title: Blood-extracted DNA_affected_Seq_I-3345

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_I-1627

status: Public on Feb 18 2011

type: SRA

city: Madrid

first: Javier

last: Benitez

address: Melchor Fernandez Almagro 3

department: Human Cancer Genetics Program

country: Spain

institute: National Cancer Research Centre CNIO

description: DNA from affected individual

library_source: genomic

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.

molecule: genomic DNA

organism: Homo sapiens

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.

tag: tissue

value: whole blood

tag: disease status

value: breast cancer patient


title: Blood-extracted DNA_affected_Seq_07S581

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_07S576

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_I-4347

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_07S636

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_04-168

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_07S722

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_07S723

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_I-1408

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_07S724

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_07S635

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_07S725

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_I-904

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_96-652

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_06-240

description: DNA from affected individual


title: Blood-extracted DNA_affected_Seq_96-265

description: DNA from affected individual


title: colfloral-23-rep2

status: Public on Feb 11 2011

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

country: Germany

institute: Max Planck Institute for Developmental Biology

description: small RNA

library_source: transcriptomic

data_processing:
Sequencing adapters were removed and sequences without adapter were discarded. The txt files list unique sequences together with their counts.
Note that due to a backup error three of the sRNA lanes could not be recovered. You can find trimmed reads as a supplementary file on Sample record.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: floral tissue

growth_protocol: 23°C, 16 hour light period

extract_protocol: Libraries were constructed as per (Mosher RA et al., 2009), except small RNA were isolated by PAGE, and RNA amplicons were reverse transcribed using the Fermentas Revertaid kit (Fermentas Life Sciences) and then amplified by PCR using the Phusion DNA polymerase (Finnzymes).

tag: strain

value: floral

tag: developmental stage

value: stage 1-14


title: burfloral-23-rep2

description: small RNA


title: burfloral-23-rep1

description: small RNA


title: Chickpea salt stressed and control roots and nodules - Untreated Roots

status: Public on Feb 01 2011

city: Dijon

first: Carlos

middle: Mauricio

last: Molina

state: Bourgogne

address: 17 Rue Sully

department: UMRLEG

country: France

institute: INRA

description:
Sequencing Instrument: First gerenration 454-Machine
Place of sequencing: 454 Life Sciences, Branford, CT, USA

data_processing: Discovery Space software data processing

molecule: polyA RNA

organism: Cicer arietinum

source_name: Chickpea variety Inrat-93 roots

growth_protocol: Chickpea seedlings from variety I-93 were further grown for 20 days in a temperature-controlled glasshouse with a day/night temperature regime of 28/20°C and a 16h photoperiod with additional light of 400 µmol PAR m-2s-1. Micro- and macro-nutrient concentrations in the growth medium were adjusted to 0.7mM K2SO4, 1mM MgSO4.7H2O, 1.65 mM CaCl2, 22.5 mM H2PO4 (macronutrients), and 6.6 mM Mn2+, 4 mM Bo3+, 1.5 mM Cu2+, 1.5 mM Zn2+(micronutrients) and additionally 2.0 g L-1 CaCO3 as pH regulator. After one round of compression and filtering, a constant air flow of 400 mL (compressed air) / liter of solution / minute was applied to each bucket through ‘‘spaghetti” tubes system

extract_protocol: CTAB LiCl gradient; PolyA+ RNA capture

treatment_protocol: no Treatment

tag: treatment


title: Chickpea salt stressed and control roots and nodules - Untreated Nodules

source_name: Chickpea variety Inrat-93 nodules

growth_protocol: Seedlings were further grown for 20 days in a temperature-controlled glasshouse with a day/night temperature regime of 28/20°C and a 16h photoperiod with additional light of 400 µmol PAR m-2s-1. Micro- and macro-nutrient concentrations in the growth medium were adjusted to 0.7mM K2SO4, 1mM MgSO4.7H2O, 1.65 mM CaCl2, 22.5 mM H2PO4 (macronutrients), and 6.6 mM Mn2+, 4 mM Bo3+, 1.5 mM Cu2+, 1.5 mM Zn2+(micronutrients) and additionally 2.0 g L-1 CaCO3 as pH regulator. After one round of compression and filtering, a constant air flow of 400 mL (compressed air) / liter of solution / minute was applied to each bucket through ‘‘spaghetti” tubes system


title: T. nigroviridis gills_Low calcium 12h

status: Public on Jan 03 2011

city: Gambelas

first: Patricia

middle: I. S.

last: Pinto

address: Ed.7, University of Algarve, Campus de Gambelas

country: Portugal

institute: Centro de Ciências do Mar (CCMAR), CIMAR-Laboratório Associado

description:
anchor: NlaIII
tag_length: 22
tag_count: 2263471
This sample was used for the comparison with the gills of fish transferred to artificial water with control (2.9 mM), low (0.01 mM) or high (10 mM) Ca2+ concentrations for 2 or 12h.

data_processing: Tag extraction and counting was performed with SuperSAGE Perl scripts by Terauchi et al. 2008 (SuperSAGE: the most advanced transcriptome technology for functional genomics. In: Handbook of Plant Functional Genomics: Concepts and Protocols. Edited by Kahl G, Meksem K. John Wiley & Sons, NY).

organism: Tetraodon nigroviridis

source_name: Gills, exposed to low calcium water (containing 0.01 mM Ca2+), 12h

extract_protocol:
Total RNA was extracted from individual gills with TRI Reagent (Sigma-Aldrich, Madrid, Spain)and polyA RNA purified from pooled total RNA (250 µg) for each experimental group using the Oligotex mRNA Mini Kit (Qiagen, Hilden, Germany). Libraries were constructed using the SuperSAGE procedure by Matsumura et al. 2003 (Gene expression analysis of plant host-pathogen interactions by SuperSAGE. PNAS 100(26):15718-23), with adaptations to massively parallel pyrosequencing described in Terauchi et al. 2008 (SuperSAGE: the most advanced transcriptome technology for functional genomics. In: Handbook of Plant Functional Genomics: Concepts and Protocols. Edited by Kahl G, Meksem K. John Wiley & Sons, NY).
Ditags were directly sequenced by pyrosequencing using a GS20 sequencer (454 Life Sciences, Branford, CT, USA).

treatment_protocol: Acclimatized fish (natural water at 10 ppt salinity, 2.9 mM Ca2+) were transferred to artificial water at 10 ppt containing 0.01mM Ca2+ (Low calcium water). Gills were collected 12h after transfer.

tag: common name

value: green spotted puffer fish

tag: origin

value: wild, imported from Thailand

tag: stage

value: adult

tag: body weight

tag: gender

value: both


title: Chickpea salt stressed and control roots and nodules - Salt stressed Roots

source_name: Chickpea variety Inrat-93 roots - salt-stressed

treatment_protocol: 2h 25 Mm NaCl

value: salt


title: AP1GRap1cal_3hMockDexCHX_set6

status: Public on Jan 01 2011

type: RNA

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

institute: Center for Research in Agricultural Genomics

description: US81303221_252313710007_S01_GE2-v5_10_Apr08_1_4.txt

hyb_protocol: Agilent microarrays were used following manufacturer's instructions. Microarray hybridizations (65ºC, 16h) and washes were performed with Agilent reagents and following standard protocols.

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 9.5.3.1.

data_processing: Data were processed with the Resolver version 7.1 data analysis system (Rosetta Biosoftware, Seattle, WA), using the Agilent Ratio data processing pipeline with default settings. Resolver uses an error model-based approach to stabilize the variance estimation to improve the specificity and sensitivity in differential gene expression detection (Weng, L., Dai, H., Zhan, Y., He, Y., Stepaniants, S.B., and Bassett, D.E. (2006). Rosetta error model for gene expression analysis. Bioinformatics 22, 1111-1121).

label_protocol: Agilent microarrays were used following manufacturer's instructions. RNA samples were labeled with fluorescent dyes using the Quick Amp Labeling Kit (Agilent).

growth_protocol: Plants were grown on a soil:vermiculite:perlite (2:1:1) mixture at 20ºC under constant illumination with cool white fluorescent light.

extract_protocol: Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich) according to the manufacturer’s instructions. Quality of RNA samples was evaluated using a Bioanalyzer and a RNA Nano 6000 kit (Agilent). RNA concentrations were determined using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: For all experiments, we used approximately 4 week-old 35S:AP1-GR ap1-1 cal-1 plants. For each sample, inflorescence tissue from ~25 plants was collected using jeweler’s forceps. Four biologically independent sets of samples were generated. Inflorescences were treated with a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol, and 0.015% (v/v) Silwett L-77 (De Sangosse), or with an identical mock solution that lacked dexamethasone, or with identical solutions that contained in addition 10 μM cycloheximide. We then collected inflorescence tissue after 3 hours.

tag: genome/variation

value: AP1-GR ap1 cal inflorescences

tag: treatment group

value: Mock

value: DexCHX


title: T. nigroviridis gills_control2h

description:
anchor: NlaIII
tag_length: 22
tag_count: 65378
This sample was used for the comparison with the gills of fish transferred to artificial water with control (2.9 mM), low (0.01 mM) or high (10 mM) Ca2+ concentrations for 2 or 12h.

source_name: Gills, exposed to control water containing 2.9 mM Ca2+, 2h

extract_protocol:
Total RNA was extracted from individual gills with TRI Reagent (Sigma-Aldrich, Madrid, Spain) and polyA RNA purified from pooled total RNA (250 µg) for each experimental group using the Oligotex mRNA Mini Kit (Qiagen, Hilden, Germany). Libraries were constructed using the SuperSAGE procedure by Matsumura et al. 2003 (Gene expression analysis of plant host-pathogen interactions by SuperSAGE. PNAS 100(26):15718-23), with adaptations to massively parallel pyrosequencing described in Terauchi et al. 2008 (SuperSAGE: the most advanced transcriptome technology for functional genomics. In: Handbook of Plant Functional Genomics: Concepts and Protocols. Edited by Kahl G, Meksem K. John Wiley & Sons, NY).
Ditags were directly sequenced by pyrosequencing using a GS20 sequencer (454 Life Sciences, Branford, CT, USA).

treatment_protocol: Acclimatized fish (natural water at 10 ppt salinity, 2.9 mM Ca2+) were transferred to artificial water at 10 ppt containing 2.9mM Ca2+ (control group). Gills were collected 2h after transfer.


title: Disease p53-NF-kB ChIP-Seq

city: Cambridge

first: Mun-Kit

last: Choy

state: Cambridgeshire

address: Box 110, Level 6, ACCI Building, Addenbrooke’s Hospital, Hills Road

department: Division of Cardiovascular Medicine

country: United Kingdom

institute: University of Cambridge

description:
Chromatin IP against p53 and RELA.
End-stage cardiomyopathies.

data_processing:
High-throughput sequencing of the sequential-ChIP fragments from human hearts was performed using the Illumina Genome Analyzer II by GeneService, UK following manufacturer's protocols. Two flowcell lanes were used for sequencing of each pooled sample (control vs. disease) on the Genome Analyzer (GA) II. The Genome Analyzer was run for 36 cycles. Images from the GA were analyzed with the GA pipeline software (version 1.3, Illumina software) for base calling and sequence alignment to the reference human genome. The reference genome used for sequence alignment was the NCBI Human Build 36.1 (hg18) finished human genome assembly (Mar. 2006) (http://hgdownload.cse.ucsc.edu/downloads.html#human ). The length and abundance of ChIP fragments were modelled from sequencing reads using Model-Based Analysis of ChIP-Seq (MACS).

