIP-on-chip protocol (version 9.1, Nov 2006).  In summary, mES cells were grown as described above and cross-linked for 15 minutes at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution (11% formaldehyde, 50mM Hepes pH7.3, 100mM NaCl, 1mM EDTA pH8.0, 0.5mM EGTA pH8.0) to the growth media followed by two washes with PBS.  Cells were scraped and frozen in liquid nitrogen.  100ul of Dynal magnetic beads (Sigma) were blocked with 0.5% BSA (w/v) in PBS.  Magnetic beads were bound with 10ug of the indicated antibody.  Antibodies used are as follows: Pol II (all; Rpb1 N-terminus): Santa Cruz sc-899; Ser5P Pol II: Abcam ab5131; Ser2P Pol II: Abcam (H5 clone) ab24758 with Upstate IgG-IgM linker antibody 12-488; Spt5: gift from Yuki Yamaguchi and Hiroshi Handa (Wada et al., 1998); NelfA: Santa Cruz (A-20) sc-23599;; Ctr9: Bethyl labs A301-395; and Max: Santa Cruz sc-197.  For all of the experiments analyzing Pol II occupancy following shRNA-mediated knockdown, flavopiridol, or 10058-F4 treatment, the Pol II (all; Santa Cruz sc-899, Pol II N-20) antibody was used.  Crosslinked cells were lysed with lysis buffer 1 (50mM Hepes pH7.3, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) and washed with lysis buffer 2 (10mM Tris-HCl pH8.0, 200mM NaCl, 1mM EDTA pH8.0 and 0.5mM EGTA pH8.0).      For Spt5 ChIPs, cells were resuspended and sonicated in lysis buffer 3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA pH8.0, 0.5mM EGTA pH8.0, 0.1% Na-Deoxycholate and 0.5% N-lauroylsarcosine) for 8 cycles at 30 seconds each on ice (18 watts) with 60 seconds on ice between cycles. Triton X-100 was added to a final concentration of 1% to the sonicated lysates. Sonicated lysates were cleared and incubated overnight at 4oC with magnetic beads bound with antibody to enrich for DNA fragments bound by the indicated factor.  Beads were washed four times with RIPA (50mM Hepes pH7.3, 500mM LiCl, 1mM EDTA, 1% NP-40 and 0.7% Na-Deoxycholate) and once with TE + 50mM NaCl.  Bound complexes were eluted in elution buffer (50mM Tris-HCl pH8.0, 10mM EDTA pH8.0, 1% SDS) at 65oC for 15 minutes with occasional vortexing.  Cross-links were reversed overnight at 65oC.  RNA and protein were digested using RNAse A and Proteinase K, respectively and DNA was purified with phenol chloroform extraction and ethanol precipitation.      For Pol II Ser5P, Pol II (all), NelfA, Ctr9 and Max ChIPs,  cells were resuspended and sonicated in sonication buffer (50mM Tris-HCl pH7.5, 140mM NaCl, 1mM EDTA, 1mM EGTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS) for 8 cycles at 30 seconds each on ice (18 watts) with 60 seconds on ice between cycles.  Sonicated lysates were cleared and incubated overnight at 4oC with magnetic beads bound with antibody to enrich for DNA fragments bound by the indicated factor.  Beads were washed three times with sonication buffer, one time with sonication buffer with 500mM NaCl, one time with LiCl wash buffer (20mM Tris pH8.0, 1mM EDTA, 250mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and one time with TE.  DNA was eluted in elution buffer.  Cross-links were reversed overnight.  RNA and protein were digested using RNAse A and Proteinase K, respectively and DNA was purified with phenol chloroform extraction and ethanol precipitation.    For Pol II Ser2P ChIP, cells were resuspended and sonicated in sonication buffer II (50mM Tris-HCl pH7.5, 140mM NaCl, 1mM EDTA, 1mM EGTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS) for 8 cycles at 30 seconds each on ice, at 18 watts with 60 seconds on ice between cycles.  Sonicated lysates were cleared and incubated overnight at 4oC with magnetic beads bound with antibody to enrich for DNA fragments bound by Pol II Ser2P.  Beads were washed two times with sonication buffer II, one time with LiCl wash buffer (2mM Tris pH8.0, 0.02mM EDTA, 50mM LiCl, 0.1% NP-40, 0.1% Na-deoxycholate) and one wash with TE.  DNA was eluted in elution buffer.  This protocol is similar to that used in (Stock et al., 2007).  Cross-links were reversed overnight.  RNA and protein were digested using RNAse A and Proteinase K, respectively and DNA was purified with phenol chloroform extraction and ethanol precipitation.      DNA was prepared for sequencing according to a modified version of the Illumina/Solexa Genomic DNA protocol. Fragmented DNA was prepared for ligation of Solexa linkers by repairing the ends and adding a single adenine nucleotide overhang to allow for directional ligation. A 1:100 dilution of the Adaptor Oligo Mix (Illumina) was used in the ligation step. A subsequent PCR step with limited (18) amplification cycles added additional linker sequence to the fragments to prepare them for annealing to the Genome Analyzer flow-cell. After amplification, a narrow range of fragment sizes was selected by separation on a 2% agarose gel and excision of a band between 150-300 bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence). The DNA was purified from the agarose and diluted to 10 nM for loading on the flow cell.    The DNA library (2-4 pM) was applied to the flow-cell (8 samples per flow-cell) using the Cluster Station device from Illumina. The concentration of library applied to the flow-cell was calibrated such that polonies generated in the bridge amplification step originate from single strands of DNA. Multiple rounds of amplification reagents were flowed across the cell in the bridge amplification step to generate polonies of approximately 1,000 strands in 1μm diameter spots. Double stranded polonies were visually checked for density and morphology by staining with a 1:5000 dilution of SYBR Green I (Invitrogen) and visualizing with a microscope under fluorescent illumination. Validated flow-cells were stored at 4 degrees C until sequencing.    Flow-cells were removed from storage and subjected to linearization and annealing of sequencing primer on the Cluster Station. Primed flow-cells were loaded into the Illumina Genome Analyzer 1G. After the first base was incorporated in the Sequencing-by-Synthesis reaction the process was paused for a key quality control checkpoint. A small section of each lane was imaged and the average intensity value for all four bases was compared to minimum thresholds. Flow-cells with low first base intensities were re-primed and if signal was not recovered the flow-cell was aborted. Flow-cells with signal intensities meeting the minimum thresholds were resumed and sequenced for 26 or 32 cycles.

