title: PGK12.1ES_RNASeq

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description: RNAseq of PGK12.1

data_processing:
Sequences (total 200M 36bp reads) from four lanes were aligned to the mouse reference genome (mm9) using TopHat with default parameters, except that the "min-isoform-fraction" flag was set to zero, "--no-novel-juncs" was specified to constrain the search to annotated exon:exon boundaries, and the RefSeq mouse gene annotation was used.
FPKM values were obtained using Cufflinks with default parameters and "min-isoform-fraction" set to zero.

source_name: PGK12.1 ES cells

growth_protocol: ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for experiments and cell collection.

extract_protocol: purified mRNA was fragmented into ~200 bases and reverse transcribed by random hexamers into cDNA, to prepare a library for Illumina sequencing using the RNA-Seq Sample Prep kit (Illumina)

value: Derived from blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

tag: cell line

value: PGK12.1 ES

tag: gender

value: Female


title: input_0hr_WCE_ChIPSeq

status: Public on Jul 19 2011

type: SRA

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

country: USA

institute: Stowers Institute for Medical Research

description: input DNA

library_source: genomic

data_processing:
Alignment: Sequencing reads were acquired through the primary Solexa image analysis pipeline, where bases were called and reads were filtered for quality, according to default Solexa standards. Filtered reads were then aligned to the mouse genome (NCBI build 37, UCSC mm9) or the human genome (UCSC hg19) using the bowtie (Langmead et al., 2009) alignment tool, version 0.12.7. Only those sequences that matched uniquely to the genome with up to two mismatches were retained.
Peaks: Enriched regions of ChIP-seq signal were determined by the "MACS" (Zhang et al.,2008) peak-finding program, version 1.4.0rc2. Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively. The effective genome size was configured appropriately for mouse and human datasets, and the p-value cutoff was set to 1.00e-08 or FDR <= 1%, and a foldchange greater than five.

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse embryonic stem cells (KH2) were cultured under feeder-free medium ESGRO (Millipore).  HCT-116 cells were grown in McCoyâs 5A medium supplemented with 10% FBS.

extract_protocol: Chromatin immunoprecipitation (ChIP) was performed according to previously described protocols (Wang et al. 2009 [MCB]).  Briefly,  ES cells were cross-linked by 1% formaldehyde and sonicated. 10 ug of antibodies were used in the ChIP assays. The ChIP Libraries were prepared with the Illumina DNA Sample Kit (Part# 0801-0303) according to Illumina's instructions and sequenced on the Genome Analyzer IIx following the manufacturer's protocols.  Antibodies for Pol II are from Covance, 8WG16, catalog #MMS-126R.  Other antibodies were sourced from the original work of Lin et al. 2010 (Mol. Cell)

treatment_protocol: For RA induction, mouse ES cells were treated with 0.3 uM of all-trans retinoic acid for 6 hours. For serum stimulation, cells were first starved by washing cells 2x in PBS, then culturing for 40 hours in McCoy's 5A without serum. Cells were then either left untreated or treated with serum for 30 minutes before harvesting.

tag: strain

value: C57BL/6 (female)  x 129/S (male)

tag: cell type

value: mES

tag: cell passage

tag: chip antibody


title: Trypanosoma brucei brucei strain STIB 247 procyclic culture library 2

status: Public on Jul 28 2011

city: Glasgow

first: Anneli

last: Cooper

address: GBRC, 120 University Place

department: Wellcome Centre for Molecular Parasitology

country: United Kingdom

institute: University of Glasgow

library_source: transcriptomic

data_processing: Read sequences were trimmed to 21bp (4bp NlaIII site + 17bp), then tag counts collated for each read sequence in each library using a custom written script with Perl 5.10.0.

molecule: total RNA

organism: Trypanosoma brucei brucei

source_name: Trypanosoma brucei brucei strain STIB 247 procyclic culture 2

growth_protocol: Procyclic form T.b.brucei strains STIB 247 and  247MelCyR were grown in SDM-79 media supplemented with 10% fetal bovine serum and harvested during mid-log phase (approximately 4,500,000 cells per library).

extract_protocol: The cells were pelleted at 1100g for 10 mins at 4ºC and immediately re-suspended in RLT buffer (Qiagen RNeasy kit). The cells were disrupted by serial passage through a 26 gauge needle and stored at -80ºC before use. RNA was isolated from the cells using RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase treatment step, to ensure that there was no DNA contamination. The RNA was measured for quantity and quality by Nanodrop ND-1000 spectrophotometer and Agilent 2100 Bioanalyzer according to the manufacturer’s instructions. Sequence tag preparation was performed with Digital Gene Expression Tag Profile Kit (Illumina) using NlaIII, according to the manufacturer’s instructions.

value: STIB 247

tag: drug sensitivity

value: Cymelarsan sensitive

tag: lifecycle stage

value: procyclic culture

tag: library


title: wild type control 111U-2

status: Public on Jul 20 2011

city: Bethesda

first: David

middle: Johannes

last: Clark

state: MD

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

data_processing: ELAND was used to align the reads to the NCBI Saccharomyces cerevisiae genome sequence Build 2.1

organism: Saccharomyces cerevisiae

source_name: wild type control

growth_protocol: Cells grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium (control), or in synthetic complete medium lacking histidine, with 10 mM 3-aminotriazole for 20 mins prior to harvesting (+3AT).

extract_protocol: The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

treatment_protocol: Nuclei were prepared and digested to mono-nucleosomes with micrococcal nuclease. Mono-nucleosomal DNA was gel-purified.

tag: genotype

tag: average length (bp) +/-sd

tag: assayed molecule

value: nucleosomal DNA


title: Pol_II_6hr_WCE_ChIPSeq

description: input DNA


title: Trypanosoma brucei brucei strain 247MelCyR procyclic culture library 1

source_name: Trypanosoma brucei brucei strain 247MelCyR procyclic culture 1

value: Cymelarsan resistant


title: Pol_II_0hr_WCE_ChIPSeq

description: input DNA


title: Pol_II_0hr_ChIPSeq

description: Chromatin IP against Pol II

value: Pol II  8WG16 Covance (Mono)


title: ELL2_0hr_ChIPSeq

description: Chromatin IP against ELL2

value: Lin et al. 2010 (Mol. Cell)


title: starved_2_RNAseq

description: ctrl mRNA

data_processing: Alignment: Sequencing reads were acquired through the primary Solexa image analysis pipeline, where bases were called and reads were filtered for quality, according to default Solexa standards. Filtered reads were then aligned to the human genome (UCSC hg19) using the tophat (Trapnell et al. 2009) alignment tool, version 1.2.0, allowing unique matches only, and the full human ENSEMBL 59 GTF.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: HCT-116 cells were grown in McCoyâs 5A medium supplemented with 10% FBS.

extract_protocol: Total RNA was extracted from serum-treated and untreated HCT-116 cells with RNeasy kit following manufacturer's protocol. And 2 ug of total RNA from each sample was used to prepare the libraries with the Illumina mRNA-Seq Sample Prep Kit (RS-100-0801) according to Illumina's instructions and sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

treatment_protocol: For serum stimulation, cells were first starved by washing cells 2x in PBS, then culturing for 40 hours in McCoyâs 5A without serum. Cells were then either left untreated or treated with serum for 30 minutes before harvesting.

tag: passages

value: passage 4-15

tag: treatment


title: serum_1_RNAseq

description: serum mRNA

value: serum-induced


title: starved_1_RNAseq

description: ctrl mRNA


title: AFF4_serum_ChIPSeq

description: Chromatin IP against AFF4

value: colon cancer cell line


title: ELL2_serum_ChIPSeq

description: Chromatin IP against ELL2


title: serum_WCE_ChIPSeq

description: input DNA


title: serum_2_RNAseq

description: serum mRNA


title: AFF4_starved_ChIPSeq

description: Chromatin IP against AFF4


title: Pol_II_serum_ChIPSeq

description: Chromatin IP against Pol II


title: Pol_II_starved_ChIPSeq

description: Chromatin IP against Pol II


title: starved_WCE_ChIPSeq

description: input DNA


title: ELL2_starved_ChIPSeq

description: Chromatin IP against ELL2


title: Col x Ler embryo RNA-seq

status: Public on Jul 18 2011

city: Cambridge

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: mRNA-seq

data_processing: Sequencing reads were aligned to the TAIR 9.0 version of the Arabidopsis reference genome (www.arabidopsis.org) using the TopHat read aligner (http://tophat.cbcb.umd.edu/). Low quality reads and reads that mapped to more than one position in the genome with the same alignment score were discarded. Reads that mapped to more than one gene due to overlapping exons were not considered in further analyses. SAM files for each sequencing run of the same library are deposited separately.

organism: Arabidopsis thaliana

source_name: embryo 6-7 days after pollination

growth_protocol: Plants were grown on soil in 16h days at 22 C.

extract_protocol: Seeds (600-1000) from crosses between multiple individuals were hand-dissected and total embryo or endosperm RNA isolated using the Ambion RNaqueous Kit with Plant RNA Isolation Aid. LIbraries were constructed using the Illumina mRNA-seq kit and protocol. 1 microgram of total RNA was poly-A selected twice, fragmented, and converted into double-stranded cDNA. The cDNA was end-repaired, adenylated, and adapters ligated. Adapter-ligated DNA approximately 200 bp in length was gel purified and amplified using Illumina PCR primers PE1.0 and PE2.0 with 15 amplification cycles.

tag: genetic background

value: Col-0 female X Ler male

tag: tissue

value: embryo

tag: age

value: 6-7 days after pollination


title: Col x Ler endosperm RNA-seq

description: mRNA-seq

source_name: endosperm 6-7 days after pollination

value: endosperm


title: Ler x Col embryo RNA-seq

description: mRNA-seq

value: Ler female X Col-0 male


title: Ler x Col endosperm RNA-seq

description: mRNA-seq


title: Juveniles_2

status: Public on Jul 21 2011

city: Changsha

first: Yunsheng

last: Wang

state: Hunan

address: Nongda road 1

department: Bioinformatics

country: China

institute: Hunan Agricultural University

description: Mi library.

data_processing:
The Sample data table includes the unique tag sequences processed with a bioinformatics pipline as follows: (1) remove low quality reads; (2) trim 3-prime adaptor sequences; (3) remove adaptor-only contaminants; (4) collect short RNAs ranged from 18-30 nt; (5) remove those sequences with polyA tail.