Alignment: Sequence reads were obtained and mapped to the human hg18 (March, 2006) genome using the Illumina Genome Analyzer Pipeline. The sequence alignment stage was performed using the ELAND algorithm with the 'ELAND extended' option to enable better handling of reads >32bp. All reads mapping with two or fewer mismatches were retained.

Peaks: Peak detection was performed with the MACS 1.3.7.1 algorithm (http://liulab.dfci.harvard.edu/MACS/ ).

source_name: human hearts, cardiomyopathy, ChIP-Seq

extract_protocol:
ChIP: Chromatin IP was performed using human heart tissues finely chopped, cross-linked and homogenised prior to manufacturer's protocol of ChIP Assay Kit (Upstate). DNA molecules were fragmentised to around 1kb by sonication. Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with antibody. For sequential chIP assays, complexes from the primary chIP (anti-p53; DO-1/sc-126; Santa Cruz) were eluted twice with 10 mM DTT for 20 min at 37°C, diluted 10 times with re-chIP buffer (20 mM Tris-HCl pH 8.1, 0.1% Triton X-100, 2 mM EDTA, 150 mM NaCl) followed by re-immunoprecipitation with anti-NF-kB (C-20/sc-372; Santa Cruz) and were again subjected to the ChIP procedure.

Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, library fragments of ~1000 bp were band isolated from an agarose gel, and DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

value: heart

tag: disease

value: cardiomyopathy

tag: antibody 1

tag: antibody 1 name

tag: antibody 1 catalog number

tag: antibody 1 vendor

value: Santa Cruz Biotechnology

tag: antibody 2

value: anti-NF-kB

tag: antibody 2 name

tag: antibody 2 catalog number

tag: antibody 2 vendor


title: T. nigroviridis gills_control 12h

description:
anchor: NlaIII
tag_length: 22
tag_count: 2267996
This sample was used for the comparison with the gills of fish transferred to artificial water with control (2.9 mM), low (0.01 mM) or high (10 mM) Ca2+ concentrations for 2 or 12h.

source_name: Gills, exposed to control water containing 2.9 mM Ca2+, 12h

treatment_protocol: Acclimatized fish (natural water at 10 ppt salinity, 2.9 mM Ca2+) were transferred to artificial water at 10 ppt containing 2.9mM Ca2+ (control group). Gills were collected 12h after transfer.


title: Chickpea salt stressed and control roots and nodules - salt stressed Nodules

source_name: Chickpea variety Inrat-93 nodules - salt stressed

tag: treatment


title: T. nigroviridis gills_Low calcium 2h

description:
anchor: NlaIII
tag_length: 22
tag_count: 2287388
This sample was used for the comparison with the gills of fish transferred to artificial water with control (2.9 mM), low (0.01 mM) or high (10 mM) Ca2+ concentrations for 2 or 12h.

source_name: Gills, exposed to low calcium water (containing 0.01 mM Ca2+), 2h

treatment_protocol: Acclimatized fish (natural water at 10 ppt salinity, 2.9 mM Ca2+) were transferred to artificial water at 10 ppt containing 0.01 mM Ca2+ (Low calcium water). Gills were collected 2h after transfer.

tag: common name

value: adult; Body weight:4.4±1.6g


title: Small RNAs from Capsicum annuum leaves

status: Public on Apr 30 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

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: Capsicum annuum

source_name: Leaves

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.

tag: tissue

value: leaves, fully grown middle or upper


title: AP1GRap1cal_3h_CHX vs DexCHX_set4

description: US81303221_252313710017_S01_GE2-v5_10_Apr08_1_2.txt

value: CHX


title: AP1GRap1cal_3h_CHX vs DexCHX_set6

description: US81303221_252313710017_S01_GE2-v5_10_Apr08_1_4.txt


title: small RNAs from C. elegans, daf-2(e1379), day 0 of adulthood

city: NEW HAVEN

first: ALEXANDRE

last: DE LENCASTRE

address: 219 PROSPECT ST KBT 924

country: USA

institute: YALE UNIVERSITY

description: C.elegans genome WS190

data_processing: Sequences corresponding to cloning and sequencing adapters or size-selection markers were trimmed from raw data. Sequencing reads were then aligned to the C. elegans genome (version WS190), using NCBI megablast (BLAST version 2.2.17 with the following options: -W 12 -p 100. Only perfect alignments were retained (full length, 100% identity). The number of sequence reads that correspond to known miRNAs was assessed using perfect sequence matching to a database of known miRNAs (miRBase, v.13.0). To compare the differential expression of miRNAs across samples, the number of miRNA reads in each sample was normalized to the total number of reads in each sample that matched the C. elegans genome.

organism: Caenorhabditis elegans

source_name: daf-2(e1379) mutant, day 0

growth_protocol: Synchronized L1s of N2 (wild-type) and mutant daf-2(e1370) strains were fed on OP50 and grown at 16oC until L4 stage to avoid dauer formation in the daf-2 temperature sensitive mutants. 5-fluorodeoxyuridine (FUDR) (0.1g/ml) was added to the plates to prevent progeny production and the plates where shifted to 25oC. FUDR does not affect lifespan of C. elegans adults [6, 7] (and Supplementary Figure 4). Day 0 worms were harvested ~20 hours after addition of FUDR and 25oC temperature shift. The remaining worms were kept at 25oC for 4 days, and then moved to 20oC. Day 10 worms were harvested 10 days after the addition of FUDR

extract_protocol: 18-26-nucleotide small RNAs from 85 - 305 micrograms of TOTAL RNA were gel extracted from denaturing 15% PAGE. Bands were visualized by the addition of trace amounts of radiolabelled 24-nt and 18-nt RNA markers. After elution and precipitation, a pre-adenylated-3'adaptor (miRNA cloning linker from IDT) was ligated (T4 RNA ligase) to the 5'-phosphate of small RNAs, purified by PAGE and bands representing ~35-41-nt bands were excised, eluted and precipitated. A 5'-adaptor was then ligated, followed by PAGE purification, and bands representing ~52-58-nt bands were excised, eluted and precipitated. 1st strand cDNA synthesis of the samples was done with Superscript III and primer specific to adaptor sequence. cDNA was PCR amplified, digested with BanI, and finally concatemerized with T4 DNA ligase (30 minutes at room temperature). The concatemerized samples were purified with Min. Elute PCR Purification Kit (Qiagen), thus removing salts, enzyme, primers and dsDNA <70bp while eluting the desired dsDNA in size range >70bp. The quality of the dsDNA was confirmed on nanospec (A260/280 > 1.8) and by running 300ng on 2% Nusieve GTG Gel, showing a smear of concatemers from ~70bp-600bp. Purified concatemers were then submitted for deep sequencing to 454 Lifesciences/Roche.

tag: strain

value: daf-2(e1379) mutant

tag: developmental stage

value: Adult

tag: age

value: Day 0


title: AP1GRap1cal_3hDexCHXMock_set5

description: US81303221_252313710007_S01_GE2-v5_10_Apr08_1_1.txt

tag: genome/variation


title: AP1GRap1cal_3hMockDex_set6

description: US81303221_252313710007_S01_GE2-v5_10_Apr08_1_2.txt

tag: treatment group

value: Dex


title: small RNAs from C. elegans, wild-type, day 0 of adulthood

description: C.elegans genome WS190

source_name: wild-type (N2), day 0

value: N2 wild-type


title: small RNAs from C. elegans, wild-type, day 10 of adulthood

description: C.elegans genome WS190

source_name: wild-type (N2), day 10

value: Day 10


title: small RNAs from C. elegans, daf-2(e1379), day 10 of adulthood

description: C.elegans genome WS190

source_name: daf-2(e1379) mutant, day 10


title: AP1GRap1cal_3h_DexCHX vs CHX_set5

description: US81303221_252313710017_S01_GE2-v5_10_Apr08_1_3.txt


title: AP1GRap1cal_3hMockCHX_set6

description: US81303221_252313710007_S01_GE2-v5_10_Apr08_1_3.txt


title: AP1GRap1cal_3hMockDexCHX_set4

description: US81303221_252313710006_S01_GE2-v5_10_Apr08_1_2.txt


title: AP1GRap1cal_3h_DexCHX vs CHX_set3

description: US81303221_252313710017_S01_GE2-v5_10_Apr08_1_1.txt


title: AP1GRap1cal_3hCHXMock_set5

description: US81303221_252313710006_S01_GE2-v5_10_Apr08_1_4.txt


title: AP1GRap1cal_3hMockCHX_set4

description: US81303221_252313710006_S01_GE2-v5_10_Apr08_1_1.txt


title: AP1GRap1cal_3hDexMock_set5

description: US81303221_252313710006_S01_GE2-v5_10_Apr08_1_3.txt


title: AP1GRap1cal_3hMockDex_set4

description: US81303221_252313710005_S01_GE2-v5_10_Apr08_1_4.txt


title: T. nigroviridis gills_High calcium 12h

description:
anchor: NlaIII
tag_length: 22
tag_count: 2260142
This sample was used for the comparison with the gills of fish transferred to artificial water with control (2.9 mM), low (0.01 mM) or high (10 mM) Ca2+ concentrations for 2 or 12h.

source_name: Gills, exposed to high calcium water (containing 10 mM Ca2+), 12h

treatment_protocol: Acclimatized fish (natural water at 10 ppt salinity, 2.9 mM Ca2+) were transferred to artificial water at 10 ppt containing 10mM Ca2+ (High calcium water). Gills were collected 12h after transfer.

value: green spotted puffer fish

tag: origin

value: wild, imported from Thailand

tag: stage

value: adult

tag: body weight

tag: gender

value: both


title: Control p53-NF-kB ChIP-Seq

description:
Chromatin IP against p53 and RELA.
Road traffic accident victims.

source_name: human hearts, control, ChIP-Seq

value: heart

tag: disease

value: control

tag: antibody 1

tag: antibody 1 name

tag: antibody 1 catalog number

tag: antibody 1 vendor


title: AP1GRap1cal_3hCHXMock_set3

description: US81303221_252313710005_S01_GE2-v5_10_Apr08_1_2.txt

value: AP1-GR ap1 cal inflorescences

value: Mock


title: ypl150w-del-2-b

status: Public on Dec 09 2010

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Features were extracted using Imagene software from Biodiscovery.

data_processing:
genes, no bg corr, dye corr: as genes, no bg corr, but followed by gene-specific dye bias correction. Identical to genes, no bg corr if the dye bias correction is 0.0, which is the default. So far (jan 2008), we have only  dye-bias corrections for yeast.
limma: A software package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. Author(s): Gordon Smyth.  The limma R package version 2.12.0 is used. P-values are Benjamini-Hochberg FDR corrected.