treatment_protocol:
For location analysis following Spt5 and NelfA knockdown, shRNA plasmids targeting the mouse Spt5 and NelfA mRNAs and an empty plasmid (control) (Open Biosystems, Huntsville, AL RMM4534-NM_013676, RMM4534-NM_011914, and RMM4534_NM_010849, RHS4080) were used.  We purchased and tested each set of shRNA hairpins for ability of each hairpin to knockdown the mRNA of the factor of interest.  We then selected the hairpin that performed the best for use in ChIP-seq analysis.  For Spt5, hairpin TRCN0000092761 was used.  For NelfA, hairpin TRCN0000124874 was used.  For c-Myc, hairpin TRCN0000042516 was used.  293T cells were plated in 6-well dishes at 6x10^5 cells/well. The shRNA plasmids and lentiviral components were co-transfected into 293T cells. V6.5 mES cells were plated in T-75 flasks at 2x10^6 cells/flask. Viral media was collected 48 hours after co-transfection and the V6.5 mES cells were directly infected with the viral media 24 hours after initial plating of the mES cells. The infection media was 1:2 viral media:mES cell media with 2mM polybrene. The efficiently infected cells were selected for 24 hours post infection with mES cell media containing 2μM puromycin. V6.5 cells were cross-linked 72 hours post selection and frozen for ChIP-Seq experiments and western blotting.
For location analysis on mES cells following treatment with small molecule inhibitors, cells were grown two passages off feeders and prior to formaldehyde crosslinking, the cells were treated by addition of the indicated final concentration of flavopiridol (1μM for 1 hour for ChIP-chip and ChIP-seq experiments, or the indicated concentration and time for Western blot analysis), or c-Myc/Max inhibitor 10058-F4 (50μM for 6 hours for ChIP-seq experiments or the indicated time for Western blot analysis), both dissolved in DMSO, to the growth medium. 50μM is within the concentration range commonly used for 10058-F4 in vivo to investigate c-Myc function (Arabi et al., 2005; Fang et al., 2008; Faumont et al., 2009; Follis et al., 2008; Hammoudeh et al., 2009; Khanna et al., 2009; Lee et al., 2009; Sampson et al., 2007; Wang et al., 2007).  As a control, vehicle alone (DMSO) was added to the growth medium at the same final volume as with drug.  Small molecule inhibitors used were: Flavopiridol (Sigma cat #F3055), and c-Myc inhibitor 10058-F4 (Sigma cat #F3680).
For location analysis following Oct4 shutdown, ZHBTc4 mES cells (Niwa et al., 2000) were grown under standard mES cell culture conditions and expanded for two passages off MEF feeders. ES cell culture media with 2 μg/ml doxycycline was added to the cells for 0 hours, 12 hours and 24 hours prior to formaldehyde crosslinking.  Loss of Oct4 was assessed using Western Blot analysis.

