title: iso31

city: Belgrade

first: Predrag

middle: M

last: Kalajdzic

address: Despota Stefana 142

department: Department for population genetics and ecogenotoxicology

country: Serbia

institute: Institute for biological research "Sinisa Stankovic"

data_processing: We downloaded the dmel-all-transcript-r5.29.fasta file from Flybase containing the sequences of every predicted transcript from genome release 5.29 (FB2010_06), availiable at ftp://flybase.net/genomes/Drosophila_melanogaster/dmel_r5.29_FB2010_06/fasta/dmel-all-transcript-r5.29.fasta.gz. The reads were aligned against the transcripts using the RMAP software (Version 2.05) for short-read mapping (Smith et al.,Bioinformatics 2009). RNAseq expression values corresponding to total reads per transcript and reads per kilobase mapped (RPKM) values were computed using custom AWK scripts. Genes with 10 or less reads for one line and 50 reads or less for the other line were excluded from further analysis. The minimum difference threshold between lines was set to 2-fold. References: Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z and Zhang MQ (2009) Updates to the RMAP short-read mapping software. Bioinformatics 25(21):2841-2842.

source_name: susceptible line

extract_protocol: Total RNA from 3 days old Drosophila melanogaster  flies was extracted using standard Trizol RNA isolation protocol (http://quantgen.med.yale.edu/). Preparation of cDNA for sequencing was done with the Illumina mRNA Seq V2 protocol. Formation of single molecule arrays, cluster growth and sequencing was all done according to the standard protocols from Illumina, Inc. Sequencing was performed on a 2008 Illumina Genome Analyzer, version 2 (GA2).

treatment_protocol: No treatment. D. melanogaster stocks were maintained on standard cornmeal-agar-yeast medium at 24oC with a 12-hour light/12-hour dark cycle.

value: adults

tag: line source


title: 4DPFVD3 rep3

status: Public on Jun 29 2012

type: SRA

city: Baltimore

first: Yuji

last: Zhang

state: MD

address: 660 W. Redwood Street

country: USA

institute: University of Maryland

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
mRNA-seq reads were aligned to the ZV9 assembly using Bowite 0.12.7 with the following configurations…
Gene and exon level count data were generated by HTSeq 0.5.3p3
Genome_build: ZV9
Supplementary_files_format_and_content: tab-delimited text files include raw count numbers at gene and exon level for each Sample ...

molecule: total RNA

organism: Danio rerio

source_name: Zebrafish embryos/larvae

growth_protocol: Zebrafish embryos were obtained from mating of Segrest wild-type (SWT) parents under controlled barrier conditions, in the Mayo Clinic Zebrafish Core Facility, in Instant Ocean media .  Zebrafish embryos (25-30) were placed in 20 mL embryo medium (pH 7.2) containing 1-phenyl-2-thiourea (PTU) (0.003% (w/v) and were maintained at 28-30 oC.  At 24 hpf (1 day post fertilization, dpf), 10 microliters of 1a,25(OH)2D3  in ethanol was added to embryos maintained in 20 mL fresh embryo medium with PTU.  The final concentration of 1a,25(OH)2D3 was 300 pM.  Control zebrafish were treated with 10 microliters ethanol alone (vehicle controls).  The medium containing either 300 pM 1a,25(OH)2D3 or vehicle was changed every 24 h .   In experiment 1, at 2, 4, 6 and 7 dpf embryos/larvae were removed and immediately frozen at -80 0C for later RNA preparations.  25-30 embryos per set were used for preparation on RNA.  At the same times, 7-12 embryos were fixed in 4% paraformaldehyde in 0.75 X Dulbecco’s phosphate buffered saline (DPBS).  In experiment 2, 6 dpf larvae were treated with 1a,25(OH)2D3 (300 pM) or vehicle for 24 h.  RNA was prepared from three sets of larvae.

extract_protocol: RNA preparation for RNA-seq and QPCR:  RNA was prepared using RNA/protein spin columns (Clontech, Mountain View, CA).  Lysis solution was added to 25-30 frozen embryos and embryos were lysed by passage of tissue successively through 21 and 27 gauge needles.  Individual embryo lysates were applied to RNA spin columns for purification.  Preparation of libraries:  mRNA-seq libraries are prepared using the mRNA v1 sample prep kit following the manufacturer’s protocol (Illumina).  Poly-A containing mRNA is purified using poly-T oligo attached magnetic beads. The purified mRNA is fragmented using divalent cations at 95°C for 5 minutes and ethanol precipitated. The RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis is performed using DNA polymerase I and RNase H. The cDNA is purified using Qiaquick PCR columns from Qiagen. The ends are repaired and phosphorylated using Klenow, T4 polymerase, and T4 polynucleotide kinase, after which an “A” base is added to the 3’ ends of double-stranded DNA using Klenow exo- (3’ to 5’ exo minus).  Paired end DNA adaptors (Illumina) with a single “T” base overhang at the 3’ end are ligated and the resulting constructs are separated on a 2% agarose gel. DNA fragments of approximately 250-300 bp are excised from the gel using GeneCatcher tips and purified using Qiagen Gel Extraction Kits.  The adapter-modified DNA fragments are enriched by 15 cycles of PCR using primers PE 1.0 and PE 2.0 (Illumina). The concentration and size distribution of the libraries is determined on an Agilent Bioanalyzer DNA 1000 chip.  Libraries are loaded onto paired end flow cells at concentrations of 6 pM to generate cluster densities of 400,000/mm2 following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 2.  The flow cells are sequenced as 51 X 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 1 or version 3 and SCS version 1.1.37.0 or HCS version 1.4.8 data collection software, respectively. Base-calling is performed using Illumina’s RTA version 1.7.45.0.

tag: genotype

value: Segrest wild type

tag: age

value: 4 days post fertilization

tag: treatment


title: input w DNA

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

library_source: genomic

data_processing:
*.sgr : Smoothed ratio values in 35 bp steps, The reads were aligned against the Drosophila reference sequence (version 5.25) using the classical mapping in Applied Biosystems Bioscope software v1.2.1. The number of uniquely mapping reads was 21,667,438 (wild-type input), 17,131,635 (wild type CBP), 25,683,953 (gd7 input) and 18,325,130 (gd7 CBP). Average read-count per nucleotide was calculated for IP and input samples. For regions where the IP sample had at least the average read-count, a ratio of IP-input (in log2 scale) was calculated. If the read count in the input was below the average read-count (in the input sample) it was set to the average. All ratio values were then adjusted by reducing each value with the average read-count in IP minus the average read-count in input. This linear adjustment was to normalize for differences in sequencing depth of IP and input. Then the ratio value at an interval of 35 bp was extracted across the genome and median smoothed using a window size of 350 bp. Windows with fewer than 5 data points were discarded. The dynamic range of CBP in wild type was -2.0 – 5.1 and CBP in gd7 -1.8 – 5.1.
*.gff : High confidence peaks, To calculate peaks and bound regions, the 5% highest ratio values in both wild type and gd7 were extracted, corresponding to a cut-off of 1.9 in wild type and 1.9 in gd7. Bound regions were then defined as regions of at least 200 bp and a region was extended as long as there was a value within 200 bp of the previous value. The value of each detected region was set to the average of the highest five consecutive ratio values. The center of the peak was set to the middle position of the five highest consecutive ratio values.

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Embryos collected on apple juice plates with yeast at 2 hour intervals, and aged an additional 2 hours.

extract_protocol: Embryos were dechorionated in bleach, homogenised with a Dounce homogeniser to release nuclei and crosslinked in 1% formaldehyde. Nuclei were washed and sonicated using a Bioruptor (Diagenode) to generate chromatin extract. Chromatin extract was cleared by centrifugation and used in ChIP with affinity-purified anti-Drosophila CBP antibody generated in rabbit, pre-bound to a mix of Protein A and G dynabeads. CBP bound DNA was purified, and sent to Uppsala Genome Center for SOLiD (TM) ChIP-Seq Library preparation (Rev date 18 March 2010), size selection (100-150 bp + adapters 90bp ≈250 bp), and SOLiD sequencing.

tag: genotype/variation

value: w1118 (wild type)

tag: developmental stage

value: 2-4h embryo


title: MiT[w-]3R2

status: Public on Jun 28 2012

source_name: resistant line

growth_protocol: D. melanogaster stocks were maintained on standard cornmeal-agar-yeast medium at 24oC with a 12-hour light/12-hour dark cycle.

value: retrieved from Minos-based insertional mutagenesis screen


title: AACCTA

first: Sten

last: Linnarsson

address: Scheeles väg 2

department: MBB

institute: Karolinska Institutet

data_processing:
Base-calling was performed using CASAVA on the Genome Analyzer IIx
Raw reads were demultiplexed into 96 files (one per barcode, but 4 barcodes were unused)
Reads were aligned using Bowtie version 0.12.7 with standard parameters
Reads were then annotated using gene models obtained from UCSC on 2012-02-03.
Genome_build: hg19
Supplementary_files_format_and_content: RPM (reads per million) was calculated by considering all reads mapped onto all known exons of each gene (including spliced reads)
Supplementary_files_format_and_content: L127_RPM.tab (supplementary)  contains a matrix of RPM values for each sample and each gene, in tab-delimited text format

organism: Homo sapiens

source_name: FB

growth_protocol: MSCs were isolated from human subcutaneous adipose tissue, passed through a 100 µm nylon mesh and replated in 10% FBS growth medium. After 48 h   medium was replaced to remove non-adherent cells. Further cultivation was performed under standard cell culture conditions. Fibroblasts were isolated from dermal skin of the same donors   as MSCs and primary culture was established by fibroblast outgrowth from skin explants placed onto Primaria dish (BD Falcon) in 10% FBS and 1% penicillin-streptomycin DMEM-High Glucose (Gibco) growth medium.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen).  Following a phenol/chloroform extraction and isopropanol precipitation, RNA samples were treated with DNase I using DNA-free kit (Ambion). RNA-seq libraries were prepared according to the STRT protocol ("Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing" Islam et al. Nature Protocols vol. 7 no. 5, 2012)

treatment_protocol: Passage three or four cells were plated 72 hours prior to induction of differentiation. 10% FBS and 1% penicillin-streptomycin containing growth medium was supplemented with:   1µM dexamethasone, 500µM IBMX (3-isobutyl-1methylxanthine), 100µM indomethacin and 10µg/ml insulin for adipogenic induction;  100nM dexamethasone, 50µM L-ascorbic acid 2-phosphate and 10mM glycerol 2-phosphate for osteogenic induction; 50µM L-ascorbic acid 2-phosphate, 6,25µg/ml insulin and 10ng/ml TGFbeta-1   (Peprotech) for chondrogenic induction.