organism: Saccharomyces cerevisiae

label_protocol: robot amplification and labeling v1.0

extract_protocol: yeast RNA isolation for robotic amplification v1.0

tag: strain (or line)

tag: genotype/variation

source_name: refpool

value: refpool


title: ypl150w-del-2-a


title: yvh1-del-1-a


title: ypr106w-del-1-b


title: AP1GRap1cal_3hDexCHXMock_set3

description: US81303221_252313710005_S01_GE2-v5_10_Apr08_1_3.txt

value: DexCHX


title: ypl141c-del-1-a


title: ypl236c-del-1-a


title: ypl236c-del-1-b


title: AP1GRap1cal_3hDexMock_set3

description: US81303221_252313710005_S01_GE2-v5_10_Apr08_1_1.txt


title: ypl109c-del-2-a


title: ynr047w-del-1-b

extract_protocol: yeast mRNA extraction v1.3


title: ypk1-del-2-a


title: ypk1-del-2-b


title: ynr047w-del-1-a


title: ylr253w-del-2-b


title: yvh1-del-1-b


title: ykl171w-del-1-b


title: ylr253w-del-2-a


title: ypk2-del-2-a


title: ypl109c-del-2-b


title: ypk2-del-2-b


title: ypl141c-del-1-b


title: ypr106w-del-1-a


title: ymr291w-del-2-b


title: ymr291w-del-2-a


title: ygr203w-del-1-b


title: yil042c-del-1-b


title: ygk3-del-2-b


title: yil042c-del-1-a


title: yck3-del-1-a


title: yck3-del-1-b


title: ygl059w-del-1-a


title: ykl161c-del-1-b

hyb_protocol: Hybridization protocol v2.2

label_protocol: aminoallyl labeling v2.1.1


title: yck2-del-1-b


title: wt-tm007-1-a

source_name: wt

value: wt


title: ykl161c-del-1-a


title: yck1-del-2-b


title: Calli_Undifferentiated

status: Public on Mar 07 2011

city: Orsay

first: Chong-Jian

last: CHEN

address: IGM, Bat 400, Université Paris-Sud

institute: Institut de Génétique et Microbiologie

data_processing:
All sequenced reads were mapped to the Oryza sativa genome (TIGR v6.0) using the Bowtie program. Only reads with more than one perfect match to the genome were reported. Reads were then searched against small RNA databases for perfect matches using the Bowtie program and assigned to different annotation classes with the following priority: tRNA (RAP-DB release 2), rRNA (RAP-DB release 2), Repeat (TIGR repeat database v3.3, and RAP-DB release 2 predicted repeats), snoRNA&snRNA (NONCODE), and miRNA (miRBase v13). Reads that couldn't be mapped to any class above were classified as other small RNAs. All reads were normalized as transcripts per million (TPM) according to the total sequenced reads in each sample.

The supplementary file "GSM686039.fasta" is a fasta format file of the small RNA sequences in the undifferentiated callus library. The Sample data table includes the counts from "GSM686039.fasta".

organism: Oryza sativa

source_name: Undifferentiated calli

growth_protocol: Mature seeds of Japonica rice variety Nipponbare were dehulled and sterilized at surfaces with 75% ethanol and 1.5% sodium hypochlorite, respectively. After being washed three times with sterile water, the sterilized seeds were plated on NB medium (a mixed medium of N6 and B5) with 2mg/L 2, 4-D (Sigma) and cultured in darkness at 25C for 30 days. The primary calli were then carried out on subculture NB medium until embryogenic calli were induced. For induction of callus differentiation, embryogenic calli were conducted on a differentiation NB medium with 1mg/L NAA (Sigma) and 3 mg/L 6-BA (Sigma) and then transferred to a tissue culture room at 25C under a 16-h-light/8-h-dark photoperiod for 20 days.

extract_protocol: Total RNA from undifferentiated and differentiated calli of Japonica rice variety Nipponbare were isolated with Trizol (Invitrogen, Carlsbad, CA) according to manufacturer instructions. Small RNA library preparation and sequencing were performed with Solexa sequencing Technology (BGI, Shenzhen, China). Briefly, total RNA was size-fractionated on a 15% Tris-borate-EDTA (TBE) urea polyacrylamide gel and a 15-30nt fraction was excised, eluted from the polyacrylamide gel slice by Spin-X filter (Fisher) and precipitated. The dissolved RNA was dephosphorylated and ligated sequentially to 5' adapter and 3' adapter with T4 RNA ligase (Promega). Ligated RNA was size-fractionated on a 10% TBE urea polyacrylamide gel, and the 70-90nt RNA was excised, eluted, precipitated and resuspended in DEPC water. Reverse transcription reaction was performed after ligation with adapters using Superscript II reverse transcriptase (Invitrogen) and Solexa's small RNA RT-Primer, and followed by PCR amplification with Hotstart Phusion DNA Polymerase (NEB). PCR products were purified on a 6% TBE polyacrylamide gel and small RNAs about 92bp in size were excised, dissolved in EB buffer and diluted for sequencing on the Solexa Genome Sequencer.

tag: cultivar

value: Japonica

tag: variety

value: Nipponbare

tag: tissue

value: calli

value: undifferentiated


title: yck1-del-2-a


title: ydl025c-del-2-a


title: wt-tm007-1-b


title: ygl059w-del-1-b


title: wt-tm006-1-a


title: ybr028c-del-1-b


title: ydl025c-del-2-b


title: ygk3-del-2-a


title: ygr203w-del-1-a


title: wt-tm006-1-b


title: Liver RiboMinus Random Rep1Sci1 CTS4 9-16-2009 fc2.ch16 Reads4_9_16fc2ch16

status: Public on Mar 24 2011

first: John

middle: F

last: Thompson

state: MA

address: One Kendall Square

department: Genomic Sciences

institute: Helicos BioSciences

description: Reads counts with no normalization

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.

source_name: Liver

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: RiboMinus

tag: cdna primer

value: Random

tag: comment

value: Rep1 Sci1

value: Liver

tag: replicate


title: ybr028c-del-1-a


title: ykl171w-del-1-a


title: yck2-del-1-a


title: yak1-del-2-b


title: Calli_Differentiated

data_processing:
All sequenced reads were mapped to the Oryza sativa genome (TIGR v6.0) using the Bowtie program. Only reads with more than one perfect match to the genome were reported. Reads were then searched against small RNA databases for perfect matches using the Bowtie program and assigned to different annotation classes with the following priority: tRNA (RAP-DB release 2), rRNA (RAP-DB release 2), Repeat (TIGR repeat database v3.3, and RAP-DB release 2 predicted repeats), snoRNA&snRNA (NONCODE), and miRNA (miRBase v13). Reads that couldn't be mapped to any class above were classified as other small RNAs. All reads were normalized as transcripts per million (TPM) according to the total sequenced reads in each sample.

The supplementary file "GSM686040.fasta" is a fasta format file of the small RNA sequences in the differentiated callus library. The Sample data table includes the counts from "GSM686040.fasta".