value: V6.5 mES cells

tag: shrna

value: c-Myc

tag: small molecule

value: no

tag: chip antibody

value: RNA Pol II (Rpb1 N-terminus)


title: PolII_Nterm_Doxycycline12hr_ChIP_Seq

description: Chromatin IP against total Pol II in cells treated with doxycycline for 12 hours

source_name: ZHBTc4 mES cells

value: ZHBTc4 mES cells

value: Doxycycline 12 hour


title: PolII_Nterm_Doxycycline0hr_ChIP_Seq

description: Chromatin IP against total Pol II in cells treated with doxycycline for 0 hours

value: Doxycycline 0 hour


title: MeDIP-Seq_AA-Liver_AG

description: meDIP against methylated DNA

data_processing:
The reads generated during a Illumina/Solexa Sequencing run are 35 bp in length. The resulting FASTQ files were aligned to the chicken reference genome (galGal3) by the open-source aligner the Mapping and Assembly with Qualities (MAQ).
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

extract_protocol: DNA was isolated by phenol-chloroform extraction. DNA was sonicated to small segments and DNA fragments ranging from 200-350bp were retracted by gel excision with gel extraction kit (Qiagen,). The recovered DNA was first 5’ and 3’ end blunting, phosphorylating and repairing by T4 Polynucleotide Kinase and T4 DNA Polymerase (NEB). After addition of an ATP in the 3’ end, an Illumina sequencing primer adapter was ligated to the DNA using the Quick LigationTM Kit (Qiagen). DNA was recovered by MinElute® PCR Purification Kit (Qiagen) and used for meDIP. Our meDIP method was modified from previous study. For each sample, we incubated 4μg denatured DNA with 32μg anti-5-methylcytosine mouse monoclonal antibody in 400μl IP buffer (10mM Tris-HCl, pH7.5, 280mM NaCl, 1mM EDTA) at 4°C for 5.5 hr. Then we added 100μl Dynabeads Protein G and Protein A (Dynal) to the mix and incubated at 4℃ for 5.5 hr. The following step was the same as in the method described by Xiaoyu Zhang. After meDIP, the DNA was divided into three fractions: the unbound, washed and bound fractions. With a high methylated region as a positive control verified by bisulfite sequencing and a region without CpG dinucleotides as a negative control, we carried out realtime-PCR to determine the relative enrichment of the control region in the above three fractions. DNA in the bound fraction from qualifying meDIP experiment was PCR amplified with sequencing primers provided by Illimina using PhusionTM High-Fidelity PCR Master Mix (Finnzymes) under the following conditions: 3min at 98°C; followed by 18 cycles of  98°C for 15s, 65°C for 30s, 72°C for 20s; and a final extension for 5min. PCR products were recovered using MinElute PCR Purification Kit (Qiagen) and used for Solexa sequencing.