tag: cell type

value: Fibroblasts

value: Chondrogenesis

tag: day

tag: patient code name

value: Daphne

tag: barcode

value: AACCTA


title: CTGAAA

value: CTGAAA


title: ACCTGA

value: ACCTGA


title: ACACCC

value: ACACCC


title: CAACAA

value: CAACAA


title: TGCAAT

value: TGCAAT


title: TGCGGA

value: Charlotte

value: TGCGGA


title: TGTCAC

value: TGTCAC


title: GTATAC

value: GTATAC


title: TTCCGC

value: TTCCGC


title: CTCGCA

value: CTCGCA


title: TGATCA

value: Osteogenesis

value: TGATCA


title: CGTATT

value: Fibroblasts

value: Noninduced

value: CGTATT


title: GACACT

value: Chondrogenesis

value: GACACT


title: TATTGT

value: Daphne

value: TATTGT


title: ACTTAT

value: ACTTAT


title: TGGATG

value: TGGATG


title: GAACGC

value: GAACGC


title: ACGTTG

value: ACGTTG


title: GAATTA

value: GAATTA


title: GCGTCC

value: Charlotte

value: GCGTCC


title: CGCTTG

value: CGCTTG


title: CGTGGC

value: Osteogenesis

value: CGTGGC


title: ACGAGC

value: Fibroblasts

value: ACGAGC


title: TCTACC

value: TCTACC


title: TGTGCG

value: TGTGCG


title: TCAAAG

value: Adipogenesis

value: TCAAAG


title: AGTCGT

value: AGTCGT


title: GCAGGA

value: GCAGGA


title: GCCTAG

value: Daphne

value: GCCTAG


title: ATCTCT

value: ATCTCT


title: AGATGG

value: AGATGG


title: GCTGTG

value: Noninduced

value: GCTGTG


title: GTAATG

value: GTAATG


title: AGGGTC

value: AGGGTC


title: CCATCT

value: Osteogenesis

value: CCATCT


title: AACGCC

value: Fibroblasts

value: Charlotte

value: AACGCC


title: GGCTGC

value: Adipogenesis

value: GGCTGC


title: TTCATA

value: TTCATA


title: ATGGCG

value: ATGGCG


title: CGGCAG

value: Chondrogenesis

value: CGGCAG


title: TCGGGT

source_name: MSC

value: Mesenchymal Stem Cells

value: Daphne

value: TCGGGT


title: CCTAGA

value: CCTAGA


title: TAGCAT

value: TAGCAT


title: GTGGTA

value: Noninduced

value: GTGGTA


title: AAAACG

value: AAAACG


title: CTCCAT

value: CTCCAT


title: CATGAT

value: Fibroblasts

value: Charlotte

value: CATGAT


title: GAGATC

value: GAGATC


title: CCGACG

value: CCGACG


title: CTTCTG

value: CTTCTG


title: ATACAG

value: Chondrogenesis

value: ATACAG


title: GCGAAT

value: Mesenchymal Stem Cells

value: GCGAAT


title: CCGCTA

value: CCGCTA


title: TGAAGC

value: TGAAGC


title: GATCTT

value: GATCTT


title: AAGTAC

value: AAGTAC


title: AAAGTT

value: Osteogenesis

value: Daphne

value: AAAGTT


title: GTTGCC

value: Noninduced

value: GTTGCC


title: TAAGGG

value: TAAGGG


title: TTAACT

value: Charlotte

value: TTAACT


title: GTCCCG

value: GTCCCG


title: TACTTC

value: TACTTC


title: GGGTTT

value: Fibroblasts

value: Adipogenesis

value: GGGTTT


title: TAGAGA

value: Mesenchymal Stem Cells

value: TAGAGA


title: TAGTCG

value: TAGTCG


title: CACAAG

value: CACAAG


title: input DNA

city: Madrid

first: Pilar

last: Santisteban

state: Madrid

address: Arturo Duperier 4

department: Physiopathology of the Endocrine and Nervous System

country: Spain

institute: Biomedical Research Institute-CSIC

description: input DNA

data_processing:
Alignment: Sequence reads were obtained and mapped to the rat (November, 2004) genome using the MIRO pipeline. All reads mapping with two or fewer mismatches were retained
The reads were directionally extended to 300 bp, and for each base pair in the genome the number of overlapping sequence reads was determined and averaged over a 10 bp window to create a wig file to visualize the data in the University of California Santa Cruz genome browser (http://genome.ucsc.edu)

organism: Rattus norvegicus

growth_protocol: PCCl3 thyroid cells were grown in Coon’s modified Ham’s F-12 medium supplemented with 5% donor calf serum and a six-hormone mixture [1 nM TSH, 10  g/ml insulin, 10 ng/ml somatostatin, 5  g/ml transferrin, 10 nM hydrocortisone, and 10 ng/ml glycyl-L-histidyl-L-lysine acetate]

extract_protocol: IP and non-IP DNAs were modified for sequencing following the ChIP-Seq manufacturer’s protocol (Illumina, San Diego, CA). Briefly, DNAs were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK. Then, a single 3′-end “A” base was added using Klenow exo (3′-to-5′ exo minus). Adapters provided by Illumina were then ligated to the ends of the modified DNA before size selection of ∼200-bp fragments via PAGE extraction. The isolated DNA samples were used as the template for amplification by 18 cycles of PCR, and used for cluster generation on the Illumina 1G genome analyzer. Amplified products were column purified with the QIAquick PCR Purification Kit (Qiagen, Dusseldorf, Germany) and assayed for quantity and quality with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: ChIP samples were prepared from PCCl3 cells as follows: cultures of 10 × 106 cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature. Cross-linking was stopped by the addition of glycine to 125 mM final concentration, and cells were washed twice with 1× PBS. The cell pellet was then resuspended consecutively in different ChIP lysis buffer and sonicated for 90 minutes (30 second pulsing and resting, high frequency) using the Bioruptor sonicator (Diagenode, Denville, NJ) to produce chromatin fragments of 200-500 bp on average. After isolating chromatin, we incubated it with previously prepared PAX8-coated magnetic beads. To prepare beads, 100 ul of magnetic sheep anti-rabbit IgG beads (Invitrogen, Carlsbad, CA) were incubated overnight with 10 ug PAX8 rabbit monoclonal antibody (Biopat, Milan, Italy). The following day, the beads were rinsed and added to shear chromatin and incubated overnight at 4°C. Samples were then rinsed five times with RIPA buffer, and the antibody was stripped from the beads by incubating in 1% SDS at 65°C for 15 minutes; cross-linking was reversed by incubating overnight at 65°C. The next day, samples were sequentially treated with RNAse A and Proteinase K, phenol-chloroform extracted, ethanol precipitated with 20 ug glycogen and resuspended in 50 ul 10 mM Tris pH 8.0.

value: Thyroid cells

tag: antibody


title: ATCAAC

value: Osteogenesis

value: Daphne

value: ATCAAC


title: PAX8_Chip-seq

description: Chromatin IP against PAX8

tag: antibody vendor

value: Biopat, Milan, Italy

tag: antibody catalog number


title: ATGCTT

value: ATGCTT


title: ACAATA

value: Charlotte

value: ACAATA


title: AGTTTA

value: AGTTTA


title: TATGTA

value: TATGTA


title: AATAAA

value: AATAAA


title: AAGCGG

value: Adipogenesis

value: AAGCGG


title: TCGTAA

value: Mesenchymal Stem Cells

value: TCGTAA


title: GCCCTC

value: GCCCTC


title: ATTTGC

value: ATTTGC


title: GTCGGT

value: GTCGGT


title: AGCGAG

value: AGCGAG


title: CATCCC

value: CATCCC


title: GGACAT

value: GGACAT


title: TTGGAC

value: TTGGAC


title: CAAAGT

value: Noninduced

value: Daphne

value: CAAAGT


title: GGTACA

value: GGTACA


title: ATTCCA

value: Charlotte

value: ATTCCA


title: GCTCAA

value: Adipogenesis

value: GCTCAA


title: CTGTGT

value: Mesenchymal Stem Cells

value: CTGTGT


title: CCAGAC

value: Osteogenesis

value: CCAGAC


title: Lib 6

status: Public on Jun 26 2012

city: Davis

first: Richard

last: Michelmore

state: CA

address: Genome & Biomedical Sciences Facility, 451 East Health Sciences Drive

department: Genome Center

institute: University of California, Davis

description:
Small RNA.
At-CHS silenced, strongly silenced.

data_processing:
Sequences and intensity scores were extracted from the GAII image files using the standard Illumina IPAR pipeline.
Filtering for high-quality reads and adaptor trimming were done with a custom script.
FASTA files were generated based on analysis of calibrated peak intensities per channel in sig2 files.
All details of sig2 data processing are at http://atgc-illumina.googlecode.com/files/ILLUPA_Overview_AKozik_100108_A.pdf, slides 19-24, and in the script http://code.google.com/p/atgc-illumina/wiki/IlluminaFiltering .
Supplementary_files_format_and_content: FASTA files include clean trimmed high-quality reads that were used for the analysis and read counts.

organism: Arabidopsis thaliana

source_name: whole rosette, three weeks old, strongly At-CHS silenced

growth_protocol: Light intensity of ~300 μE, 14h light/10h dark photoperiod, 15°C during the day and 5°C during the night.

extract_protocol: The libraries were made using Small RNA Sample Prep Kits (Illumina Inc.; http://www.illumina.com/) following the manufacturer's protocol. 41 (Libs 0, 5 and 6) or 45 (Libs 1-4) cycles of Illumina sequencing.

treatment_protocol: Pooled 120 individual plants from ten independent T2 progenies.

tag: ecotype

value: transgenic

tag: ihprna construct

value: gusa-chsa^chss-guss

tag: tissue

value: whole rosette

value: 3 weeks


title: Lib 5

value: chss-guss^gusa-chsa


title: Lib 4

description:
Small RNA.
At-CHS silenced.

source_name: whole rosette, three weeks old, At-CHS silenced


title: Lib 2

description:
Small RNA.
At-CHS silenced.


title: Lib 3

description:
Small RNA.
At-CHS silenced.

value: chsa-gusa^guss-chss


title: AGGACT

value: Noninduced

value: AGGACT


title: GAGGAG

value: Daphne

value: GAGGAG


title: Lib 0

description:
Small RNA.
Not silenced.

source_name: whole rosette, three weeks old, not At-CHS silenced

value: wild-type


title: HepG2

city: Barcelona

first: Julien

last: Lagarde

address: Dr. Aiguader 88

department: Bioinformatics and Genomics

institute: CRG

description: pooled RT-PCR products

data_processing:
The reads were mapped with BLAT v.34 with defaults parameters = blat.out.psl
Genome_build: hg19
Supplementary_files_format_and_content: PSL files contain the BLAT mapping of the 454 reads on the human genome (hg19 build)

molecule: polyA RNA

source_name: Liver carcinoma cells

growth_protocol: Cells are grown according to ENCODE standards

extract_protocol: Oligo-dT was used to prime batch RNA.  96-well PCR was then conducted using junction-specific primers on the resulting cDNA. The resultant RT-PCR products were pooled according to cell line and sequenced on the Roche 454 FLX.