The clean tag sequences were mapped to the genome of M. incognita (WormBase WS205) by SOAPalign, and microRNA genes were identified with MIREAP.

The 'GSM611102_Mi_clean.fa' file contains the M. incognita non-redundant reads sequence in fasta format. The 'GSM611102_Mi_map.txt' file contains the alignment results of these unique reads to the M. incognita genome with an exact match.

organism: Meloidogyne incognita

source_name: J2 juveniles

growth_protocol: Nematode inoculums were obtained from a population of Meloidogyne incognita (Kofoid and White), and reproduced in a greenhouse with pepper cultivar Qiemen (Capsicum annuum L. cv), a root-knot nematode (RKN)-susceptible cultivar. Inoculums consisted of freshly hatched juveniles from egg masses. RKN J2 were concentrated and filtered off foreign matter through a 1mm pore size nylon sieve.

extract_protocol: Total RNA was extracted from the samples using Trizol reagent according to the manufacturer’s recommended protocol (Invitrogen, USA). For small RNA library construction and deep sequencing, the 18-30 nt size range of RNA was enriched by polyacrylamide gel electrophoresis (PAGE). 20 µg of the purified small RNA from each library was subjected to DNA sequencing with an Illumina Genome Analyzer according to the manufacturer’s instructions.

tag: developmental stage

value: juvenile 2 (J2)

value: whole body


title: EGF replicate 2

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium supplemented with EGF for 6 additional hours. Biological replicate 2 of 3

data_processing:
Raw sequence base calls and probability scores (.srf files generated from _seq.txt and _prb.txt files): Raw data were processed using the Illumina pipeline version 0.3.0.
removal of adaptor sequences (.fa files): 3’ adapters were recognized and trimmed using a perl script that penalizes mismatches to a lesser extent at read ends, following the distribution of sequencing errors along Solexa reads (Dohm et al. 2008). Where no adaptor could be recognized, sequence was cut down to 18 nt.
mapping to RefSeq (_seq.txt files): The compiled collection of expression tags with removed adapters was aligned against the reduced-complexity set of RefSeq entries generated by in silico identification of DpnII cut sites and retrieval of 30 nt sequences on either side of each cut site. The mapping was performed by applying Eland iteratively in order to include all possible product sizes.
raw transcript counts (_nonfiltered_tab.txt file): Reads mapping unambiuously were counted for each unique transcript within the reduced-complexity RefSeq reference set. File available as supplementary file on the Series record.
per gene transcript counts (_collapsed_tab.txt file): Raw transcript counts were first filtered by removal of RefSeq probes with values smaller than 'mean minus standard error' in at least 90% of the samples, where 'mean = average counts of RefSeq probes corresponding to the same gene within one sample' and 'standard error = standard error of counts of RefSeq probes corresponding to the same gene within one sample' Normalized counts of RefSeq probes corresponding to the same gene (defined by gene symbol) were summed up. Subsequently, counts were normalized by making sample-wise total numbers of reads equal to the median total number of reads for all samples. Finally, normalized counts of RefSeq probes corresponding to the same gene (defined by gene symbol) were summed up. File available as supplementary file on the Series record.

source_name: Cervical cancer cell line (HeLa)

growth_protocol: Cells were cultured at 37ºC in a 95/5 Air/CO2 water saturated  atmosphere in Dulbecco’s  modified  Eagle’s medium (DMEM) containing 10% heat inactivated foetal bovine serum (FBS), 2 mM  L-glutamine and 100U/ml Penicilin/streptomycine (complete growth medium).

extract_protocol:
Total RNA from HeLa cells was extracted using the RNeasy RNA Isolation kit (Qiagen) followed by treatment with RNase-free DNase I (Ambion, Austin, TX) following manufacturer's instructions. RNA quantification was performed with a Nanodrop spectrophotometer, and the RNA integrity was assessed using the Bioanalyzer 2100 nanoelectrophoresis Lab-on-a–chip system (Agilent, Wilmington, DE).
library selection: 18 nt tag selection by restriction enzyme digestion (DpnII), oligo-dT selection of most 3' fragments, ligation of adapter with MseI site, followed by type II restriction enzyme cut (MseI)
library construction protocol: 2 ug of total RNA were used following Illumina's protocol for sequencing of DGE tags. Briefly, libraries of cDNA fragments were generated by capturing transcripts on oligo-dT beads, followed by synthesis of first and second strand cDNA in situ. Cleavage with DpnII resulted in recovery of the most 3' portion of the cDNA molecules, still attached to beads. A 5' adaptor containing a cut site for the type II restriction endonuclease MmeI was ligated to the cDNA. Cleavage with MmeI released fragments of 17-18 bp from the beads. Following 3' adapter ligation, the resulting library was enriched by PCR amplification (15 cycles), and purified by PAGE.
planned read length (bp): 36

treatment_protocol: For treatments, the cells were transferred to 60 mm dishes and cultured for 48h in complete growth medium, after which they were starved for 24h in DMEM containing 2% FBS after which they were grown in complete growth medium or the same supplemented with EGF (150 ng/ml) during 6 hours

value: EGF

tag: biological replicate

tag: cell line

value: HeLa

value: Cervical cancer cell line


title: ZLD cycle 8

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

description: ChIP for Zelda at wt Dmel embryo (Oregon R) at mitotic cycles 8-9 (hand sorted)

data_processing:
Alignment: Sequenced reads were mapped to the April 2006 assembly of the D. melanogaster genome, (UCSC version dm3, BDGP Release 5) using Bowtie (version 0.12.5). Sequenced reads were trimmed to 36 bp and mapped to the genomes using the Bowtie command-line options -n 2 -l 36 -m 2, thereby keeping for further analyses only tags that mapped uniquely to the genome with at most two mismatch.
Peaks: Each read was extended to 150 bp based on its orientation, and the total number of reads per time point was normalized to 10,000,000 reads. Peak calling was then performed using a Model-based Grizzly Peak algorithm (http://eisenlab.org/software/grizzly)

organism: Drosophila melanogaster

source_name: Embryos

extract_protocol:
The chromatin obtained was fragmented to sizes ranging from 100-300 bp using a Bioruptor for a total of processing time of 140 min (15s on, 45s off), with power setting at H. We used 3.7 µg chromatin from cycle 8, 6.6 µg for cycle 13 and 6 µg for stage 5 in the chromatin immunoprecipitation reaction using the affinity purified anti-ZLD antibody, following the procedure described previously (Li-XY et al, PLoS Biology, 2008). The sequencing libraries were prepared from the ChIP and Input DNA samples, and subjected to ultra-high throughput sequencing on a Solexa GAIIx platform as previously described (Bradley-RK et al, PLoS Biology, 2010), except that the DNA fragments ranged from 200-350 bp in size.
ZLD antibody purification -
As described in Harrison-MM et al. (Dev. Biology, 2010), rabbits were immunized with GST fused to amino acids 1117-1487 of ZLD and purified against the same portion of the protein fused to maltose binding protein (MBP). As this portion of ZLD includes the zinc-finger DNA-binding domain, we further purified these antibodies using MBP fused to the four zinc fingers, amino acids 1318-1444. For our experiments, we recovered the antibodies that failed to bind to this MBP fusion protein and confirmed by immunoblot that these antibodies could recognize the full-length ZLD, but not the DNA-binding domain alone.

tag: strain

value: Oregon R

value: mitotic cycles 8-9

tag: antibody

value: anti-ZLD


title: Control replicate 3

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium for 6 additional hours. Biological replicate 3 of 3

value: Control

tag: cell type


title: EGF replicate 1

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium supplemented with EGF for 6 additional hours. Biological replicate 1 of 3


title: ZLD cycle 13

description: ChIP for Zelda at wt Dmel embryo (Oregon R) at mitotic cycles 13-14 (hand sorted)

value: mitotic cycles 13-14


title: ZLD cycle 14

description: ChIP for Zelda at wt Dmel embryo (Oregon R) at late mitotic cycle 14 (hand sorted)

value: late mitotic cycle 14


title: Control replicate 2

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium for 6 additional hours. Biological replicate 2 of 3


title: EGF replicate 3

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium supplemented with EGF for 6 additional hours. Biological replicate 3 of 3


title: EBV_EBNA1_Raji_ChIP-Seq

status: Public on Jul 16 2011

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description: Raji cells per IP with EBNA1 monoclonal antibody

data_processing:
Alignment: Alignment was performed using Illumina software
Solexa ChIP-Seq experiments were performed with 2x106 Raji cells per IP with either EBNA1 monoclonal antibody or control mouse IgG.  Raji cells are EBV positive human Burkitt lymphoma cell line.  For Peak calling, A combination of fold ratio and Poisson model for the tag distribution was used to define peaks as follows: (i) Identification of genomic regions (of length 1000bp) enriched with ChIP-seq sequence tags using fold ratio â A genomic region is considered as sequence enriched if the fold ratio, calculated using number of reads normalized to the total reads within that region in ChIP (antibody treatment) sample divided by the number of reads normalized to the total reads in control sample (IgG control) in the same region, is higher than the given cutoff. Nearby enriched regions were merged to make broader enriched genomic regions. A cutoff of 3 was applied to find the initial genomic regions of enrichment at this stage. (ii) Creating the read overlapping profile for each identified region from step 1, by extending the sequence reads from the 5â end to the 3â end of the reads up to 300 bps (the average length of the ChIP-DNA fragment sequenced from the Solexa GA with Illumina standard ChIP-seq protocol) for the experiment sample. (iii) Peak identification, by using Poisson model â by counting the number of overlapped reads at each nucleotide position and defining the genomic position with the highest number as the peak position within the significant region.  Finally, only those genomic regions that have fold ratio > 10 and peak score > 8 and p value < 0.001 (as determined by Poisson background model) are considered as statistically significant.   Peak score is calculated as the average value of raw counts within a given region of significant fold enrichment relative to control IgG levels.  The average is measured for overlapping tags at every base after extending the tags to their average tag length within the significant region.

growth_protocol: 10% FBS in RPMI with antibiotics

extract_protocol: Illumina Library Preparation Protocol

value: Burkitt lymphoma

value: Raji cells

tag: chip-antibody

value: EBNA1 monoclonal antibody

tag: chip-antibody vendor

value: Advance Biotechnology.

tag: chip-antibody cat. number


title: BMP-4_Input_Seq

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: Input genomic DNA.