tag: medip antibody

value: anti-5-methycytosine mouse mAb


title: MeDIP-Seq_RJF-Muscle_YJ

description: meDIP against methylated DNA


title: Expression_AA-Liver_AG

description: RNA sequencing


title: muscle_pre-training_rep6

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description: NlaIII digested polyA RNA

data_processing: reps 1-3 were processed using the illumina IPAR v1.01 pipeline. Reps 4-7 were processed using Illumina pipeline v1.4. Tag counts correspond to equCab2 ensembl 49 build.

organism: Equus caballus

source_name: gluteus medius muscle

extract_protocol: The Illumina cDNA library was prepared according to the Illumina procotol document "Preparing Samples for Digital Gene Expression-Tag profiling with NlaIII" Part # 11251702 Rev. A   (icom.illumina.com).

value: gluteus medius muscle

tag: training timepoint

value: pre

tag: horse number


title: PolII_Nterm_shSpt5_ChIP_Seq

description: Chromatin IP against total Pol II in cells infected and selected with Spt5 shRNA


title: MeDIP-Seq_AA-Muscle_AJ

description: meDIP against methylated DNA


title: PolII_Nterm_shControl2_ChIP_Seq

description: Chromatin IP against total Pol II in cells infected and selected with control shRNA

value: empty


title: ChIP_RNAPII_4H8_KCl_b1

city: boston

first: jesse

middle: M

last: gray

address: 77 avenue louis pasteur, NRB 356

institute: Harvard Medical School

description: ChIP

data_processing:
Corona lite read alignment to mm9; discard non-uniquely aligned reads; conversion of uniquely aligned reads (0-3 mismatches) into bigWig (.bw) file
For ChIP-Seq, the .bw file reflects extended 120bp fragments corresponding to each ChIP-Seq read
For RNA-Seq, the .bw files contain information only about the 5' most base of each read; there are separate bigWig files for + and - genomic strands
The .bedgraph files from which the .bw files were derived are also provided.

source_name: 7 DIV E16.5 mouse cortical neurons, before and after membrane depolarization induced by extracellular potassium

growth_protocol: 7 DIV E16.5 mouse cortical neurons grown in B27/NB on PO-coated plastic 15-cm plates