tag: cell line

value: transformed cells

value: Liver carcinoma cells


title: H1 ES Cells

description: pooled RT-PCR products

source_name: embryonic stem cells

value: stem cells

value: embryonic stem cells


title: 7DPFETOH rep4

treatment_protocol: Zebrafish embryos were obtained from mating of Segrest wild-type (SWT) parents under controlled barrier conditions, in the Mayo Clinic Zebrafish Core Facility, in Instant Ocean media .  Zebrafish embryos (25-30) were placed in 20 mL embryo medium (pH 7.2) containing 1-phenyl-2-thiourea (PTU) (0.003% (w/v) and were maintained at 28-30 oC.  At 24 hpf (1 day post fertilization, dpf), 10 microliters of 1a,25(OH)2D3  in ethanol was added to embryos maintained in 20 mL fresh embryo medium with PTU.  The final concentration of 1a,25(OH)2D3 was 300 pM.  Control zebrafish were treated with 10 microliters ethanol alone (vehicle controls).  The medium containing either 300 pM 1a,25(OH)2D3 or vehicle was changed every 24 h .   In experiment 1, at 2, 4, 6 and 7 dpf embryos/larvae were removed and immediately frozen at -80 0C for later RNA preparations.  25-30 embryos per set were used for preparation on RNA.  At the same times, 7-12 embryos were fixed in 4% paraformaldehyde in 0.75 X Dulbecco’s phosphate buffered saline (DPBS).  In experiment 2, 6 dpf larvae were treated with 1a,25(OH)2D3 (300 pM) or vehicle for 24 h.  RNA was prepared from three sets of larvae.

value: Segrest wild type

value: 7 days post fertilization

value: ethanol


title: HUVEC

description: pooled RT-PCR products

source_name: Umbilical vein epithelial cells

value: HUVEC

value: primary cells

value: Umbilical vein epithelial cells


title: TTTAGG

value: Mesenchymal Stem Cells

value: Charlotte

value: TTTAGG


title: pGES-1 _HPL-2_YL416_3-4-10_L1_rep1_GFP_ACGT

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

description: Chromatin IP against HPL-2 using anti-GFP

data_processing: Sequence reads were aligned to the reference genome (WS182), and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200-bp. Peaks were determined using Peakseq program.

organism: Caenorhabditis elegans

source_name: pGES-1  HPL-2:GFP:FLAG whole animal

extract_protocol: Chromatin was sheared to 200-800 bp using a Branson sonifier microtip, immunoprecipitated using anti-GFP antibody and purified using Qiangen PCR purification kit. The protocol for library preparation was modified from the protocol "Preparing Samples for sequencing genomic DNA" by Illumina. The antibody to GFP was provided by the laboratory of A.A. Hyman, at Max-Planck Institution in Dresden, Germany.

tag: strain

tag: Stage

tag: chip antibody

value: GFP


title: pGES-1_LIN-35_YL398_3-4-10_L1_rep1 _Input _GTAT

description: No immunoprecipitated sheared genomic DNA from the same preparation

source_name: pGES-1 LIN-35:GFP:FLAG whole animal


title: pGES-1_LIN-35_YL398_6-14-10_L1_rep2 _Input _CATT


title: pGES-1_DPL-1_YL448_6-7-10 _L1_rep2_Input _GTAT

source_name: pGES-1 DPL-1:GFP:FLAG whole animal


title: pGES-1_LIN-35_YL398_6-14-10_L1_rep2 _GFP _GTAT

description: Chromatin IP against LIN-35 using anti-GFP


title: pGES-1_LIN-35_YL398_3-4-10_L1_rep1 _GFP _GTAT


title: pGES-1 _HPL-2_YL416_3-4-10_L1_rep1_Input_ACGT


title: pGES-1 _HPL-2_YL416_3-4-10_L1_rep2_Input_ACGT


title: pGES-1 _HPL-2_YL416_3-4-10_L1_rep2_GFP_ACGT


title: pGES-1_DPL-1_YL448_3-22-10_L1_rep1_GFP_TGCT

description: Chromatin IP against DPL-1 using anti-GFP


title: pGES-1_EFL-1_YL418_6-21-10_L1_rep3 _GFP_ACGT

description: Chromatin IP against EFL-1 using anti-GFP

source_name: pGES-1 EFL-1:GFP:FLAG whole animal


title: pGES-1_DPL-1_YL448_3-22-10_L1_rep1_Input_TGCT


title: pGES-1_EFL-1_YL418_6-21-10_L1_rep3 _Input_TGCT


title: Lib 1

description:
Small RNA.
At-CHS silenced.

tag: genotype

value: transgenic

value: guss-chss^chsa-gusa

value: whole rosette

tag: age

value: 3 weeks


title: pGES-1_EFL-1_YL418_5-31-10_L1_rep2_Input_CATT


title: Plin-35_LIN-35_YL409_4-12-10_L1_rep2.2_GFP_CATT

source_name: Plin-35_LIN-35:GFP:FLAG whole animal


title: Plin-35_LIN-35_YL409_4-9-10_L1_rep1_Input _GTAT


title: Plin-35_LIN-35_YL409_4-12-10_L1_rep2.1_GFP_CATT


title: pGES-1_EFL-1_YL418_5-31-10_L1_rep2_GFP_CATT


title: Plin-35_LIN-35_YL409_4-9-10_L1_rep1.2_GFP _GTAT


title: Plin-35_LIN-35_YL409_4-12-10_L1_rep2_Input_CATT


title: Plin-35_LIN-35_YL409_4-9-10_L1_rep1.1_GFP _GTAT


title: Pdpl-1_DPL-1_YL425_5-3-10_L1_rep2 _GFP _GTAT

source_name: Pdpl-1_DPL-1:GFP:FLAG whole animal


title: Pdpl-1_DPL-1_YL425_2-14-10_L1_rep1_GFP _GTAT


title: pGES-1 _HPL-2_YL416_3-4-10_L1_rep3_GFP_ACGT


title: Pdpl-1_DPL-1_YL425_2-14-10_L1_rep1_Input_CATT


title: pGES-1_DPL-1_YL448_6-7-10 _L1_rep2_GFP _GTAT


title: Pmex-5_LIN-35_YL468_10_18_10_yAd_rep2_Input_CATT

source_name: Pmex-5 LIN-35:GFP:FLAG whole animal

value: Young adult


title: Pefl-1_EFL-1_YL424_3-1-10_L1_rep1_Input_TGCT

source_name: Pefl-1 EFL-1:GFP:FLAG whole animal


title: Pefl-1_EFL-1_YL424_3-1-10_L1_rep1_GFP_ACGT


title: Ppie-1_LIN-35_YL402_4-2-10_Ad_rep3_Input_TGCT

source_name: Ppie-1 LIN-35:GFP:FLAG whole animal


title: Pefl-1_EFL-1_YL424_4-30-10_L1_rep2 _GFP_CATT


title: Pmex-5_LIN-35_YL468_10-6-10_yAd_rep1_GFP_GTAT


title: Pmex-5_LIN-35_YL468_10_18_10_yAd_rep2_GFP_CATT


title: Pmex-5_LIN-35_YL468_10-6-10_yAd_rep1_Input_GTAT


title: Ppie-1_LIN-35_YL402_4-2-10_Ad_rep3 _GFP_TGCT


title: Pdpl-1_DPL-1_YL425_5-3-10_L1_rep2 _Input _GTAT


title: Ppie-1 _DPL-1_YL390_4-23-10_Ad_rep4_Input_ACGT

source_name: Ppie-1_DPL-1:GFP:FLAG whole animal


title: Ppie-1_LIN-35_YL402-3-31-10_Ad_rep2.1_GFP_TGCT


title: Ppie-1_EFL-1_YL445_3-31-10_Ad_rep3_Input_TGCT

source_name: Ppie-1 EFL-1:GFP:FLAG whole animal


title: Ppie-1_DPL-1_YL390_12-31-09_Ad_rep1_Input_GTAT


title: Ppie-1_DPL-1_YL390_12-31-09_Ad_rep1_ GFP_GTAT


title: Ppie-1_EFL-1_YL445_3-25-10_Ad_rep2_Input_TGCT


title: Ppie-1 _DPL-1_YL390_4-23-10_Ad_rep4_GFP_ACGT


title: Col_PAC_PPZ repeat

status: Public on Jun 25 2012

city: Jinan

first: Mingyi

last: Bai

state: Shandong

address: 27 Shandananlu

department: Life of Scienec

country: China

institute: Shandong University

data_processing: The sequence reads were mapped to the Arabidopsis genome using Tophat software, and differential gene expression was analyzed using DeSeq software.

growth_protocol: Wild type Arabidopsis and bzr1-1D were grown in media containing 1 μM PAC and 0 or 2 μM PPZ for 4.5 days in dark

extract_protocol: Libraries were constructed with barcodes using TruSeqTM RNA Sample Preparation Kit (Ilumina)

treatment_protocol: Added 5 ml liquid solution with 10 μM GA3 or mock to the plate, incubated 5 min and pooled out the liqid and keep the plate another 12 hr.

tag: genotype/variation

value: wild type

value: Hypocotyl


title: Ppie-1_EFL-1_YL445_3-31-10_Ad_rep3_GFP_TGCT


title: bzr1-1D_PAC_PPZ repeat


title: Col_PAC_PPZ GA repeat

source_name: Col_PAC_PPZ GA


title: Pefl-1_EFL-1_YL424_4-30-10_L1_rep2 _Input_CATT


title: Ppie-1_EFL-1_YL445_3-25-10_Ad_rep2_GFP_ACGT


title: 1809_7day

city: Dunsany

first: David

middle: J

last: Lynn

address: Grange

department: Animal & Bioscience

country: Ireland

institute: Teagasc

description: mRNA

data_processing:
CASAVA version 1.6 used for base calling and FastQC version 0.9.1 for QC checks.
Alignments to Btau4.0 using Bowtie (version 0.12.7).
Gene counts calculated with HTseq (version 0.4.6p2) and Ensembl v61 of the bovine genome.
EdgeR (version 1.6.12) used for identification of DEG.