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006; hg18) genome using the Illumina Genome Analyzer Pipeline.
Peaks: Peaks were called using CisGenome v1.2 by two-sample analysis, where input genomic DNA was used as a negative control.

source_name: PASMCs stimulated with BMP-4 for 1.5 h, input

growth_protocol: PASMCs were maintained in SmGM-2 medium (Lonza). Cells were grown in a humidified incubator with 5% CO2 at 37C.

extract_protocol: ChIP was performed as described (Koinuma et al., Mol Cell Biol 29: 172-186, 2009 [PMID 18955504]). SMAD1/5-DNA complexes were isolated with anti-SMAD1/5 antibody. Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: Cells were treated with 50 ng/ml of BMP-4 for 1.5 h.

value: human pulmonary arterial smooth muscle cells

value: 50 ng/ml BMP-4

tag: treatment duration

tag: chip antibody


title: BMP-6_SMAD1_5_ChIPSeq

description: Chromatin IP against SMAD1/5

data_processing: Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline.

source_name: HUVECs stimulated with BMP-6 for 1.5 h

growth_protocol: HUVECs were maintained in EGM-2 medium (Lonza).  Cells were grown in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: ChIP were performed as described (Koinuma et al, Mol Cell Biol 29: 172-186, 2009). SMAD1/5-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were treated with either 50 ng/ml of BMP-6 or 1 ng/ml of BMP-9 for 1.5 h.

value: human umbilical vein endothelial cells (Lonza)

tag: stimulation

value: 50 ng/ml BMP-6 for 1.5 h

tag: vendor

value: Matrix Research, Chiba, Japan

tag: catalog#

tag: lot#


title: Frankia sp. 5dNH4 cells

status: Public on Jul 15 2011

city: Beltsville

first: Derek

middle: Martens

last: Bickhart

address: Building 005, Rm 318, BARC-West 10300 Baltimore Ave

department: BARC

institute: USDA ARS

data_processing: CLC Bio Genomic Workbench using NC_007777.1 as reference genome

organism: Frankia casuarinae

source_name: culture flask

growth_protocol: Frankia CcI3 cultures were grown in Frankia Defined Minimal (FDM) broth (5.13 M Sodium Pyruvate, 4mM CaCl2*2H20, 800mM MgSO4*7H20, 4uM NaEDTA, 5mM KH2PO4, 5.5 mM MOPS) , with no agitation, at 30Â°C.

extract_protocol: Three mililiters of gravity settled cells were extracted from each culture flask. RRNA isoforms were depleted using a Microbexpress RNA enrichment kit. Sequence libraries were created using the guidelines provided in the Illumina mRNA-seq kit (cat # RS-100-0801) with only one modification: the Superscript III reverse transcriptase (Invitrogen) was used for cDNA synthesis at a temperature of 50Â°C.

treatment_protocol: Cells were subcultured once (for three days of growth) prior to the experiment. The N2 sample was grown with a modified iron stock and deprived of NH4Cl. The two NH4 samples were grown with NH4Cl added to the medium.

tag: culture time

value: 5 days

tag: ammonium chloride addition

value: yes

tag: iron stock

value: 201nM iron sulfate


title: Frankia sp. 3dN2 cells

value: 3 days

value: no

value: 35uM iron sulfate


title: HMLE/Twist-ER induced (Mesenchymal)

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description: RNA-seq of HMLE/Twist-ER cells induced to undergo EMT

data_processing: MAQ (PMID: 18714091) was used for mapping reads to the hg18 human genome and junction database. A junction database was generated by concatenating exonic sequences at junctions. The Acembly gene annotation (PMID: 16925834) was used to define exon boundaries and exon splicing junctions. The reference transcriptome on which reads were mapped was the union of the junction database and the genome.

source_name: HMLE/Twist-ER

growth_protocol: Immortalized human mammary epithelial cells (HMLEs) expressing pWZL-Twist-ER were obtained from Robert Weinbergâs laboratory at the Whitehead Institute for Biomedical Research (Cambridge, MA) and cultured as described in Elenbaas B, Spirio L, Koerner F, Fleming MD, Zimonjic DB, et al. (2001) Human breast cancer cells generated by oncogenic transformation of primary mammary epithelial cells. Genes Dev 15: 50-65.

extract_protocol: Total RNA was extracted from untreated HMLE/Twist-ER cells (epithelial sample) and after prolonged 4-OHT treatment (mesenchymal sample) using RNeasy Plus Mini kit (Qiagen). Poly-T capture beads were used to isolate mRNA from 10 mg of total RNA. mRNA was fragmentedand used for a first-strand cDNA synthesis by random hexamer-primed reverse transcription andsubsequent second-strand cDNA synthesis. Sequencing adaptors were ligated using the IlluminaGenomic DNA sample prep kit. Fragments 200 bp long were isolated by gel electrophoresis, amplified by 16 cycles of PCR, and sequenced on the Illumina Genome Analyser.

treatment_protocol: 4-hydroxy tamoxifen (4-OHT) treatment was performed as described in Mani SA, Guo W, Liao MJ, Eaton EN, Ayyanan A, et al. (2008) The epithelial-mesenchymal transition generates cells with properties of stem cells. Cell 133: 704-715

tag: background cell line

value: HMLE

tag: genotype/variation

value: expressing pWZL-Twist-ER

tag: cell state

value: Mesenchymal

tag: tamoxifen treatment


title: HMLE/Twist-ER Pre-induction (Epithelial)

description: RNA-seq of HMLE/Twist-ER cells (not induced)

value: Epithelial


title: Control replicate 1

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium for 6 additional hours. Biological replicate 1 of 3

tag: treatment

value: Control

tag: biological replicate

tag: cell line

value: HeLa

tag: cell type

value: Cervical cancer cell line


title: BMP-9_SMAD1_5_ChIPSeq

description: Chromatin IP against SMAD1/5

source_name: HUVECs stimulated with BMP-9 for 1.5 h

value: 1 ng/ml BMP-9 for 1.5 h


title: [E-MTAB-513] HCT20173, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCB_s_7_sequence

status: Public on Jul 14 2011

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

description:
100bp_Stranded_RNA_Seq_FCB_s_7_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

data_processing: processed data not provided

extract_protocol:
nucleic_acid_extraction | 100ng of total RNA was fragmentated, end repared and ligated with illumina small RNA v1.5 adaptors. The ligated RNA was reverse transcribed and PCR amplified with 15 cycles. The PCR product was normalized by DSN digestion and used for sequencing.
sequencing | Illumina sequencing was performed at HiSeq 2000 at Illumina
bioassay_data_transformation | FASTQ files (Illumina format) of sequencing reads were retrieved from the sequencing machine

tag: organismpart

value: 16 Tissues mixture

tag: material type

tag: libraryprep

value: totalRNA-stranded+DSN


title: [E-MTAB-513] HCT20173, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCA_s_8_sequence

description:
100bp_Stranded_RNA_Seq_FCA_s_8_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20173, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCB_s_5_sequence

description:
100bp_Stranded_RNA_Seq_FCB_s_5_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20173, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCB_s_6_sequence

description:
100bp_Stranded_RNA_Seq_FCB_s_6_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20173, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCB_s_8_sequence

description:
100bp_Stranded_RNA_Seq_FCB_s_8_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20173, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCA_s_7_sequence

description:
100bp_Stranded_RNA_Seq_FCA_s_7_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: ChIP-Seq_IgG

description: Raji cells per IP with control IgG

value: Burkitt lymphoma

value: Raji cells

tag: chip-antibody

value: purified IgG


title: Frankia sp. 3dNH4 cells

tag: strain

value: yes

value: 201nM iron sulfate


title: [E-MTAB-513] HCT20170, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCA_s_1_sequence

description:
100bp_Stranded_RNA_Seq_FCA_s_1_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

extract_protocol:
nucleic_acid_extraction | 1ug of total RNA was subjected to two rounds of oligo-dT beads binding. The purified RNA was fragmentated, end repared and ligated with illumina small RNA v1.5 adaptors. The ligated RNA was reverse transcribed and PCR amplified with 15 cycles, and used for illumina sequencing.
sequencing | Illumina sequencing was performed at HiSeq 2000 at Illumina
bioassay_data_transformation | FASTQ files (Illumina format) of sequencing reads were retrieved from the sequencing machine

value: mRNA-stranded


title: [E-MTAB-513] HCT20172, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCA_s_4_sequence

description:
100bp_Stranded_RNA_Seq_FCA_s_4_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

extract_protocol:
nucleic_acid_extraction | Final product from mRNA-stranded protocol was normalized by DSN digestion and used for sequencing.
sequencing | Illumina sequencing was performed at HiSeq 2000 at Illumina
bioassay_data_transformation | FASTQ files (Illumina format) of sequencing reads were retrieved from the sequencing machine

value: mRNA-stranded+ DSN


title: [E-MTAB-513] HCT20172, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCA_s_5_sequence

description:
100bp_Stranded_RNA_Seq_FCA_s_5_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20172, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCB_s_3_sequence

description:
100bp_Stranded_RNA_Seq_FCB_s_3_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20170, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCB_s_1_sequence

description:
100bp_Stranded_RNA_Seq_FCB_s_1_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20170, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCB_s_2_sequence

description:
100bp_Stranded_RNA_Seq_FCB_s_2_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20149, white blood cells, male, 58 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCA_s_4_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

extract_protocol:
nucleic_acid_extraction | 1ug of total RNA was subjected to two rounds of  oligo-dT beads binding. Purified mRNA was fragmented and random primed for cDNA synthesis. cDNA fragements were end repared, added dATP, and liagted to illumina pair end sample prep adaptor. The ligated material was amplified by PCR for 15 cycles, and used for illumina sequencing.
sequencing | Illumina sequencing was performed at HiSeq 2000 at Illumina
bioassay_data_transformation | FASTQ files (Illumina format) of sequencing reads were retrieved from the sequencing machine

value: white blood cells

tag: Sex

value: male

tag: age

value: 58 years

tag: phenotype

value: caucasian

value: mRNA-Seq

tag: biosourceprovider

value: Human White Blood Cells total RNA


title: [E-MTAB-513] HCT20170, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCA_s_3_sequence

description:
100bp_Stranded_RNA_Seq_FCA_s_3_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: BMP-4_SMAD1_5_ChIPSeq

description: Chromatin IP against SMAD1/5.