extract_protocol:
Whole Transcriptome sequencing (WT-Seq, RNA-Seq: sequencing of total RNA): WT-Seq was performed according to a protocol/kit now available from Life Technologies, with minor modifications that are included below.  Briefly, 5–10ug of RNA isolated from mouse cortical cultures was depleted of ribosomal RNAs using two rounds of Human/Mouse RiboMinus treatment (Life Technologies) with overnight ethanol precipitations for sample re-concentration.  The removal of ribosomal RNAs was confirmed on a Bioanalyzer Nano Chip (Agilent).  500–1000ng of riboRNA-depleted total RNA was fragmented with 10–18 minutes 37° RNAseIII treatment, and 10 minutes of RNAseIII inactivation at 65°.  Fragmentation was followed by size selection of ~50 to ~150bp fragments using the flashPAGE denaturing PAGE-fractionator (Life Technologies) and ethanol precipitation overnight.  The resulting RNA was directionally ligated, reverse-transcribed, and RNAseH treated. After trial PCR to assess library quality and quantity, 30ul cDNA was run on a native 6% PAGE gel.  The 90–120bp size window (corresponding to 50–80bp RNA insert size) was cut from the gel, shredded, and inserted directly into a 400ul PCR reaction using standard WT-Seq kit components and submitted to 11–15 cycles of PCR.  The PCR product was phenol-chloroform extracted, ethanol precipitated, and resuspended in 20ul WT-Seq gel loading buffer.  The resulting sample was run on a 6% native PAGE gel, and the 150–175bp size range (corresponding to 60–85bp) was cut from the gel, shredded, and extracted overnight in WT-Seq PAGE elution buffer.  The resulting library was filtered through 0.45um spin filters (Life Technologies) to remove gel pieces and ethanol precipitated. We note that WT-Seq can detect neither the 5'-most fragment from transcripts with 5'-modified ends (such as mRNA 5' 7-methyl-guanosine caps) nor the 3'-most fragment from transcripts with 3'-modified ends.  However, for transcripts long enough to produce multiple 50+ bp fragments, WT-Seq should detect the remaining fragments. Mouse cortical neuron WT-Seq data presented in this manuscript are from one specific biological replicate, but each result was confirmed in at least one additional replicate.
Chromatin immunoprecipitation-sequencing (ChIP-Seq): Forty million mouse cortical neurons cultured to in vitro day 7 were used for each ChIP-Seq library construction.  ChIP was performed as described2 using antibodies listed above.  The immuno-precipitated DNA fragments were repaired by the End-It DNA End Repair Kit (Epicentre Biotechnology) according to the manufacturer’s instructions.  The end-repaired ChIP DNA fragments were purified by MinElute Reaction Cleanup Kit (Qiagen) and eluted in 20 ul in EB buffer.  The resulting DNA fragments were ligated with P1 and P2 adaptors for SOLiD genome analyzer (adaptor sequences can be available upon request) for 20 minutes at room temperature using the Quick Ligase Kit (NEB), followed by purification using MinElute Reaction Cleanup Kit (Qiagen).  The purified, adaptor-ligated ChIP DNA fragments were subject to 6% native-PAGE for an in-gel PCR reaction.  A gel slice containing 175–200 bp adaptor-ligated ChIP DNA fragments (corresponding to 125–150bp genomic fragment sizes) was cut and shredded.  PCR Platinum Supermix (100–200 ul, Invitrogen), 50 pmoles of PCR primers (available upon request), 0.5 ul Taq DNA polymerase (NEB), and 0.15 ul Pfu Turbo DNA polymerase (Stratagene) were added into the shredded gel slice.  The adaptor-ligated ChIP DNA fragments were amplified by 15 cycles of in-Gel PCR.  After the PCR reaction, gel pieces were filtered out by 0.45 um filter spin column, and the amplified ChIP-Seq library was purified by MinElute PCR purification kit (Qiagen).  The library was purified by one more round of 6% PAGE.  A gel slice containing 200–250 bp PCR products (110–150bp fragment size) was cut and shredded, and the amplified library was extract out of the gel by passive elution in elution buffer (1.5M ammonium acetate in 1X TE).  Gel pieces were filtered out by filter spin column, and the resulting ChIP-Seq library was purified using the Qiaquick PCR purification kit (Qiagen).

treatment_protocol: 0, 1, 2, or 6 hours of 55mM KCl, with overnight quieting with TTX/APV

tag: protein immunoprecipitated

value: RNAPII

tag: agent

value: KCL

tag: kcl treatment time (hours)

value: cortical neuron

tag: biological rep

tag: technical rep


title: PolII_Nterm_shControl1_ChIP_Seq


title: MeDIP-Seq_RJF-Liver_YG

description: meDIP against methylated DNA

value: red junglefowl


title: HCV(+) HCC Tissue Sample

description: 18-30 nt small RNA

source_name: HCV(+) HCC Tissue

tag: tumor stage

value: HCV-related HCC Tissue

tag: clinical characteristics

value: Primary HCV-related HCC


title: HCV(+) Adjacent Tissue Sample

description: 18-30 nt small RNA

source_name: HCV(+) Adjacent Tissue

tag: tissue

value: liver

value: HCV-related HCC Adjacent Tissue

value: Adjacent liver tissue of primary HCV-related HCC


title: muscle_pre-training_rep7

description: NlaIII digested polyA RNA


title: PolII_Nterm_10058F4_ChIP_Seq

description: Chromatin IP against total Pol II in cells treated with 10058-F4 for 6 hours