The processed data file 'read_counts.txt' is available as a supplementary file from the Series record.
Genome_build: Btau4.0

organism: Bos taurus

source_name: Leukocytes from calves housed and simultaneously weaned, day 7 post-weaning

extract_protocol: Single-read, 36 bp libraries were prepared for 6 animals per treatment, selected at random, on day 0, 1, 2 and 7 of the study. All 48 libraries were prepared from a starting material of 10 µg of high-quality total RNA. Briefly, total RNA was heated at 65˚C for 5 min to disrupt secondary structures and the mRNA was isolated using 100 µL of Dyna oligo(dT) beads. This step was repeated in order to ensure the removal of genomic DNA, ribosomal RNA and other contaminating RNA. Fragmentation Reagent (Ambion) was used to fragment mRNA prior to synthesis of double-stranded cDNA. cDNA was synthesised using random hexamer primers and SuperScript II reverse transcriptase. Following second strand cDNA synthesis, each sample was purified using a QIAquick PCR spin column. Fragments were end repaired with T4 DNA polymerase and E. coli DNA Polymerase I Klenow fragment to remove 3'-overhangs and fill in 5'-overhangs. In order to prepare the cDNA fragments for adapter ligation, an additional "A" base was added to the 3' end of the phosphorylated DNA fragments using Klenow Fragment 3'-to-5' exo-. Adapters were ligated to the DNA fragments using Quick T4 DNA Ligase at room temperature for 15 min. Following adapter ligation, 10 µL of sample was loaded onto a 2% agarose gel in 1X TAE buffer. The gel was run at 120 V for 70 min. The gel was then visualised on a Dark Reader Transilluminator and a band of gel corresponding to the 250 bp ladder band was excised using a GeneCatcher Disposable Gel Excision tip. The DNA was then purified from this gel band using the QIAquick Gel Extraction kit and eluted in 30 µL of EB solution. PCR reactions were performed on the gel-purified cDNA in a 50 µL reaction using Illumina supplied PCR primers 1.1 and 2.1 and Phusion High-Fidelity DNA polymerase for 15 cycles. Following the PCR step, the final libraries were purified using a QIAquick PCR spin column, quantified with a Qubit Fluorometer and stored at -80 ˚C until sequencing. Library size was confirmed by running 5 µL of each library on a gel and visually inspecting for the sole presence of a 250 bp band. Each library was sequenced in an individual lane on one of eight flowcells using a 36 bp single-end sequencing kit (version 4) at a concentration of 8.5 pM. Sequencing was carried out using an Illumina Genome Analyzer II at the Conway Institute, University College Dublin (Dublin, Ireland).

tag: breed

value: Continental

tag: developmental stage

value: calf

value: leukocytes

tag: treatment

value: housed and simultaneously weaned

tag: day post-weaning


title: 1809_1day

description: mRNA

source_name: Leukocytes from calves housed and simultaneously weaned, day 1 post-weaning


title: 1809_0day

description: mRNA

source_name: Leukocytes from calves housed and simultaneously weaned, day 0 post-weaning


title: Ppie-1_LIN-35_YL402-3-31-10_Ad_rep2_Input_TGCT


title: Ppie-1_LIN-35_YL402-3-31-10_Ad_rep2.2_GFP_TGCT


title: Col_PAC GA repeat

source_name: Col_PAC GA


title: Cunninghamia lanceolata: small RNAs from five tissues

city: Beijing

first: Jinxing

last: Lin

address: No.20 Nanxincun, Xiangshan

institute: Institute of botany

description:
Mixed small RNAs from five tissues
Illumina 1G Genome Analyzer

data_processing:
The raw data were processed with the BGI sRNA analysis pipeline to filter low- quality reads, trim 3'-prime adaptor sequences, and remove poly(A) sequences, and adaptor contaminants formed by adaptor ligation. Sequences shorter than 18-nt and longer than 30-nt were discarded. Nonredundant sRNAs ranging from 18 to 30-nt were collected and stored in the Clean file. Unique sRNAs in the Clean file were mapped to the A. thaliana and P. trichocarpa genomes using SOAP (http://www.arabidopsis.org/, http://www.phytozome.net/poplar).
1) For A. thaliana: araTha5 - Jun 2004 - RepeatMasker open-3.1.9 - Repeat Library 20071204
http://www.repeatmasker.org/PreMaskedGenomes.html
2) For P. trichocarpa: P. trichocarpa v1.1
http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.download.ftp.html
The sRNAs with perfect genomic matches are used for further analysis.

The Clean file is presented in the Data table and linked as a supplementary file.

organism: Cunninghamia lanceolata

source_name: seeds, calluses, two-week-old young shoots, leaves and stems

growth_protocol: Cunninghamia lanceolata plants were grown under standard greenhouse conditions. Callus derived from immature C. lanceolata seeds was maintained on C. lanceolata-specific culture medium.

extract_protocol:
Total RNAs were extracted from seed and callus using RNAiso-mate for plant tissue and RNAiso plus. Moreover, total RNAs from leaves and stems were isolated with Concert Plant RNA Reagent. 16-30 nt sRNAs were purified and two adaptors were sequentially ligated to the 5' and 3' ends of purified sRNAs.

To separate the small RNA (16-30 nt) from total RNA:
1) Mix total RNA with 2X loading Buffer of equal volume and then incubate it at 65C for 5 minutes to break the second structure within RNA.
2) After pre-running of the 15% TBU PAGE for 15 minutes, load the samples, 10bp DNA ladder and 14-30nt RNA ladder into the gel separately. Run the gel at 180V for 1 hour.
3) Cut out the band of gel corresponding to the 16-30nt in the marker lane.

Adapter sequences:
5' RNA Adapter: 5' GUUCAGAGUUCUACAGUCCGACGAUC
3' RNA Adapter: 5' P-UCGUAUGCCGUCUUCUGCUUGUidT

The ligation products were further purified and then RT-PCR amplified. The amplification products were purified and utilized for sequencing on an Illumina 1G Genome Analyzer at the Beijing Genomics Institute, Shenzhen.

tag: seed

value: fully mature; store at 4ºC

tag: callus

value: originating/derived from immature seed

tag: young shoot

value: two-weeks old

tag: leaves

value: five-years old

tag: stem

value: age:five-year old


title: 1803_7day

description: mRNA

source_name: Leukocytes from calves housed with their dam, day 7 post-weaning

tag: tissue

value: housed with their dam

tag: sample type

value: control


title: 1803_1day

description: mRNA

source_name: Leukocytes from calves housed with their dam, day 1 post-weaning


title: 1803_2day

description: mRNA

source_name: Leukocytes from calves housed with their dam, day 2 post-weaning


title: 1803_0day

description: mRNA

source_name: Leukocytes from calves housed with their dam, day 0 post-weaning


title: Col_PAC_PPZ

tag: ecotype


title: Col_PAC_PPZ_GA


title: Col_PAC_GA


title: bzr1-1D_PAC_PPZ


title: 1773_2day

description: mRNA

source_name: Leukocytes from calves housed and simultaneously weaned, day 2 post-weaning


title: 1773_1day

description: mRNA


title: Col_PAC


title: 1802_7day

description: mRNA


title: 1773_0day

description: mRNA


title: 1802_2day

description: mRNA


title: 1802_0day

description: mRNA


title: 1802_1day

description: mRNA


title: 1789_7day

description: mRNA


title: 1789_0day

description: mRNA


title: 1789_1day

description: mRNA


title: 1789_2day

description: mRNA


title: 1770_2day

description: mRNA


title: 1770_1day

description: mRNA


title: 1770_7day

description: mRNA


title: 1770_0day

description: mRNA


title: 1769_7day

description: mRNA


title: Col _PAC repeat

source_name: Col _PAC


title: 1769_2day

description: mRNA


title: 1773_7day

description: mRNA


title: 1763_7day

description: mRNA


title: 1769_0day

description: mRNA


title: 1763_2day

description: mRNA


title: 1763_1day

description: mRNA


title: 1763_0day

description: mRNA


title: 1762_1day

description: mRNA


title: 1762_7day

description: mRNA


title: 1769_1day

description: mRNA


title: 1762_2day

description: mRNA


title: 1759_2day

description: mRNA


title: 1762_0day

description: mRNA


title: 1759_7day

description: mRNA


title: 1759_1day

description: mRNA


title: 1758_7day

description: mRNA


title: 1759_0day

description: mRNA


title: 1758_1day

description: mRNA


title: 1758_0day

description: mRNA


title: 1758_2day

description: mRNA


title: 1755_2day

description: mRNA


title: 1755_7day

description: mRNA


title: 1755_1day

description: mRNA


title: miR-146a HEK293T cells

city: Belfast

middle: Arthur

last: Simpson

state: N. Ireland

address: QUB Institue of clinical Science, Block A, RVH

department: Centre for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Fastq files generated with Illumina 1.3+ encoded quality scores
Adaptor sequences trimmed and reads aligned to miRBase (Release 17) using  Genomics Workbench (CLC bio) software
Genome_build: miRBase (Release 17)
Supplementary_files_format_and_content: 'annotated' tab-delimited text files include Reads Per Million Mapped (RPMM) values for each sample
Supplementary_files_format_and_content: 'unannotated'  tab-delimited text files include read counts each sample

source_name: HEK293T cell line

extract_protocol: Total RNA was extracted and small RNA libraries were prepared using a sample prep kit v1.5 kit (Illumina).

tag: cell type

value: HEK293T human embryonic kidney cell line

value: overexpression of miR-146a

tag: miRNA source

value: cells


title: 1755_0day

description: mRNA


title: miR-146a HEK293T EVs

value: extracellular vesicles


title: Untreated HEK293T cells


title: WT_2h_Mic_GRO_Seq

status: Public on Jun 21 2012

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

data_processing:
Library strategy: GRO-Seq
Reads containing any non-A/C/G/T bases and reads derived from rRNAs, tRNAs, snRNAs and the mitochondrial genome were removed. The first 25 nt of each GRO-seq read was used to uniquely map the representative Mic loci.

organism: Tetrahymena thermophila

source_name: mating wild-type cells at 2 h post-mixing

growth_protocol: Wild-type Tetrahymena thermophila strains B2086 and CU428 were used for preparation of micronuclei. Mating of cells was induced as described (Gorovsky et al. 1975).