source_name: Differentiated calli

tag: developmental stage

value: differentiated


title: yak1-del-2-a


title: wt-tm004-1-b


title: wt-sv096-b


title: wt-sv076-a


title: wt-sv085-b


title: wt-tm002-1-a


title: wt-sv082-b


title: wt-sv082-a


title: wt-sv081-b


title: wt-sv079-a


title: wt-sv081-a


title: wt-tm001-1-b


title: wt-sv071-a


title: wt-sv071-b


title: wt-tm003-1-b


title: wt-tm003-1-a


title: wt-sv073-a


title: wt-sv079-b


title: wt-sv097-b


title: wt-tm004-1-a


title: wt-sv075-b


title: wt-sv077-a


title: wt-sv097-a


title: wt-sv077-b


title: wt-tm002-1-b


title: wt-sv076-b


title: wt-sv075-a


title: wt-sv073-b


title: wt-sv085-del-1-a


title: wt-tm001-1-a


title: wt-sv096-a


title: wt-sv070-b


title: wt-sv057-b


title: wt-sv061-b


title: wt-sv057-a


title: wt-sv067-a


title: wt-sv047-b


title: wt-sv067-b


title: wt-sv052-b


title: wt-sv061-a


title: wt-sv043-b


title: wt-sv019-b


title: wt-sv064-b


title: wt-sv052-a


title: wt-sv030-b


title: wt-sv040-a


title: wt-sv047-a


title: wt-sv019-a


title: wt-sv024-b


title: wt-sv018-b


title: wt-sv040-b


title: wt-sv024-a


title: wt-sv064-a


title: wt-sv035-b


title: wt-sv035-a


title: wt-sv070-a


title: wt-sv022-b


title: wt-sv043-a


title: wt-sv022-a


title: wt-sv030-a


title: wt-sv018-a


title: wt-sv017_2-del


title: wt-sv017_1-a


title: wt-sv008_3-b


title: wt-sv014-a


title: wt-sv016-a


title: wt-sv012-b


title: wt-sv014-b


title: wt-sv015-a


title: wt-sv010-a


title: wt-sv006_1-b


title: wt-sv010-b


title: wt-sv017_1-b


title: wt-sv006_2-a


title: wt-sv017_2-b


title: wt-sv005_1-b


title: wt-nbr031-a


title: wt-mbr005-b


title: wt-sv005_2-b


title: wt-sv006_1-a


title: wt-mbr005-a


title: wt-sel01-b


title: wt-sv006_2-b


title: wt-nbr031-b


title: wt-sv012-a


title: wt-jb010b-1-b


title: wt-sv015-b


title: wt-sel01-a


title: wt-sv005_2-a


title: wt-sv005_1-a


title: wt-sv008_3-a


title: wt-jb010-1-a


title: wt-ic022-b


title: wt-ic025-a


title: wt-jb010b-1-a


title: wt-ic024-b


title: wt-ic024-a


title: wt-ic026-b


title: wt-ic019-b


title: wt-ic022-a


title: wt-ic020-a


title: wt-ic025-b


title: wt-ic020-b


title: wt-ic026-a


title: wt-ic018-b


title: wt-ic016-b


title: wt-ic018-a


title: wt-ic015-a


title: wt-ic016-a


title: wt-ic012-a


title: wt-ic014-a


title: wt-ic019-a


title: wt-ic014-b


title: wt-ic015-b


title: wt-ic010-a


title: wt-ic011-a


title: wt-ic011-b


title: wt-ic010-b


title: wt-ic012-b


title: wt-jb010-1-b


title: wt-ic007-a


title: wt-ic007-b


title: wt-ic005-b


title: wt-ic008-a


title: wt-ic004-a


title: wt-ic004-b


title: wt-ic008-b


title: wt-htp98-b


title: wt-ic003-a


title: vps15-del-1-a


title: vhs1-del-1-b


title: wt-ic006-b


title: wt-ic006-a


title: wt-ic003-b


title: wt-htp98-a


title: wt-ic002-b


title: wt-SV013-a


title: wt-htp96-b


title: wt-ic002-a


title: wt-htp96-a


title: wt-ic005-a


title: wt-ea017-1-a


title: wt-ea011-1-a


title: wt-ea017-1-b


title: vhs1-del-1-a


title: vps15-del-1-b


title: wt-SV013-b


title: wt-ea011-1-b


title: twf1-del-1-b


title: twf1-del-1-a


title: tpk3-del-2-b


title: tpk2-del-2-b


title: tos3-del-1-b


title: tpk1-del-2-b


title: tpk1-del-2-a


title: tpk2-del-2-a


title: tel1-del-1-b


title: tos3-del-1-a


title: wt-sv016-b


title: tor1-del-1-b


title: tel1-del-1-a


title: tor1-del-1-a


title: ste20-del-3-b


title: swe1-del-1-a


title: ste11-del-2-b


title: swe1-del-1-b


title: ssk2-del-1-a


title: ste7-del-1-a


title: snf1-del-2-a


title: ste20-del-3-a


title: sps1-del-3-a


title: ste7-del-1-b


title: snf1-del-2-b


title: ste11-del-2-a


title: sps1-del-3-b


title: ssk22-del-1-b


title: ssk2-del-1-b


title: snf1-del+rim11-del-1-b


title: slt2-del+ptp3-del-1-b


title: slt2-del-2-a


title: smk1-del-2-a


title: smk1-del-2-b


title: slt2-del-2-b


title: slt2-del+cla4-del-2-a


title: skm1-del-3b


title: slt2-del+ptp3-del-1-a


title: tpk3-del-2-a


title: sky1-del-2-b


title: sky1-del-2-a


title: ssk22-del-1-a


title: slt2-del+cla4-del-2-b


title: siw14-del-2-b


title: sdp1-del-1-a


title: rim15-del-1-a


title: scy1-del-1-a


title: siw14-del-2-a


title: sha3-del-1-a


title: sit4-del-1-b


title: sat4-del-2-b


title: rim15-del-1-b


title: scy1-del-1-b


title: snf1-del+rim11-del-1-a


title: sak1-del-1-b


title: sit4-del-1-a


title: sak1-del-1-a


title: sha3-del-1-b


title: skm1-del-3a


title: sat4-del-2-a


title: sdp1-del-1-b


title: rim11-del-2-a


title: rim11-del-2-b


title: rck2-del-1-b


title: ptp2-del-1-a


title: rck1-del-1-b


title: rck1-del-1-a


title: ptp3-del-1-b


title: ptp3-del-1-a


title: ptp2-del-1-b


title: ptp2-del+ptp3-del-1-b


title: ptp2-del+ptp3-del-1-a


title: ptk1-del-1-b


title: ptk2-del-3-b


title: ptp2-del+ptc2-del-1-b


title: ptk2-del-3-a


title: ptp2-del+ptc2-del-1-a


title: ptc2-del-1-b


title: ptc7-del-1-a


title: ptc3-del-1-a


title: ptc7-del-1-b


title: ptp1-del-1-a


title: ptp1-del-1-b


title: ptc5-del-a


title: ptc5-del-1-b


title: ptk1-del-1-a


title: ptc4-del-1-b


title: ptc2-del-1-a


title: ptc3-del-1-b


title: ptc4-del-1-a


title: rck2-del-1-a


title: ptc1-del-2-b


title: ptc1-del-2-a


title: ptc1-del+ptc2-del-1-a


title: ptc1-del+pph3-del-1-b


title: psr2-del-1-b


title: psr1-del-1-a


title: psr1-del-1-b


title: psk2-del-2-b


title: prr2-del-1-b


title: psk2-del-2-a


title: psk1-del-2-b


title: ptc1-del+ptc2-del-1-b


title: psk1-del-2-a


title: prr2-del-1-a


title: prr1-del-1-a


title: prr1-del-1-b


title: pho85-del-2-b


title: pkh3-del-1-b


title: pkh1-del-1-b


title: pkh3-del-1-a


title: ppg1-del-1-a


title: ppq1-del-2-a


title: pkh1-del-1-a


title: ppg1-del-1-b


title: pph21-del-1-a


title: pph22-del-3-b


title: pho85-del-2-a


title: pbs2-del-2-a


title: prk1-del-1-b


title: ptc1-del+pph3-del-1-a


title: pbs2-del-2-b


title: oca1-del-4-b


title: npr1-del-1-a


title: oca2-del-1-b


title: pbs2-del+ptk2-del-1-b


title: ppt1-del-1-b


title: pps1-del-1-b


title: pbs2-del+ptk2-del-1-a


title: ppz2-del-2-a


title: prk1-del-1-a


title: psr2-del-1-a


title: ppq1-del-2-b


title: pps1-del-1-a


title: pph3-del-1-b


title: ppz1-del-1-b


title: npr1-del-1-b


title: pph3-del-1-a


title: ppt1-del-1-a


title: nem1-del-1-b


title: oca1-del-4-a


title: ppz2-del-2-b


title: nem1-del-1-a


title: pph21-del-1-b


title: msg5-del-1-b


title: mkk2-del-1-a


title: mkk2-del-1-b


title: pph22-del-3-a


title: mrk1-del-1-a


title: mrk1-del-1-b


title: mck1-del-1a


title: mih1-del-1-b


title: mck1-del-1-b


title: mek1-del-2-a


title: lcb5-del-1-a


title: mkk1-del-1-b


title: ltp1-del-2-a


title: mek1-del-2-b


title: mih1-del-1-a


title: ltp1-del-2-b


title: oca2-del-1-a


title: ppz1-del-1-a


title: lcb5-del-1-b


title: lcb4-del-1-b


title: ksp1-del-1-b


title: lcb4-del-1-a


title: kss1-del+fus3-del+hog1-del-1-a


title: kss1-del-2-a


title: msg5-del-1-a


title: kss1-del-2-b


title: ksp1-del-1-a


title: kns1-del-1-b


title: kkq8-del-1-b


title: mkk1-del-1-a


title: kin82-del-1-a


title: kss1-del+fus3-del+hog1-del-1-b


title: kin82-del-b


title: kcc4-del-1-a


title: kin3-del-1-b


title: kin3-del-1-a


title: kns1-del-1-a


title: kin2-del-1-b


title: kin4-del-1-b


title: kin2-del-1-a


title: kkq8-del-1-a


title: ire1-del-2-b


title: ime2-del-1-b


title: kcc4-del-1-b


title: kin1-del-1-a


title: ire1-del-2-a


title: iks1-del-1-b


title: kin4-del-1-a


title: kin1-del-1-b


title: ime2-del-1-a


title: hrk1-del-1-a


title: hsl1-del-1-b


title: hsl1-del+cla4-del-1-b


title: iks1-del-1-a


title: hsl1-del-1-a


title: hsl1-del+cla4-del-1-a


title: hog1-del-2-b


title: hog1-del-2-a


title: hrk1-del-1-b


title: hal5-del-2-a


title: hal5-del-2-b


title: hal5-del+sat4-del-1-b


title: hal5-del+sat4-del-1-a


title: gin4-del-2-b


title: gin4-del-2-a


title: cmk1-del-1-b


title: cmk1-del-1-a


title: cmk2-del-1-a


title: dbf20-del-1-b


title: dun1-del-2-a


title: fus3-del-1-b


title: fus3-del-1-a


title: cla4-del-3-a


title: cla4-del-3-b


title: gcn2-del-1-b


title: cmk2-del-1-b


title: eki1-del-1-b


title: fus3-del+kss1-del-1-b


title: dun1-del-2-b


title: eki1-del-1-a


title: cka1-del-3-b


title: cki1-del-1-a


title: cka2-del-3-b


title: elm1-del-3-a


title: bck1-del-1-b


title: cki1-del-1-b


title: gcn2-del-1-a


title: cka1-del-3-a


title: dbf20-del-1-a


title: chk1-del-2-a


title: chk1-del-2-b


title: fus3-del+kss1-del-1-a


title: cka2-del-3-a


title: cdk8-del-2-b


title: fab1-del-3-a


title: bck1-del+ptp3-del-1-b


title: elm1-del-3-b


title: bck1-del-1-a


title: cdk8-del-2-a


title: ark1-del+prk1-del-1-b


title: cna1-del-1-b


title: akl1-del-1-b


title: ark1-del-1-a


title: ark1-del+prk1-del-1-a


title: atg1-del-1-b


title: atg1-del-1-a


title: rosettes_drought_h3k4me3

status: Public on Dec 07 2010

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

data_processing: See Methods from van Dijk et al. The Plant Cell. 2008 (submitted) for detailed protocol on data processing.

source_name: Histone H3K4 trimethyl antibody ChIP on vegetative rosettes under drought stress conditions

growth_protocol: Arabidopsis thaliana cultivar Columbia 0 plants were grown in pots with soil covered with miracloth to prevent soil contamination in 12 hr light for 4 weeks. Control plants continued to receive water while water was withheld from water deficit treated pla

extract_protocol: See Methods from van Dijk et al. The Plant Cell. 2008 (submitted) for detailed protocol on extract production, immunoprecipitation, and sequencing.

value: vegetative rosettes

tag: age

value: approx. 5 weeks


title: alk2-del-2-a


title: fmp48-del-1-a


title: rosettes_watered_h3k4me3

source_name: Histone H3K4 trimethyl antibody ChIP on vegetative rosettes under watered conditions


title: rosettes_drought_h3k4me1

source_name: Histone H3K4 monomethyl antibody ChIP on vegetative rosettes under drought stress conditions


title: rosettes_drought_h3k4me2

source_name: Histone H3K4 dimethyl antibody ChIP on vegetative rosettes under drought stress conditions


title: abc1-del-2-b


title: akl1-del-1-a


title: ark1-del-1-b


title: bck1-del+ptp3-del-1-a


title: alk2-del-1-b


title: fab1-del-3-b


title: cna1-del-1-a


title: fmp48-del-1-b


title: cmp2-del-1-a


title: ctk1-del-3-b


title: alk1-del-1-a


title: cmp2-del-1-b


title: abc1-del-2-a


title: alk1-del-1-b


title: ctk1-del-3-a


title: rosettes_watered_h3k4me2

source_name: Histone H3K4 dimethyl antibody ChIP on vegetative rosettes under watered conditions


title: rosettes_watered_h3k4me1

source_name: Histone H3K4 monomethyl antibody ChIP on vegetative rosettes under watered conditions


title: unassigned_run1

status: Public on Nov 13 2010

city: Worcester

first: Scot

last: Wolfe

address: 364 Plantation Street, LRB 619

department: MCCB

institute: UMass Medical School

description: all the reads that did not match the expected sequences (barcoded restriction enzyme fragments) exactly from illumina run 1 were grouped together

library_source: synthetic

data_processing:
Two barcoded, multiplexed samples were sequenced using Illumina Genome Analyzer machines.  Each experiment was associated with one or more expected sequence.  Expected sequences were determined based on the restriction enzyme and barcode used to uniquely identify each experimental sample.  Each read was assigned to an experiment if it matched the constant region of an expected sequence exactly.  Reads that did not match one of the expected sequences exactly were placed in the 'unassigned' category.
The Sample tables contain two columns. The first column contains all of the observed unique randomized regions for an experiment.  The second column contains an integer values which indicates the number of times each unique randomized region was observed.
Note: Randomized regions which contained 'N' characters were discarded.  Only reads which matched an expected sequence exactly were considered.  The sequences from multiple experiments were pooled and multiplexed.  The sequences from each experiment were uniquely labeled using a combination of different restriction enzymes and different barcodes.  The expected sequence for each experimental data set is determined by the restriction enzyme and barcode used. In order to be assigned to a specific experiment, a read had to match an expected sequence exactly at all constant (i.e. non randomized) bases.  For example, the expected sequence for the Zen2_omegaUV2zf_rep1 data set is GGTCATGGATCCNNNNNNNNNNTGGGCGGCTGATAG.  The read GGTCATGGATCCGTCCAGATTGTGGGCGGCTGATAG matches the expected sequence for Zen2_omegaUV2zf_rep1, but the sequence GGTCATGGATCCGTCCAGATTGTGGGCAAAAAAAAA does not.

molecule: other

organism: Drosophila melanogaster

source_name: B1H selection; unassigned reads

extract_protocol: After each selection, all of the cells were scraped of the plate.  The randomized portion of the prey vector containing the selected transcription factor binding sites were extracted and amplified using PCR.  The PCR products from different experiments were digested with different restriction enzymes  in the first step of uniquely encoding sequences from different experiments.  The restriction enzyme fragments were then barcoded, pooled and sequenced using the Illumina Genome Analyzer II or IIx.  the supplemental material of Noyes et al. (2008). Cell. 133(7):1277-1289 for a more detailed description of the experimental protocol employed.

tag: homeodomain protein

tag: iptg concentration

value: 10 uM

tag: 3-at concentration

tag: duration of experiment

value: 36-48 hours


title: Zen2_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Zen2

tag: bait_plasmid variant


title: Zen_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Zen

value: Zen


title: Vis_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Vis

value: Vis


title: Unpg_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Unpg

value: Unpg


title: Unc4_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Unc4


title: Tin_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Tin

value: Tin


title: Scr_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Scr

value: Scr


title: Tup_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Tup

value: Tup


title: Rx_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Rx

value: Rx


title: Slou_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Slou

value: Slou


title: Pb_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Pb

value: Pb


title: Oc_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Oc

value: Oc


title: Ptx1_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Ptx1


title: Odsh_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Odsh

value: Odsh


title: Otp_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Otp

value: Otp


title: Repo_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Repo

value: Repo


title: Vnd_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Vnd

value: Vnd


title: Optix_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Optix

value: Optix


title: PhdP_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: PhdP

value: PhdP

value: 10 uM


title: Ubx_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Ubx

value: Ubx

value: 36-48 hours


title: Lim3_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Lim3


title: So_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: So

value: So


title: Ro_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Ro

value: Ro


title: Six4_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Six4


title: Six4_omegaUV5zf_rep1


title: NK7.1_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: NK7.1


title: Pph13_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Pph13


title: onecut_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: onecut

value: onecut


title: Lim1_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Lim1


title: Mirr_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Mirr

value: Mirr


title: Lbl_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Lbl

value: Lbl


title: Hmx_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Hmx

value: Hmx


title: Lag1_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Lag1


title: Lab_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Lab

value: Lab


title: Hth_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Hth

value: Hth


title: Lbe_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Lbe

value: Lbe


title: Exd_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Exd

value: Exd


title: Hgtx_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Hgtx

value: Hgtx


title: H2.0_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: H2.0


title: Ind_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Ind

value: Ind


title: Eve_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Eve

value: Eve


title: Ftz_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Ftz

value: Ftz


title: Hbn_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Hbn

value: Hbn

value: 10 uM


title: Inv_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Inv

value: Inv

value: 36-48 hours


title: CG9876_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG9876


title: Ct_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Ct

value: Ct


title: CG7056_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG7056


title: CG4328_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG4328


title: Dr_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Dr

value: Dr


title: En_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: En

value: En


title: Ems_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Ems

value: Ems


title: En_R3K_I47N_A54R_K55R_omegaUV2zf_rep1

description: En synthetic mutant

source_name: B1H selection; homeodomain protein: En mutant R3K_I47N_A54R_K55R

value: En mutant R3K_I47N_A54R_K55R


title: Exex_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Exex

value: Exex


title: E5_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: E5


title: En_R3K_K55R_omegaUV2zf_rep1

description: En synthetic mutant

source_name: B1H selection; homeodomain protein: En mutant R3K_K55R

value: En mutant R3K_K55R


title: CG4136_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG4136


title: Dfd_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Dfd

value: Dfd


title: En_147N_A54R_omegaUV2zf_rep1

description: En synthetic mutant

source_name: B1H selection; homeodomain protein: En mutant 147N_A54R

value: En mutant 147N_A54R


title: Dll_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Dll

value: Dll


title: Gsc_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Gsc

value: Gsc


title: En_R3K_I47N_Q50A_A54R_K55R_omegaUV2zf_rep1

description: En synthetic mutant

source_name: B1H selection; homeodomain protein: En mutant R3K_I47N_Q50A_A54R_K55R

value: En mutant R3K_I47N_Q50A_A54R_K55R


title: CG34031_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG34031


title: CG32532_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG32532


title: CG33980_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG33980


title: CG15696_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG15696


title: CG18599_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG18599


title: CG32105_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG32105


title: CG12361_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG12361


title: CG11617_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG11617


title: CG13424_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG13424


title: CG11085_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG11085


title: CG11294_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: CG11294


title: Caup_A8F_E59Q_omegaUV2zf_rep1

description: Caup synthetic mutant

source_name: B1H selection; homeodomain protein: Caup mutant A8F_E59Q

value: Caup mutant A8F_E59Q


title: Caup_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Caup

value: Caup


title: Caup_E59Q_omegaUV2zf_rep1

description: Caup synthetic mutant

source_name: B1H selection; homeodomain protein: Caup mutant E59Q

value: Caup mutant E59Q

value: 10 uM


title: Caup_A8F_omegaUV2zf_rep1

description: Caup synthetic mutant

source_name: B1H selection; homeodomain protein: Caup mutant A8F

value: Caup mutant A8F

value: 36-48 hours


title: Bcd_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Bcd

value: Bcd


title: BH1_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: BH1


title: Bcd_I47N_omegaUV2zf_rep1

description: Bcd synthetic mutant

source_name: B1H selection; homeodomain protein: Bcd mutant I47N

value: Bcd mutant I47N


title: Bcd_K50A_omegaUV2zf_rep1

description: Bcd synthetic mutant

source_name: B1H selection; homeodomain protein: Bcd mutant K50A

value: Bcd mutant K50A


title: Cad_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Cad

value: Cad


title: Awh_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Awh

value: Awh


title: BH2_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: BH2


title: Ap_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Ap

value: Ap


title: Bcd_I47N_K50A_omegaUV2zf_rep1

description: Bcd synthetic mutant

source_name: B1H selection; homeodomain protein: Bcd mutant I47N_K50A

value: Bcd mutant I47N_K50A


title: Btn_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Btn

value: Btn


title: Ara_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Ara

value: Ara


title: Bap_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Bap

value: Bap


title: Antp_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Antp

value: Antp


title: unassigned_run2

description: all the reads that did not match the expected sequences (barcoded restriction enzyme fragments) exactly from illumina run 2 were grouped together

source_name: B1H selection; unassigned reads


title: AbdB_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: AbdB

value: AbdB


title: Achi_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Achi

value: Achi


title: Al_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: Al

value: Al


title: Slou_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Slou

value: Slou

value: 10 uM


title: Repo_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Repo

value: Repo

value: 36-48 hours


title: Rx_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Rx

value: Rx


title: Six4_omegaUV5zf_rep2

source_name: B1H selection; homeodomain protein: Six4


title: Lag1_omegaUV5zf_rep1

source_name: B1H selection; homeodomain protein: Lag1


title: Tin_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Tin

value: Tin


title: Ptx1_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Ptx1


title: Tup_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Tup

value: Tup


title: Scr_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Scr

value: Scr


title: Optix_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Optix

value: Optix


title: Lim1_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Lim1


title: Odsh_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Odsh

value: Odsh


title: Lbl_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Lbl

value: Lbl


title: Gsc_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Gsc

value: Gsc


title: Exd_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Exd

value: Exd


title: Inv_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Inv

value: Inv


title: En_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: En

value: En


title: AbdA_omegaUV2zf_rep1

source_name: B1H selection; homeodomain protein: AbdA

value: AbdA


title: CG34031_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: CG34031


title: CG33980_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: CG33980


title: Exex_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Exex

value: Exex


title: E5_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: E5


title: Zen2_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Zen2


title: CG32105_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: CG32105


title: Lab_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Lab

value: Lab


title: lacZ dsRNA

status: Public on Oct 21 2010

city: New York

first: Jessica

middle: E

last: Treisman

state: NY

address: 540 First Avenue

department: Cell Biology (Skirball)

institute: NYUMC

data_processing: Raw images were analyzed by Illumina RTA version 1.6 using Phix control lane for estimating base calling parameters. Reads were generated and aligned to the D. melanogaster genome (dm3) and exon-exon splice junction database (prepared using a UCSC annotation database downloaded on 4/23/10) by Illumina CASAVA version 1.6 using default filtering parameters. The first and last two nucleotides were trimmed out. In total, 22,537,621 and 21,130,945 50bp reads for LacZ and Mago samples, respectively, were sequenced. 46% of LacZ and 44% of Mago reads had eligible alignments after filtering for contaminants, repeats, and reads aligned to multiple genes. We normalized gene counts using the RPKM method (reads per kilobase of transcript per million mapped sequence reads)(Mortazavi et al., 2008), and calculated the fold-change of RPKM between the LacZ and Mago samples.

source_name: S2R+ cells treated with lacZ dsRNA

growth_protocol: Cells were maintained in Schneider's medium supplemented with 10% fetal calf serum

extract_protocol: Total RNA was extracted using TRIzol, cleaned using RNeasy Mini Kit (Qiagen) and treated with RQ1 RNase-Free DNase (Promega). Isolation of Poly(A)+ mRNA, RT reactions, and purification of the cDNA templates were performed following the mRNA-Seq Sample Preparation kit protocol from Illumina.

treatment_protocol: 10^6 cells per well were treated with 15 micrograms dsRNA for 3 days and placed in fresh medium with 15 micrograms dsRNA for another 3 days

tag: cell type

tag: treatment

value: 6 days with 15 micrograms lacZ dsRNA


title: CG12361_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: CG12361

value: 10 uM


title: BH2_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: BH2

value: 36-48 hours


title: Cad_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Cad

value: Cad


title: AbdB_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: AbdB

value: AbdB


title: B73_wild-type_2mm_ear_rep3

status: Public on Oct 20 2010

city: St. Louis

first: Andrea

middle: L

last: Eveland

state: MO

address: 975 N. Warson Road

institute: Donald Danforth Plant Science Center

description: 3' tag DGE libraries with DpnII and NlaIII from wild-type B73 2mm maize ears

data_processing:
Unique tag consolidation:  Raw sequences were extracted from the resulting image files using the open source Firecrest and Bustard applications (Illumina). Data were consolidated by read counts for unique sequences.  The consolidated, unfiltered sequence tags and raw read counts are provided as processed data files for each sample (lane of sequence).  All downstream analyses are detailed in Eveland et al., Digital gene expression signatures for Maize Development, Plant Physiol. 2010 Sep 10. [Epub ahead of print], PMID: 20833728
Alignment:  Vmatch (www.vmatch.de) sequence analysis software to map the collapsed reads to the maize reference genome.  The Vmktree feature was used to construct persistent indices for each of the 10 unmasked, assembled maize chromosomes and for an additional chromosome 0, which includes non-assembled sequence (B73 RefGen_v1).  For each of the 11 indices, the unique DpnII and NlaIII tags were queried for complete matches to all possible 20- and 21-mer sequences, respectively, using the Vmatch algorithm.  This included both sense and antisense matches and strand information for each tag was retained.  Processed data files include Vmatch alignments for sequence tags represented by at least 2 reads that align completely to the maize genome (B73 RefGen_v1) 1-3 times (alignments_complete_vmatch_DGE_comsensus_tags.txt) and the associated .gff3 file for viewing on a genome browser (DGE_complete_genomic_alignment.gff3).