value: V6.5 mES cells

value: no

value: RNA Pol II (Rpb1 N-terminus)


title: Spt5_ChIP_Seq

description: Chromatin IP against Spt5


title: PolII_Nterm_DMSO6hr_ChIP_Seq

description: Chromatin IP against total Pol II in cells treated with DMSO for 6 hours

value: DMSO 6 hours


title: muscle_post-training_rep4

description: NlaIII digested polyA RNA

value: post


title: PolII_Nterm_Flavopiridol_ChIP_Seq

description: Chromatin IP against total Pol II in cells treated with Flavopiridol for 1 hour

value: Flavopiridol 1 hour


title: muscle_pre-training_rep5

description: NlaIII digested polyA RNA

value: gluteus medius muscle

value: pre


title: NelfA_ChIP_Seq

description: Chromatin IP against NelfA

value: NelfA


title: PolII_Ser2P_ChIP-Seq

description: Chromatin IP against Ser2 phospho Pol II

value: RNA Pol II (Ser2 phospho CTD)


title: PolII_Nterm_Doxycycline24r_ChIP_Seq

description: Chromatin IP against total Pol II in cells treated with doxycycline for 24 hours

value: ZHBTc4 mES cells

value: Doxycycline 24 hour


title: PolII_Ser5P_ChIP_Seq

description: Chromatin IP against Ser5 phospho Pol II

value: RNA Pol II (Ser5 phospho CTD)


title: PolII_Nterm_DMSO1hr_ChIP_Seq

description: Chromatin IP against total Pol II in cells treated with DMSO for 1 hour

value: DMSO 1 hour


title: PolII_Nterm_shNelfA_ChIP_Seq

description: Chromatin IP against total Pol II in cells infected and selected with NelfA shRNA


title: Ctr9_ChIP_Seq

description: Chromatin IP against Ctr9


title: Co-culture_cDNASeq_11

city: Taichung

first: Li-Ching

last: Hsieh

address: 145 Xingda Rd.

department: Graduate Institute of Genomics and Bioinformatics

country: Taiwan

institute: National Chung Hsing University

description: MAT-a type

data_processing: The sequence reads of each sample were mapped on each reference yeast genome (the BY reference genome was downloaded from the Saccharomyces Genome Database ftp://ftp.yeastgenome.org/yeast/ (Apr. 2008), and the RM reference genome was downloaded from the Saccharomyces cerevisiae RM11-1a Database http://www.broadinstitute.org/annotation/genome/saccharomyces_cerevisiae/Home.html) and all reads mapping with two or fewer mismatches were retained . In addition, 4442 reliable orthologous gene pairs with single nucleotide polymorphism (SNP) sites were identified between the two strains. The sequence reads mapped on the SNPs for each of the gene pairs were counted and then allele-specific expression can be measured between BY and RM.

organism: Saccharomyces cerevisiae

growth_protocol: Overnight subcultures were used to prepare four technical replicates each of BYxRM hybrid (WL201) cultures and BY+RM co-cultures with starting OD600 at 0.1 and harvested overnight subcultures were used to prepare four technical replicates each of hybrid (WL201) cultures and BY+RM co-cultures with starting OD600 at 0.1 and harvested when cell density reached OD600=1.0 at 30'C, 250rpm

extract_protocol: The hybrid and co-culture mRNA was purified on Invitrogen's oligo-dT Dynabeads according to the manufacturer's protocol.  Subsequent reverse transcription was carried out with oligo-dT primers and the Superscript II

treatment_protocol: Each of the replicated subcultures of BYxRM hybrid and BY+RM co-culture harvested at OD600=1.0 was used to extract total RNA by the hot acid phenol method (Kohrer and Domdey 1991)

tag: strains

value: BY4741 and RM11-1a


title: Co-culture_cDNASeq_12

description: MAT-a type


title: Co-culture_cDNASeq_09

description: MAT-a type


title: Blood_male_pooled

city: Mainz

last: Castle

address: Langenbeckstr. 1

department: Genomics

institute: Institute for Translational Oncology and Immunology

data_processing: Reads were aligned to the Hs genome hg18 using alignment program BWA

source_name: DNA dervied from a pool of male blood

extract_protocol: To develop and evaluate a sequencing based platform for assaying CNV, we prepared genomic DNA libraries from a pool of DNA derived from blood from non-diseased males; a pool of DNA derived from blood from non-diseased females; and DNA from the UMC-11 cell line, a lung carcinoid-derived cell line.  DNA was fragmented using DNase.  We did not test whether DNase can shear heterochromatin sequence such as in centromeres; however, we used only sequence reads that align uniquely to the genome and thus would not use sequence reads from regions of low sequence-complexity.  The ends of the fragmented DNA were filled in or cleaved to produce blunt ends.  This blunted DNA was ligated to adapters containing reverse complements on like adapters for suppression PCR as well as priming sites for a set of universal PCR primers and the Illumina sequencing primer.  These "DNA Libraries" were then amplified using standard PCR conditions.  We did not use size-selection after fragmentation, allowing lab-automation of library construction.

value: blood

tag: gender

value: male


title: Blood_female_pooled

source_name: DNA dervied from a pool of female blood

value: female


title: UMC11_CellLine

source_name: DNA dervied from the UMC-11 cell line

tag: cell line


title: Co-culture_cDNASeq_08

description: MAT-a type


title: Co-culture_cDNASeq_10

description: MAT-a type


title: Co-culture_cDNASeq_06

description: MAT-a type


title: Co-culture_cDNASeq_05

description: MAT-a type


title: Co-culture_cDNASeq_07

description: MAT-a type


title: Co-culture_cDNASeq_04

description: MAT-a type


title: Co-culture_cDNASeq_03

description: MAT-a type


title: Hybrid_cDNASeq_12

description: a/alpha diploid

tag: strain


title: Co-culture_cDNASeq_02

description: MAT-a type


title: Co-culture_cDNASeq_01

description: MAT-a type


title: Hybrid_cDNASeq_11

description: a/alpha diploid


title: muscle_post-training_rep6

description: NlaIII digested polyA RNA


title: Hybrid_cDNASeq_10

description: a/alpha diploid


title: Hybrid_cDNASeq_09

description: a/alpha diploid


title: Hybrid_cDNASeq_08

description: a/alpha diploid


title: Hybrid_cDNASeq_07

description: a/alpha diploid


title: Hybrid_cDNASeq_02

description: a/alpha diploid


title: Hybrid_cDNASeq_03

description: a/alpha diploid


title: Hybrid_cDNASeq_04

description: a/alpha diploid


title: Hybrid_cDNASeq_05

description: a/alpha diploid


title: Hybrid_cDNASeq_01

description: a/alpha diploid


title: Hybrid_cDNASeq_06

description: a/alpha diploid


title: muscle_pre-training_rep1

description: NlaIII digested polyA RNA


title: muscle_post-training_rep5

description: NlaIII digested polyA RNA


title: dcr-1(-/-)K39A_2

status: Public on Apr 01 2010

city: Salt Lake City

first: Noah

last: Welker

state: UT

address: 15 N Medical Drive E. Rm. 4800

department: Biochemistry

institute: University of Utah

description: dcr-1(ok247) animals expressing transgene containing Dicer with K39A mutation

data_processing: Alignment: Reads were aligned to the May_2008 release of the C. elegans genome (ce6). Adapter sequences were trimmed and a gapped alignment was performed using the Novoalign software package (http://www.novocraft.com). In order to make these data useful for as many downstream users as possible, the provided novoalign .txt output files were created use a non-stringent posterior probability for alignment. These files should therefore be parsed based on the desired posterior probability before carrying out downstream analysis. The USeq software package contains one such parser and is available at: http://sourceforge.net/projects/useq/.