extract_protocol: Nuclear fractions were isolated from wild-type strains B2086 and CU428 at 2 h post-mixing as described previously (Sweet et al 2006) with some modifications. All fractionation steps were performed at 4°C or on ice. Cells (1.2 x 108) were suspended in 100 ml of Medium B and blended for 30 sec at the highest speed (WARING Commercial Blender 7009G). Samples were divided among two 50-ml conical tubes and centrifuged with a swing rotor at 1,750 g, 2,750 g, 3,300 g, and 4,200 g for 5 min each and twice at 4,500 g for 10 min. The supernatants of each step were blended as above for 20 sec and then centrifuged at the subsequent speed. Each pellet was washed once in modified nuclei resuspension buffer (NRB; 50 mM Tris-Cl pH 8.0, 30% glycerol, 5 mM MgCl2, 0.1 mM EDTA), resuspended in 200 µl NRB (per 50 ml tube), and stored at -80°C. A portion of the pellet was removed for DAPI-staining,and the ratios between Mac and Mic and the concentrations of nuclei were examined on a hemocytometer. The Mic-enriched nuclear fraction used for the experiments shown in Fig. 5 and Fig. S1 consisted of ~99.5% Mic and ~0.5% Mac, as judged by the sizes of the nuclei.     Mic-enriched nuclear fractions were used to identify nascent transcription by applying the GRO-seq technique (Core et al. 2008) with some modifications. Briefly, ~1.3 x 107 nuclei of the Mic-enriched fraction were used for the run-on reaction, which contained 500 µM ATP, 500 μM GTP, 500 μM BrUTP and 0.33 µM α-32P-CTP. After DNase I treatment, the total RNA was isolated with Trizol LS Reagent (Invitrogen) and resuspended in 20 µl of water. Base hydrolysis was performed for 20 min on ice to digest RNA products to ~30-250 nt. The RNAs were treated with DNase I again, and RNA was purified twice through P30 spin columns (Bio-Rad). BrdU-incorporated RNA was enriched on anti-BrdU beads (Santa Cruz Biotech) at 4°C for 2 h and resuspended in 21 µl of water. A 20-µl aliquot of the RNA was end-repaired and resuspended in 10.5 µl of water.     cDNA was synthesized as described (Hafner et al. 2008) with some modifications. For 3’ adapter ligation, 10 µl of the end-repaired RNAs was incubated with 1 µl 50 µM 3’ adapter (5’-App-TCG TAT GCC GTC TTC TGC TTG-L-3’; L = 3'OH blocking group; IDT), 0.5 µl Ribolock (Fermentas), 2.15 µl ATP-free T4 RNA ligase buffer, 6 µl 50% PEG8000 and 2 µl T4 RNA ligase 2 truncated K227Q (NEB) at 16°C overnight. The RNAs were enriched on anti-BrdU beads as above and resuspended in 10 µl of water. For 5’ adapter ligation, 10 µl 3'-adapter ligated RNAs was incubated with 1 µl 50 µM 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), 0.5 µl Ribolock, 2.2 µl T4 RNA ligase buffer, 1 µl 10 mM ATP, 6 µl 50% PEG8000 and 2 µl T4 RNA ligase (Ambion) at 16°C overnight. The RNAs were purified again with anti-BrdU beads and resuspended in 10 µl of water. The adapter-ligated RNA was incubated with 2 µl 10 µM Sol-rv primer (5’-CAA GCA GAA GAC GGC ATA CGA-3’) and 1 µl 10 mM dNTP mix at 65°C for 5 min and on ice for 2 min. Then, 4 µl 5x First-Strand buffer, 1 µl 0.1 M DTT, 1 µl Ribolock, and 1 µl SuperScript III Reverse Transcriptase (Invitrogen) were added. The mixture was incubated at 50°C for 30 min, 55°C for 30 min, and 70°C for 15 min. Then, 5 U of RNase H (Ambion) was added, followed by incubation at 37°C for 10 min. The cDNA was amplified by subjecting 9.5 µl of the reaction to 17 cycles of PCR with KAPA Hifi Hot Start DNA polymerase (Kapa Biosystems) and Sol-fw (5’-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3’) and Sol-rv primers. The amplified cDNA library was fractionated in a 2% agarose gel; ~100-200 bp products were extracted, and single-read 50-base sequences were generated on a HiSeq 2000 platform (Illumina) to obtain ~200 million reads. Reads containing any non-A/C/G/T bases and reads derived from rRNAs, tRNAs, snRNAs and the mitochondrial genome were removed. The first 25 nt of each GRO-seq read was used to uniquely map the representative Mic loci.

tag: rna subtype

value: Nuclear run-on RNAs


title: H3K27me3 24hpf

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

description: chromatin IP against H3K27me3

data_processing:
Reads were mapped to the D. rerio genome (ENSEMBL version Zv8) with the ELAND software (Ilumina pipeline). Only the alignments within 2 mismatches were included in further analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: whole embryo

growth_protocol: Danio rerio embryos used for ChIP assays were obtained from a natural mating procedure and dechorionated by pronase treatment prior to immunoprecipitation.

extract_protocol: The DNA ends were repaired and the 3-dA overhangs added. The adapters were then ligated. The library was size-selected (200-300 bp) and amplified by PCR.

value: 24 hpf

value: whole embryo

tag: chip antibody

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #

tag: chip antibody lot #

tag: genetic background

value: mixed Ab and Tubingen


title: Heart_Nkx2-5_ChIP-seq

status: Public on Jun 22 2012

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: Sample 4

data_processing:
Sequencing results were run through the standard Illumina GAPipeline (v1.0 for GAI runs and v1.3 for GAII runs) to convert images to reads of 36bp in length (unaligned sequences produced by the Illumina Genome Analyzer) and edit for quality (FIRECREST, Bustard and GERALD). Reads were then processed and aligned to the mouse reference genome (NCBI Build 37, mm9) as previously described, allowing a maximum of two mismatches and retaining only sequences with unique alignments
Genome Build:
Heart_Nkx2-5_ChIP-seq.WIG: mm9
Heart_Nkx2-5_ChIP-seq_bed.txt: mm9

organism: Mus musculus

extract_protocol: Material was used for library preparation with standard NEBNext library kit protocol for Illumina sequencing (New England BioLabs, #E6000S/L, #E6040S/L).

tag: strain background

value: FVB/N

tag: genotype/variation

value: wildtype

tag: Stage

value: adult

value: heart

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat#

tag: chip antibody lot#


title: Foxa1 ChIP rep5

city: Cambridge

first: Irina

last: Bochkis

state: MA

address: 7 Cambridge Center

institute: Broad Institute

data_processing: Alignment:Foxa1 ChIP libraries for five biological replicates in a total of five lanes to 36 nucleotides.  The reads were aligned to the mouse genome (mm8; NCBI Build 36) using the ELAND aligner (Illumina).

source_name: liver

extract_protocol: Snap-frozen mouse liver (100 mg) from wild type mice was used to prepare chromatin. Foxa1–specific antiserum (a kind gift of G. Schütz, Heidelberg, Germany) was used for immunoprecipitation. For ChIPSeq experiments, the immunoprecipitated DNA was modified for sequencing following the manufacturer’s protocol (Illumina). Briefly, DNAs were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK, then a single 3′-end “A” base was added using Klenow exo (3′-to-5′ exo minus). Adapters provided by Illumina were then ligated to the ends of the modified DNA before size selection of ∼200-bp fragments via PAGE extraction. The isolated DNA samples were used as the template for amplification by 18 cycles of PCR. Amplified products were column purified with the QIAquick PCR Purification Kit (Qiagen) and assayed for quantity and quality with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Liver was dissected and frozen prior to preparation of chromatin

tag: tissue

value: liver

tag: strain

value: CD1 outbred mice

tag: age

value: 2-3 months

tag: Sex

value: male

tag: ChIP


title: Heart_Tbx3_ChIP-seq

description: Sample 1

data_processing:
Sequencing results were run through the standard Illumina GAPipeline (v1.0 for GAI runs and v1.3 for GAII runs) to convert images to reads of 36bp in length (unaligned sequences produced by the Illumina Genome Analyzer) and edit for quality (FIRECREST, Bustard and GERALD). Reads were then processed and aligned to the mouse reference genome (NCBI Build 37, mm9) as previously described, allowing a maximum of two mismatches and retaining only sequences with unique alignments
Genome Build:
Heart_Tbx3_ChIP-seq.WIG: mm9
Heart_Tbx3_ChIP-seq_bed.txt: mm9


title: Heart_control_ChIP-seq

description: Sample 2

data_processing:
Sequencing results were run through the standard Illumina GAPipeline (v1.0 for GAI runs and v1.3 for GAII runs) to convert images to reads of 36bp in length (unaligned sequences produced by the Illumina Genome Analyzer) and edit for quality (FIRECREST, Bustard and GERALD). Reads were then processed and aligned to the mouse reference genome (NCBI Build 37, mm9) as previously described, allowing a maximum of two mismatches and retaining only sequences with unique alignments
Genome Build:
Heart_Control_ChIP-seq.WIG: mm9


title: Foxa1 ChIP rep3


title: Foxa1 ChIP rep1


title: Foxa1 ChIP rep2


title: RCC without recurrence 42T2Y_s5_CACACC

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

institute: Leiden University Medical Center

data_processing:
truncate the sequence reads on the 3'adapter sequence: CGCCTTGG
calculate the frequency of the unique sequences after truncation
Genome_build: Hg19
Supplementary_files_format_and_content: Tab delimited: sequence <tab> frequency

source_name: renal

extract_protocol: Modifier Solid SREK protocol to run on the Illumina Flowcells. Previously published by Buermans et al, BMC Genomics. 2010 Dec 20;11:716.

tag: tumor group

value: RCC without recurrence

value: clear cell renal cell carcinoma

tag: disease state

value: clear cell renal cell carcinoma  without recurrence


title: RCC without recurrence 42T2Y_s6_CCCCTT


title: SKRC7 4306M_s8_CATCGG

source_name: renal cell line

tag: cell line


title: RCC without recurrence 42T2Y_s5_CATCGG


title: RCC without recurrence 42T2Y_s6_TCGTTG


title: MZ1257 4306M_s8_TCGTTG


title: Untreated HEK293T EVs

tag: cell type

value: HEK293T human embryonic kidney cell line

value: control

tag: miRNA source

value: extracellular vesicles


title: Heart_Gata4_ChIP-seq

description: Sample 3

data_processing:
Sequencing results were run through the standard Illumina GAPipeline (v1.0 for GAI runs and v1.3 for GAII runs) to convert images to reads of 36bp in length (unaligned sequences produced by the Illumina Genome Analyzer) and edit for quality (FIRECREST, Bustard and GERALD). Reads were then processed and aligned to the mouse reference genome (NCBI Build 37, mm9) as previously described, allowing a maximum of two mismatches and retaining only sequences with unique alignments
Genome Build:
Heart_Gata4_ChIP-seq.WIG: mm9
Heart_Gata4_ChIP-seq_bed.txt: mm9

tag: chip antibody


title: Heart_p300_ChIP-seq

description:
Sample run through SOLiD v3.0
Sample 5

data_processing:
Sequencing results were run through the standard Illumina GAPipeline (v1.0 for GAI runs and v1.3 for GAII runs) to convert images to reads of 36bp in length (unaligned sequences produced by the Illumina Genome Analyzer) and edit for quality (FIRECREST, Bustard and GERALD). Reads were then processed and aligned to the mouse reference genome (NCBI Build 37, mm9) as previously described, allowing a maximum of two mismatches and retaining only sequences with unique alignments
Genome Build:
Heart_p300_ChIP-seq.bigwig: mm9

extract_protocol: Material was used for library preparation with standard SOLiD library construction kit for SOLiD sequencing (Applied Biosystems, #4443713, #4400413).