source_name: PASMCs stimulated with BMP-4 for 1.5 h, SMAD1/5 ChIP

tag: tissue

value: human pulmonary arterial smooth muscle cells

value: 50 ng/ml BMP-4

tag: treatment duration

tag: chip antibody

tag: antibody vendor

value: Matrix Research, Chiba, Japan

tag: antibody catalog#

tag: antibody lot#


title: [E-MTAB-513] HCT20149, white blood cells, male, 58 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCB_s_5_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20152, thyroid, female, 60 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCA_s_1_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: thyroid

value: female

value: 60 years

value: Human thyroid total RNA, lot 0908003


title: [E-MTAB-513] HCT20152, thyroid, female, 60 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCB_s_8_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20151, testes, male, 19 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCA_s_2_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: testes

value: 19 years

value: Human testes total RNA, lot 05060392


title: [E-MTAB-513] HCT20147, prostate, male, 73 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCB_s_3_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: prostate

value: 73 years

value: Human prostate total RNA, lot 0906002


title: [E-MTAB-513] HCT20151, testes, male, 19 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCB_s_7_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: male


title: [E-MTAB-513] HCT20147, prostate, male, 73 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCA_s_6_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: caucasian


title: [E-MTAB-513] HCT20170, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCA_s_2_sequence

description:
100bp_Stranded_RNA_Seq_FCA_s_2_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: 16 Tissues mixture

value: mRNA-stranded


title: [E-MTAB-513] HCT20150, ovary, female, 47 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCB_s_6_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: ovary

value: 47 years

value: african american

value: mRNA-Seq

value: Human ovary total RNA, lot 0812002


title: [E-MTAB-513] HCT20146, lymph node, female, 86 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCA_s_7_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: lymph node

value: female

value: 86 years

value: Human lymph node total RNA, lot 026P010305032B


title: [E-MTAB-513] HCT20146, lymph node, female, 86 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCB_s_2_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20144, liver, male, 37 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCB_s_8_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: liver

value: 37 years

value: Human liver total RNA, lot 040000124


title: [E-MTAB-513] HCT20145, lung, male, 65 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCB_s_1_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: lung

value: 65 years

value: Human lung total RNA, lot 0904002


title: [E-MTAB-513] HCT20142, kidney, female, 60 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCA_s_6_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: kidney

value: 60 years

value: caucasian

value: Human kidney total RNA, lot 0908002


title: [E-MTAB-513] HCT20144, liver, male, 37 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCA_s_8_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: male


title: [E-MTAB-513] HCT20143, heart, male, 77 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCB_s_7_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: heart

value: 77 years

value: mRNA-Seq

value: Human heart total RNA, lot 07040023


title: [E-MTAB-513] HCT20161, breast, female, 29 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCA_s_4_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: breast

value: female

value: 29 years

value: Human breast total RNA, lot 04060013


title: [E-MTAB-513] HCT20160, brain, female, 77 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCB_s_3_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: brain

value: Human brain total RNA, Ambion


title: [E-MTAB-513] HCT20162, colon, female, 68 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCA_s_5_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: colon

value: 68 years

value: Human colon total RNA, lot 05060063


title: [E-MTAB-513] HCT20161, breast, female, 29 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCB_s_4_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA


title: [E-MTAB-513] HCT20148, skeletal muscle, male, 77 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCB_s_4_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: skeletal muscle

value: Human skeletal muscle total RNA, lot 046P021205086A


title: [E-MTAB-513] HCT20160, brain, female, 77 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCA_s_3_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: caucasian


title: [E-MTAB-513] HCT20148, skeletal muscle, male, 77 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCA_s_5_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: male


title: [E-MTAB-513] HCT20159, adrenal, male, 60 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCB_s_2_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: adrenal

value: 60 years

value: Human adrenal total RNA, lot 0812003


title: [E-MTAB-513] HCT20158, adipose, female, 73 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCB_s_1_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: adipose

value: 73 years

value: mRNA-Seq

value: Human adipose total RNA, lot 05060581


title: [E-MTAB-513] HCT20172, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCB_s_4_sequence

description:
100bp_Stranded_RNA_Seq_FCB_s_4_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: 16 Tissues mixture

value: mRNA-stranded+ DSN


title: [E-MTAB-513] HCT20150, ovary, female, 47 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCA_s_3_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: ovary

value: female

value: 47 years

value: african american

value: Human ovary total RNA, lot 0812002


title: [E-MTAB-513] HCT20162, colon, female, 68 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCB_s_5_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: colon

value: 68 years

value: Human colon total RNA, lot 05060063


title: [E-MTAB-549] Day6.1_1TachNC

description: Performer: SC

organism: Neospora caninum

growth_protocol: grow | Neospora caninum-Liverpool isolate tachyzoites were maintained as described previously (Cohen et al. 2002). Briefly,  parasites were cultured by twice weekly passage into African Green Monkey Kidney Fibroblasts (Vero cells) using Iscove's Modified Dulbecco's Medium (IMDM, Lonza, Walkersville, USA) supplemented with 5% (v/v) foetal calf serum (FCS, Labtech international, UK) and 100Uml-1 penicillin/100Âµgml-1 streptomycin (Sigma-Aldrich). Parasites were harvested 2, 3, 4 or 6 days post-infection in aliquots of 108 tachyzoites and stored at -20oC either resuspended in TRIÂ® Reagent (Sigma-Aldrich) for RNA extraction or as pellets for proteomics.

extract_protocol:
nucleic_acid_extraction | RNA was extracted from Trizol with chloroform (as per the Invitrogen protocol), ethanol precipitated and then resuspended in RNAse free water. Poly A+ mRNA was purified from total RNA using oligo dT dyna bead selection followed by metal ion hydrolysis fragmentation with the Ambion RNA fragmentation kit. 1st strand cDNA is synthesized using randomly primed oligos followed by 2nd strand synthesis to produce dscDNA. This was followed by end repair with T4 and Klenow DNA polymerases and T4 polynucleotide kinase to blunt-end the DNA fragments. A single 3' A nucleotide was added to the repaired ends using Klenow exo- and dATP to deter concatemerization of templates, limit adapter dimers and increase the efficiency of adapter ligation. Adapters were then ligated (containing primer sites for sequencing). Ligated fragments were run on an agarose gel, size selected for 200-250bp inserts and DNA extracted as per Qiagen gel extraction kit protocol but with dissolution of gel slices at room temperature (rather than 50oC) to avoid heat induced bias. Libraries were then amplified by PCR to enrich for properly ligated template strands, to generate enough DNA and to add primers for flowcell surface annealing followed by a clean up with AMPure SPRI beads. These libraries were quantified using Agilent Bioanalyser chip and Kapa Illumina SYBR Fast qPCR kit.
scanning | The samples were sequenced on an Illumina Genome Analyser II.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.3. There were 152 cycles of sequencing with 2 reads per cluster.

tag: cellline

value: Vero cells

tag: developmentalstage

value: 6 days post infection


title: [E-MTAB-549] Day4.1_1TachNC

description: Performer: SC

value: 4 days post infection


title: [E-MTAB-549] Day3.1_1TachNC

description: Performer: SC

value: 3 days post infection


title: [E-MTAB-549] Day6_1TachNC

description: Performer: SC


title: [E-MTAB-513] HCT20145, lung, male, 65 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCA_s_8_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

tag: organismpart

value: lung

value: male

value: 65 years

value: caucasian

value: Human lung total RNA, lot 0904002


title: Cucumber_gall_infected

description: GC library.

data_processing:
The Sample data table includes the unique tag sequences processed with a bioinformatics pipline as follows: (1) remove low quality reads; (2) trim 3-prime adaptor sequences; (3) remove adaptor-only contaminants; (4) collect short RNAs ranged from 18-30 nt; (5) remove those sequences with polyA tail.

The clean tag sequences were mapped to the genome of M. incognita (WormBase WS205) by SOAPalign, and microRNA genes were identified with MIREAP.

The 'GSM611103_GC_clean.fa' file contains the M. incognita and C. annuum non-redundant reads sequence in fasta format. The 'GSM611103_GC_map.txt' file contains the alignment results of these unique reads to the M. incognita genome with an exact match.

organism:
Capsicum annuum
Meloidogyne incognita

source_name: M. incognita from infected gall of cucumber root

tag: developmental stage

value: juvenile 3 (J3) to adult

value: whole body


title: [E-MTAB-549] Day4_1TachNC

description: Performer: SC

tag: material type


title: [E-MTAB-549] NC4_exo_depleted

description: Performer: SC

extract_protocol:
nucleic_acid_extraction | RNA was extracted from Trizol with chloroform (as per the Invitrogen protocol), ethanol precipitated and then resuspended in RNAse free water. mRNA was purified from total RNA using terminator exonuclease to digest RNA species that have 5' phosphate followed by metal ion hydrolysis fragmentation with the Ambion RNA fragmentation kit. 1st strand cDNA is synthesized using randomly primed oligos followed by 2nd strand synthesis to produce dscDNA. This was followed by end repair with T4 and Klenow DNA polymerases and T4 polynucleotide kinase to blunt-end the DNA fragments. A single 3' A nucleotide was added to the repaired ends using Klenow exo- and dATP to deter concatemerization of templates, limit adapter dimers and increase the efficiency of adapter ligation. Adapters were then ligated (containing primer sites for sequencing). Ligated fragments were run on an agarose gel, size selected for 200-250bp inserts and DNA extracted as per Qiagen gel extraction kit protocol but with dissolution of gel slices at room temperature (rather than 50oC) to avoid heat induced bias. Libraries were then amplified by PCR to enrich for properly ligated template strands, to generate enough DNA and to add primers for flowcell surface annealing followed by a clean up with AMPure SPRI beads. These libraries were quantified using Agilent Bioanalyser chip and Kapa Illumina SYBR Fast qPCR kit.
scanning | The samples were sequenced on an Illumina Genome Analyser.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.0. There were 74 cycles of sequencing with 2 reads per cluster.


title: [E-MTAB-549] NC3_oligodT

description: Performer: SC

extract_protocol:
nucleic_acid_extraction | RNA was extracted from Trizol with chloroform (as per the Invitrogen protocol), ethanol precipitated and then resuspended in RNAse free water. Poly A+ mRNA was purified from total RNA using oligo dT dyna bead selection followed by metal ion hydrolysis fragmentation with the Ambion RNA fragmentation kit. 1st strand cDNA is synthesized using randomly primed oligos followed by 2nd strand synthesis to produce dscDNA. This was followed by end repair with T4 and Klenow DNA polymerases and T4 polynucleotide kinase to blunt-end the DNA fragments. A single 3' A nucleotide was added to the repaired ends using Klenow exo- and dATP to deter concatemerization of templates, limit adapter dimers and increase the efficiency of adapter ligation. Adapters were then ligated (containing primer sites for sequencing). Ligated fragments were run on an agarose gel, size selected for 200-250bp inserts and DNA extracted as per Qiagen gel extraction kit protocol but with dissolution of gel slices at room temperature (rather than 50oC) to avoid heat induced bias. Libraries were then amplified by PCR to enrich for properly ligated template strands, to generate enough DNA and to add primers for flowcell surface annealing followed by a clean up with AMPure SPRI beads. These libraries were quantified using Agilent Bioanalyser chip and Kapa Illumina SYBR Fast qPCR kit.
scanning | The samples were sequenced on an Illumina Genome Analyser.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.0. There were 74 cycles of sequencing with 2 reads per cluster.


title: [E-MTAB-513] HCT20143, heart, male, 77 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCA_s_7_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: heart

value: 77 years

tag: libraryprep

value: mRNA-Seq

value: Human heart total RNA, lot 07040023


title: [E-MTAB-549] NC3_exo_depleted

description: Performer: SC


title: [E-MTAB-549] NC4_oligodT

description: Performer: SC


title: [E-MTAB-612] polyA+_testis_7060321

description: Performer: LGTF

extract_protocol:
nucleic_acid_extraction | RNA from tissues was isolated by a modified guanidium thiocynate methods followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns. Selected targets were then amplified by RT-PCR.
sequencing | Standard Illumina protocol, performed at the University of Lausanne, Lausanne, Switzerland
bioassay_data_transformation | Standard method from the Illumina platform

value: testis

tag: biosourcetype

value: Clontech


title: [E-MTAB-612] polyA+_spleen_6090097

description: Performer: LGTF

value: spleen

tag: Sex


title: [E-MTAB-549] Day3_1TachNC

description: Performer: SC

value: Vero cells


title: [E-MTAB-502] ICC169-476, 3601_1

description: Performer: SC

organism: Citrobacter rodentium

source_name: RNA from Citrobacter rodentium ICC169-476

growth_protocol: grow | Citrobacter rodentium strains were grown at 37 degrees C in Luria-Bertani (LB) medium.

extract_protocol:
nucleic_acid_extraction | The whole genome transcriptome of Citrobacter rodentium ICC169-476 was sequenced using Illumina sequencing technology as previously described (Croucher NJ et al. (2009) A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res 37: e148).  Removal of genomic DNA from the RNA sample and subsequent successful cDNA generation was confirmed by PCR using the four primer pairs NKP125-132 that generate amplicons internal to C. rodentium housekeeping genes.
sequencing | cDNA was made into a standard Illumina library with a fragment size of 200 to 250 bp. Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina pipeline v1.3.4. There were 54 cycles of sequencing with 1 read per cluster.

tag: genotype


title: [E-MTAB-612] polyA+_lung_1100350

description: Performer: LGTF


title: [E-MTAB-502] ICC169-476, 2158_6

description: Performer: SC

extract_protocol:
nucleic_acid_extraction | The whole genome transcriptome of Citrobacter rodentium ICC169-476 was sequenced using Illumina sequencing technology as previously described (Croucher NJ et al. (2009) A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res 37: e148).  Removal of genomic DNA from the RNA sample and subsequent successful cDNA generation was confirmed by PCR using the four primer pairs NKP125-132 that generate amplicons internal to C. rodentium housekeeping genes.
sequencing | cDNA was made into a standard Illumina library with a fragment size of 200 to 250 bp. Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina pipeline v1.3rc1. There were 37 cycles of sequencing with 1 read per cluster.


title: [E-MTAB-475] Trypanosoma vivax Y486 RNA

description: Performer: SC

organism: Trypanosoma vivax

growth_protocol: grow | Trypanosoma vivax Y486 was grown from stabilate in BALB/c mice immunosuppressed with cyclophosphamide (250 mg.kg-1) and was amplified at patent parasitaemia in three immunosuppressed mice, from which whole blood was collected.  The blood was treated with the erythrocyte lysis buffer (EL; QIAGEN), following the manufacturer's instructions, and RNA was isolated from the pellet using the RNeasy mini kit protocol (QIAGEN).

extract_protocol:
nucleic_acid_extraction | Poly A+ mRNA was purified from total RNA using oligo dT dyna bead selection followed by metal ion hydrolysis fragmentation with the Ambion RNA fragmentation kit. 1st strand cDNA was synthesized using randomly primed oligos followed by 2nd strand synthesis to produce dscDNA. This was followed by end repair with T4 and Klenow DNA polymerases and T4 polynucleotide kinase to blunt-end the DNA fragments. A single 3' A nucleotide was added to the repaired ends using Klenow exo- and dATP to deter concatemerization of templates, limit adapter dimers and increase the efficiency of adapter ligation. Adapters were then ligated (containing primer sites for sequencing). Ligated fragments were run on an agarose gel, size selected for 275-325bp inserts and DNA extracted as per Qiagen gel extraction kit protocol but with dissolution of gel slices at room temperature (rather than 50oC) to avoid heat induced bias. Libraries were then amplified by PCR to enrich for properly ligated template strands, to generate enough DNA and to add primers for flowcell surface annealing followed by a clean up with AMPure SPRI beads. These libraries were quantified using Agilent Bioanalyser chip and Kapa Illumina SYBR Fast qPCR kit.
sequencing | Libraries were denatured with 0.1M sodium hydroxide and diluted in a hybridisation buffer to allow the template strands to hybridise to adapters attached to the flowcell surface. Cluster amplification was performed on the Illumina cBOT using the V4 cluster generation kit following the manufacturer's protocol and then a SYBRGreen QC was performed to measure cluster density and determine whether to pass or fail the flowcell for sequencing. This was followed by linearization, blocking and hybridization of the R1 sequencing primer. The hybridized flowcells were loaded onto the Illumina Genome Analyser IIX for 76 cycles of sequencing-by-synthesis using the V4 SBS sequencing kit then, in situ, the linearization, blocking and hybrdization step was repeated to regenerate clusters, release the 2nd strand for sequencing and to hybridise the R2 sequencing primer followed by another 76 cycles of sequencing to produce paired end reads. These steps were performed using proprietary reagents according to manufacturer's recommended protocol.
scanning | Data was analysed from the Illumina GAII sequencing machines using RTA1.6

tag: strainorline


title: [E-MTAB-612] polyA+_muscle_7040106

description: Performer: LGTF

value: muscle

tag: biosourceprovider


title: [E-MTAB-612] polyA+_brain_6120217

description: Performer: LGTF

value: brain


title: [E-MTAB-612] polyA+_heart_7082801A

description: Performer: LGTF


title: [E-MTAB-533] K562_GM12878_cell_lines

description: Performer: LGTF

extract_protocol:
nucleic_acid_extraction | RNA from human cell lines was isolated by a modified guanidium thiocynate methods followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns. Selected targets were then amplified by RT-PCR.
sequencing | Standard Illumina protocol, performed at the University of Lausanne, Lausanne, Switzerland
bioassay_data_transformation | Qseq files were produced by the sequencing machine.

value: cell

value: female

value: ATTC & Coriell Inst. Medical Res.


title: [E-MTAB-599] c57xdba_Thymus6

description: Performer: SC

source_name: c57xdba_Thymus6 160271

extract_protocol:
tissue collection | Mouse tissues where obtained from 8 weeks old mice from the Jackson lab Maine USA.
nucleic_acid_extraction | Total RNA extraction using trizol as per manufacturer instructions
scanning | The samples were sequenced on an Illumina Genome Analyser II.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.6.0a14. There were 152 cycles of sequencing with 2 reads per cluster.

value: adult

value: thymus

value: Jackson laboratory


title: [E-MTAB-612] polyA+_liver_6100188

description: Performer: LGTF

value: liver

value: male


title: [E-MTAB-513] HCT20158, adipose, female, 73 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCA_s_1_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: adipose

tag: age

value: 73 years

tag: phenotype

value: caucasian

value: Human adipose total RNA, lot 05060581


title: [E-MTAB-513] HCT20159, adrenal, male, 60 years, 1x75 single mRNA-Seq

description:
75bp_mRNA_Seq_FCA_s_2_sequence
1x75 single mRNA-Seq
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

value: adrenal

value: 60 years

value: mRNA-Seq

value: Human adrenal total RNA, lot 0812003


title: [E-MTAB-599] c57xdba_Thymus3

description: Performer: SC

source_name: c57xdba_Thymus3 160268


title: [E-MTAB-599] c57xdba_Thymus2

description: Performer: SC

source_name: c57xdba_Thymus2 160267


title: [E-MTAB-599] c57xdba_Thymus5

description: Performer: SC

source_name: c57xdba_Thymus5 160270


title: [E-MTAB-599] c57xdba_Thymus1

description: Performer: SC

source_name: c57xdba_Thymus1 160266


title: [E-MTAB-587] Inflorescences-Low_amount_material-OverAmplified-SEP3_IP-rep1

description: Performer: PLANT & FOOD RESEARCH

growth_protocol: grow | Arabidopsis thaliana, wild-type (Col-0),  plants were grown under standard greenhouse conditions (20Â°C, long day light regime: 16 h light, 8 hours dark cycle). Flower material was harvested from primary and secondary inflorescences of 5-7 weeks old plants.

extract_protocol:
specified_biomaterial_action | Inflorescences were harvested and fixed using FAA following a protocol published in Gomez-Mena et al. 2005 (PMID: 15634696) with modifications in de Folter et al. 2007 (PMID: 17868439)
sequencing | ChIP library preparation was performed using the standard protocol starting with very low amount of DNA material recovered from the ChIPseq step. This results in  overamplification of a limited number of DNA fragments.
scanning | Reads were mapped to the unmasked Arabidopsis reference genome (ATH1.1con.01222004; ftp://ftp.arabidopsis.org/) using the SOAP software.Only uniquely mapped reads were retained.

value: 5-7 weeks

value: Inflorescence

tag: chip-antibody

value: Antibody against a C-terminal peptide of SEP3

value: Over-amplified


title: [E-MTAB-599] c57xdba_Spleen6

description: Performer: SC

source_name: c57xdba_Spleen6 140973

value: adult

value: spleen


title: [E-MTAB-587] Inflorescences-Low_amount_material-SEP3_IP-rep2

description: Performer: PLANT & FOOD RESEARCH

value: control


title: [E-MTAB-599] c57xdba_Spleen5

description: Performer: SC

source_name: c57xdba_Spleen5 140972

value: Jackson laboratory


title: [E-MTAB-599] c57xdba_Spleen4

description: Performer: SC

source_name: c57xdba_Spleen4 140971


title: [E-MTAB-599] c57xdba_Spleen1

description: Performer: SC

source_name: c57xdba_Spleen1 140968


title: [E-MTAB-599] c57xdba_Spleen2

description: Performer: SC

source_name: c57xdba_Spleen2 140969


title: [E-MTAB-587] Inflorescences-Low_amount_material-SEP3_IP-rep1

description: Performer: PLANT & FOOD RESEARCH


title: [E-MTAB-599] c57xdba_Spleen3

description: Performer: SC

source_name: c57xdba_Spleen3 140970


title: [E-MTAB-599] c57xdba_Lung6

description: Performer: SC

extract_protocol:
tissue collection | Mouse tissues where obtained from 8 weeks old mice from the Jackson lab Maine USA.
nucleic_acid_extraction | Total RNA extraction using trizol as per manufacturer instructions
scanning | The samples were sequenced on an Illumina Genome Analyser II.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.6.1. There were 152 cycles of sequencing with 2 reads per cluster.

value: lung


title: [E-MTAB-599] c57xdba_Thymus4

description: Performer: SC

source_name: c57xdba_Thymus4 160269

value: thymus


title: [E-MTAB-599] c57xdba_Lung4

description: Performer: SC


title: [E-MTAB-599] c57xdba_Lung3

description: Performer: SC


title: [E-MTAB-460] Zebrafish adult swim bladder, 5625_5

description: Performer: SC

organism: Danio rerio

source_name: Zebrafish adult swim bladder

growth_protocol: grow | Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at -70 C.

extract_protocol:
nucleic_acid_extraction | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions. Pellets were re-suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments).
specified_biomaterial_action | Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented, LiCl precipitated, reverse transcribed with random primers, a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.
sequencing | Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.
SRF file were generated using the standard method for the Illumina platform. Base calling was performed using Illumina RTA pipeline 1.8.70.0 (Bustard 1.8.1a2) with phred quality scores at 64 levels using Illumina pipeline 1.8.70.0 (GERALD). There were 160 cycles of sequencing with two 76 base reads per cluster along with an unused 8 base barcode tag.  The forward read starts at cycle 1 and the reverse read starts at cycle 85.  The sequence in cycles 77 to 84 is only present for technical reasons and should be ignored.
nucleic_acid_extraction | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions. Pellets were re-suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments).
specified_biomaterial_action | Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented, LiCl precipitated, reverse transcribed with random primers, a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.
sequencing | Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.

value: swim bladder

value: Singapore

value: mixed


title: [E-MTAB-460] Zebrafish adult head kidney, 5625_3

description: Performer: SC

source_name: Zebrafish adult head kidney

value: head kidney


title: [E-MTAB-460] Zebrafish adult heart, 5625_2

description: Performer: SC

source_name: Zebrafish adult heart

value: heart


title: [E-MTAB-610] Pachycladon enysii - PE2

description: Performer: AWCGS

organism: Pachycladon enysii

extract_protocol:
nucleic_acid_extraction | RNA from three native populations of P. enysii and P. fastigiatum was isolated as described in Voelckel et al. 2008. Replicate RNAs of each species were pooled and underwent sample preparation according to manufacturer instructions (DGE-Tag Profiling DpnII Sample Prep Kit, Illumina Inc., San Diego, USA). mRNA was isolated from total RNA and DpnII-restricted to generate 16 bp tags. DpnII-anchored tags were then enriched for sequencing. After tag library construction, libraries were titrated resulting in three flow cell lanes being loaded for each species.
sequencing | Cluster generation and sequencing were conducted according to Illumina protocols (DGE-Tag Profiling DpnII Cluster Generation Kit, 18 Cycle Solexa Sequencing Kit, Illumina Inc., San Diego, USA).
scanning: FASTQ files of sequencing reads were retrieved from the sequencing machine.

value: cell

tag: population

tag: tissue

value: 15 leaves

value: middle-aged, rosette-stage


title: [E-MTAB-460] Zebrafish adult brain, 5625_1

description: Performer: SC

source_name: Zebrafish adult brain

value: brain


title: [E-MTAB-460] Zebrafish adult swim bladder, 3212_5

description: Performer: SC

extract_protocol:
nucleic_acid_extraction | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions. Pellets were re-suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments).
specified_biomaterial_action | Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented, LiCl precipitated, reverse transcribed with random primers, a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.
sequencing | Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.
SRF file were generated using the standard method for the Illumina platform. Base calling was performed using Illumina pipeline 1.3 (Bustard 1.3.4) with phred quality scores at 64 levels using Illumina pipeline 1.3 (Gerald). There were 152 cycles of sequencing with 2 reads per cluster, a forward read starting at base 1 and a reverse read starting at base 77.
nucleic_acid_extraction | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions. Pellets were re-suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments).
specified_biomaterial_action | Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented, LiCl precipitated, reverse transcribed with random primers, a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.
sequencing | Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.


title: [E-MTAB-610] Pachycladon enysii - PE1

description: Performer: AWCGS

value: 16 leaves


title: [E-MTAB-599] c57xdba_Lung1

description: Performer: SC


title: [E-MTAB-460] Zebrafish adult swim bladder, 4191_5

description: Performer: SC

extract_protocol:
nucleic_acid_extraction | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions. Pellets were re-suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments).
specified_biomaterial_action | Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented, LiCl precipitated, reverse transcribed with random primers, a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.
sequencing | Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.
SRF file were generated using the standard method for the Illumina platform. Base calling was performed using Illumina pipeline 1.6.0a14 (Bustard 1.6.0a14) with phred quality scores at 64 levels using Illumina pipeline 1.6.0a14 (GERALD). There were 152 cycles of sequencing with 2 reads per cluster, a forward read starting at base 1 and a reverse read starting at base 77.
nucleic_acid_extraction | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions. Pellets were re-suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments).
specified_biomaterial_action | Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented, LiCl precipitated, reverse transcribed with random primers, a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.
sequencing | Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.


title: [E-MTAB-610] Pachycladon enysii - PE3

description: Performer: AWCGS


title: [E-MTAB-599] c57xdba_Liver6

description: Performer: SC

source_name: c57xdba_Liver6 139644

value: liver


title: [E-MTAB-552] Mature Tuber

description: Performer: AAU

organism: Solanum tuberosum

source_name: Mature Tuber

growth_protocol: grow | RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested.

extract_protocol:
nucleic_acid_extraction | A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.
Illumina Genome Analyzer Classic. Analyzed with Illumina Pipeline 0.3.
scanning | All samples were base called with the standard settings. Samples RHs01.tx-RHs08.txt: CHASTITY>=0.6, using a chastity threshold of 0.6, on the first 12 cycles. Samples RHs09.tx-RHs16.txt:  failed-chastity<=1, using a chastity threshold of 0.6, on the first 25 cycles.

value: tuber

value: mature


title: [E-MTAB-599] c57xdba_Liver5

description: Performer: SC

source_name: c57xdba_Liver5 139643

value: adult


title: [E-MTAB-552] Young Tuber

description: Performer: AAU

source_name: Young Tuber

value: young


title: [E-MTAB-460] Zebrafish adult head kidney, 4191_6

description: Performer: SC


title: [E-MTAB-599] c57xdba_Lung2

description: Performer: SC

value: lung

value: Jackson laboratory


title: [E-MTAB-599] c57xdba_Lung5

description: Performer: SC


title: [E-MTAB-460] Zebrafish adult head kidney, 3212_8

description: Performer: SC


title: [E-MTAB-552] Stolon

description: Performer: AAU

source_name: Stolon

value: stolon


title: [E-MTAB-599] c57xdba_Liver4

description: Performer: SC

source_name: c57xdba_Liver4 139642


title: [E-MTAB-460] Zebrafish adult heart, 4191_7

description: Performer: SC

value: Singapore


title: [E-MTAB-552] Stem

description: Performer: AAU

source_name: Stem

value: stem


title: [E-MTAB-552] Shoot apex

description: Performer: AAU

source_name: Shoot apex

value: shoot apex


title: [E-MTAB-599] c57xdba_Liver3

description: Performer: SC

source_name: c57xdba_Liver3 139641


title: [E-MTAB-552] Petiole

description: Performer: AAU

source_name: Petiole

value: petiole


title: [E-MTAB-552] Leaf

description: Performer: AAU

source_name: Leaf

value: leaf


title: [E-MTAB-599] c57xdba_Liver2

description: Performer: SC

source_name: c57xdba_Liver2 139640


title: [E-MTAB-460] Zebrafish adult heart, 3212_7

description: Performer: SC

value: heart

value: mixed


title: [E-MTAB-552] Flower

description: Performer: AAU

source_name: Flower

value: flower


title: [E-MTAB-599] c57xdba_Liver1

description: Performer: SC

source_name: c57xdba_Liver1 139639


title: [E-MTAB-445] uninfected control Gastric LN_146

description: Performer: ROSLIN

organism: Ovis aries

source_name: gastric lymph node, uninfected control

extract_protocol:
nucleic_acid_extraction | Gastric lymph nodes were collected from all lambs, diced and placed in RNAlater (Ambion) at 20C, incubated at 4C overnight and stored at -70C. Total RNA was isolated from tissues using the Ambion Ribopure (http://www.ambion.com/techlib/prot/fm_1924.pdf). Approximately 100 mg tissue was thawed to 20C and excess RNALater removed by blotting. 2 ml TRI Reagent was added and tissues homogenized using a rotor-stator homogenizer. Insoluble material was removed by centrifugation at 12,000 x g. 1 ml  supernatant from each sample was dispensed into 1.5 ml microcentrifuge tubes with 100 ul of bromochloropropane (BCP). Tubes were vortexed and incubated at 20C for 15 min. Tubes were centrifuged at 12,000 x g for 10 min at 4C. 400 ul of the aqueous phase (top layer) was transferred to a new 1.5 ml microcentrifuge tube with 200 ul 100% ethanol, vortexed for 5 s. Each sample was transferred to a Filter Cartridge-Collection Tube assembly, centrifuged at 12,000 x g for 30 s at 20C. 500 ul of Wash Solution was added to the Filter Cartridge-Collection Tube centrifuged for 30 s at 20C and rewashed. RNA was eluted by the addition of 100 ul Elution Buffer incubated at 20C for 2 min and centrifuged for 30 s to elute the RNA from the filter. RNA quality and integrity was assessed using a RNA 6000 Nano LabChip on the Agilent 2100 Bioanalyzer and quantified using a NanoDrop ND-1000 spectrophotometer.
Illumina Solexa standard protocols for preparing samples for digital gene expression-tag profiling with NlaIII     (http://arrayconsortium.tgen.org/np2/docs/PreparingSamplesforDigitalGeneExpression-TagProfilingwithNlaIII.pdf)

treatment_protocol: Uninfected control lambs, were sham dosed with water at the same time as three times a week starting at approximately 12 weeks of age and continuing until sacrifice at approximately 27 weeks.

value: gastric lymph node

value: 185 days

value: lamb

value: female

tag: clinicalinformation

value: not applicable


title: [E-MTAB-445] uninfected control Gastric LN_130

description: Performer: ROSLIN

value: 190 days


title: [E-MTAB-599] c57xdba_Hippocampus6

description: Performer: SC

source_name: c57xdba_Hippocampus6 237736

extract_protocol:
tissue collection | Mouse tissues where obtained from 8 weeks old mice from the Jackson lab Maine USA.
nucleic_acid_extraction | Total RNA extraction using trizol as per manufacturer instructions
scanning | The samples were sequenced on an Illumina Genome Analyser II.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.8.67.0. There were 152 cycles of sequencing with 2 reads per cluster.

value: adult

value: hippocampus


title: [E-MTAB-445] uninfected control Gastric LN_124

description: Performer: ROSLIN

value: 193 days


title: [E-MTAB-460] Zebrafish adult brain, 3212_6

description: Performer: SC

source_name: Zebrafish adult brain

value: brain

value: Singapore


title: [E-MTAB-445] T. circumcincta infected Gastric LN_183

description: Performer: ROSLIN

source_name: gastric lymph node, T. circumcincta infected

treatment_protocol: Lambs were experimentally infected with approximately 2,300 infective L3 Teladorsagia circumcincta larvae three times a week starting at approximately 12 weeks of age and continuing until sacrifice at approximately 27 weeks.

value: 181 days

value: susceptible


title: [E-MTAB-445] T. circumcincta infected Gastric LN_114

description: Performer: ROSLIN


title: [E-MTAB-445] T. circumcincta infected Gastric LN_109

description: Performer: ROSLIN

value: 197 days


title: [E-MTAB-434] RNA from Zebrafish embryo 3 dpf

description: Performer: SC

source_name: Zebrafish embryo 3 dpf

growth_protocol: grow | Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at -70 C

extract_protocol:
nucleic_acid_extraction | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions. Pellets were resuspended RNase-free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments).   Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.
scanning | Base calling was performed using Illumina pipeline 1.8.67.0 (Bustard 1.8.1a1) with phred quality scores at 64 levels using Illumina pipeline 1.8.67.0 (GERALD).    There were 152 cycles of sequencing with 2 reads per cluster, a forward read starting at base 1 and a reverse read starting at base 77.

value: 3 days

value: embryo

tag: stainorline

value: Tuebingen

value: whole organism


title: [E-MTAB-445] T. circumcincta infected Gastric LN_173

description: Performer: ROSLIN

value: gastric lymph node

value: 187 days

tag: developmentalstage


title: [E-MTAB-599] c57xdba_Hippocampus5

description: Performer: SC

source_name: c57xdba_Hippocampus5 237735

tag: organismpart

value: Jackson laboratory


title: [E-MTAB-445] T. circumcincta infected Gastric LN_92

description: Performer: ROSLIN

value: 184 days

value: lamb

value: female

value: resistant


title: [E-MTAB-599] c57xdba_Hippocampus4

description: Performer: SC

source_name: c57xdba_Hippocampus4 237734

value: adult

value: hippocampus


title: [E-MTAB-445] T. circumcincta infected Gastric LN_58

description: Performer: ROSLIN

value: 188 days


title: [E-MTAB-599] c57xdba_Hippocampus3

description: Performer: SC

source_name: c57xdba_Hippocampus3 237733


title: [E-MTAB-445] uninfected control Gastric LN_57

description: Performer: ROSLIN

value: 185 days

value: not applicable


title: [E-MTAB-434] RNA from Zebrafish embryo 6hpf

description: Performer: SC

source_name: Zebrafish embryo 6hpf

growth_protocol: grow | Zebrafish embryos or tissues were collected from a Tuefel long fin strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at -70 C

value: mixed

value: 6 hours

value: Tupfel long fin


title: [E-MTAB-460] Zebrafish adult brain, 3537_7

description: Performer: SC

value: brain

value: Singapore


title: [E-MTAB-445] T. circumcincta infected Gastric LN_50

description: Performer: ROSLIN

value: gastric lymph node

value: 189 days


title: [E-MTAB-434] RNA from Zebrafish embryo 2cells

description: Performer: SC

source_name: Zebrafish embryo 2cells

value: cell

value: 2-cell embryo

value: Tuebingen


title: [E-MTAB-445] T. circumcincta infected Gastric LN_38

description: Performer: ROSLIN

value: 192 days

value: lamb

value: female

value: susceptible


title: [E-MTAB-445] uninfected control Gastric LN_47

description: Performer: ROSLIN

value: 190 days


title: [E-MTAB-599] c57xdba_Hippocampus1

description: Performer: SC

source_name: c57xdba_Hippocampus1 237731

value: adult

value: hippocampus

value: Jackson laboratory


title: [E-MTAB-434] RNA from Zebrafish embryo 5 dpf

description: Performer: SC

source_name: Zebrafish embryo 5 dpf

extract_protocol:
nucleic_acid_extraction | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions. Pellets were resuspended RNase-free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments).   Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.
scanning | Base calling was performed using Illumina pipeline 1.3 (Bustard 1.3.4) with phred quality scores at 64 levels using Illumina pipeline 1.3 (Gerald).    There were 108 cycles of sequencing with 2 reads per cluster, a forward read starting at base 1 and a reverse read starting at base 55.

value: mixed

value: 5 days

value: embryo

value: whole organism


title: [E-MTAB-599] c57xdba_Hippocampus2

description: Performer: SC

source_name: c57xdba_Hippocampus2 237732


title: [E-MTAB-445] T. circumcincta infected Gastric LN_20

description: Performer: ROSLIN

extract_protocol:
nucleic_acid_extraction | Gastric lymph nodes were collected from all lambs, diced and placed in RNAlater (Ambion) at 20C, incubated at 4C overnight and stored at -70C. Total RNA was isolated from tissues using the Qiagen RNeasy Mini kit (www.qiagen.com/literature/render.aspx?id=353). Approximately 30 mg tissue was thawed to 20C and excess RNALater removed by blotting. 600ul Buffer RTL (including 6?l ?-mercaptoethanol) was added and tissues homogenized using a rotor-stator homogenizer. Insoluble material was removed by 3 min centrifugation at 12,000 x g. 600ul of 70% ethanol was added to the cleared supernatant, mixed and immediately applied to an RNAeasy mini column, which was centrifuged at 8,000 x g for 15 s. The columns were washed by the addition of 700 ul Buffer RW1 and centrifugation at 8,000 x g for 15 s. RNeasy column was transferred into a new 2 ml collection tube, 500 ul Buffer RPE was added and centrifuged at 8,000 x g for 15 s, which was repeated. RNA was eluted by the addition of 50 ul RNase-free water directly onto the RNeasy silica-gel membrane and centrifugation 8,000 x g for 1 min. RNA quality and integrity was assessed using a RNA 6000 Nano LabChip on the Agilent 2100 Bioanalyzer and quantified using a NanoDrop ND-1000 spectrophotometer.
Illumina Solexa standard protocols for preparing samples for digital gene expression-tag profiling with NlaIII     (http://arrayconsortium.tgen.org/np2/docs/PreparingSamplesforDigitalGeneExpression-TagProfilingwithNlaIII.pdf)

value: gastric lymph node

value: resistant


title: [E-MTAB-434] RNA from Zebrafish embryo 2 dpf

description: Performer: SC

source_name: Zebrafish embryo 2 dpf

value: 2 days


title: [E-MTAB-434] RNA from Zebrafish embryo 1 dpf

description: Performer: SC

source_name: Zebrafish embryo 1 dpf

value: 1 day


title: [E-MTAB-315] mts 2 B

description: Performer: DKFZ

growth_protocol: grow | S2 cells adjusted to growth in serum-free media (D.Mel-2, Invitrogen, Carlsbad, CA) were grown in Express Five SFM (Invitrogen, Carlsbad, CA) supplemented with 20 mM Glutamax I, 100 U/ml penicillin, 100 microgram/ml streptomycin.