source_name: whole organism

growth_protocol: worm strains were grown on NGM agar plates at 20 C and mixed stage worms were isolated

extract_protocol: Total RNA was isolated from C. elegans strains using trizol. Total RNA (10 µg) was subjected to 5’ ligation-dependent library preparation (Illumina small RNA sequencing protocol V1.0). small RNAs were selected by gel purification.

tag: stage

value: mixed

tag: genotype/variation


title: dcr-1(-/-)K39A_1

value: dcr-1(ok247) animals expressing transgene containing Dicer with K39A mutation


title: muscle_pre-training_rep4

description: NlaIII digested polyA RNA


title: dcr-1(-/-)WT

description: dcr-1(ok247) animals expressing transgene containing WT Dicer


title: SRS009476.1_CBP_T0.fq

status: Public on Mar 30 2010

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

description: Chromatin IP against CBP

data_processing: Alignment (also enrichment): We ran the Illumina GAPipeline, ran GAPSS (www.lgtc.nl/GAPSS to remove first bps, aligned with Rmap to human NCBI build 36, and construct UCSC wiggle  files) and to make wiggle file size manageable and reduce background base pairs with only a single tag aligning were not reported.

source_name: Human glioblastoma T98G cells

growth_protocol: Human glioblastoma T98G cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), penicillin (100 ug/ml), and streptomycin (100 ug/ml). Then serum starved for 2-3 days (DMEM supplemented with 0.1% FBS).

extract_protocol: Chromatin was prepared  and ChIPs were carried out as previously described, including  fragmentation by sonication (Denissov et al. 2007) (fragment size around 500 bp). For ChIP-seq all samples were prepared with Illumina's DNA sampleprep Kit (FC-102-1001) according to the manufacturer's protocol. Single ends of each sample were then sequenced on a single lane of the Illumina Genome Analyzer for 36 cycles.

treatment_protocol: stimulation with serum (20%) and Tetradecanoyl phorbol acetate (TPA 100 ng/ml; Sigma)

tag: time after stimulation

value: T0 (minutes)

tag: antibody

value: CBP


title: SRS009457.1_CBP_T30-1.fq

description: Chromatin IP against CBP

value: T30 (minutes)


title: Metatranscriptome of M oxyfera enrichment culture

status: Public on Mar 25 2010

city: Bremen

first: Marc

last: Strous

address: Celciusstrasse 1

department: Microbial Fitness Group

institute: MPI Bremen

description: enrichment culture, 80% methylomirabilis oxyfera

data_processing:
reads were mapped to the Methylomirabilis oxyfera complete genome (accession number FP565775); mapping was performed with maq, with standard arguments
average coverage was calculated for each orf

growth_protocol: see Raghoebarsing et al, 2006 Nature 440, p918-921

extract_protocol: Total cell RNA was extracted from enrichment culture “Twente” biomass using the RiboPureTM-Bacteria Kit (Ambion) following manufacturers instructions. An additional DNase I treatment was done (provided within the RiboPureTM-Bacteria Kit (Ambion)). RNA quality was checked by agarose gel electrophoresis and the RNA concentration was measured with the Nanodrop® ND-1000 spectrophotometer (Isogen Life science). First-strand cDNA was generated with RevertAidTM H Minus M-MuLV Reverse Transcriptase (Fermentas Life Sciences), according to the manufacturers protocol. Second-strand cDNA synthesis was performed using RNase H (Fermentas Life Sciences) and DNA polymerse I (Fermentas Life Sciences) according to the manufacturer’s protocol. Purification of the dsDNA for sequencing was performed with the Qiaquick PCR Purification Kit (Qiagen) according to manufacturers instructions and single-end Illumina sequencing performed.

tag: cell type


title: SRS009479.1_p300_T30-1.fq

description: Chromatin IP against p300


title: SRS009477.1_CBP_T30-2.fq

description: Chromatin IP against CBP


title: SRS009478.1_p300_T0.fq

description: Chromatin IP against p300