tag: strain background


title: Foxa1 ChIP rep4


title: RCC without recurrence 42T2V_s2_TCGTTG


title: Orange_WT_120DAF

city: Ithaca

first: Qiang

last: Xu

state: NY

address: Tower Road, Cornell University

institute: Cornell University

description: fruit transcriptome of sweet orange

data_processing: Sequences without adapters were discarded. The sequence sets were filtered to remove low quality sequences including ambiguous nucleotides, adaptor-only sequences and below 3 transcript per million (TPM)

organism: Citrus sinensis

source_name: sweet orange fruits

growth_protocol: The orange fruits were pick up from 3 different trees which cultivated at the Institute of Citrus Research located in Guilin, Guangxi Province, China

extract_protocol: Total RNA were extracted from the sweet orange fruits according to previous protocol (Liu et al. 2006). 10 μg total RNA were reverse-transcribed, the resultant cDNA was digested with NlaIII, and then ligated with the first adapter containing the recognition site of MmeI, a Type IIs endonuclease which cleave at sites 21bp from the recognition site. After digestion by MmeI, the transcripts were ligated with the second adapter. With the sequencing primers designed based on the two adaptors, the sequence of the 21 bp representing each transcript can be determined via sequencing by synthesis mode.

tag: genotype/variation

value: wild type

tag: developmental stage

value: 120 Days after flowering


title: Orange_WT_190DAF

description: fruit transcriptome of sweet orange

value: 190 Days after flowering


title: RCC stage IV 4306M_s8_AAGCCC

value: RCC stage IV

value: clear cell renal cell carcinoma  stage IV


title: RCC without recurrence 42T2V_s2_CACACC


title: RCC stage IV 4306M_s8_CACACC


title: RCC stage IV 4306M_s8_CCCCTT


title: Orange_WT_170DAF, 2

description: fruit transcriptome of sweet orange

value: 170 Days after flowering


title: Orange_MT_190DAF

description: fruit transcriptome of sweet orange

value: mutant


title: Orange_WT_150DAF

description: fruit transcriptome of sweet orange

value: 150 Days after flowering


title: RCC stage IV 42T2V_s1_TCGTTG


title: Orange_MT_120DAF

description: fruit transcriptome of sweet orange


title: Orange_MT_170DAF, 2

description: fruit transcriptome of sweet orange


title: Orange_MT_220DAF

description: fruit transcriptome of sweet orange

value: 220 Days after flowering


title: RCC stage IV 30K1R_s5_CACACC


title: RCC recurrence 42T2Y_s6_AAGCCC

value: RCC recurrence

value: clear cell renal cell carcinoma  recurrence


title: RCC recurrence 4306M_s7_CCCCTT


title: RCC recurrence 4306M_s7_CACACC


title: Orange_WT_220DAF

description: fruit transcriptome of sweet orange


title: RCC recurrence 42T2V_s1_CACACC


title: RCC recurrence 30K1R_s5_CATCGG


title: RCC without recurrence 42T2V_s2_CATCGG

value: RCC without recurrence


title: WT_8 h

description: WT_8 h

data_processing:
Following the removal of the adapter sequences from the sequence reads, we removed reads containing any non-A/C/G/T bases; reads from rRNAs, tRNA, snRNAs, and the mitochondrial genome; and reads from mixed phiX174 phage DNA. Then, sequences from 26-32 nt RNAs were used as scnRNA sequences. The first 25 nt of each scnRNA sequence was mapped to the annotated Mic genome, the selected Mic loci,or the selected 218 Mac genome scaffolds.
Supplementary_files_format_and_content: The first 25-nt sequences of filtered 26- to 32-nt small RNAs

source_name: 26-32nt small RNAs

growth_protocol: Wild-type Tetrahymena thermophila strains B2086 and CU428, nullisomic 4 strains CU357 and CU367, the complete (germ plus soma) TWI1 KO (Mochizuki and Gorovsky 2004) strains 20-1 and 20-4, or the somatic EMA1 KO strains (7)-17-1 and (8)-6-1 (Aronica et al. 2008) were used for total RNA preparation. Mating of cells was induced as described (Gorovsky et al. 1975), and asynchronous mating initiation was limited by adding quarter of the total volume of 4x SPP at ~3, 4.5, 6 or 8 hr post-mixing.

extract_protocol: RNA was isolated from 2.5 x 106 mating cells at the indicated times post-mixing using the mirVana miRNA isolation kit (Ambion). For periodate oxidation of small RNAs (Akbergenov et al. 2006), the RNA pellet was dried and resuspended in 17.5 µl borax buffer (4.375 mM borax, 50 mM boric acid; pH 8.6). Next, 2.5 µl 0.2 M sodium periodate was added, and the reaction was incubated for 10 min at RT in the dark. Then, 2 µl of glycerol was added, the reaction was incubated for another 10 min at RT in the dark, and the small RNAs were purified by ethanol precipitation.   The cDNA library of small RNAs was constructed as described (Hafner et al. 2008) with some modifications. In brief, approximately one-tenth of the purified RNA (with or without periodate oxidation) was mixed with radiolabeled 26- and 32-nt oligoribonucleotides (5’-GUC GUA CGC GGA AUA GUU UAA ACU GU-3’ and 5'-AUC UUG GUC GUA CGC GGA AUA GUU UAA ACU GU-3’, respectively; the PmeI restriction site is underlined), fractionated in a sequencing gel, and the gel region containing the two radiolabeled markers and a few bases on each side were excised. RNA was recovered from the gel and ligated to a 5'-adenylated 3' adapter oligonucleotide (5’-App-TCG TAT GCC GTC TTC TGC TTG-L-3’; L = 3'OH blocking group; a gift from Markus Landthaler from the Tuschl lab) using truncated T4 Rnl2tr (NEB). After gel fractionation and purification as above, the product was ligated to the 5' adapter oligoribonucleotide (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3') using T4 RNA ligase (Ambion). The gel-purified final ligation product was then reverse-transcribed using the primer 5’-CAA GCA GAA GAC GGC ATA CGA-3’ and PCR-amplified using that reverse transcription primer and the primer 5’-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3’. After phenol-chloroform extraction followed by ethanol precipitation, the PCR product was digested with PmeI (to cut the size markers) and fractionated by agarose gel electrophoresis, and the uncut PCR product was purified from the gel. The amplified cDNA libraries were mixed with phiX174 phage DNA at one-tenth of the amount of DNA, and single-read 36-base sequences were generated on the Illumina GAII platform obtaining 2-30 million reads.

tag: rna subtype

value: Whole RNAs

value: mating wild-type cells at 8 h post-mixing


title: RCC stage IV 4306M_s7_TCGTTG

value: clear cell renal cell carcinoma


title: RCC recurrence 4306M_s7_AAGCCC


title: NRC 42T2Y_s6_CATCGG

value: NRC

value: non-tumoral renal cortex


title: RCC recurrence 4306M_s7_CATCGG


title: RCC stage IV 42T2V_s1_CATCGG


title: NRC 42T2Y_s6_CACACC


title: NRC 42T2Y_s5_TCGTTG


title: Orange_MT_150DAF

description: fruit transcriptome of sweet orange


title: NRC 42T2Y_s5_CCCCTT


title: EMA1_KO_4.5 h_Ox

description: EMA1_KO_4.5 h_Ox

value: Oxidation resistant RNAs

value: mating EMA1 KO cells at 4.5 h post-mixing


title: EMA1_KO_6 h_Ox

description: EMA1_KO_6 h_Ox

value: mating EMA1 KO cells at 6 h post-mixing


title: WT_6 h_Ox

description: WT_6 h_Ox

value: mating wild-type cells at 6 h post-mixing


title: EMA1_KO_8 h_Ox

description: EMA1_KO_8 h_Ox

value: mating EMA1 KO cells at 8 h post-mixing


title: NRC 42T2V_s2_AAGCCC


title: WT_4.5 h_Ox

description: WT_4.5 h_Ox

value: mating wild-type cells at 4.5 h post-mixing


title: TWI1_KO_3 h

description: TWI1_KO_3 h

value: matingTWI1 KO cells at 3 h post-mixing


title: WT_3 h_Ox

description: WT_3 h_Ox

value: mating wild-type cells at 3 h post-mixing


title: WT_3 h

description: WT_3 h


title: NRC 30K1R_s5_AAGCCC


title: NRC 42T2V_s2_CCCCTT


title: NRC 42T2V_s1_AAGCCC


title: NRC 42T2V_s1_CCCCTT


title: Nanoarchaeum equitans sRNAs

status: Public on Jun 20 2012

city: Marburg

first: Lennart

last: Randau

address: Karl-von-Frisch Strasse 10

country: Germany

institute: MPI for terrestrial microbiology

description: Total small RNA (<200 bases).

data_processing:
Illumina Software CASAVA 1.8 was used for basecalling and removal of adaptor sequences.
Sequencing reads were trimmed ((i) removal of poly-A tails, (ii) removal of sequences using a quality score limit of 0.05)) and mapped to the reference genome (RefSeq: NC_005213.1) with CLC Genomics Workbench 5.0 (CLC Bio, Aarhus, Denmark). A total of 16614433 reads with an average length of 62.3 nt were obtained after trimming. The following mapping parameters were employed (mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.5, similarity: 0.8). Reads below 15 nt were removed.
CLC Genomics Workbench 5.0 was utilized to determine the coverage for the individual RNA molecules.
Genome_build: RefSeq: NC_005213.1
Supplementary_files_format_and_content: Tab-delimited text file indicating the coverage of mapped sequence reads at single-nucleotide resolution for the N. equitans genome (NC_005213.1).

organism: Nanoarchaeum equitans

source_name: Cultured organism

growth_protocol: Nanoarchaeum equitans was grown in the Archaeenzentrum Regensburg (H. Huber, M. Thomm, K. Stetter) in a  300 l fermenter in simultaneous culture with Ignicoccus hospitalis KIN4-I and was purified by gradient centrifugation as described (Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO: A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 2002, 417:63-67 (PMID 11986665)).

extract_protocol: Total RNA was isolated by SDS-lysis of the cell pellet and phenol/chloroform extraction. Small RNAs were purified from total RNA using the MirVana RNA extraction kit (Ambion). N. equitans small RNA were treated with T4 polynucleotidekinase to ensure proper termini for ligation: 1 μg of RNA was incubated at 37 ˚C for 6 hours with 10 Units T4 PNK and 10 μl 5x T4PNK buffer (NEB) in a total volume of 50 μl. Subsequently, 1 mM ATP was added and the reaction mixture was incubated for 1 hour at 37 ˚C to generate monophosphorylated 5' termini. The RNAs were treated with poly(A) polymerase to add a poly-A tail that was used for cDNA synthesis and were prepared with an Illumina TruSeq RNA Sample Prep Kit (Cat# FC-122-1001). Library preparation and sequencing on an Illumina HiSeq 2000 sequencer were performed at the Max-Planck Genomecentre Cologne.