organism: Zea mays

source_name: 2mm maize ear (female inflorescence)

extract_protocol: Typically 500–2000 ng of DNase I-treated total RNA was used in library construction. Briefly, after double-stranded cDNA synthesis using oligo(dT) beads (Invitrogen) the cDNA was digested with an anchoring restriction enzyme (NlaIII or DpnII) and ligated to Illumina specific adapter, Adapter A, containing a recognition site for the TypeIIS restriction enzyme MmeI (New England Biolabs).  Following MmeI digestion, dephosphorylation with shrimp alkaline phosphatase (USB Corp), and purification, a second Illumina adapter, Adapter B, containing a 2-bp degenerate 3’ overhang was ligated. Tags flanked by both adapters were enriched by PCR using Phusion DNA polymerase (Finnzymes) and Gex PCR primers 1 and 2 (Illumina) following the manufacturer’s instructions. The PCR products were run on a 12% PAGE gel and the 85-bp DNA band was excised and purified using Spin-X filter column (Costar) followed by ethanol precipitation. The DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent) and the DNA sample was diluted to 10 nM.  Each sample (multiplexed DpnII and NlaIII libraries) was sequenced in a single lane of an Illumina GA flow cell.

tag: genotype

value: wild-type (B73)

tag: replication

value: Biological rep 3:pool of 4-5 ears


title: ramosa3_2mm_ear_rep3

description: 3' tag DGE libraries with DpnII and NlaIII from ra3 mutant 2mm maize ears

value: ramosa3_mutant (B73 background)


title: ramosa3_2mm_ear_rep3b

value: Technical rep of ra3 biol rep 3


title: ramosa3_2mm_ear_rep2

value: Biological rep 2:pool of 4-5 ears


title: ramosa3_2mm_ear_rep1

value: Biological rep 1:pool of 4-5 ears


title: mago dsRNA

source_name: S2R+ cells treated with mago dsRNA

value: 6 days with 15 micrograms mago dsRNA


title: B73_wild-type_2mm_ear_rep2


title: BH1_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: BH1


title: N2_L4_dsDNALigSeq

city: Stanford

first: Ayelet

last: Lamm

state: CA

address: 300 Pasteur Drive, Lane Bldg Room L302

department: Pathology

institute: Stanford University School of Medicine

data_processing: The processed data files in fasta format contain the parsed RNA reads for each sample (without 5' barcode sequence). The raw files each correspond to a single lane of sequence sequences. The 5’ barcode was trimmed from the barcoded samples and the homopolymer A tail was trimmed from all reads that were obtained using the CircLigSeq method. Identical sequences were collapsed in each sample to avoid PCR "jackpots".

source_name: whole L4 hermaphrodite

extract_protocol: single-strand-capture, double-strand-capture, and circligase-based RNA-seq

value: whole L4 hermaphrodite

value: wild type

tag: strain

tag: rna-seq method

value: dsDNALigSeq

tag: gender

value: hermaphrodite


title: B73_wild-type_2mm_ear_rep1


title: Ap_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: Ap

value: Ap


title: CG13424_omegaUV2zf_rep2

source_name: B1H selection; homeodomain protein: CG13424


title: Tissue:Adult_ovaries:EL:1 extraction1_seq1 aliquote 1_Ago1IP_2749

status: Public on Oct 18 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is RIP RNA; Antibody information listed below: official name: Ago1;target name: Ago1;host: Rabbit;antigen: Synthetic peptide derived from within residues 1 - 100 of Fruit fly (Drosophila melanogaster) Ago1.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab5070;reference: http://www.biocompare.com/ProductCompare.aspx?i=304729 http://www.biocompare.com/ProductCompare.aspx?i=470260

data_processing: sequence analysis protocol. 1. 3' adapter sequences starting with 'CTGTAGG' were mapped and trimmed, allowing 2 mismatches when starting from base 20 in a read. Only reads with recognized 3' adapter and longer than 18 bases were considered in further analysis.2. The trimmed sequences were mapped to genome by BLAT. only sequences can perfectly match to genome were acceptable.  Processed data are obtained using following parameters: genome version is 5

growth_protocol: Young adult flies were fed with fly food supplemented with yeast for 3-4 days.Agef flies were anesthetized with CO2 and collected in an eppendorf tube.The flies were frozen on dry ice and stored at -80C until use.

extract_protocol:
1. Freeze 3-5 days old adult flies at -80C 2. Vortex frozen flies in a 15ml conical tube. 3. Sieve heads and bodies by mesh # 20 and  # 40. Bodies are recovered   from #20 fraction. Legs and wings are mostly lost in this procedure.   Proceed directly to total RNA isolation or freeze the samples at -80C.
Samples are homogenized in 100ul Hepes-NP40 buffer using plastic pestles and then 900ul Hepes-NP40 is added .Lysates are cleared by centrifugation at 4C for 10 minutes at 10,000g. Cleared extract was split and incubated with rabbit polyclonal AGO1 antibody (1:20; lot number 113754, Abcam) for 4 h at 4 uC. AGO1 antibodies were isolated by adding protein G beads (1:10; Roche) for 1 h. Beads were washed six times each for 10 min in buffer B (30 mM HEPES, pH 7.4, 800 mM NaCl, 2 mM MgCl2, 0.1% NP-40), which contained equal supplements as buffer A. The immunoprecipitation was analysed by western blotting using anti-AGO1 (1:2,000; Abcam). AGO1-associated RNAs were isolated with phenol/chloroform and ethanol precipitated.
A Gel purification of RNA sample1. Spike 50 ug of total RNA with 32P-labeled 19bp and 24bp oligos (~10,000 counts per second) and load the sample in a 15% polyacrylamide/urea gel (Sequagel, National Diagnostics). Run the gel in 1x TBE at constant 10W for 1-2 hours. Expose the gel for 10 minutes in Phosphoimager.2. Excise the band corresponding to the desired size of small RNA (~19-24 nt) into Eppendorf tubes, including the radio-labeled oligos. Add 400uL of 0.4M NaCl. Freeze rapidly in dry ice. Incubate (thaw) for 16 hours at room temperature with agitation to maximize RNA elution.3. Spin down gel slice homogenate through micropore filter (Ultrafree-MC, 0.22um, Millipore) for 1 minute at room temperature. Add 20ug of glycogen and 2 volumes of 100% Ethanol (RNase-free). Incubate at -20oC for 4 hours.4. Spin the sample at 4oC for 30 minutes. Wash the pellet with 70% EtOH, air dry for 2 min and resuspend in DEPC MQ water and proceed to section B.B 3'-linker ligation and gel purification of the ligated RNA product5. Ligate 50 pmol of Modban oligo (IDT:miRNA cloning linker 1) to the 3' terminus of the purified RNA sample in 1X ATP-free T4 RNA ligase buffer (50mM Tris-HCl (pH 7.5-7.6), 10mM MgCl2, 10mM DTT, 60ug/mL BSA) and 10% DMSO, with 5-10 pmol of T4 RNA ligase 2 Rnl2(1-249) (Ho et al, 2004). Incubate at room temperature for 1 hour 30 min. 6. Load the sample on a 15% polyacrylamide/urea gel as described above and expose the gel for 30 minutes.7. Excise the band corresponding to the desired size of small RNA (~36-41 nt) into Eppendorf tubes, including the ligated radio-labeled oligos.8. Proceed again with overnight elution and precipitation as in steps 2-4.C 5'-linker ligation and gel purification of the ligated RNA product.9. Ligate 50 pmol of Solexa linker to the 5' terminus of the RNA sample in 1XT4 RNA ligase buffer (Ambion) and 10% DMSO with 5-10 Units of T4 RNA ligase (Ambion). Incubate at 37oC for 1 hour 30 min.10. Load the sample on a 15% polyacrylamide/urea gel as described above and expose the gel for 1 hour.11. Excise the band corresponding to the desired size of small RNA (~68-73 nt) into Eppendorf tubes, including the ligated radio-labeled oligos.12. Proceed again with overnight elution and precipitation as in steps 2-4.D Reverse transcription and cDNA amplification.13. Reverse-transcribe the ligated RNA product by using 21 pmol of BanOne primer and 1 ul Superscript III Reverse Transcriptase (Invitrogen), for 1 hour at 50oC in 20 ul of reaction. Then, amplify 5 ul of the cDNA product with 100 pmol of primers Sol_5_SBS3 and Sol_3_Modban, and 5 Units of Taq Polymerase (New England Biolabs): [94oC 15 sec; 54oC 30 sec; 72oC 30 sec] x 5 cycles and [94oC 15 sec; 60oC 30 sec; 72oC 30 sec] x 17 cycles.14. Clean up the PCR product with phenol:chloroform and chloroform. Precipitate the amplified cDNA with Ethanol 100%.E Digestion of the spikes and gel-purification of the amplified cDNA.15. Perform PmeI (New England Biolabs) digestion of radiolabeled oligos (spikes) for 3-4 hours at 37oC and purify the amplified cDNA in a 2% low-melt agarose gel (SeaKem).16. Excise the ~ 120 bp DNA band and proceed to hot-phenol-based gel purification. Transfer aqueous phase to a new eppendorf tube and clean up with phenol:chloroform and chloroform. Precipitate the DNA with Ethanol 100% and resuspend it in 20uL water. 17. Perform Agilent test and dilute the sample to 10nM for Solexa sequencing.Required oligosModban:   AMP-5 p=5'pCTGTAGGCACCATCAATdideoxyC-3'   IDT  Product name: miRNA cloning linker 1      Solexa linker:   5'-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrC                                                   rUrCrUrUrCrCrGrArUrC-3'   IDT 'Custom oligo' HPLC purified      BanOne primer:   5'-ATTGATGGTGCCTACAG-3'                                                IDT 'Custom oligo' HPLC purified      Sol_5_SBS3 primer:   5'-AATGATACGGCGACCACCGAACACTCTTTCCCT                                                  ACACGACG-3'   IDT 'Custom oligo' Desalt      Sol_3_Modban primer: 5'-CAAGCAGAAGACGGCATACGATTGATGGTGCCT ACAG-3'   IDT 'Custom oligo' HPLC purified
1. cluster generation2. the length of short reads, i.e., the number of sequencing cycles is 35 cycles of sequencing.3. after each cycle, a CCD camera will scan the cells to make a image.

value: Adult Female

tag: Sex

value: Female


title: Pex33-overxpressing rice leaf

status: Public on Oct 01 2010

city: Ueda

first: Hideo

last: Matsumura

state: Nagano

address: Tokita 3-15-1

department: Gene Research Center

country: Japan

institute: Shinshu University

description: Pex33 gene (derived from Magnaporthe grisea) was transformed into rice callus (Sasanishiki).  Leaf was harvested from its regenerated plant.

data_processing:
Sequece reads were sorted by barcode into separate files. From each read in each file, 26-bp sequence upstream anchoring enzyme site (CATG, GTAC or CTAG) was extracted. Extracted 26-bp sequences (tags) were count. These process was done by script written in Perl.
Tags were extracted from sequence data of multiplexed samples, which were analyzed by Illumina Genome Analyzer IIx.

source_name: rice mature leaf

extract_protocol: ds-cDNA was synthesized using biotinylated dT primer. After digestion of cDNA with anchoring enzymes (NlaIII, DpnII or BfaI), digested fragments were associated with streptavidin magnetic beads. Adapters were ligated to cDNA ends on the beads and adapter-cDNA was digested with EcoP15I. Released fragments after enzyme digestion were ligated to adapter encoding barcode. Obtained fragments were once amplified PCR and applied to sequence analysis.

tag: anchor

value: NlaIII

tag: tag length

tag: tag count

tag: cultivar

value: Sasanishiki

tag: genome/variation

value: overexpressing Pex33 gene (regenerated plant from tissue culture)

tag: tissue

value: leaf


title: wild type rice (cv. Sasanishiki) leaf

description: Mature leaf from regenerated plant of rice (Sasanishiki) was applied to RNA extraction.

value: (regenerated plant from tissue culture)


title: SuperSAGE analysis of the Nicotiana attenuata transcriptome after wounding (F library 2)

status: Public on Oct 06 2010

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

description:
Sample_anchor = NlaIII
Sample_tag_length = 22
Sample_tag_count = 120119

'Utah' is a genotype of N. attenuata found in the Great Basin Desert of Southwestern USA, Utah.
The F library was generated from N. attenuata leaves elicited with fatty acid-amino acid conjugates (FACs). Tissue was collected 30 min after the treatment.
SuperSAGE library was generated as described by Matsumura et al. (2003) PNAS 100:15718-15723

Instrument model: 454 GS 20

data_processing: number of tag copies in the library

organism: Nicotiana attenuata

source_name: leaves

extract_protocol: Library construction protocol: 5 ug of mRNA were isolated from total RNA by using the mRNA Purification Kit (Amersham Biosciences). This mRNA was reverse-transcribed (cDNA synthesis system, Invitrogen) to generate single-stranded cDNA by using reverse transcription-primer with the sequence 5'-CTGATCTAGAGGTACCGGATCCCAGCAGTTTTTTTTTTTTTTTTT-3' containing the 5'-CAGCAG-3' recognition site of the type III restriction enzyme EcoP15I. The product was converted to double-stranded cDNA and digested with NlaIII (NEB, Beverly, MA). A suspension of streptavidin magnet beads (Promega) was added to the digestion reaction and the 3'-end fragments of the cDNAs were bound to streptavidin magnetic beads. The streptavidin-bound cDNA was washed and divided into two portions in separate tubes. Two FITC-labeled linkers (1E and 2E) were prepared by annealing commercially synthesized oligonucleotides (linker-1E, FITC-5'-TACAACTAGGCTTAATACAGCAGCATG-3' and 5'-CTGCTGTATTAAGCCTAGTTGTA-3'-NH2; linker-2E, FITC-5'-TTCTAACGATGTACGCAGCAGCATG-3' and 5'-CTGCTGCGTACATCGTTAGAA-3'-NH2; Qiagen, Valencia, CA). The unblocked 5' termini of linker-1E and -2E were phosphorylated by T4 polynucleotide kinase (NEB). Both linker-1E and -2E harbor the EcoP15I recognition sequence (5'-CAGCAG-3'). To each of the two tubes containing cDNA bound to magnet beads, linker-1E or -2E, respectively, were added and ligated to the cDNA ends by T4 DNA ligase (NEB). Consequently, each cDNA fragment is flanked by two inverted repeats of 5'-CAGCAG-3'. The type III restriction enzyme EcoP15I recognizes the asymmetric hexameric sequence 5'-CAGCAG-3' and cleaves the DNA 25 nt (in one strand) and 27 nt (in the other strand) downstream of the recognition site leaving a 5' overhang of two bases. Two unmethylated and inversely oriented recognition sites in head-to-head configuration (5'-CAGCAG-N(i)-CTGCTG-3') are essential for efficient cleavage. Linker-ligated cDNA on the magnetic beads was digested with 10 units of EcoP15I in the reaction mixture (10 mM Tris-HCl, pH 8.0/10 mM KCl/10 mM MgCl2/0.1 mM EDTA/0.1 mM DTT/5 mg/ml BSA/2 mM ATP) at 37°C for 90 min. Released fragments after EcoP15I digestion were separated on PAGE, and the ~69-bp 'linker-tag' fragments (linker, 42 bp; tag, ~27 bp) were visualized by FITC fluorescence on a UV transilluminator and collected from the gel. Linker-1E-tag and linker-2E-tag fragments were mixed, blunt-ended by filling-in with KOD DNA polymerase (from Thermococcus kodakaraensis strain KOD1, Toyobo, Osaka), and ligated to each other. The resulting ditags were amplified by PCR with biotinylated primers (ditag primer 1E, biotin-5'-CTAGGCTTAATACAGCAGCA-3'; ditag primer 2E, biotin-5'-TTCTAACGATGTACGCAGCAGCA-3'). After digestion of ditag PCR products with NlaIII, digested fragments were separated on PAGE and the fragment of ~54 bp was isolated from the gel. Amplified ditags were directly sequenced by a GS 20 sequencer (454 Life Sciences).

value: Utah

tag: developmental stage

value: rosette

tag: protocol

value: elicitation with fatty acid-amino acid conjugates (FACs)


title: rice pollen cells

description: Pollen cells were collected from rice anthers using Laser Microdissection

source_name: Pollens from rice plants

value: heading

value: pollens


title: SuperSAGE analysis of the Nicotiana attenuata transcriptome after wounding (W library 2)

description:
Sample_anchor = NlaIII
Sample_tag_length = 22
Sample_tag_count = 215585

'Utah' is a genotype of N. attenuata found in the Great Basin Desert of Southwestern USA, Utah.
The W library was generated from wounded N. attenuata leaves. Tissue was collected 30 min after the treatment.
SuperSAGE library was generated as described by Matsumura et al. (2003) PNAS 100:15718-15723

Instrument model: 454 GS 20

value: wounding


title: SG0807 seedling (allele of lm1)

description: One of three allelic mutants of rice.

source_name: seedling of rice SG0807 mutant

value: SG0807 mutant

tag: age


title: rice germinating seed (c.v. Kakehashi at low temp)

description:
Seeds were imbibed and incubated at 15˚C for germination.
RNA was extracted from whole germinating seeds.

source_name: rice germinating seed

value: Kakehashi

value: germinating seed

value: low temperature (15˚C)


title: Arabidopsis stems (DpnII)

description: RNA was extracted from stem tissues. Synthesized cDNA was separated in three tubes and digested with each different enzyme (NlaIII, DpnII, BfaI).

source_name: Arabidopsis stem tissues

tag: ecotype

value: Wassilevskija

value: stem tissues


title: Arabidopsis leaves (BfaI)

description: RNA was extracted from leaves. Synthesized cDNA was separated in three tubes and digested with each different enzyme (NlaIII, DpnII, BfaI).

source_name: Arabidopsis mature leaves

value: BfaI

value: rosetta leaves


title: Arabidopsis stems (BfaI)


title: M.grisea-infected rice cells (30h)

description: Compatible Magnaporthe grisea-infected rice leaf cells were collected with laser microdissection after 30h of infection.

source_name: Rice seedling inoculated with Magnaporthe grisea

value: NlaIII

value: leaf sheath

tag: treatment

value: Magnaporthe grisea infection, time after inoculation:30h


title: rice seedling-3 (5-cycles of PCR)

description:
One of the three independently grown seedlings.
Adapter-tags were amplified by five cycles of PCR reaction.

source_name: Rice seedlings

value: leaf


title: M.grisea-infected rice leaf tissue

description: Epidermal cell tissues were removed from infected leaf sheath and applied to RNA extraction.

value: Sasanishiki

value: Magnaporthe grisea infection


title: rice leaf (5-cycle PCR)

description: Adapter-tags were amplified by five cycles of PCR reaction.


title: rice anther wall tissue

description: Anther walls were collected from rice anthers using Laser Microdissection

source_name: Anther wall tissues from rice plants

value: heading

value: anther walls


title: zebrafish embryo 16.5h after fertilization

description: Embryo was collected at 16.5h after fertilization.

organism: Danio rerio

source_name: zebrafish developing embryo

value: Tg(fli1:EGFP)y1albino b4/b4)

value: whole embryo after fertilization

value: 16.5h after fertilization


title: M.grisea-infected rice cells (48h)

description: Compatible Magnaporthe grisea-infected rice leaf cells were collected with laser microdissection after 48h of infection.

value: Kakehashi

value: Magnaporthe grisea infection, time after inoculation:48h


title: lm1 rice mutant seedling

description: One of three allelic mutants of rice.

source_name: seedling of rice lm1 mutant

value: lm1 mutant


title: rice germinating seed (c.v.Dunghan shali at low temp)

value: Dunghan shali

value: germinating seed

value: low temperature (15˚C)


title: CM552 seedling (allele of lm1)

description: One of three allelic mutants of rice.

source_name: seedling of rice CM552 mutant

value: NlaIII

value: CM552 mutant


title: rice germinating seed (c.v. Kakehashi,submerged)

description:
Seeds were imbibed and incubated in submerged condition.
RNA was extracted from whole germinating seeds.

value: submergence


title: rice leaf (10-cycle PCR)

description: Adapter-tags were amplified by ten cycles of PCR reaction.

value: leaf


title: rice mature leaf (3-cyclePCR)

description: Adapter-tags were amplified by  three cycles of PCR reaction.

data_processing:
Tags were extracted from sequence data of multiplexed samples, which were analyzed by Illumina Genome Analyzer IIx.
Sequece reads were sorted by barcode into separate files. From each read in each file, 26-bp sequence upstream anchoring enzyme site (CATG, GTAC or CTAG) was extracted. Extracted 26-bp sequences (tags) were count. These process was done by script written in Perl.


title: rice seedling-2 (5-cycles of PCR)


title: rice germinating seed (c.v.Dunghan shali,submerged)


title: Arabidopsis stems (NlaIII)

value: Wassilevskija

value: stem tissues


title: rice seedling-1 (5-cycles of PCR)


title: Myers_GM12878_cell_1x32_ilNA_1

status: Public on Sep 11 2010

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCaltechRnaSeq

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/human/GM12878_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCaltechRnaSeq

tag: cell line

tag: cell organism

value: Human

tag: cell description

value: lymphoblastoid

tag: cell karyotype

value: relatively normal

tag: cell lineage

value: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus

tag: cell sex

value: F

tag: localization

value: cell

tag: readtype

tag: insertlength

value: ilNA

tag: replicate


title: Myers_K562_cell_1x32_ilNA_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/human/K562_protocol.pdf

value: leukemia

value: cancer

value: "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC


title: Myers_GM12878_cell_2x75_200_2


title: Myers_K562_cell_2x75_200_1


title: Myers_GM12878_cell_1x32_ilNA_2


title: Myers_GM12878_cell_2x75_200_1


title: Yeast-Ecoli control, Mnase

status: Public on Aug 20 2010

city: Piscataway

first: George

last: Locke

state: NJ

address: 136 Frelinghuysen Rd

department: Physics

institute: Rutgers University

data_processing:
Mononucleosome size DNA fragments were sequenced using Illumina Genome Analyzer, and mapped to the S.cerevisiae genome (SGD April 2008 build) and to the E.coli K12 genome (U00096), allowing up to 2 mismatches per read.
Raw sequence read data are unavailable

organism:
Escherichia coli
Saccharomyces cerevisiae

source_name: Yeast-Ecoli mixture

extract_protocol: Genomic DNA from S.cerevisiae and E.coli was purified using Qiagen genomic tip 500/G, and mixed in a 3:1 mass ratio. The mixture was treated with MNase (USB) to yield a small average fragment size (< 300 bp), and DNA fragments of approximately 150 bp were purified by excision from an agarose gel.

tag: strain (yeast)

value: BY4730 (MAT a, leu2∆0, met15∆0, ura3∆0)

tag: strain (e. coli)


title: Myers_K562_cell_1x32_ilNA_1


title: Arabidopsis leaves (DpnII)

tag: anchor

tag: tag length

tag: tag count

tag: tissue

value: rosetta leaves


title: Arabidopsis leaves (NlaIII)

value: NlaIII

tag: ecotype


title: zebrafish embryo 10.5h after fertilization

description: Embryo was collected at 10.5h after fertilization.

tag: strain

value: Tg(fli1:EGFP)y1；albino b4/b4)

value: whole embryo after fertilization

tag: developmental stage

value: 10.5h after fertilization


title: zebrafish embryo 15h after fertilization

description: Embryo was collected at 15h after fertilization.

value: Tg(fli1:EGFP)y1albino b4/b4)

value: 15h after fertilization


title: liver-rep1

status: Public on Jul 31 2010

city: Adelaide

first: Jan

middle: Marek

last: Szubert

state: South Australia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

description: 20nt from 5' monophospate RNA end

data_processing: To generate the processed data BED files (with UCSC type track headers), we trimmed from the read ends up to tissue barcodes starts, leaving 20/21 nucleotides, removed all those with mitochondrial mappings (no-missmatch) and non-unique-genomic mapping (1missmatch permitted), removing also any with long homopolymeric tracts ( >9nt ) and low average read quality (< Phred 20 ). Allowing 1 missmatch, only mappings to unique locations in the mm9 genome were taken and non-unique read sequences consolidated into a single BED file entry having the read sequence as a name, followed by the accumulated number of identical reads. Read mapping was carried out with Bowtie using indexing against the UCSC mm9 genome sequences, the filtering and processing pipeline being Perl script based.

organism: Mus musculus

source_name: whole liver

extract_protocol: RNA was extracted from adult mouse tissues using trizol and PARE libraries prepared as described in German et al, Nature Protocols, 2008. Polyadenylated RNA was isolated from 200ug total RNA (from adult mouse brain, liver or lung) using oligo(dT) dynabeads (Invitrogen) and an RNA adaptor (5’-GUUCAGAGUUCUACAGUCCGAC-3’) ligated using T4 RNA ligase (Ambion). RNA was extracted with phenol / chloroform, ethanol precipitated and re-purified with oligo(dT) dynabeads. RNA was then reverse transcribed (SuperscriptIII, Invitrogen) using the primer (5’-CGAGCACAGAATTAATACGACT(18)V-3’) and amplified by PCR (Phusion DNA Polymerase, Finnzymes) using the primers (5’-GTTCAGAGTTCTACAGTCCGAC-3’ and 5’-CGAGCACAGAATTAATACGAC-3’). PCR conditions were 7 cycles of 94 °C for 30s, 60 °C for 20s and 72 °C for 3 min. Products were gel purified, cleaved with MmeI (New England Biolabs) and dephosphorylated (Shrimp alkaline phosphatase, New England Biolabs). Samples were run on a 12% polyacrylamide gel and a 42nt band excised. DNA was eluted from the gel overnight with 0.3M NaCl, filtered through a Millex 0.45uM column and ethanol precipitated. Products were then ligated using T4 DNA ligase (Ambion) to one of 6 double-stranded DNA adaptors (top 5’-P-TCGTATGCCGTCTTCTGCTTG-3’, bottom NN: 3’-NNAGCATACGGCAGAAGACGAAC-5’) that varied in the composition of an additional first 6 nucleotides (not in the given sequence) to enable barcoding of the separate tissue samples. Another 12% polyacrylamide gel was run and a 92nt band excised and purified as above followed by PCR amplification using the following conditions : 25 cycles of 94 °C for 20s, 60 °C for 20s and 72 °C for 20s. The product was again run on a polyacrylamide gel and purified prior to high-throughput sequencing using the Illumina GA platform.

tag: genetic background

value: BALB-c

value: whole liver


title: lung-rep1

description: 20nt from 5' monophospate RNA end

source_name: whole lung

value: whole lung


title: brain-rep1

description: 20nt from 5' monophospate RNA end

source_name: whole brain

value: whole brain


title: ovary-rep1

description: 20nt from 5' monophospate RNA end

source_name: whole ovary

value: whole ovary


title: zebrafish embryo 12h after fertilization

description: Embryo was collected at 12h after fertilization.

value: 12h after fertilization


title: zebrafish embryo 13.5h after fertilization

description: Embryo was collected at 13.5h after fertilization.

value: 13.5h after fertilization


title: spleen-rep1

description: 20nt from 5' monophospate RNA end

source_name: whole spleen

value: whole spleen


title: kidney-rep1

description: 20nt from 5' monophospate RNA end

source_name: whole kidney

value: whole kidney


title: ER_WT-ChIPSeq

status: Public on Jun 30 2010

city: La Jolla

first: Joshua

middle: D

last: Stender

address: 9500 Gillman

institute: University of California at San Diego

description: Chromatin IP against Estrogen Receptor

data_processing:
Alignment: Reads were truncated to 25 bp and aligned to the human hg18 genome (NCBI Build 36) using eland.  Only reads that mapped to a single, unique position were used for downstream analysis.
Peak Identification: Peaks were identified using custom software (HOMER, available at http://biowhat.ucsd.edu/homer/).  Peaks were found by identifying 200 bp regions with tag density exceeding a threshold set at a 0.1% false discovery rate (determined by tag randomization).  Only peaks with >4x normalized tag density relative to control sequencing and >4x normlaized tag density to the sourrounding 10kb of region were considered for analysis

source_name: MDA-MB-231 Cells

growth_protocol: Cells were grown in phenol-red free DMEM-Ham's F-12 media with 10 mM HEPES, 10% Charcoal-dextran stripped media, 6 ng/ml bovine insulin, 3.75 ng/ml Hydrocortisone and 16 ug/ml glutathione.

extract_protocol: Chromatin was sonicated and precipitated using an specific antibody for ERa (HC20,Santa Cruz)

treatment_protocol: Cells were treated with 10 nM E2 for 45 minutes, fixed with 1% formaldehyde for 10 minutes and sonicated to shear chromatin.

tag: cell type

value: MDA-MB 231 cells stably expressing ER

tag: genotype/variation

value: WT-ER

tag: antibody

value: ERa

tag: antibody manufacturer

value: HC20 Santa Cruz

tag: cell amount

value: 20 million Cells


title: ER_DBDmut-ChIPSeq

description: Chromatin IP against Estrogen Receptor

value: DBDmut-ER


title: Illumina: Human-superior frontal gyrus-88 years old

status: Public on Jun 10 2010

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

country: China

institute: PICB

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 32120 day old human individual

data_processing: supplementary files contain small RNA sequences from purified low molecular weight RNA

source_name: Dissected human post-mortem superior frontal gyrus

extract_protocol: Total RNA was isolated from the frozen prefrontal cortex tissue using the Trizol (Invitrogen, USA) protocol with no modifications. Low molecular weight RNA was isolated, ligated to the adapters, amplified, and sequenced following the Small RNA preparation protocol (Illumina, USA) with no modifications.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used.

tag: sex

value: male

tag: age

value: superior frontal gyrus of the brain

tag: batch

value: human batch 2


title: Illumina: Human-superior frontal gyrus-4 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 4 day old human individual

value: 4 days


title: Illumina: Human-superior frontal gyrus-98 years old rep2

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 35770 day old human individual


title: Illumina: Human-superior frontal gyrus-34 days old rep2

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 34 day old human individual

value: 34 days


title: Illumina: Human-superior frontal gyrus-66 years old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 24090 day old human individual


title: Whole Brain small RNAs 1

status: Public on Jun 25 2010

city: Cambridge

first: Jin-Wu

last: Nam

address: Nine Cambridge Center

institute: Whitehead Institute

description: Size fraction(18-30nt)

data_processing:
Small RNA sequences from same total RNA samples were mapped to the human genome (hg18), requiring a perfect match, and reads co-localizing to annotated miRNA loci (miRBase, version 11.0) were counted.
sequence reads are summarized as frequency counts

source_name: Whole Brain

extract_protocol: The small RNA cDNA libraries were made as described (Grimson et al. 2008), except for the 3' adaptor ligation, which was 5' adenylated pTCGTATGCCGTCTTCTGCTTGidT. For a detailed protocol, see http://web.wi.mit.edu/bartel/pub/protocols.html.

tag: data type

value: small RNAs

value: brain


title: A1_ovaries_total

status: Public on Jul 19 2010

city: Cold Spring Harbor

first: Nikolay

middle: V

last: Rozhkov

email: nik.rozhkov@gmail.com, rozhkov@cshl.edu

address: 1 Bungtown Rd.

institute: CSHL

description:
19-30nt RNA isolated from ovaries of strain A1
processed_file_build: dm3

data_processing: Sequenced reads were clipped to remove 3' adapter, collapsed to obtain multiplicity, then mapped to relevant genome with no mismatches. Annotations were made based on genomic co-ordinates after mapping. Mapping count refers to number of times a sequence is mapped to the genome.

source_name: ovaries

extract_protocol: RNA was size selected (19-30nt) or small RNA-protein complexes were immunoprecipitated from extracts using specific polyclonal antibodies. These were then ligated to linkers at the 3' and 5' end using T4 RNA ligase, then PCR amplified and gel purified.

value: ovaries


title: Illumina: Human-superior frontal gyrus-13 years 360 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 5105 day old human individual

value: 5105 days


title: Illumina: Human-superior frontal gyrus-80 years old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 29200 day old human individual

value: Age 29200 days

value: human batch 1


title: Whole Brain small RNAs 2

description: Size fraction(18-30nt)


title: Illumina: Human-superior frontal gyrus-25 years 152 day old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 9277 day old human individual

value: 9277 days


title: Illumina: Human-superior frontal gyrus-204 days old

description: miRNA sequencing raw reads from post-mortem superior frontal gyrus of a 204 day old human individual

value: 204 days