title: EMSA-Seq of p52p52 round 2 of SELEX

tag: selex round


title: EMSA-Seq of p52p52 round 3 of SELEX

status: Public on May 24 2011

type: SRA

city: Oxford

first: Jiannis

last: Ragoussis

address: Roosevelt Drive

department: Wellcome Trust Centre for Human Genetics

country: United Kingdom

institute: University of Oxford

description: EMSA-Seq selection of ligands that bind a transcription factor

library_source: genomic

data_processing: Raw data in the form of reads (FASTQ format) obtained after deep sequencing has been subsequently processed using both UNIX and perl scripts. Briefly, only sequenced reads that contained matches to at least 4 bp-sequences flanking the degenerate region were considered acceptable for   further processing. In addition, for reads to be acceptable the three regions on the DNA ligand (two flanks and degenerate) must not contain bases annotated as 'N' and furthermore, bases must have a Phred quality score of at least 20. For ligands with 10-mer degnerate regions, a 10-mer sequence was extracted. For ligands with 20-mer degenerate region, 20-mer sequences corresponding to the degenerate segment of DNA ligands were then extracted and 'lower' order 11-mer sequences were derived from these. 11-mer or 10-mer sequence counts obtained from these processed reads have been normalized against the dataset with the lowest number of acceptable reads for that sequence. A binomial distribution model has been used to determine enrichment (z-score) of 11-mer or 10-mer for all datasets.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Purified protein was  mixed with 60  base pair long double-stranded DNA molecules in a 20 ul-reaction, in the presence of 125 ug/ul poly dI-dC buffered in 12 mM HEPES pH7.8, 75 mM KCl, 1 mM EDTA, 4 mM GTP and 12.5 % glycerol.The mixture was incubated at room temperature for 1 h. A DNA: protein of 8:1 molecules was maintained in all the experiments. TF-DNA mixtures were subsequently loaded onto a 6 % DNA Retardation Gel (Invitrogen #EC6365BOX) alongside 'no protein' and 'no DNA' controls, and migrated in Novex 0.5 X TBE Running Buffer (Invitrogen #LC6675) for 1.5 h. Gels were stained using Invitrogen's EMSA-Kit (#E33075) following manufacturer's procedures. Visualization of gels was performed using either a DR46B Transilluminator (Clare Chemical Research, USA) or LAS-4000 system (Fujifilm, Japan). Bands containing TF-DNA complexes were excised from gels, elution of DNA carried out overnight at room temperature using a diffusion buffer (0.5 M ammonium acetate; 10 mM magnesium acetate; 1 mM EDTA pH 8.0; 0.1 % SDS) and the DNA purified using QIAGEN's Polyacrylamide Gel Extraction Protocol (QIAGEN #20021). This was then processed for deep sequencing. The libraries were created using standard 'Paired-End' adaptor-molecules  as described in Illumina's ChIP-protocol and the NEBNext DNA Sample Prep kit (NEB#E6000S). 10 ng of DNA was used for each library-preparation.
For experiments in which several rounds of SELEX were carried out the following procedure was adopted. DNA obtained after the first round of TF-DNA binding followed by EMSA, elution and purification was amplified using a high-fidelity PCR procedure . Briefly, multiple 100 ul reactions each comprised of 0.2 mM dNTPs, 1uM of Primers 1 and 2, together with 2 units of KOD Hot Start Polymerase (Merck #71086-3) buffered in accompanying 1X PCR Buffer were incubated for 15 s at 95°C, then subjected to 25 PCR cycles (5 s 95°C, 5 s 60°C, 5 s 70°C). DNA was pooled, purified using phenol-chloroform and concentrated via ethanol precipitation. This was subsequently used as starting material for TF-DNA binding in the second round of SELEX.

tag: 4nf-kb dimer


title: EMSA-Seq of p52p52 round 1 of SELEX


title: EMSA-Seq of RELARELA

source_name: RELARELA

value: RELARELA


title: 5 DPF PCB-126_embryo_SC4_Cy3

status: Public on Jun 06 2011

type: RNA

city: Miami

first: Marjorie

middle: F.

last: Oleksiak

state: FL

address: 4600 Rickenbacker Causeway

department: Marine Biology and Fisheries

country: USA

institute: University of Miami

hyb_protocol: Labeled aRNA samples (2 pmol dye/ul) were hybridized to slides in 10 ul of hybridization buffer [50% formamide buffer, 5x SSPE, 1% sodium dodecyl sulfate, 0.2 mg/ml bovine serum albumin, 1 mg/ml denatured salmon sperm DNA (Sigma), and 1 mg/ml RNAse free poly(A) RNA (Sigma)] for 44 hours at 42º C.

scan_protocol: Arrays were scanned using  a ScanArray Express 4000 (Perkin Elmer).  Resulting 16 bit Tiff Images were quantified using ImaGene® (Biodiscovery, Inc.) spotfinding software.

data_processing: Log2 measures of gene expression were normalized using a linear mixed model in JMP Genomics 3.2 (SAS, Cary, NC, USA) to remove the effects of dye (fixed effect) and array (random effect) following a joint regional and spatial Lowess transformation in MAANOVA version 0.98.8 for R to account for both intensity and spatial bias.  The model was of the form yij = μ  + Ai + Dj + (AxD)ij + εij where, yij is the signal from the ith array with dye j, μ is the sample mean, Ai and Dj are the overall variation in arrays (arrays 1-80) and dyes (Cy3 and Cy5), (AxD)ij is the array x dye interaction and εij is the stochastic error.  Because we were not interested in differences due to developmental stage, we analyzed residuals from the above model separately by time (e.g., separately for times 5, 10 and 15 dpf).  Thus, residuals from this model were used for gene-by-gene analyses by time of population and treatment effects, using population, treatment and dye as fixed effects, and array as a random effect.  The model was rijn = μ  + Ai + Dj + Pn + Tk + PnxTk + εijn where Pn is the nth population and Tk is the kth treatment (DMSO or PCB-126).  For all mixed model analyses, we used a false discovery rate (FDR) p-value of < 0.01 to control for multiple testing

molecule: total RNA

organism: Fundulus heteroclitus

source_name: 5 DPF PCB-126_embryo_SC4_Cy3

label_protocol: RNA for hybridization was prepared by one round of amplification (aRNA) using the Amino Allyl MessageAmp aRNA Kit (Ambion, Austin, TX, USA) to form copy template RNA by T7 amplification.  Amino-allyl UTP was incorporated into targets during T7 transcription, and resulting amino-allyl aRNA was coupled to Cy3 and Cy5 dyes (GE Healthcare, Piscataway, NJ, USA).

growth_protocol: F. heteroclitus adults were collected from New Bedford Harbor, MA USA and Scorton Creek, MA USA in May and June of 2007. For each site, eggs from 8 females (~1100 total) were fertilized using minced testes from 5 males. After non-fertile eggs were culled, embryos were exposed to vehicle (DMSO; 0.1%) or PCB-126 (50 nM) in filtered seawater (salinity 25 part per thousand, 65 embros per 20 ml in glass petri dish) for 4 hr at 20º C. After exposure, the embryos were washed in filtered seawater and incubated at 20º C under a 14-h light, 10-h dark cycle.  At 5-, 10-, and 15-dpf, embryos were collected as three pools of 20 embryos from each treatment group and flash frozen in liquid nitrogen and stored at -80º C until used for RNA isolation

extract_protocol: Total RNA was isolated from pools of embryos (20 embryos per pool) using STAT-60 (Tel-Test).

tag: population

value: Scorton Creek

tag: tissue

value: Whole embryo

tag: treatment

tag: days post-fertilization


title: LNCaP-H3K4me1-vehicle-siFoxA1-ChIP-Seq

status: Public on May 15 2011

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: Chromatin IP against H3K4me1 in LNCaP cells treated with siRNA against FoxA1 and with vehicle for 1h

data_processing:
Alignment: Reads were truncated to 25 bp (ChIP-Seq) or 32 bp (RNA, GRO-Seq) and aligned to the human hg18 genome (NCBI Build 36) using Bowtie.  Only reads that mapped to a single, unique position were used for downstream analysis.
Data analysis was performed using HOMER, a software suite for high-throughput sequencing analysis and created in part to support this study (http://biowhat.ucsd.edu/homer/).  Each sequencing experiment was normalized to a total of 10 million uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.  UCSC Genome Browser bedGraph files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.  GRO-Seq bedGraph files are strand specific and contain pileups assuming a RNA fragment size of ~75 bp.  Focal peaks (~200 bp) were found for transcription factors/co-factors, and broad, variable lengthed regions of enrichment were found for histone modifications using the default settings in HOMER.  GRO-Seq data was initially pooled across all samples to identify contigous regions of nascent RNA enrichment to identify transcription units without prior knowledge of genes.

source_name: Prostate cancer cell line (LNCaP)

extract_protocol: Chromatin immunoprecipitation was performed using ~10 million cell crosslinked with 1% formaldehyde at room temperature for 15 min. After sonication, the soluble chromatin was incubated with 1-5ug of antibody. Specific immunocomplexes were precipitated with Protein A or G beads (Sigma-Aldrich). Complexes were washed and the DNA was extracted and purified by QIAquick Spin columns (Qiagen). For ChIP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing in the Solexa GAII system according to manufacturer's instruction (Illumina).

treatment_protocol: LNCaP cells were cultured in RPMI 1640 supplemented with 10% FBS.  Control (1027280) and the specific siRNA against  FOXA1 (M-010319) were purchased from Qiagen or Dharmacon. One day prior to transfection, LNCaP cells were seeded in RPMI 1640 medium. Six hours after transfection with Lipofectamine 2000 (Invitrogen), cells were washed twice with PBS and then maintained in hormone-deprived phenol-free RPMI 1640 media.  Cells were then cultured for 96 hours following transfection and then treated with DHT or vehicle for 1 hrs.

tag: cell line

value: LNCaP

tag: sirna transfection

tag: agent

value: vehicle

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog#

tag: transgenes


title: LNCaP-H3K4me1-dht-siCTRL-ChIP-Seq

description: Chromatin IP against H3K4me1 in LNCaP cells treated with control siRNA and with DHT for 1h

value: DHT


title: LNCaP-H3K4me1-vehicle-siCTRL-ChIP-Seq

description: Chromatin IP against H3K4me1 in LNCaP cells treated with control siRNA and with vehicle for 1h


title: LNCaP-FoxA1-dht-siCTRL-ChIP-Seq

description: Chromatin IP against FoxA1 in LNCaP cells treated with control siRNA and with DHT for 1h


title: LNCaP-AR-dht-siFoxA1-ChIP-Seq

description: Chromatin IP against AR in LNCaP cells treated with siRNA against FoxA1 and with DHT for 1h

value: AR

value: Santa Cruz


title: LNCaP-FoxA1-vehicle-siCTRL-ChIP-Seq

description: Chromatin IP against FoxA1 in LNCaP cells treated with control siRNA and with vehicle for 1h


title: LNCaP-AR-vehicle-siFoxA1-ChIP-Seq

description: Chromatin IP against AR in LNCaP cells treated with siRNA against FoxA1 and with vehicle for 1h


title: LNCaP-AR-dht-siCTRL-ChIP-Seq

description: Chromatin IP against AR in LNCaP cells treated with control siRNA and with DHT for 1h


title: LNCaP-H3K4me1-dht-siFoxA1-ChIP-Seq

description: Chromatin IP against H3K4me1 in LNCaP cells treated with siRNA against FoxA1 and with DHT for 1h


title: LNCaP-AR-vehicle-siCTRL-ChIP-Seq

description: Chromatin IP against AR in LNCaP cells treated with control siRNA and with vehicle for 1h


title: 5 DPF PCB-126_embryo_SC4_Cy5

source_name: 5 DPF PCB-126_embryo_SC4_Cy5

treatment_protocol: After non-fertile eggs were culled, embryos were exposed to vehicle (DMSO; 0.1%) or PCB-126 (50 nM) in filtered seawater (salinity 25 part per thousand, 65 embros per 20 ml in glass petri dish) for 4 hr at 20º C. After exposure, the embryos were washed in filtered seawater and incubated at 20º C under a 14-h light, 10-h dark cycle.  At 5-, 10-, and 15-dpf, embryos were collected as three pools of 20 embryos from each treatment group and flash frozen in liquid nitrogen and stored at -80º C until used for RNA isolation


title: 5 dpf DMSO_embryo_SC1_Cy3

source_name: 5 dpf DMSO_embryo_SC1_Cy3

value: vehicle control (DMSO)


title: HEK293T_Input_DNA_rep1

status: Public on May 13 2011

city: Berlin

first: Hans-Jörg

last: Warnatz

address: Ihnestrasse 63-73

department: Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Input DNA

data_processing:
Alignment: Sequencing reads of 26 bases length were aligned to the human genome (UCSC hg18) using Eland from the Illumina Gerald module (v1.27) allowing up to two mismatches without insertions or deletions. The genomic coverage was calculated for 10 bp windows using MACS 1.4 (Zhang et al. Genome Biol. 9(9):R137 (2008)).
Peaks: Redundant reads were removed for identification of candidate peak regions enriched in ChIP reads as compared to control reads using QuEST 2.4 (Valouev et al. Nature Methods 5, 829-834 (2008)) with a ChIP seeding fold enrichment of 30, a ChIP extension fold enrichment of 3 and a ChIP to background fold enrichment of 3. Artifactual peaks with an absolute peak shift (distance between peaks of forward and reverse reads) of less than 20 and a Bonferroni-corrected p-value for read enrichment larger than 10-60 were filtered out to obtain the final list of 84 peak regions significantly enriched in ChIP reads.
Processed data files:
HEK293T.BACH1.U0-2.hg18.reads.bed: aligned reads in BED 12 format
HEK293T.BACH1.U0-2.hg18.wig: genomic coverage in WIG format
HEK293T.BACH1.U0-2.hg18.peaks.bed: peaks in BED 6 format
HEK293T.Input.U0-2.hg18.reads.bed: aligned reads in BED 12 format

source_name: HEK293T cells

growth_protocol: The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2.

extract_protocol: A final concentration of 1% formaldehyde was added to 50 million adherent cells in five 175 cm2 cell culture dishes to crosslink the proteins to the DNA for 10 min at room temperature. After cell lysis, the nuclei were collected and sonicated with a Branson Sonifier W250 to shear the chromatin to a final size of 200-500 bp. The sonicated chromatin was cleared by centrifugation for 10 min with 10,000 g and incubated with 10 µg goat anti-BACH1 antibody (Santa Cruz Biotechnology sc-14700X) coupled to Protein G-magnetic beads (Invitrogen) overnight at 4°C. The control input DNA was chromatin that was reverse crosslinked, digested with RNase A and Proteinase K, phenol-chloroform extracted, and purified by ethanol precipitation with glycogen as carrier. The ChIP DNA was purified in parallel. Sequencing libraries were prepared according to the manufacturer's instructions for the Illumina 1G   Genome Analyzer, with some modifications. End-repair for the ChIP and control DNA was carried out with T4 DNA  polymerase, Klenow DNA polymerase and  T4 polynucleotide kinase (all from New England Biolabs) for 30 min at 20°C. Following DNA purification with the DNA Clean&Concentrator-5 kit (Zymo Research), addition of adenosine overhangs was performed with Klenow 3'-5' exo minus (New England Biolabs) for 30 min at 37 °C. After DNA purification with the DNA Clean&Concentrator-5 kit, sequencing adapters (Genomic Adapter Oligo mix from Illumina) were ligated using Quick T4 DNA Ligase (New England Biolabs) for 15 min at 20°C. Following DNA purification with the DNA Clean&Concentrator-5 kit, the adapter-modified DNA was amplified by PCR with the genomic PCR primers 1.1 and 2.1 (Illumina) using the Phusion Master Mix with HF Buffer (New England Biolabs). The PCR program was Step 1: 98°C for 30 sec, Step 2: 98°C for 10 sec, Step 3: 65°C for 30 sec, Step 4: 72°C for 30 sec, Step 5: goto Step 2 (17 times), Step 6: 72°C for 5 min. After DNA purification with the DNA Clean&Concentrator-5 kit, the DNA libraries were seperated on 2% agarose TAE gels. The 150-250 bp fragments were excised from the gel on a Dark Reader (Claire Chemical Research) and purified with a Qiagen MinElute Gel Extraction Kit (Qiagen). The purified libraries were sequenced on an Illumina 1G Genome Analyzer according to the manufacturer's instructions.

value: embryonic kidney cell line HEK 293T

tag: passages

tag: chip antibody catalog #


title: 15 DPF PCB-126_embryo_NBH33_Cy5

source_name: 15 DPF PCB-126_embryo_NBH33_Cy5

value: New Bedford Harbor


title: HEK293T_ChIP-seq_BACH1_rep1

description: Chromatin IP against BACH1

value: BACH1 (C-20)X

value: Santa Cruz Biotechnology


title: Small RNAs from Picea abies silenced

status: Public on May 10 2011

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

description:
Lateral bud meristem
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

library_source: transcriptomic

data_processing: Small RNA reads were analyzed after removal of 3' adapter (5' -TCGTATGCCGTCTTCTGCTTG) and filtering of 5' adapter (5'-GTTCAGAGTTCTACAGTCCGACGATC) or 3' adapter artefacts.

organism: Picea abies

source_name: Lateral bud meristem

extract_protocol: Total RNA was extracted  with the TriReagent (Molecular Research Center) for leaves and phloem sap and the Plant RNA Purification Reagent (Invitrogen) for flowers. Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000).

value: lateral bud meristem


title: Small RNAs from Picea abies wild-type flowers

description:
Immature female cones
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Immature cones

value: cones

tag: gender

value: female

tag: age

value: immature


title: Small RNAs from Mimulus guttatus leaves

description:
Leaves
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Erythranthe guttata

source_name: Leaves

value: leaves


title: Small RNAs from Picea abies leaves

description:
Needles
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Needles

value: needles


title: Small RNAs from Panicum virgatum drought-treated leaves

description:
Drought-treated leaves (5 days of complete water deprivation)
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Panicum virgatum

value: drought


title: Small RNAs from Marsilea quadrifolia roots

description:
Roots
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Marsilea quadrifolia

source_name: Roots

value: roots


title: Small RNAs from Populus trichocarpa leaves

organism: Populus trichocarpa


title: Small RNAs from Panicum virgatum leaves


title: Small RNAs from Marsilea quadrifolia leaves

description:
Young unfurled leaves
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: young


title: Small RNAs from Hordeum vulgare leaves infected with Blumeria

description:
7-day old  seedlings (1st leaf) inoculated with Blumeria
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Hordeum vulgare

source_name: Infected leaves

tag: infection

value: Blumeria

value: 7 d


title: Small RNAs from Panicum virgatum flowers

description:
Flowers
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Flowers

value: flowers


title: Small RNAs from Mimulus guttatus flowers

description:
Flowers, flower buds
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: flower buds


title: Small RNAs from Populus trichocarpa xylem

description:
Xylem
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Xylem

value: xylem


title: Small RNAs from Nuphar advena flowers

description: Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Nuphar advena

value: Flowers


title: Small RNAs from Cycas rumphii microsporangia

description:
Microsporangia (pollen sacs)
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Cycas rumphii

source_name: Microsporangia

value: Microsporangia


title: Small RNAs from Marsilea quadrifolia drought-treated leaves

description:
Drought-treated young unfurled leaves
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Drought-treated leaves


title: Small RNAs from Gossypium arboreum flowers

description:
Flowers, a mixture of -3 to 0 dpa (days post anthesis)
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Gossypium arboreum

value: -3 to 0 dpa


title: RNA-Seq on DS isolated EPCs

status: Public on May 05 2011

city: Naples

first: Valerio

last: Costa

address: Via P. Castellino 111

institute: Institute of Genetics and Biophysics “A. Buzzati-Traverso”, CNR, Naples, Italy

description:
rRNA-depleted total RNA
Massive-scale transcriptome analysis of cEPCs on total RNA depleted from abundant rRNA species

data_processing: Total reads produced were filtered out accordingly to quality values, and secondly, to the mapping to adapters and to rRNA. RNA-MATE software version 1.1 was used to map the usable reads either to the genome (hg19) and to a custom-designed library of exon-junction sequences containing 2010842 sequences. RNA-MATE mapping to the genome was customized using the following cycles: 50.5.1, 45.4.1, 40.4.1, 35.3.1, 30.3.1, 25.1.1, 23.0.0, 22.0.0, 21.0.0 In the pipeline, all multiple reads (with at most 10 mapping positions) underwent the rescue procedure with default parameters. Bedgraph and BED files were automatically produced after the mapping.

growth_protocol: Total mononuclear cells were isolated by density gradient centrifugation of peripheral blood samples on Histopaque-1077 (Sigma). Cells were washed twice with PBS, plated on culture dishes pre-coated with gelatin and fibronectin and maintained in endothelial growth medium-2 (EGM2; Cell Systems). Cells were cultured at 37°C with 5% CO2 in a humidified atmosphere. After four days, non-adherent cells were removed and adherent cells were collected for RNA isolation.