title: NRC 30K1R_s5_CCCCTT


title: EMA1_KO_3 h_Ox

description: EMA1_KO_3 h_Ox

value: mating EMA1 KO cells at 3 h post-mixing


title: Nulli4_3 h

description: Nulli4_3 h

value: mating nullisomic 4 cells at 3 h post-mixing


title: HSF1 STHdhQ7/Q7 Heat Shock ChIP-seq

status: Public on Jun 19 2012

first: Laura

last: Riva

address: 77 Massachusetts Avenue

department: Biological Engineering

institute: MIT

description: Chromatin IP against HSF1

data_processing:
Alignment: sequence reads were mapped to the mouse genome (UCSC, mm9) using eland extended with the default parameters.
Only ChIP-Seq reads that aligned to exactly one location in the reference mouse genome were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) to identify bound regions by comparing the enrichment of the IP sample against a control IgG IP for background correction. MACS version 1.4.0rc2 was run with all parameters at their default settings and with an enrichment p-value cutoff of 1e-9
Genome_build: mm9
Supplementary_files_format_and_content: peak files, that are bed files, were generated using MACS version 1.4.0rc2.

source_name: STHdhQ7/Q7 striatal cells

growth_protocol: STHdhQ7/Q7 and STHdhQ111/Q111 striatal cells derived from wild type HdhQ7/Q7 and HdhQ111/Q111 knock-in embryonic mice were used in this study. Cells were grown at 5% CO2 at 33°C in Dulbecco’s modified Eagle’s medium (DMEM, from CellGro, Manassas, VA) with 10% fetal bovine serum (HyClone, Logan, UT), Pen/Strep/Glutamine and 400 μg/ml G418 (both from CellGro). The cells were only used up to passage 15.

extract_protocol: The cells were crosslinked with 1% formaldehyde and immunoprecipitated using antibody sc-9144 (Santa Cruz Biotech) for HSF-1. Library preparation for sequencing was performed according to the standard Illumina protocol. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments around 200-300bp were cut from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Samples were sequenced on the Illumina Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: cells were heat-shocked at 42°C for six hours

value: striatal cells derived from wild type HdhQ7/Q7 embryonic mice

tag: genotype

tag: treatment

tag: chip antibody catalog #

tag: chip antibody manufacturer

value: Santa Cruz


title: HSF1 STHdhQ7/Q7 no treatment ChIP-seq

description: Chromatin IP against HSF1

value: no treatment


title: WT_8 h_Ox

description: WT_8 h_Ox

value: mating wild-type cells at 8 h post-mixing


title: HSF1 STHdhQ111/Q111 Heat Shock ChIP-seq

description: Chromatin IP against HSF1

source_name: STHdhQ111/Q111 striatal cells

value: striatal cells derived from  HdhQ111/Q111 knock-in embryonic mice

value: cells were heat-shocked at 42°C for six hours


title: NRC 42T2Y_s5_AAGCCC

value: NRC

tag: tissue

value: non-tumoral renal cortex


title: STHdhQ7/Q7 control reads

description: Control IgG


title: STHdhQ111/Q111 control reads

description: Control IgG


title: HSF1 STHdhQ111/Q111 no treatment ChIP-seq

description: Chromatin IP against HSF1


title: CC189_G2

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

description:
Sample 10
processed data file: CC189cer_normalized.wig [genome build: sacCer1]
processed data file: CC189bay_normalized.wig [genome build: CBS7001 (Scannell et al., 2011)]

data_processing: Reads were mapped to the references genome for each organisms and uniquely mapping reads were retained. Replication timing profiles were generated from the ratio of uniquely mapped reads in the replicating (S phase) sample to the non-replicating (G2 sample) in 1 kb windows. Windows where fewer than 250 reads were mapped in either sample were excluded. The resulting absolute ratios reflect the read numbers; therefore data was normalized  by dividing by an empirically determined factor. This resulted in >95% of the data points lying between 1 and 2 (a biologically imposed restraint).  Processed files (*.wig) are available as Series supplementary files.

organism: Saccharomyces bayanus x Saccharomyces cerevisiae

source_name: G2 phase cells

growth_protocol: Cells were harvested from mid-log phase cultures grown in rich medium

extract_protocol: Sequencing libraries were made using the NEB Next kit (New England Biolabs) as advised by the manufacturer.

treatment_protocol: Cells were sorted by DNA content, selecting S phase and G2 phase cells

tag: strain

tag: cell cycle stage

value: G2 phase


title: BY4743_G2

description:
Sample 2
processed data file: BY4743_normalized.wig [genome build: sacCer1]

organism: Saccharomyces cerevisiae


title: CC189_S

description:
Sample 9
processed data file: CC189cer_normalized.wig [genome build: sacCer1]
processed data file: CC189bay_normalized.wig [genome build: CBS7001 (Scannell et al., 2011)]

source_name: S phase cells

value: S phase


title: OS24_G2

description:
Sample 8
processed data file: OS24_normalized.wig [genome build: CBS7001 (Scannell et al., 2011)]

organism: Saccharomyces bayanus


title: BY4743_S

description:
Sample 1
processed data file: BY4743_normalized.wig [genome build: sacCer1]


title: total amplified RNA, Ler seed coat at 2-4cells embryo stage # SC_2

city: Glarus

first: Marc

middle: William

last: Schmid

address: Hauptstrasse 34

country: Switzerland

institute: MWSchmid GmbH

description: linear amplified

data_processing:
50 base reads generated by SOLiD v3 were aligned to the TAIR8.0 version of the Arabidopsis Col genome using the SOLiD™ System Analysis Pipeline Tool (Corona Lite 4.0r2.0, Applied Biosystems, USA), allowing up to 4 color-space mismatches with the additional rule “count valid adjacent errors as single errors”. For transcriptome profiles, reads were excluded if they mapped to more than one genomic position, mapped at splice junctions or were partially overlapping. Consequently, full-length reads uniquely mapping inside a transcript were taken.
Genome_build: Arabidopsis thaliana, TAIR8
Supplementary_files_format_and_content: Processed data file contains transcript coverage, read count (full-length), transcript type

source_name: seed coat (dissected)

growth_protocol: Plants were grown under 16h light.

extract_protocol: 1-RNA extraction: PicoPure RNA Isolation Kit (Arcturus). 2-RNA amplification: WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies, USA) producing single-stranded cDNA. 3- Second strand synthesis: poly-A tails added using Terminal Transferase (New England Biolabs, USA) in presence of dATPs (1 PCR cycle using Ex Taq Polymerase , (TaKaRa, Japan), and oligo(dT)12-18 primers (Invitrogen). 4-Library preparation: from 500 ng ds cDNA, Covaris S2 system (Covaris, Inc.), sheared into 80–130 bp fragments , DNA ends were repaired and ligated to SOLiD P1 and P2 adaptors, followed by enrichment by PCR (7 cycles) and a size selection on gel

tag: Stage

value: seed coat from seeds with embryos at 2-to-4 cells stage

tag: parental strains

value: Landsberg erecta (Ler)

tag: parental genotype/variation

value: wildtype


title: OS24_S

description:
Sample 7
processed data file: OS24_normalized.wig [genome build: CBS7001 (Scannell et al., 2011)]


title: OS27_S

description:
Sample 3
processed data file: OS27_normalized.wig  [genome build: CBS432 (Liti et al., 2009; PMID: 19212322)]

organism: Saccharomyces paradoxus


title: 1809_2day

description: mRNA

data_processing:
CASAVA version 1.6 used for base calling and FastQC version 0.9.1 for QC checks.
Alignments to Btau4.0 using Bowtie (version 0.12.7).
Gene counts calculated with HTseq (version 0.4.6p2) and Ensembl v61 of the bovine genome.
EdgeR (version 1.6.12) used for identification of DEG.

The processed data file 'read_counts.txt' is available as a supplementary file from the Series record.
Genome_build: Btau4.0

tag: breed

value: Continental

value: calf

value: leukocytes

value: housed and simultaneously weaned

tag: day post-weaning


title: OS27_G2

description:
Sample 4
processed data file: OS27_normalized.wig  [genome build: CBS432 (Liti et al., 2009; PMID: 19212322)]


title: RCC recurrence 30K1R_s5_TCGTTG

tag: tumor group

value: RCC recurrence

value: clear cell renal cell carcinoma

tag: disease state

value: clear cell renal cell carcinoma  recurrence


title: longissimus muscle_pooled 3 Lantang postnatal 28 day pigs

status: Public on Jun 18 2012

city: College Station

first: Jason

last: Karpac

state: Texas

address: Reynolds Medical Building

department: Molecular and Cellular Medicine

institute: Texas A&M University Health Sciences Center

data_processing:
Data processed by the Beijing Genomics Institute (BGI, commercial service). Clean tags were obtained by filtering raw data to remove adaptor tags, low quality tags and tags of copy number = 1. The clean tags were classified according their copy number in the library and the proportion of each category in relation to total clean tags was determined. Similar analyses were carried out for clean distinct tags.
All possible CATG+17-nt tag sequences were created from the sus scrofa RefSeq and UniGene (NCBI36.1, 20090827) databases and used as reference sequences to align and identify the sequencing tags. All clean tags were aligned to the reference database, and then unambiguous tags were annotated. One mismatch in each alignment was allowed to tolerate polymorphisms across samples. Mismatch could be caused by a sequencing error, but the frequency is very low (1 or 2 per million).
Software/programs used in our analysis:
1. BLAST v2.2.21. (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.21/)
2. BLAT v.34, (http://genome.ucsc.edu/FAQ/FAQblat)
3. SOAP v1.11. . http://soap.genomics.org.cn/#down2.
4. Bowtie v0.12.3. http://bowtie-bio.sourceforge.net/index.shtml
5. Cluster v1.47. http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/
6. Java TreeView v1.1.4r3. http://sourceforge.net/projects/jtreeview/
7. Medusa v1.5.1. http://coot.embl.de/medusa/ Applet. http://coot.embl.de/medusa/Stringlet2Applet.shtml
8. Blast2GO Blast2GO. v2.3.5. http://www.blast2go.org/

organism: Sus scrofa

source_name: pooled longissimus muscle of three pigs (postnatal day 28)

growth_protocol: All animal procedures were performed according to guidelines developed by the China Council on Animal Care and protocol approved by Animal Care and Use Committee of Guangdong Province, P.R. China.