extract_protocol:
nucleic_acid_extraction | Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), followed by Rneasy cleanup (Qiagen, Hilden, Germany) including on-column DNAse digest. RNA integrity was verified on an Agient 2100 Bioanalyzer. mRNA was isolated with the Dynabeads mRNA DIRECT Kit (Invitrogen, Carlsbad,CA). For each sample, a library for SOLiD sequencing was prepared with the 'Whole transcriptome analysis kit' (4409491 Rev. D, Invitrogen, Carlsbad,CA). Briefly, polyA RNA was fragmented using RNAseIII, purified, hybridized and ligated to RNA adapters. Ligation products were reverse transcribed, purified and ca. 200 nt cDNA fragments selected after electrophoresis on a 6% TBE-Urea gel. cDNA was PCR amplified with SOLiD sequencing primers and purified to produce a library suitable as a template for emulsion PCR. DNA concentrations were determined using qPCR and a pooled library was generated by combining equimolar amounts from all samples.
sequencing | Emulsion PCR and sequencing with the SOLiD v.3 system was performed according to the manufacturers' protocol (Applied Biosystems, Foster City, CA).
scanning | Base calling and quality scoring done during SOLiD primary analysis. csfasta and qual files of sequencing reads were retrieved from the sequencing machine. These files were converted to srf format using solid2srf_v0.7.5.

treatment_protocol: specified_biomaterial_action | RNAi knockdown was performed by seeding 0.75 Mio cells in 1.5 ml Express-5 medium containing 20 microgram dsRNA and 8 microliter 0.4 mg/ml dimethyldioctadecylammonium bromide (DDAB) per well of a 6-well plate. Cells were incubated at 25 degr. C for 5 days and harvested by centrifugation at 1500xg for 5 min.

value: cell

tag: RNAi

value: mts


title: [E-MTAB-599] c57xdba_Heart5

description: Performer: SC

source_name: c57xdba_Heart5 149877

tag: material type

value: heart


title: [E-MTAB-434] RNA from Zebrafish adult female head

description: Performer: SC

source_name: Zebrafish adult female head

value: female

value: Tuebingen

value: head


title: [E-MTAB-533] L3_L4_stages

description: Performer: LGTF

organism: Caenorhabditis elegans

extract_protocol:
nucleic_acid_extraction | Total RNA from N2 worms was isolated using Trizol. Selected targets were then amplified by RT-PCR.
sequencing | Standard Illumina protocol, performed at the University of Lausanne, Lausanne, Switzerland
bioassay_data_transformation | Qseq files were produced by the sequencing machine.

value: L2 and L4 stage

value: hemaphrodite

value: Guilin Wand/Valerie Reinke (Yale, USA)


title: [E-MTAB-599] c57xdba_Heart6

description: Performer: SC

organism: Mus musculus

source_name: c57xdba_Heart6 149878

value: adult

value: Jackson laboratory


title: [E-MTAB-315] gap1 1 A

description: Performer: DKFZ


title: [E-MTAB-315] gap1 1 B

description: Performer: DKFZ


title: [E-MTAB-599] c57xdba_Heart4

description: Performer: SC

source_name: c57xdba_Heart4 392846

extract_protocol:
tissue collection | Mouse tissues where obtained from 8 weeks old mice from the Jackson lab Maine USA.
nucleic_acid_extraction | Total RNA extraction using trizol as per manufacturer instructions
scanning | The samples were sequenced on an Illumina Genome Analyser II.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.8.70.0. There were 152 cycles of sequencing with 2 reads per cluster.


title: [E-MTAB-315] mts 2 A

description: Performer: DKFZ


title: [E-MTAB-451] adult2, 7 weeks

description:
Performer: SC
Provider: Wellcome Trust Sanger Institute

organism: Schistosoma mansoni

source_name: adult2, 7 weeks

growth_protocol: grow | A  Peurto Rican strain of S. mansoni was used in this study.  Mixed-sex worms (including female worms) were perfused from percutaneously infected Golden Syrian hamsters challenged 7-weeks earlier with cercariae and provided by Dr. Phil LoVerde (University of Texas, San Antonio, Texas, U.S.). Cercariae were shed from Biomphalaria glabrata intermediate snail hosts. Mechanically transformed schistosomula were prepared by mechanical transformation of cercariae and cultured at 37C in DMEM (Sigma, UK) supplemented with 10% foetal calf serum, 2 mM L-glutamine, and 100 ug/ml penicillin/streptomycin in an atmosphere of 5% CO2 for 3hr or 24hr. Skin transformed schistosomula were prepared by allowing cercariae to penetrate a layer of freshly excised mouse skin. After penetration, schistosomula were cultured at 37C in DMEM (Sigma, UK) supplemented with 10% foetal calf serum, 2 mM L-glutamine, and 100 ug/ml penicillin/streptomycin in an atmosphere of 5% CO2 for 24hr. Cercarial tails were obtained using the same procedure as for mechanically transformed schistosomula. (Parameters: time unit = seconds, temperature unit = C).

extract_protocol:
nucleic_acid_extraction| S. mansoni total RNA was extracted from parasites homogenised in TRIzol reagent (Invitrogen UK) using an Ultra-Turrax T10 dispersing tool (IKA-Labortechnik, Janke & Kunkel, GmbH & Co). Cercariae total RNA was isolated using a modified TRIzol/RNeasy (Invitrogen UK; Qiagen UK) procedure as previously described, RNA from the rest of the samples was extracted using  TRIzol(Invitrogen, UK)according to manufacturers instructions. All RNA was subsequently quantified with a NanoDrop ND-1000 UV-Vis spectrophotometer and visualized for quality using an Agilent 2100 bioanalyzer. (Parameters: Extracted product = total_RNA, Amplification = none)
sequencing | Total RNA was used to produce RNA-seq libraries as described in Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5, 621-628 (2008). Exceptions to the protocol included: i) fragmentation of mRNA was performed by incubating the samples in a 5x fragmentation buffer (Ambion, UK) and at 70C for 5 minutes followed by removal of fragmentation buffer using sodium acetate/isopropanol precipitation of RNA; ii) after second strand cDNA synthesis, the Illumina Genomic DNA Sample Preparation Kit (Illumina, UK) was used according to manufacturer instructions and with modifications described in Quail, M. A. et al. A large genome center's improvements to the Illumina sequencing system. Nat Methods 5, 1005-1010 (2008).The samples were sequenced on an Illumina Genome Analyser II.
scanning | Image processing and base calling were done using the Illumina pipeline.

value: 7 weeks

value: mixed

value: puerto rican


title: [E-MTAB-599] c57xdba_Heart3

description: Performer: SC

source_name: c57xdba_Heart3 149875


title: [E-MTAB-315] mts 1 B

description: Performer: DKFZ


title: [E-MTAB-451] somule6, 24 hours

source_name: somule6, 24 hours

value: 24 hours

value: larva


title: [E-MTAB-315] fireflyLuc tech2 2 B

description: Performer: DKFZ

value: firefly luciferase


title: [E-MTAB-315] mts 1 A

description: Performer: DKFZ

value: cell


title: [E-MTAB-445] T. circumcincta infected Gastric LN_21

description: Performer: ROSLIN

source_name: gastric lymph node, T. circumcincta infected

value: gastric lymph node

value: 195 days

value: lamb

value: resistant


title: [E-MTAB-599] c57xdba_Heart2

description: Performer: SC

source_name: c57xdba_Heart2 149874

value: heart


title: [E-MTAB-315] fireflyLuc tech2 2 A

description: Performer: DKFZ


title: [E-MTAB-451] somule5, 24 hours

source_name: somule5, 24 hours


title: [E-MTAB-315] fireflyLuc tech1 2 B

description: Performer: DKFZ


title: [E-MTAB-315] fireflyLuc tech1 2 A

description: Performer: DKFZ


title: [E-MTAB-451] somule4, 24 hours

source_name: somule4, 24 hours


title: [E-MTAB-442] 0ON562: do851_Input_liver_none_mmuBL60ON562

description: Performer: CRUK-CRI

extract_protocol:
nucleic_acid_extraction | Samples were prepared by direct perfusion of the tissue with buffered salt solution, followed by % formaldehyde.  After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde.  After homogenization, the cells were rinsed with PBS.
immunoprecipitate | The animal tissues were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. No antibody was added in the immunoprecipitation step.  Following the non-ChIP step, DNA was not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA Fragments using 2 Âµl of fortyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 Âµl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 Âµl of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 cycles.
sequencing | The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 cycles. doi:10.1016/j.ymeth.2009.03.001

value: liver

value: male

tag: strain

tag: chip antibody

value: none, input DNA


title: [E-MTAB-315] fireflyLuc tech2 1 A

description: Performer: DKFZ


title: [E-MTAB-315] fireflyLuc tech1 1 B

description: Performer: DKFZ


title: [E-MTAB-451] somule3, 24 hours

source_name: somule3, 24 hours

tag: Sex

tag: biosourcetype


title: [E-MTAB-315] fireflyLuc tech2 1 B

description: Performer: DKFZ

tag: strainorline


title: [E-MTAB-451] cerc13, 4 hours

source_name: cerc13, 4 hours

value: 4 hours


title: [E-MTAB-315] fireflyLuc tech1 1 A

description: Performer: DKFZ


title: [E-MTAB-315] p38b 1 B

description: Performer: DKFZ


title: [E-MTAB-442]  0ON489: do566_Input_liver_none_mmu0ON488

description: Performer: CRUK-CRI

value: adult


title: [E-MTAB-451] cerc12, 4 hours

source_name: cerc12, 4 hours


title: [E-MTAB-315] p38b 2 A

description: Performer: DKFZ


title: [E-MTAB-315] p38b 1 A

description: Performer: DKFZ


title: [E-MTAB-315] kay 2 B

description: Performer: DKFZ

value: kay


title: [E-MTAB-315] kay 2 A

description: Performer: DKFZ