extract_protocol: Total RNA was isolated from endothelial progenitor cells by standard Trizol protocol. Integrity and quantity of RNA was evaluated by Experion (Biorad) following the manufacturer's instructions. Ribosomal RNA depletion was performed on 10μg of total RNA by using magnetic beads (RiboMinus Eukaryote Kit for RNA-Seq, Invitrogen) according to the manufacturer's protocol. 10 μg of total RNA were incubated at 72°C for 5 min with sequence-specific 5'-biotin labeled oligonucleotide probes. Streptavidin-coated RiboMinus Magnetic Beads were used to capture rRNA-probes to discard. The efficiency of rRNA depletion was evaluated on the Experion. RNA was fragmented with RNase III and, after cleanup with RiboMinus Concentration Module (Invitrogen) according to the manufacturer's protocol, and quantified on Qubit Fluorometer (Invitrogen). The appropriate size distribution of fragmented RNA was evaluated on the Experion. 100 ng of fragmented RNA was hybridized and ligated to double stranded oligonucleotides adapter suited for the 5' SOLiD System sequencing. Reverse transcription was performed using ArrayScript Reverse Transcriptase. Purified cDNA samples were denatured on 6% TBE Urea gel, and size selection (150-250 bp) was performed. PCR amplification on gel slices was then performed using AmpliTaq DNA Polymerase, and yield of purified PCR products was assessed on the Qubit Fluorometer and NanoDrop spectrophotometer (Invitrogen). Size distribution of cDNA libraries was evaluated on the Experion.

treatment_protocol: Isolated cells were not treated with any drug/exonegous chemical

tag: cell type

value: Circulating endothelial progenitor cells

tag: genotype

value: trisomy 21

tag: phenotype

value: Down syndrome


title: Small RNAs from Persea americana leaves

organism: Persea americana

tag: tissue

value: Leaves


title: RNA-Seq on euploid isolated EPCs

value: euploid


title: Small RNAs from Nuphar advena roots

value: Roots


title: input DNA

status: Public on May 03 2011

city: Los Angeles

first: susan

middle: a

last: krum

state: cA

address: 615 Charles E Young Dr. South; OHRC 410

institute: UCLA

description: input DNA

data_processing: Alignment: Sequence reads were obtained and mapped to the human (Feb, 2009) genome using the Illumina Genome Analyzer Pipeline.

source_name: U2OS-ERalpha cells

growth_protocol: U2OS-ERalpha cells were maintained as in Monroe DG et. al. J Cell Biochem 90:315-326

extract_protocol: Immunoprecipitated DNA was prepared for sequencing with the ChIP-Seq DNA Sample Prep Kit from Illumina

treatment_protocol: 24 hours before treatment with 17beta-estradiol, ERalpha expression in U2OS-ERalpha cells was induced by treatment with 100 ng/ml doxycycline. U2OS-Eralpha cells were treated with 10nM 17beta-estradiol for 45 minutes.


title: Small RNAs from Mimulus guttatus roots


title: Small RNAs from Gossypium arboreum fibers

description:
Fibers, from bolls 8-11 dpa
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Fibers

value: Fibers


title: Small RNAs from Persea americana flowers


title: Small RNAs from Cucurbita maxima phloem sap

description:
Phloem sap, from 5-week old plants
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Cucurbita maxima

source_name: Phloem sap

value: phloem

value: 5 wk


title: Small RNAs from Gossypium arboreum leaves

description:
Leaves, newest from top of plant
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: newest, from top of plant


title: G. hirsutum Verticillium inoculated

status: Public on Apr 30 2011

city: Anyang

first: Zujun

last: Yin

state: Henan

address: 38 Huanghe Dadao, Anyang 455000, Henan, China

department: Cotton Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

description: genomic small RNAs

data_processing: For non-coding RNAs identification, clean reads were compared with rRNA, tRNA, snRNA, and snoRNA deposited in NCBI and Rfam database  using the SOAP 2.0 program. Next, sequence tags were searched against the miRNA database, miRBase, in order to identify conserved miRNAs in cotton.

organism: Gossypium hirsutum

source_name: Verticillium dahliaeâinoculated cotton roots

growth_protocol: The sterilized seeds of each variety were put on pasteurized sands for germination. Seedlings were grown in a growth chamber at 25â 28Â°C and watered with Hogland culture liquid every 3 days for 15 days.

extract_protocol: Total RNA was isolated from roots using a modified CTAB method with isopropanol instead of lithium chloride for RNA precipitation. The total RNAs from roots which were harvested at 12 and 24 hours after inoculation were pooled in an equal fraction ratio. Small RNA cloning was performed as described previously by Sunkar and Zhu ( 2004). Briefly, 0.5 M NaCl and 10% PEG8000 were used to precipitate and enrich RNAs with low molecular weight. After that, about 100 Î¼g of low molecular weight RNA were processed by 15% denaturing polyacryl amide gel electrophoresis (PAGE). After gel electrophoresis, the small RNA fragments in the range of 10â32 nt were excised and eluted with 0.4 M NaCl overnight at 4Â°C. The RNA was dephosphorylated using alkaline phosphatase (New England Biolabs, Beijing China) and recovered by ethanol precipitation. The isolated small RNAs were then sequentially ligated to RNA/DNA chimeric oligonucleotide adapters, and were converted to DNA by RT-PCR. Finally, the DNA was sequenced by Solexa sequencing technology (BGI, Beijing China).

treatment_protocol: Seedlings of each cotton variety with two fully expanded leaves were infected with the pathogen by root-dip inoculation into a suspension of fungal conidia for 5 min, and returned to the Hogland liquid medium for discrete post-inoculation time intervals. Control seedlings were inoculated with water.

value: roots

value: Verticillium dahliae-inoculated cotton roots


title: G. hirsutum water-inoculated

description: genomic small RNAs

source_name: waterâinoculated cotton roots

value: water-inoculated cotton roots


title: Small RNAs from Hordeum vulgare leaves

description:
7-day old  seedlings (1st leaf) non treated
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: leaves

value: 7 d


title: Small RNAs from Nuphar advena leaves


title: ERalpha ChIP-Seq

description: Chromatin IP against ERalpha

value: ERalpha


title: Small RNAs from Cycas rumphiis leaves

description:
Leaves, young, female
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: young


title: G. barbadense Verticillium inoculated

description: genomic small RNAs

organism: Gossypium barbadense


title: G. barbadense water-inoculated

description: genomic small RNAs


title: Small RNAs from Hordeum vulgare inflorescence

description:
inflorescence, pre-anthesis, green anthers but not dehisced
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Inflorescence

value: inflorescence


title: Small RNAs from Cycas rumphii ovules

description:
Ovules, female cones
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: ovules

value: ovules


title: Small RNAs from lettuce leaves infected with the fungus Bremia lactucae, strain CA-III

description:
small RNAs
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina. Library code: LSA3.

data_processing: Small RNA reads were analyzed after removal of 3' adapter (5' -TCGTATGCCGTCTTCTGCTTG) and filtering of 5' adapter (5'-GTTCAGAGTTCTACAGTCCGACGATC) or 3' adapter artefacts. Custom-written perl scripts were used for data extraction from Illumina native files, trimming, small RNA size distribution analysis, inter-library comparisons and small RNA mapping to genome(s) or other reference sequences, when applied. SeqMap (Jiang and Wong, 2008)  was also used for alignments allowing multiple mismatches.

organism: Lactuca sativa

source_name: Fungus-infected leaves

extract_protocol:
Total RNA was extracted with TriReagentÂ® (Molecular Research Center). Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000).
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: Leaves infected with the fungus Bremia lactucae, strain CA-III and harvested 7 days after inoculation


title: Small RNAs from Persea americana ripening fruit

value: Ripening fruit


title: Small RNAs from Cucurbita maxima leaves

description:
Leaves, 5-week old
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.


title: Small RNAs from lettuce leaves

description:
small RNAs
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina. Library code: LSA1.

value: Leaves


title: N2 1st run

status: Public on Apr 16 2011

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description:
genomic DNA
genomic DNA from N2 worms; from 1st Solexa sequencing run

data_processing: We generated a database of all potential DAM tags with the structure 5'-(N)16GATC-3' from C. elegans genome version WS170. There are 269,049 DAM (GATC) sites per haploid genome in C. elegans. Because DALEC captures two tags (in principle) per GATC site, there are a total of 538,098 potential tags (or half sites) per haploid genome. To reduce computation time during alignment of Solexa reads to the genome, each tag was represented by a 16 nucleotide sequence that did not include the 3' GATC.    We excluded DAM tags that occurred more than once in the genome or that mapped to vector or ribosomal sequences. We also excluded tags belonging to two adjacent GATC sites that lie within 20 bp from each other. Under situations where two fully methylated adjacent GATC sites mapped within 20 bp of each other, one site will always be captured at the expense of the other, resulting in undercount of DAM accessibility at such regions. When the distances are slightly above 20 bp, it is conceivable that there may be inherent bias in Mme I sequence preference that leads to the preferential capture of one site over the other, again resulting in undercount. To avoid both situations from skewing our analysis, we excluded such "proximal tags" using the criteria described in Additional File 2, Figure S4). After filtering out proximal, repetitive, and vector/ribosome-derived sequences, we were left with 370,152 in silico tags (per haploid genome) that we could use to align Solexa reads to the genome. Described in Sha et al. (BMC Genomics 2010, 11:465)

organism: Caenorhabditis elegans

source_name: mixed stage

growth_protocol: standard C. elegans growth conditions at 23C

extract_protocol: To obtain a genome-level view of chromatin susceptibility to DAM methylation, we developed a method that captures sequences flanking methylated GATC sites for high throughput sequencing: described in Sha et al. (BMC Genomics 2010, 11:465)

tag: developmental stage

value: mixed stage

tag: genetic background

tag: strain

value: wild type

value: whole organism


title: gut 2nd run

description:
DAM-methylated genomic DNA
genomic DNA from synchronized adult worms expressing DAM driven by vit-2 promoter; from 2nd Solexa sequencing run

source_name: synchronized young/gravid adults

value: synchronized young/gravid adults

value: gut

tag: promoter for dam


title: gut 1st run

description:
DAM-methylated genomic DNA
genomic DNA from synchronized adult worms expressing DAM driven by vit-2 promoter; from 1st Solexa sequencing run


title: N2 2nd run

description:
genomic DNA
genomic DNA from N2 worms; from 2nd Solexa sequencing run


title: hypodermis 2nd run

description:
DAM-methylated genomic DNA
genomic DNA from synchronized young adult worms expressing DAM driven by rol-6 promoter; from 2nd Solexa sequencing run

source_name: synchronized L4

value: synchronized L4

value: hypodermis


title: hypodermis 1st run

description:
DAM-methylated genomic DNA
genomic DNA from synchronized young adult worms expressing DAM driven by rol-6 promoter; from 1st Solexa sequencing run


title: bodywall muscle 2nd run

description:
DAM-methylated genomic DNA
genomic DNA from synchronized L4 worms expressing DAM driven by myo-3 promoter; from 2nd Solexa sequencing run

source_name: synchronized L1/L2

value: synchronized L1/L2

value: bodywall muscle


title: Small RNAs from Populus trichocarpa mechanically-treated xylem

description:
Mechanically treated xylem
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Mechanically treated xylem

value: xylem

tag: treatment

value: mechnically treated


title: RBC 10d

status: Public on Apr 15 2011

city: Barcelona

first: David

last: Martin

address: C/ Dr. Aiguader, 88

department: Bioinformatics and Genomics

country: Spain

institute: CRG

description: Chromatin IP against CTCF

data_processing:
Alignment: Sequence reads were obtained and mapped to the chicken (Galgal3) genome using Eland (illumina pipeline). All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with SISSRs (http://sissrs.rajajothi.com/).

organism: Gallus gallus

source_name: Red blood cells

growth_protocol: We cultured PBMCs in RPMI supplemented with 2mM Glutamine, 50 Î¼M Ã-Mercaptoethanol and 10% inactivated fetal bovine serum. Cultured cells were stimulated with 50 ng/ml of PMA and 10 ng/ml Io for 4h at 37oC and 5% CO2.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. 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: Blood cells were subjected to density gradient centrifugation by Histopaque-1077 (Sigma-Aldrich) to obtain a homogeneous population of mononuclear cells (PBMCs)

value: red blood cell

tag: antibody

value: CTCF

tag: antibody manufacturer

value: Millipore

tag: antibody catalog #

value: 10 day old


title: Small RNAs from lettuce flowers

description:
small RNAs
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina. Library code: LSA2.

source_name: Flowers

value: Flowers


title: RBC 5d

description: Chromatin IP against CTCF

value: 5 day old


title: MEF cells

description: Chromatin IP against CTCF

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 genome using GEM (http://gemlibrary.sourceforge.net). All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with SISSRs (http://sissrs.rajajothi.com/).

organism: Mus musculus

source_name: MEF cells

growth_protocol: All the cells used in this study were grown in DMEM medium supplemented with 10% fetal calf serum, at 37âÂ°C, and under standard conditions

value: MEF


title: ES cells

description: Chromatin IP against CTCF

source_name: ES cells

value: ES

value: Bl3.10 and C57BL


title: HIF-1 beta ChIP-Seq

status: Public on Apr 05 2011

middle: R

last: Mole

department: The Henry Wellcome Building for Molecular Physiology

description: Chromatin IP against HIF-1 beta

data_processing: The files are the sorted.txt files from the Illumina pipeline v1.6 mapped against human genome (March, 2006/hg18)

organism: Homo sapiens

source_name: HIF-1 beta ChIP-Seq

growth_protocol: MCF-7 breast cancer cells were grown in Dulbeccoâs modified Eagleâs Medium, 2 mM L-glutamine and 10% fetal bovine serum (Sigma)

extract_protocol: Libraries were prepared from immunoprecipitated chromatin using the Illumina ChIP-Seq kit

treatment_protocol: Sub confluent cell cultures were exposed to 2 mM dimethyloxalylglycine (DMOG) or 0.5% hypoxia for 16 hours prior to harvest

tag: cell line

value: breast cancer cells

tag: chip antibody

value: HIF-1 beta


title: pre-immune ChIP-Seq control for HIF-1 beta

description: Chromatin IP pre-immune serum  control for HIF-1 beta

value: pre-immune serum


title: bodywall muscle 1st run

description:
DAM-methylated genomic DNA
genomic DNA from synchronized L4 worms expressing DAM driven by myo-3 promoter; from 1st Solexa sequencing run


title: HIF-2 alpha ChIP-Seq

description: Chromatin IP against HIF-2 alpha

data_processing: The files are the sorted.txt files from the Illumina pipeline v1.3.4 mapped against human genome (March, 2006/hg18)

source_name: HIF-2 alpha ChIP-Seq

value: HIF-2 alpha


title: pre-immune ChIP-Seq control for HIF-1/HIF-2 alpha

description: Chromatin IP pre-immune serum control for HIF-1/HIF-2 alpha


title: HIF-1 alpha ChIP-Seq

description: Chromatin IP against HIF-1 alpha

source_name: HIF-1 alpha ChIP-Seq

value: HIF-1 alpha


title: Small RNAs from Ginkgo biloba male cones

description:
Male cone (microsporophyll)
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Ginkgo biloba

source_name: Male cones

value: microsporophyll

tag: gender

value: male


title: RCOR3 ChIP-Seq

status: Public on Apr 01 2011

city: Singapore

first: hongbing

last: yu

address: 60 biopolis street, #02-01, genome

department: stem cell and development

country: Singapore

institute: genome institute of singapore

description: Chromatin IP against RCOR3

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (Build 36, Feb, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (SCISSRS) algorithm

growth_protocol: E14 cell were maintained under normal condition for mouse ES cell culture.

extract_protocol: Lysates were clarified from sonicated nuclei and REST and its cofactors DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: passages

tag: transgene

value: V5 tagged RCOR3

tag: chip antibody manufacturer

value: Invitrogen

tag: chip antibody catalog #


title: RCOR2 ChIP-Seq

description: Chromatin IP against RCOR2

value: V5 tagged RCOR2


title: Small RNAs from Ginkgo biloba female cones

description:
Female cone (macrosporophyll)
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Female cones

value: macrosporophyll

value: female


title: SIN3B ChIP-Seq

description: Chromatin IP against SIN3B

value: VG tagged SIN3B


title: Mycorrhizae_rep2

status: Public on Mar 25 2011

city: Argonne National Laboratory

first: Peter

last: Larsen

address: 970 S. Cass Ave

institute: Argonne National Labs

description: Illumia deep RNA seqeuncing

data_processing:
Bowtie was used to align short seq-reads to gene models (Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25.)
Output from 'Bowtie' aligner was used as input for 'BowStrap' (http://www.bio.anl.gov/molecular_and_systems_biology/BowStrap.html) for gene expression calculation.
Gene expression determined by 'BowStrap'.  Data normalized by Global Average.
Gene expression expressed as Reads aligned to gene model Per Kb of gene model length per Million deep RNA-seq reads (RPKM), with Standard Deviations for 10,000 random re-samplings.
JGI (http://www.jgi.doe.gov/) Best Gene Model files: Poplar 'transcripts.Poptr1_1.JamboreeModels.fasta' and Laccaria 'BestModelsv1.na.fasta'.

organism:
Populus tremuloides
Laccaria bicolor

source_name: Mycorrhizal roots after 6 weeks

growth_protocol: Mycorrhizal aspen and L. bicolor were grown in biological duplicates.  L. bicolor (Maire) Orton (strain S238N) culture was maintained on Modified Melin Norkan's (MMN) media at 20 deg C. Populus tremuloides seeds were surface sterilized and germinated on McCown's woody plant media (WPM) in Petri dishes as described. One week old germinated seedlings were transferred to Magenta vessels (Sigma, St. Louis, MO) containing the interaction medium (WPM with 1.5% of sucrose). The seedlings were grown under 16 hr light and 8 hr dark cycles at 24 deg C for 4-5 weeks until fine lateral roots were developed.  L. bicolor mycelial plugs were transferred to Magenta vessels with aspen plants for ectomycorrhizae formation. Mycorrhizal roots were visualized approximately after 6 weeks.

extract_protocol:
CTAB method (Cseke LJ: Handbook of molecular and cellular methods in biology and medicine. 2nd edn. Boca Raton: CRC Press; 2004) and RNA quality was assessed by gel electrophoresis prior to library preparation.  Total RNA was treated with RQ-DNase (Promega, Madison, WI) to remove any traces of DNA.
Deep RNA sequencing:  Ten ug of total RNA from each sample was hybridized to Sera-mag oligo (dT) beads (Thermo Scientific) for mRNA purification. Purified mRNA was fragmented by addition of 5X fragmentation buffer (Illumina, Hayward, CA) and was heated for 5 min at 94 C in a thermocycler. First strand cDNA was synthesized using random primers to eliminate the general bias towards 3' end of the transcript. Second strand cDNA synthesis was done by adding GEX second strand buffer (Illumina, Hayward, CA), dNTPs, RNaseH and DNA Polymerase I followed by incubation for 2.5 h at 16 C.  Second strand cDNA was further subjected to end repair, A-tailing, and adapter ligation in accordance with the manufacturer supplied protocols. Purified cDNA templates were enriched by PCR amplification with Phusion DNA polymerase (Illumina, Hayward, CA) and the samples were cleaned using QIAquick PCR purification columns and eluted in 30 ul EB buffer as per manufacturerâs instructions (QIAGEN, CA). Purified cDNA libraries were quantified using Nanodrop spectrophotometer and loaded onto Illumina flow cells with one of the flow cells reserved for a recurrent internal standard as control for sequencing efficiency.

treatment_protocol: Mycorrhizal roots were collected, snap frozen in liquid nitrogen and stored at -80 deg C

tag: growth media

value: WPM


title: REST ChIP-Seq

description: Chromatin IP against REST

value: REST

value: Santa Cruz


title: control

status: Public on Apr 04 2011

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: ChIP-seq control samples were prepared from ES cells with the empty vector and Cdx2 inducible cells were cultured for 48-60 hours with Dox to repress transgene induction.

data_processing: the muti-alignment file is from Eland pipeline

source_name: control

growth_protocol: ES cells grown without feeders on gelatin coated dish with an empty vector, Heat Inactivated (GIBCO); LIF (ESGRO) 1000 U/ml; Doxycyclin 0.2 ug/ml; uvate (GIBCO); 0.1 mM Non Essential Amino Acids (GIBCO), 2 mM glutamate (GIBCO), 0.1 mM beta-mercapto ethanol (GIBCO), and 1X penicillin/streptomycin (GIBCO). Cells were incubated at 37C; 5% CO2. Medium was changed daily.

extract_protocol: Chromatin from 100000000 cells was incubated at 4C over night. Purified DNA was used for sequencing preparation according to manufacturer's manuals.

tag: cell type


title: Small RNAs from Nicotiana tabacum leaves

description:
Leaves, fully grown, middle or upper leaves (50 days)
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Nicotiana tabacum

source_name: Leaves

tag: tissue

value: leaves

tag: age


title: RCOR1 ChIP-Seq

description: Chromatin IP against RCOR1

value: V5 tagged RCOR1


title: HL60-tRET polyA Random - CTS4 12-4-2009 fc1.ch5 RPM4_12_4_FC1CH5

status: Public on Mar 24 2011

city: Cambridge

first: John

middle: F

last: Thompson

state: MA

address: One Kendall Square

department: Genomic Sciences

institute: Helicos BioSciences

description: Reads normalized per million

data_processing: Reads were aligned to UCSC gene tracks using IndexDPgenomic (hg18) with a cutoff score of 4.3.  Reads with multiple equivalent alignments were fractionally distributed among the various genes.  Reads aligning to ribosomal and mitochondrial transcripts were discarded.  When channels were added together, it was done prior to any normalization.  Aligned reads were normalized to reads per million for comparison.  No length correction was performed.

growth_protocol: Liver (Clontech), brain (Clontech), and K562 (Ambion) RNAs were purchased from commercial sources.  HL60 RNA was prepared by MIR Preclinical Services from cells grown under standard conditions or treated with 0.1% DMSO and 0.1uM t-retenoic acid for 5 days.

extract_protocol: Before further fractionation, total RNA was treated with DNase I as follows: 50Î¼g of total RNA was mixed with 10Î¼l of 10X DNase I buffer (Roche), 2Î¼l of RNaseOut (Invitrogen) and 8Î¼l of recombinant DNase I (10U/Î¼l, Roche) and incubated for 45 minutes at 37Â°C. The RNA was then purified using the RNeasy MinElute kit (Invitrogen).   The DNase I-treated total RNA was either unfractionated (total RNA) or fractionated using one of the following methods: 1. Depleted of ribosomal RNA (rRNA) using the RiboMinus kit (Invitrogen) 2. polyA fraction was selected using a magnetic bead-based purification kit (Dynabeads mRNA purification kit, Invitrogen) or, 3. polyA fraction was selected using the oligo-dT cellulose method (Micro Poly(A)Purist Kit, Ambion).  Some RNA samples were fragmented by heating at 95C for 10 min prior to cDNA synthesis.  100-400 ng of DNase I -treated RNA, except where noted, was mixed with the following reagents from the SuperScript III kit (Invitrogen). First 10Î¼l of 50ng/Î¼l Random Hexamers and 2Î¼l of 10mM dNTPs were added in the total volume of 25Î¼l. When employing selected primers, the same conditions were used.  The mixture was then placed in a thermocycler and heat denatured at 65Â°C for 5 min followed by rapid cooling on ice. Next, 5Î¼l of 10X cDNA synthesis buffer, 5Î¼l of 0.1M DTT and 10Î¼l of 25mM MgCl2 were added. The samples were returned to the thermocycler and allowed to incubate at 15Â°C for 20 min. Then, 2.5Î¼l of RNaseOut and 2.5Î¼l of SuperScript III reverse transcriptase were added and the samples were incubated at 25Â°C for 10 min, 42Â°C for 40 min, 55Â°C for 50 min and 70Â°C for 10 min.  After reverse transcription, RNA was removed by adding 1Î¼l of RNaseH (Invitrogen) and 1Î¼l of RNase If (New England BioLabs) to each sample and incubating at 37Â°C for 30 min. The cDNA was then purified by two rounds of purification over Performa columns (EdgeBio) and quantified using a NanoDrop spectrophotometer.  Next, a 3â poly-A tail was added to the cDNA samples. cDNA (100ng) was mixed with a control oligo to monitor tail length and water in a total volume of 33.5Î¼l. The mixture was denatured at 95Â°C for 5 min followed by rapid cooling on ice.  5Î¼l of 2.5mM CoCl2, 5Î¼l of 10X terminal transferase (TdT) buffer (New England BioLabs), 5 Âµl of 50ÂµM dATP and 1.5Î¼l of TdT (20U/Î¼l, New England BioLabs) was then added and the samples were incubated at 42Â°C for 1 hr, and at 70Â°C for 10 min.     The 3â ends of the polyA-tailed cDNA were then blocked with biotin-ddATP.  The sample was denatured at 95Â°C for 5 min followed by rapid cooling on ice.  0.3Âµl of 1mM biotin-ddATP (Perkin Elmer) and 1.5Âµl of TdT were added followed by incubation at 37Â°C for 45 min and 70Â°C for 10 min.

tag: rna type

value: polyA bead selected

tag: cdna primer

value: Random

tag: comment

value: tRET


title: HL60-control Total-DGE oligo-dT - P11 12-11-2009 fc2.ch18 RPM11_12_11_FC2CH18

description: Reads normalized per million

value: Total/DGE

value: oligo dT

value: No tRET

tag: treatment


title: Mycorrhizae_rep1

description: Illumia deep RNA seqeuncing


title: SIN3A ChIP-Seq

description: Chromatin IP against SIN3A


title: HL60-tRET Total Random - P2 1-12-2010 fc1.ch07 RPM2_1_12_FC1CH7

description: Reads normalized per million

value: Total


title: HL60-tRET Total Random - P2 1-12-2010 fc1.ch08 RPM2_1_12_FC1CH8

description: Reads normalized per million


title: HL60-tRET Total Random - P11 12-11-2009 fc2.ch14 RPM11_12_11_FC2CH14

description: Reads normalized per million


title: Liver Frag-polyA Random Rep3Sci2 CTS4 9-25-2009 fc1.ch20 RPM4_9_25fc1ch20

description: Reads normalized per million

source_name: Liver

value: polyA bead selected then fragmented

value: Rep3 Sci2

value: Liver

tag: replicate


title: Small RNAs from Musa acuminata leaves

description:
Leaves
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Musa acuminata


title: Liver Frag-polyA Random Rep3Sci2 P9 10-16-2009 fc1.ch20 RPM9_10_16fc1ch20

description: Reads normalized per million


title: Small RNAs from Musa acuminata immature fruit

description:
Immature fruit, 2 weeks after flowering
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Roots

value: fruit

value: 2 weeks after flowering


title: Liver Frag-polyA Random Rep1Sci2 CTS4 9-25-2009 fc1.ch18 RPM4_9_25fc1ch18

description: Reads normalized per million

value: Rep1 Sci2


title: HL60-control Total Selected - CTS4 9-25-2009 fc1.ch10 RPM4_9_25fc1ch10

description: Reads normalized per million

value: Selected


title: HL60-control Total Selected - CTS4 9-25-2009 fc1.ch11 RPM4_9_25fc1ch11

description: Reads normalized per million


title: Brain Total Random - CTS4 9-16-2009 fc2.ch22 RPM4_9_16fc2ch22

description: Reads normalized per million

source_name: Brain

value: Brain


title: Small RNAs from Musa acuminata male flowers

description:
Flowers, male
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: flowers

value: male


title: HL60-control Total Selected - CTS4 9-25-2009 fc1.ch9 RPM4_9_25fc1ch9

description: Reads normalized per million


title: Brain Total-DGE oligo-dT - CTS4 12-4-2009 fc1.ch2 RPM4_12_4fc1ch2

description: Reads normalized per million


title: HL60-control Total Random - P2 1-12-2010 fc1.ch10 RPM2_1_12fc1ch10

description: Reads normalized per million


title: HL60-control polyA Random - CTS4 12-4-2009 fc1.ch4 RPM4_12_4_FC1CH4

description: Reads normalized per million

value: polyA bead selected


title: Small RNAs from Citrus sinensis fruits

data_processing: Small RNA reads were analyzed after removal of 3' adapter (5' -TCGTATGCCGTCTTCTGCTTG) and filtering of 5' adapter (5'-GTTCAGAGTTCTACAGTCCGACGATC) or 3' adapter artifacts.

organism: Citrus sinensis

source_name: Fruits

extract_protocol: Total RNA was extracted with the TriReagent (Molecular Research Center) for leaves and flowers and the Guanidinium-free for fruits. Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000). Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

tag: developmental stage

value: mature


title: Small RNAs from Citrus sinensis flowers

value: fully open


title: Small RNAs from Citrus sinensis leaves

value: leaves

value: young fully expanded


title: Brain RiboMinus Random Rep2 P5 8-21-2009 fc1.ch19 RPM5_8_21fc1ch19

description: Reads normalized per million

value: RiboMinus

value: Random

tag: cell line


title: HL60-control Total Random - P2 1-12-2010 fc1.ch9 RPM2_1_12fc1ch9

description: Reads normalized per million

value: Total

value: No tRET


title: HL60-control Total Random - P11 12-11-2009 fc2.ch15 RPM11_12_11fc2ch15

description: Reads normalized per million


title: Small RNAs from Cucurbita maxima flowers

description:
Flowers, 5-week old
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: 5 wk


title: Small RNAs from Nicotiana tabacum male flowers

description:
Flowers, pre-anthesis; petals are fully elongated but have not opened to reveal anthers/carpel (72 days)
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.


title: Liver Frag-polyA Random Rep2Sci2 P9 10-16-2009 fc1.ch19 RPM9_10_16fc1ch19

description: Reads normalized per million

value: polyA bead selected then fragmented

value: Rep2 Sci2

value: Liver


title: Small RNAs from Aristolochia fimbriata leaves

organism: Aristolochia fimbriata

extract_protocol: Total RNA was extracted  with the TriReagent (Molecular Research Center). Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000). Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: mixture, with a bias towards those from early, actively differentiating cells


title: Brain polyA Random Rep2 CTS4 9-16-2009 fc2.ch13 RPM4_9_16fc2ch13

description: Reads normalized per million

value: Brain


title: Brain polyA Random Rep1 P5 8-21-2009 fc1.ch12 RPM5_8_21fc1ch12

description: Reads normalized per million


title: Brain polyA Random Rep2 P5 8-21-2009 fc1.ch13 RPM5_8_21fc1ch13

description: Reads normalized per million


title: Brain RiboMinus Random Rep1 CTS4 9-16-2009 fc2.ch18 RPM4_9_16fc2ch18

description: Reads normalized per million


title: Brain polyA Random Rep1 CTS4 9-16-2009 fc2.ch12 RPM4_9_16fc2ch12

description: Reads normalized per million


title: Liver RiboMinus Random Rep2Sci2 P2 11-4-2009 fc1.ch15 RPM2_11_04_fc1ch15

description: Reads normalized per million


title: Liver Frag-polyA Random Rep2Sci2 CTS4 9-25-2009 fc1.ch19 RPM4_9_25FC1CH19

description: Reads normalized per million


title: Liver Total Random - P5 8-21-2009 fc1.ch21 RPM5_8_21fc1ch21

description: Reads normalized per million


title: Liver polyA-cell2 Random - CTS4 10-30-2009 fc1.ch1 RPM4_10_30fc1ch1

description: Reads normalized per million

value: polyA 2x cellulose selected


title: Liver RiboMinus Random Rep1Sci2 P2 11-4-2009 fc1.ch14 RPM2_11_04_fc1ch14

description: Reads normalized per million

value: Rep1 Sci2


title: Liver Total Random - CTS4 9-16-2009 fc2.ch21 RPM4_9_16fc2ch21

description: Reads normalized per million


title: Small RNAs from Aristolochia fimbriata flower buds

source_name: Flower buds

value: flower buds, close to anthesis


title: Liver polyA-cell2 Random - P2 11-4-2009 fc1.ch1 RPM2_11_4fc1ch1

description: Reads normalized per million


title: Liver Total Random - CTS4 9-16-2009 fc2.ch24 RPM4_9_16fc2ch24

description: Reads normalized per million


title: Brain RiboMinus Random Rep1 P5 8-21-2009 fc1.ch18 RPM5_8_21fc1ch18

description: Reads normalized per million


title: Liver polyA-cell1 Random - CTS4 10-30-2009 fc1.ch2 RPM4_10_30fc1ch2

description: Reads normalized per million

value: polyA 1x cellulose selected


title: Small RNAs from Capsicum annuum fruit

organism: Capsicum annuum

extract_protocol: Total RNA was extracted  with the TriReagent (Molecular Research Center) for leaves and flowers and the Plant RNA Purification Reagent (Invitrogen) for fruit. Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000). Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: fruit, exterior tissue (endocarp, exocarp, mesocarp), inner septa and seeds removed


title: Liver RiboMinus Random Rep2Sci1 P5 8-21-2009 fc1.ch17 RPM5_8_21fc17

description: Reads normalized per million

value: Rep2 Sci1


title: Liver polyA-cell1 Random - P2 11-4-2009 fc1.ch2 RPM2_11_4fc1ch2

description: Reads normalized per million


title: Liver RiboMinus Random Rep2Sci1 CTS4 9-16-2009 fc2.ch17 RPM4_9_16fc2ch17

description: Reads normalized per million


title: Small RNAs from Ginkgo biloba leaves

description:
Leaves, female
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: leaves

value: female


title: Liver RiboMinus Random Rep1Sci1 CTS4 9-16-2009 fc2.ch16 RPM4_9_16fc2ch16

description: Reads normalized per million

value: RiboMinus

value: Random

value: Rep1 Sci1


title: K562 Total-DGE oligo-dT - CTS4 12-4-2009 fc1.ch3 RPM4_12_4fc1ch3

description: Reads normalized per million

value: Total/DGE

value: oligo dT


title: Liver Total-DGE oligo-dT - CTS4 12-4-2009 fc1.ch1 RPM4_12_4fc1ch1

description: Reads normalized per million


title: K562 Total-DGE oligo-dT - P9 11-20-2009 fc2.ch4 RPM9_11_20fc2ch4

description: Reads normalized per million


title: HL60-tRET Total-DGE oligo-dT - P11 12-11-2009 fc2.ch17 RPM11_12_11_FC2CH17

description: Reads normalized per million

value: tRET


title: Liver Total-DGE oligo-dT - P9 11-20-2009 fc2.ch1 RPM9_11_20fc2ch1

description: Reads normalized per million

value: Liver


title: Liver RiboMinus Random Rep1Sci1 P5 8-21-2009 fc1.ch16 RPM5_8_21fc1ch16

description: Reads normalized per million


title: Liver Total-DGE oligo-dT - P9 11-20-2009 fc1.ch25 RPM9_11_20fc1ch25

description: Reads normalized per million


title: Liver polyA Random Rep3Sci2 CTS4 9-25-2009 fc1.ch14 RPM4_9_25fc1ch14

description: Reads normalized per million

value: polyA bead selected

value: Rep3 Sci2


title: Liver polyA Random Rep1Sci2 P9 10-16-2009 fc1.ch12 RPM9_10_16fc1ch12

description: Reads normalized per million


title: Liver polyA Random Rep2Sci1 P5 8-21-2009 fc1.ch11 RPM5_8_21fc1ch11

description: Reads normalized per million


title: Liver polyA Random Rep2Sci1 CTS4 9-16-2009 fc2.ch11 RPM4_9_16fc2ch11

description: Reads normalized per million


title: Liver polyA Random Rep2Sci2 CTS4 9-25-2009 fc1.ch13 RPM4_9_25fc1ch13

description: Reads normalized per million

value: Rep2 Sci2


title: Liver polyA Random Rep1Sci1 CTS4 9-16-2009 fc2.ch10 RPM4_9_16fc2ch10

description: Reads normalized per million


title: Liver polyA Random Rep1Sci1 P5 8-21-2009 fc1.ch10 RPM5_8_21fc1ch10

description: Reads normalized per million


title: Liver polyA Random Rep3Sci2 P9 10-16-2009 fc1.ch14 RPM9_10_16fc1ch14

description: Reads normalized per million


title: Liver polyA Random Rep2Sci2 P9 10-16-2009 fc1.ch13 RPM9_10_16fc1ch13

description: Reads normalized per million


title: Liver Frag-polyA Random Rep1Sci2 P9 10-16-2009 fc1.ch18 RPM9_10_16fc1ch18

description: Reads normalized per million

value: polyA bead selected then fragmented

value: Rep1 Sci2


title: K562 Total Random - CTS4 9-16-2009 fc2.ch20 RPM4_9_16fc2ch20

description: Reads normalized per million

value: Total


title: Liver polyA Random Rep1Sci2 CTS4 9-25-2009 fc1.ch12 RPM4_9_25fc1ch12

description: Reads normalized per million


title: K562 RiboMinus Random Rep2 P5 8-21-2009 fc1.ch15 RPM5_8_21fc1ch15

description: Reads normalized per million


title: K562 RiboMinus Random Rep1 CTS4 9-16-2009 fc2.ch14 RPM4_9_16fc2ch14

description: Reads normalized per million


title: K562 RiboMinus Random Rep2 CTS4 9-16-2009 fc2.ch15 RPM4_9_16fc2ch15

description: Reads normalized per million


title: K562 polyA Random Rep2 CTS4 9-16-2009 fc2.ch9 RPM4_9_16fc2ch9

description: Reads normalized per million


title: K562 polyA Random Rep2 P5 8-21-2009 fc1.ch9 RPM5_8_21fc1ch9

description: Reads normalized per million


title: K562 polyA Random Rep1 P5 8-21-2009 fc1.ch8 RPM5_8_21fc1ch8

description: Reads normalized per million


title: HL60-control Total-DGE oligo-dT - P11 12-11-2009 fc2.ch18 Reads11_12_11_FC2CH18

description: Reads counts with no normalization

value: No tRET


title: Small RNAs from Nicotiana tabacum pods

description:
Pods, green, prior to desiccation (72 days)
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: pods


title: K562 polyA Random Rep1 CTS4 9-16-2009 fc2.ch8 RPM4_9_16fc2ch8

description: Reads normalized per million


title: K562 Total Random - P5 8-21-2009 fc1.ch20 RPM5_8_21fc1ch20

description: Reads normalized per million


title: K562 Total Random - CTS4 9-16-2009 fc2.ch23 RPM4_9_16fc2ch23

description: Reads normalized per million


title: HL60-tRET polyA Random - CTS4 12-4-2009 fc1.ch5 Reads4_12_4_FC1CH5

description: Reads counts with no normalization


title: HL60-tRET Total-DGE oligo-dT - P11 12-11-2009 fc2.ch17 Reads11_12_11_FC2CH17

description: Reads counts with no normalization


title: HL60-tRET Total Random - P11 12-11-2009 fc2.ch14 Reads11_12_11_FC2CH14

description: Reads counts with no normalization


title: HL60-control polyA Random - CTS4 12-4-2009 fc1.ch4 Reads4_12_4_FC1CH4

description: Reads counts with no normalization


title: Liver Frag-polyA Random Rep3Sci2 P9 10-16-2009 fc1.ch20 Reads9_10_16fc1ch20

description: Reads counts with no normalization


title: HL60-tRET Total Random - P2 1-12-2010 fc1.ch07 Reads2_1_12_FC1CH7

description: Reads counts with no normalization


title: HL60-tRET Total Random - P2 1-12-2010 fc1.ch08 Reads2_1_12_FC1CH8

description: Reads counts with no normalization


title: Brain Total Random - P5 8-21-2009 fc1.ch22 RPM5_8_21fc1ch22

description: Reads normalized per million

value: Brain


title: K562 RiboMinus Random Rep1 P5 8-21-2009 fc1.ch14 RPM5_8_21fc1ch14

description: Reads normalized per million


title: Liver Frag-polyA Random Rep3Sci2 CTS4 9-25-2009 fc1.ch20 Reads4_9_25fc1ch20

description: Reads counts with no normalization


title: Brain RiboMinus Random Rep2 CTS4 9-16-2009 fc2.ch19 RPM4_9_16fc2ch19

description: Reads normalized per million


title: HL60-control Total Random - P11 12-11-2009 fc2.ch15 Reads11_12_11fc2ch15

description: Reads counts with no normalization


title: Liver Frag-polyA Random Rep2Sci2 CTS4 9-25-2009 fc1.ch19 Reads4_9_25FC1CH19

description: Reads counts with no normalization


title: Small RNAs from Capsicum annuum flowers

value: flowers, pre-anthesis, petals are elongating and have turned white, but have not opened or are partially opened


title: Liver Frag-polyA Random Rep1Sci2 CTS4 9-25-2009 fc1.ch18 Reads4_9_25fc1ch18

description: Reads counts with no normalization


title: Liver Frag-polyA Random Rep1Sci2 P9 10-16-2009 fc1.ch18 Reads9_10_16fc1ch18

description: Reads counts with no normalization


title: Brain polyA Random Rep2 P5 8-21-2009 fc1.ch13 Reads5_8_21fc1ch13

description: Reads counts with no normalization


title: Brain RiboMinus Random Rep1 CTS4 9-16-2009 fc2.ch18 Reads4_9_16fc2ch18

description: Reads counts with no normalization

value: RiboMinus


title: Brain RiboMinus Random Rep2 CTS4 9-16-2009 fc2.ch19 Reads4_9_16fc2ch19

description: Reads counts with no normalization

value: Random


title: HL60-control Total Random - P2 1-12-2010 fc1.ch9 Reads2_1_12fc1ch9

description: Reads counts with no normalization


title: Liver Frag-polyA Random Rep2Sci2 P9 10-16-2009 fc1.ch19 Reads9_10_16fc1ch19

description: Reads counts with no normalization


title: Brain RiboMinus Random Rep1 P5 8-21-2009 fc1.ch18 Reads5_8_21fc1ch18

description: Reads counts with no normalization


title: Brain Total-DGE oligo-dT - CTS4 12-4-2009 fc1.ch2 Reads4_12_4fc1ch2

description: Reads counts with no normalization


title: HL60-control Total Selected - CTS4 9-25-2009 fc1.ch10 Reads4_9_25fc1ch10

description: Reads counts with no normalization

value: Selected


title: HL60-control Total Selected - CTS4 9-25-2009 fc1.ch11 Reads4_9_25fc1ch11

description: Reads counts with no normalization


title: Liver RiboMinus Random Rep1Sci2 P2 11-4-2009 fc1.ch14 Reads2_11_04_fc1ch14

description: Reads counts with no normalization


title: Liver RiboMinus Random Rep2Sci2 P2 11-4-2009 fc1.ch15 Reads2_11_04_fc1ch15

description: Reads counts with no normalization


title: Brain polyA Random Rep1 CTS4 9-16-2009 fc2.ch12 Reads4_9_16fc2ch12

description: Reads counts with no normalization


title: Brain polyA Random Rep2 CTS4 9-16-2009 fc2.ch13 Reads4_9_16fc2ch13

description: Reads counts with no normalization


title: Brain Total Random - CTS4 9-16-2009 fc2.ch22 Reads4_9_16fc2ch22

description: Reads counts with no normalization


title: Brain RiboMinus Random Rep2 P5 8-21-2009 fc1.ch19 Reads5_8_21fc1ch19

description: Reads counts with no normalization


title: Brain Total Random - P5 8-21-2009 fc1.ch22 Reads5_8_21fc1ch22

description: Reads counts with no normalization


title: HL60-control Total Random - P2 1-12-2010 fc1.ch10 Reads2_1_12fc1ch10

description: Reads counts with no normalization


title: Brain polyA Random Rep1 P5 8-21-2009 fc1.ch12 Reads5_8_21fc1ch12

description: Reads counts with no normalization


title: Liver Total Random - P5 8-21-2009 fc1.ch21 Reads5_8_21fc1ch21

description: Reads counts with no normalization


title: Liver Total Random - CTS4 9-16-2009 fc2.ch24 Reads4_9_16fc2ch24

description: Reads counts with no normalization


title: Liver Total Random - CTS4 9-16-2009 fc2.ch21 Reads4_9_16fc2ch21

description: Reads counts with no normalization


title: Liver polyA-cell2 Random - P2 11-4-2009 fc1.ch1 Reads2_11_4fc1ch1

description: Reads counts with no normalization

value: polyA 2x cellulose selected


title: Liver polyA-cell2 Random - CTS4 10-30-2009 fc1.ch1 Reads4_10_30fc1ch1

description: Reads counts with no normalization


title: Liver polyA-cell1 Random - CTS4 10-30-2009 fc1.ch2 Reads4_10_30fc1ch2

description: Reads counts with no normalization

value: polyA 1x cellulose selected


title: Liver polyA-cell1 Random - P2 11-4-2009 fc1.ch2 Reads2_11_4fc1ch2

description: Reads counts with no normalization


title: Liver RiboMinus Random Rep2Sci1 P5 8-21-2009 fc1.ch17 Reads5_8_21fc17

description: Reads counts with no normalization

value: Rep2 Sci1


title: HL60-control Total Selected - CTS4 9-25-2009 fc1.ch9 Reads4_9_25fc1ch9

description: Reads counts with no normalization


title: Liver RiboMinus Random Rep1Sci1 P5 8-21-2009 fc1.ch16 Reads5_8_21fc1ch16

description: Reads counts with no normalization

value: Rep1 Sci1

value: Liver


title: Liver Total-DGE oligo-dT - CTS4 12-4-2009 fc1.ch1 Reads4_12_4fc1ch1

description: Reads counts with no normalization

value: Total/DGE

value: oligo dT


title: Small RNAs from Amborella leaves

organism: Amborella trichopoda

value: leaves

value: mixture, with a bias towards those from early, actively differentiating cells


title: K562 Total-DGE oligo-dT - P9 11-20-2009 fc2.ch4 Reads9_11_20fc2ch4

description: Reads counts with no normalization


title: Liver polyA Random Rep3Sci2 P9 10-16-2009 fc1.ch14 Reads9_10_16fc1ch14

description: Reads counts with no normalization

value: polyA bead selected

value: Rep3 Sci2


title: Liver Total-DGE oligo-dT - P9 11-20-2009 fc2.ch1 Reads9_11_20fc2ch1

description: Reads counts with no normalization


title: Liver polyA Random Rep2Sci2 P9 10-16-2009 fc1.ch13 Reads9_10_16fc1ch13

description: Reads counts with no normalization

value: Rep2 Sci2


title: Liver polyA Random Rep3Sci2 CTS4 9-25-2009 fc1.ch14 Reads4_9_25fc1ch14

description: Reads counts with no normalization


title: Liver polyA Random Rep1Sci1 CTS4 9-16-2009 fc2.ch10 Reads4_9_16fc2ch10

description: Reads counts with no normalization


title: K562 Total Random - P5 8-21-2009 fc1.ch20 Reads5_8_21fc1ch20

description: Reads counts with no normalization

value: Total


title: Liver polyA Random Rep1Sci2 CTS4 9-25-2009 fc1.ch12 Reads4_9_25fc1ch12

description: Reads counts with no normalization

value: Rep1 Sci2


title: Liver polyA Random Rep2Sci1 CTS4 9-16-2009 fc2.ch11 Reads4_9_16fc2ch11

description: Reads counts with no normalization


title: K562 RiboMinus Random Rep2 CTS4 9-16-2009 fc2.ch15 Reads4_9_16fc2ch15

description: Reads counts with no normalization

value: RiboMinus


title: Liver polyA Random Rep1Sci2 P9 10-16-2009 fc1.ch12 Reads9_10_16fc1ch12

description: Reads counts with no normalization

value: Random


title: K562 Total Random - CTS4 9-16-2009 fc2.ch23 Reads4_9_16fc2ch23

description: Reads counts with no normalization


title: K562 RiboMinus Random Rep2 P5 8-21-2009 fc1.ch15 Reads5_8_21fc1ch15

description: Reads counts with no normalization


title: Liver polyA Random Rep2Sci1 P5 8-21-2009 fc1.ch11 Reads5_8_21fc1ch11

description: Reads counts with no normalization


title: K562 RiboMinus Random Rep1 P5 8-21-2009 fc1.ch14 Reads5_8_21fc1ch14

description: Reads counts with no normalization


title: K562 Total Random - CTS4 9-16-2009 fc2.ch20 Reads4_9_16fc2ch20

description: Reads counts with no normalization


title: K562 RiboMinus Random Rep1 CTS4 9-16-2009 fc2.ch14 Reads4_9_16fc2ch14

description: Reads counts with no normalization


title: Liver polyA Random Rep2Sci2 CTS4 9-25-2009 fc1.ch13 Reads4_9_25fc1ch13

description: Reads counts with no normalization


title: K562 polyA Random Rep2 P5 8-21-2009 fc1.ch9 Reads5_8_21fc1ch9

description: Reads counts with no normalization


title: K562 polyA Random Rep2 CTS4 9-16-2009 fc2.ch9 Reads4_9_16fc2ch9

description: Reads counts with no normalization


title: K562 Total-DGE oligo-dT - CTS4 12-4-2009 fc1.ch3 Reads4_12_4fc1ch3

description: Reads counts with no normalization


title: K562 polyA Random Rep1 P5 8-21-2009 fc1.ch8 Reads5_8_21fc1ch8

description: Reads counts with no normalization


title: Liver Total-DGE oligo-dT - P9 11-20-2009 fc1.ch25 Reads9_11_20fc1ch25

description: Reads counts with no normalization


title: K562 polyA Random Rep1 CTS4 9-16-2009 fc2.ch8 Reads4_9_16fc2ch8

description: Reads counts with no normalization


title: ERA000183 STD RNA seq 1 RPMIllumina 1

description: Reads normalized per million

source_name: Placenta

value: polyA

value: Raw data from ERA000183, reanalyzed using same aligner and counting algorithms for comparability

value: Placenta


title: ERA000183 STD RNA seq 2 RPMIllumina 2

description: Reads normalized per million


title: ERA000183 STD RNA seq 1 ReadsIllumina 1

description: Reads counts with no normalization


title: Liver polyA Random Rep1Sci1 P5 8-21-2009 fc1.ch10 Reads5_8_21fc1ch10

description: Reads counts with no normalization


title: ERA000183 STD RNA seq 2 ReadsIllumina 2

description: Reads counts with no normalization


title: Liver RiboMinus Random Rep2Sci1 CTS4 9-16-2009 fc2.ch17 Reads4_9_16fc2ch17

description: Reads counts with no normalization

value: Rep2 Sci1


title: G1ME_RNApolII

status: Public on Mar 21 2011

city: Parkville

first: Matthew

middle: Daniel

last: Young

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter & Eliza Hall Institute of Medical Research

data_processing: All reads were mapped to version 9 of the mouse reference genome (mm9) using bowtie version 0.11.3 with the default settings and output to SAM format.  Any reads that appeared on the same strand at the same location more than 5 times was discarded to remove PCR artifacts (i.e. at most five reads were allowed to start at any one location).

source_name: G1ME Cells

growth_protocol: Mouse C57BL/6 Bruce 4 (B4) ES cells were adapted to culture without helper fibroblasts and expanded using standard techniques. mESCs were cultured in DMEM (Invitrogen) with 15% (v/v) FCS (batch tested for ES cell culture), 100 ug/ml streptomycin, 100 IU/ml penicillin, beta-mercaptoethanol (Sigma), non-essential amino acids, Glutamax (Gibco) and recombinant mLIF 103 IU/ml (Millipore). To prepare chromatin for ChIP, mESCs were grown to ~80% confluence and fixed with buffered formaldehyde (1%) for 10 minutes at room temperature.  G1ME cells were grown in alpha-MEM (Invitrogen) supplemented with 20% (v/v) FCS, 100 ug/ml streptomycin, 100 IU/ml penicillin and 70 ng/ml recombinant thrombopoietin (Stachura, 2006). For ChIP studies G1ME cells were grown at 5x105 cells/ml and were fixed with 1% formaldehyde for 20 minutes at room temperature.

extract_protocol: Chromatin was prepared from fixed mouse ES cells and G1ME cells and was sonicated with a Bandelin sonicator (30% amplitude, 15-25 30 second bursts with a 2 minute reprieve) to produce fragments from 200-1000 bp, with peak signal between 200-500 bp. Approximately 2 x107 cell equivalents were used for each immunoprecipitation. 1.7% of the sample was removed for use as an input control. ChIP was performed as described previously (Lee, 2006), using antibodies towards H3K27Me3 (07-449, Millipore) or phosphorylated RNA polymerase C-terminal domain (ab5131, Abcam).

tag: strain

value: C58BL/6 Bruce 4 (B4)

value: G1ME cells

tag: chip antibody

value: RNA polymerase II C-terminal domain

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog#


title: G1ME_WCE


title: ES_WCE

source_name: Embryonic Stem Cells

value: ES cells


title: ES_RNApolII


title: IgG_Control

status: Public on Mar 23 2011

city: Irvine

first: Jacob

last: Biesinger

state: CA

address: 4058 Donald Bren Hall, University of California Irvine

department: Computer Science

institute: University of California, Irvine

description: Chromatin IP with IgG

data_processing:
Alignment: Short reads of 39-bp were produced from Solexa/Illumina Genome Analyzer, and mapped to a reference genome by Ambry Genetics using ELAND, allowing one mismatch. Short sequence reads that mapped to simple and complex repeats or that were not unique by chance were removed from the analysis.
Peaks: We used GLITR (Tuteja et al., 2009) to determine where areas where there were significantly more enriched reads mapped in the ChIP sample than in the IgG.

source_name: Chromatin IP with IgG

extract_protocol: Chromatin preparation for ChIP assays and ChIP Seq using mouse livers were performed as previously described (Bennett et al., 2008; Seo et al., 2009). To prepare chromatin for the ChIP-seq, after isolating the ChIP-enriched DNA, gene-specific enrichment for known SREBP-2 target promoters relative to IgG control chromatin was verified. 20 ng of ChIP enriched DNA or control DNA was sent to Ambry Genetics (Aliso Viejo, CA) for high throughput DNA sequencing. The samples were blunt ended and adapters were ligated to the ends, according to the library preparation protocol from Illumina. Then DNA fragments with 200 ± 5bp in length were selected for the construction of the ChIP-seq DNA library. After size selection, all the resulting ChIPed DNA fragments were amplified and sequenced simultaneously using Solexa/Illumina Genome Analyzer.

value: liver

tag: antibody

value: IgG


title: ES_H3K27me3

value: Millipore


title: G1ME_H3K27me3


title: Inferior spikelets-Seq data

status: Public on Mar 19 2011

city: Zhengzhou

first: Quan-Zhi

last: Zhao

state: Henan Province

address: NO 63 Nongye Road

department: Agricultural College

institute: Henan Agricultural University

description: inferior spikelets small RNA library

data_processing: The adaptor sequences in Illumina sequencing reads were removed by using vectorstrip in the EMBOSS package. The small RNA reads with high sequencing accuracy and with length of more than 18 nt were were retained for further analysis.

organism: Oryza sativa

source_name: rice seed

growth_protocol: Oryza sativa spp. japonica cv. Xinfeng 2 were planted from the same seed lot and grown at a research farm of Henan Agricultural University, Henan Province, China (34°5' N, 113°35' E, 94m altitude) under non-stress conditions during the rice growing season (May-October) of 2009.

extract_protocol: Total RNA was isolated from superior and inferior spikelets at 18 DAF using Trizol reagent (Invitrogen), according to the manufacturer's instructions. RNase-free DNase I was used to remove the residual DNA for 30 min at 37°C. Small RNA sized at 18-30 nt was gel-purified on a 15% polyacrylamide denaturing gel from the total RNA for each sample. The isolated small RNAs were sequentially ligated to RNA/DNA chimeric oligonucleotide adapters, reversely transcribed, and amplified with 15 cycles of PCR to produce sequencing libraries. The Illumina sequencing was performed by Beijing Genomics Institute.

tag: cultivar

value: japonica Xinfeng 2

value: 18 days after fertilization

value: inferior spikelets


title: SGBS_PPARg_rep2

status: Public on Feb 23 2011

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: Chromatin IP against PPARG.

data_processing: Sequence reads from the ChIP-seq library were mapped to the human reference genome hg18 using the BWA alignment software (Li H, Durbin R, 2009, Bioinformatics, 25: 1754-1760) allowing for 2 mismatches. Peak calling was performed with MACS (Zhang Y et al., 2008, Genome Biol , 9: R137), with a p-value cutoff of e-10, and using sonicated input as a control.

source_name: Adipocytes, SGBS, PPARg ChIP

growth_protocol: SGBS cells were grown to confluence in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham’s supplemented with 10% fetal bovine serum, 33 µM biotin, 17 µM pantothenate, 100 µg/ml streptomycin, 62.5 µg/ml penicillin, 1ng/µl fibroblast growth factors (FGF) 1, and 90 µg/µl heparin. At two days postconfluency, SGBS cells were stimulated to differentiate with serum-free growth medium supplemented with 10 nM insulin, 200 pM triiodothyronine, 1 µM cortisol, 2 µM BRL 49653, 0.115 mg/ml MIX, 0.25 mmol/L DEX, and 0.01 mg/ml human transferrin. After 3 days, the medium was replaced with the differentiation medium without FGF1 and heparin, and after 6 days, Rosiglitazone/BRL49653, MIX, and DEX were removed from the medium. The cells were harvested for ChIP experiments at day 10 of differentiation.

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 minutes, sonicated for 48x30sec at high power using a Bioruptor (Diagenode), immunoprecipitated with C/EBPa  or PPARg antibodies, purified and sequenced using the Illumina Genome Analyzer as recommended by the manufacturer.

value: SGBS

value: adipocytes

tag: days of differentiation

tag: chip epitope

value: PPARG (H100)

tag: antibody vendor

value: Santa Cruz Biotechnology

tag: antibody catalog number


title: SGBS_CEBPa_rep1

description: Chromatin IP against C/EBPA.

source_name: Adipocytes, SGBS, CEBPa ChIP

tag: cell type

value: C/EBPA (14AA)


title: SGBS_PPARg_rep1

description: Chromatin IP against PPARG.


title: 3T3L1_PPARg

description: Chromatin IP against PPARG.

data_processing: Sequence reads from the ChIP-seq library were mapped to the mouse reference genome mm9 using the BWA alignment software (Li H, Durbin R, 2009, Bioinformatics, 25: 1754-1760) allowing for 2 mismatches. Peak calling was performed with MACS (Zhang Y et al., 2008, Genome Biol , 9: R137), with a p-value cutoff of e-10, and using sonicated input as a control.

source_name: Adipocytes, 3T3L1, PPARg ChIP

growth_protocol: 3T3-L1 fibroblasts were differentiated to adipocytes by the standard DMI procedure (stimulation with 3-isobutyl-1-methylxanthine, dexamethasone, and insulin; Helledie et al., 2002, J. Biol. Chem. 277: 26821-26830). The cells were harvested for ChIP experiments at day 6 of differentiation.


title: SR2_ChIPSeq

description: Chromatin IP against SREBP-2

source_name: Chromatin IP against SREBP-2

tag: tissue

value: antibody to a region of the mouse SREBP-2 within its amino-terminal nuclear targeted domain


title: Small RNAs [rmkh01_1]

status: Public on Mar 09 2011

city: Austin

middle: Wayne

last: Vaughn

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

description:
Replicate 1
Strand-specific RNAseq

data_processing: Adapters were trimmed from the sequence reads, and reads were filtered by size using the FASTXtoolkit and a shell script. Sequences were aligned to the S. japonicus genome using BWA.

organism: Schizosaccharomyces japonicus

source_name: Small RNAs

growth_protocol: S. japonicusculteres were grown to logarithmic phase, then harvested.

extract_protocol:
Total RNA was isolated using TRIZOL reagent and small RNA-enriched fraction was used to generate sRNA libraries suitable for sequencing on Illumina GAIIx DNA sequencers.
RNAs in the 10-40 nt size range were enriched from 40 ug of total RNA using flashPAGE (Ambion). The adapters (Small RNA Oligo Only, Illumina) were ligated sequentially using T4 RNA Ligase (Promega). The ligation of the 5' adapter was dependent on the 5'-monophosphate on sRNA and the ligation of the 3' adapter was dependent on the 3'- OH on sRNA. Following ligation of each adapter, reaction products were purified by denaturing 7M urea-PAGE (15% 19:1 acrylamide:bisacrylamide), eluted from the gel slice and precipitated. RNA was reverse-transcribed using Superscript II (Invitrogen) and the library was amplified by PCR using Pfusion Hot Start High Fidelity DNA Polymerase (Finnzymes). PCR products were precipitated and purified by native PAGE. The sRNA library was subject to parallel sequencing on an Illumina Genome Analyzer

tag: size

tag: growth phase

value: log-phase cells


title: Ptomaphagus hirtus whole head RNA-sequencing

city: Houston

first: Bryce

last: Daines

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing: BLASTX

organism: Ptomaphagus hirtus

source_name: Ptomaphagus hirtus heads

growth_protocol: Animals were kept in 60mm polystyrene petri dishes filled with an approximately 0.5 mm deep layer of sieved soil obtained from the natural habitats. Culture Petri dishes were kept in styrofoam boxes on a layer of moist tissue. To maintain saturated humidity, petri dishes and paper towels were sprayed with water approximately every three days. Ptomaphagus hirtus cultures were maintained in constant dark in a coolbox incubator kept at 12°C.

extract_protocol: For each library, mRNA was purified from 20µg of total RNA using an mRNA Purification Kit (Invitrogen). Double-stranded cDNAs were made from mRNA using the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) and random hexamer primers (Invitrogen, 3ug/ul). On a 2% agrose gel, 200-400bp cDNAs were selected and used as the DNA template for the Solexa library construction. The quality and quantity of the resulting double-stranded cDNAs was assessed using the Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA).

treatment_protocol: Ptomaphagus hirtus cultures derived from 25 individuals collected in Fall 2008 from the Frozen Niagara cave entrance of Mammoth Cave (Scientific Research and Collecting Permit MAC-2008-SCI-2006).Whole body samples were homogenized in 1ml of Trizol (Invitrogen, Carlsbad, California, USA) per 50-100 mg of tissue using a glass-Teflon homogenizer.  RNA was purified according to the suggested manufacturer's protocol (Invitrogen).

value: heads

value: Adults


title: 3T3L1_CEBPa

description: Chromatin IP against C/EBPA.

source_name: Adipocytes, 3T3L1, CEBPa ChIP


title: Small RNAs [rmkh02_1]

description:
Replicate 2
Strand-specific RNAseq


title: SGBS_CEBPa_rep2

description: Chromatin IP against C/EBPA.


title: 3T3L1_Input

description: Input DNA.

source_name: Adipocytes, 3T3L1, input


title: SGBS_Input

description: Input DNA.

source_name: Adipocytes, SGBS, input


title: Blood-extracted DNA_affected_Seq_I-1927

status: Public on Feb 18 2011

city: Madrid

first: Javier

last: Benitez

address: Melchor Fernandez Almagro 3

department: Human Cancer Genetics Program

institute: National Cancer Research Centre CNIO

description: DNA from affected individual

data_processing:
After the identification of the sequences belonging to each individual and before the alignment, we removed the first five bases of every sequence corresponding to each of the barcodes. We selected SOAP v1.0 to analyse our dataset using the following parameters: a seed of 12 positions, gaps allowed up to 12 bases, a maximum of 2 mismatches, and a maximum of 5 repeated regions (reporting every region on which the sequences matched equally), using the whole genome as reference sequence. One of the main advantages of SOAP v1.0 is its ability to identify short insertions and deletions (indels) in single-end data, while maintaining all input information in the output file. We developed a specific SNP caller written in the Perl programming language to extract the information contained in the SOAP output file.
Please see 'Readme.txt' (supplementary file on the Series record) for additional information about processed data files.

source_name: Blood

extract_protocol: Genomic DNA (2.5 μg) was fragmented by a triple sonication step. After ligating the modified adaptors, 150-300 bp fragments were selected by agarose gel electrophoresis and purified. To obtain a suitable amount of product, multiple parallel PCR reactions were carried out per sample.

value: whole blood

tag: disease status

value: breast cancer patient


title: Blood-extracted DNA_affected_Seq_I-2033

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_I-1928

description: DNA from affected individual


title: Blood-extracted DNA_healthy_Seq

description: DNA from healthy individuals

value: healthy control


title: Superior spikelets-Seq data

description: superior spikelets small RNA library

tag: age

value: superior spikelets