extract_protocol: The RNA library was constructed and deep sequencing preformed by the Beijing Genomics Institute (BGI, commercial service). Total RNA was extracted from frozen muscles using standard protocols (Trizol) and then treated with DNase to remove potential genomic DNA contamination according to the manufactures's protocols. RNA integrity and concentration were evaluated by Agolent 2100 Bioanalyzer (Agilent Technologies). For RNA library construction and deep sequencing, equal quantities of RNA samples from three individual pigs were pooled at every time points. Approximately 6 ug of RNA representing each group were submitted to Solexa (now Illumina Inc.) for sequencing. Sequence tag preparation was done with Illumina's Digital Gene Expression Tag Profiling Kit according to the manufacturer's protocol. In brief, mRNA was isolated from 6ug total RNA by binding the mRNA to a magnetic oligo bead. First-and second-strand cDNA were synthesized while the mRNA was attached to the beads. The double 14 stranded cDNA were digested with NlaIII to wash away all fragmens other than the 3? CATG fragment attached to the oligo bead. Then GEX NlaIII Adapter 1 was ligated at the site of NlaIII cleavage. In addition, GEX NlaIII Adapter 1 contains the sequence for the restriction enzyme MmeI, subsequently, we applied the restriction enzyme MmeI to create the 17 bp tag. The GEX Adapter 2 was ligated at the site of MmeI cleavage. A PCR with 12 cycles was performed with two primers that anneal to the ends of the adapters to enrich the adapter-ligated cDNA construct. The resulting 85 bp fragments were purified from 6% Novex TBE PAGE gel. Subsequently, the purified cDNA tags were sequenced on the Illumina Cluster Station and Genome Analyzer. Image recognition and base calling were performed using the Illumina Pipeline.

treatment_protocol: Purebred 15 Lantang (LT) and 15 Landrace (Lde) sows which have the same genetic background were artificially inseminated with semen from same purebred boars respectively.

value: Lantang

value: longissimus muscle

value: postnatal day 28


title: longissimus muscle_pooled 3 Lantang postnatal 120 day pigs

source_name: pooled longissimus muscle of three pigs (postnatal day 120)

value: postnatal day 120


title: longissimus muscle_pooled 3 Lantang postnatal 90 day pigs

source_name: pooled longissimus muscle of three pigs (postnatal day 90)

value: postnatal day 90


title: longissimus muscle_pooled 3 Lantang postnatal 180 day pigs

source_name: pooled longissimus muscle of three pigs (postnatal day 180)

value: postnatal day 180


title: longissimus muscle_pooled 3 Lantang 77 day fetals

source_name: pooled longissimus muscle of three fetals (prenatal day 77)

value: prenatal day 77


title: longissimus muscle_pooled 3 Lantang 91 day fetals

source_name: pooled longissimus muscle of three fetals (prenatal day 91)

value: prenatal day 91


title: longissimus muscle_pooled 3 Landrace postnatal 90 day pigs

value: Landrace


title: longissimus muscle_pooled 3 Landrace postnatal 28 day pigs


title: longissimus muscle_pooled 3 Lantang 35 day fetals

source_name: pooled longissimus muscle of three fetals (prenatal day 35)

value: prenatal day 35


title: longissimus muscle_pooled 3 Landrace postnatal 120 day pigs


title: longissimus muscle_pooled 3 Lantang 49 day fetals

source_name: pooled longissimus muscle of three fetals (prenatal day 49)

value: prenatal day 49


title: longissimus muscle_pooled 3 Landrace 91 day fetals


title: longissimus muscle_pooled 3 Lantang 63 day fetals

source_name: pooled longissimus muscle of three fetals (prenatal day 63)

value: prenatal day 63


title: longissimus muscle_pooled 3 Landrace 77 day fetals


title: longissimus muscle_pooled 3 Landrace 49 day fetals


title: longissimus muscle_pooled 3 Landrace postnatal 2 day pigs

source_name: pooled longissimus muscle of three pigs (postnatal day 2)

value: postnatal day 2


title: OS350_S

description:
Sample 5
processed data file: Sarb_normalized.wig [genome build: CBS10644 (Liti et al., 2012)]

organism: Saccharomyces arboricola

value: S phase


title: OS350_G2

description:
Sample 6
processed data file: Sarb_normalized.wig [genome build: CBS10644 (Liti et al., 2012)]

value: G2 phase


title: longissimus muscle_pooled 3 Landrace 35 day fetals


title: Nucleosomes_yeast_0.4mM_H2O2_20min

city: Madison

first: Dana

last: Huebert

state: WI

address: 425G Henry Mall

institute: University of Wisconsin-Madison

description:
0.4mM H2O2 Timecourse in BY4741

The majority of inserts will be about 150bp but there will be a population around 300bp as well.

data_processing: Raw data were aligned to the yeast S288C. NC_001133.7  GI:144228165 build of the yeast genome using Bowtie allowing 1 mismatch across the length of the read (-v 1), removing any read that did not match uniquely to the genome (-m 1), using a minimum end-to-end distance of paired reads of 60bp (-I 60) and a maximum distance of 400bp (-X 400).   Aligned reads were converted to sequence counts/bp across the genome using the compiler function of Maq. Nucleosome positions were called in each time point using the method of Kuan et al. Stat App Mol Bio Genet 8(1):Article 29

organism: Saccharomyces cerevisiae S288C

source_name: yeast

growth_protocol: Yeast were grown at least 10 generations to an OD(600) ~0.6 in YPD medium at 30C.

extract_protocol: Cells were treated with formaldehyde (1%) for 15 minutes at 25C and quenched with 125mM glycine. Cells were digested to spheroplasts with zymolyase and treated with micrococcal nuclease for 20 minutes at 37C. DNA was purified as described in Liu et al (PLoS Biol, 2005). Libraries were generated using Illumina's "Preparing Samples for Paired End Sequencing" guide; size selection targeted 140-310bp fragments to capture mono- and di-nucleosomes. Clusters were generated using Cluster Kits (v2) and the Illumina Cluster Station with one sample per lane. A paired end, 75 bp run was performed using standard 36bp SBS kits (v3) and SCS 2.4 software. The majority of inserts will be about 150bp but there will be a population around 300bp as well.

treatment_protocol: Yeast were treated with 0.4mM (final conc) H2O2 for varying amounts of time (range: 4-60 minutes)

tag: sequenced molecule

value: nucleosome-bound DNA

tag: time

value: 20 min


title: Nucleosomes_yeast_0.4mM_H2O2_12min

value: 12 min


title: Nucleosomes_yeast_0.4mM_H2O2_40min

value: 40 min


title: Nucleosomes_yeast_0.4mM_H2O2_60min

value: 60 min


title: Nucleosomes_yeast_0.4mM_H2O2_0min

value: none (untreated)

value: 0 min


title: H3K27me3_CTCF_knockdown_ChIPseq

city: Palo Alto

first: Kevin

last: Van Bortle

address: 3165 Porter Dr

institute: Stanford University

description: Chromatin IP against H3K27me3

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Genome Build:
H3K27me3_CTCF_KD.wig: DM3

organism: Drosophila melanogaster

source_name: Kc cells

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

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

tag: chip antibody

value: H3K27me3 Millipore Cat. # 07-449 Lot # JBC1924326

tag: cell type

value: Kc167 Drosophila Embryonic Cell line


title: H3K27me3_ChIPseq

description: Chromatin IP against H3K27me3

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Genome Build:
H3K27me3.wig: DM3


title: Nucleosomes_yeast_0.4mM_H2O2_4min

tag: treatment

value: 4 min


title: Mod(mdg4)BTB_ChIPseq

description: Chromatin IP against Mod(mdg4)BTB

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS1.4.0alpha2) algorithm using equal numbers of unique reads for input and ChIP samples and a p-value cutoff of 1e-10.
Genome Build:
Modmdg4BTB.bed: DM3
Modmdg4BTB.wig: DM3


title: Mod(mdg4)2.2_ChIPseq

description: Chromatin IP against Mod(mdg4)2.2

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS1.4.0alpha2) algorithm using equal numbers of unique reads for input and ChIP samples and a p-value cutoff of 1e-10.
Genome Build:
Modmdg42.2.bed: DM3
Modmdg42.2.wig: DM3


title: L(3)mbt_ChIPseq

description: Chromatin IP against L(3)mbt

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS1.4.0alpha2) algorithm using equal numbers of unique reads for input and ChIP samples and a p-value cutoff of 1e-10.
Genome Build:
L3mbt.bed: DM3
L3mbt.wig: DM3


title: longissimus muscle_pooled 3 Landrace postnatal 180 day pigs

value: Landrace

value: longissimus muscle

tag: developmental stage

value: postnatal day 180


title: longissimus muscle_pooled 3 Lantang postnatal 2 day pigs

value: Lantang


title: SMEU37Fe1MP1

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

description: Chlamydomonas reinhardtii 2137 - Fe-deficient - Replicate #1

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe1MP1_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe1MP1_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii 2137 - Fe-deficient (Minimal media)

growth_protocol: Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium or minimal media.

extract_protocol: Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina by whole transcriptome analysis.

treatment_protocol: To generate Fe-deficient and Fe-limited cultures, cells in the pretransfer culture are grown under Fe-replete conditions to mid to late log phase (10e6-10e7 cells/ml) and diluted to 10e4 cells/ml into fresh Fe-deficient or Fe-limited medium. Two sequential transfers (from 10e6-10e7 cells/ml into fresh Fe-deficient medium) are performed to ensure that residual iron in the Fe-deficient or Fe-limited cultures is reduced.

tag: medium

value: Minimal media


title: SMEU37Fe1MS2

description: Chlamydomonas reinhardtii 2137 - Fe-deficient - Replicate #2

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe1MS2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly


title: SMEU37Fe1MS1

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe1MS1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly


title: SMEU37Fe1MP2

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe1MP2_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe1MP2_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly


title: SMEU37Fe20MS2

description: Chlamydomonas reinhardtii 2137 - Fe replete - Replicate #2

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe20MS2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly

source_name: Chlamydomonas reinhardtii 2137 - Fe replete (Minimal media)


title: SMEU37Fe20MS1

description: Chlamydomonas reinhardtii 2137 - Fe replete - Replicate #1

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe20MS1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly


title: SMEU37Fe20MP2

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe20MP2_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe20MP2_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly


title: SMEU37Fe02MS2

description: Chlamydomonas reinhardtii 2137 - Fe-limited - Replicate #2

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe02MS2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly

source_name: Chlamydomonas reinhardtii 2137 - Fe-limited (Minimal media)


title: SMEU37Fe02MS1

description: Chlamydomonas reinhardtii 2137 - Fe-limited - Replicate #1

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe02MS1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly


title: SMEU37Fe02MP2

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe02MP2_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe02MP2_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly


title: SMEU37Fe02TP3

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe02TP3_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe02TP3_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly

source_name: Chlamydomonas reinhardtii 2137 - Fe-limited (TAP)

value: TAP


title: SMEU37Fe02TP2

description: Chlamydomonas reinhardtii 2137 - Fe-deficient - Replicate #5

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe02TP2_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe02TP2_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly


title: SMEU37Fe1TP1

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe1TP1_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe1TP1_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly

source_name: Chlamydomonas reinhardtii 2137 - Fe-deficient (TAP)


title: SMEU37Fe1TP2

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe1TP2_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe1TP2_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly


title: SMEU37Fe02TP1

description: Chlamydomonas reinhardtii 2137 - Fe-deficient - Replicate #4

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe02TP1_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe02TP1_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly