arrayexpress and gene expression atlas: mining functional genomics data emma hastings functional...
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ArrayExpress and Gene Expression Atlas: Mining Functional Genomics data
Emma HastingsFunctional Genomics Team
EBI-EMBL
[email protected]://www.ebi.ac.uk/~emma/Zagreb/
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Services available from EBI
GenomesGenomes
DNA & RNA sequenceDNA & RNA sequence
Gene expressionGene expression
Protein sequenceProtein sequence
Protein families,
motifs and domains
Protein families,
motifs and domains
Protein structureProtein structure
Protein interactionsProtein interactions
Chemical entitiesChemical entities
PathwaysPathways
SystemsSystems
Literature and ontologiesLiterature and ontologies
www.ebi.ac.uk
ArrayExpress3
Talk structure
Why do we need a database for functional genomics data?
ArrayExpress database
• Archive
• Gene Expression Atlas
Database content
Query the database
Data download
Data submission
What is functional genomics?
Functional genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects (such as genome sequencing projects) to describe gene (and protein) functions and interactions. Unlike genomics and proteomics, functional genomics focuses on the dynamic aspects such as gene transcription, translation, and protein-protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures. Functional genomics attempts to answer questions about the function of DNA at the levels of genes, RNA transcripts, and protein products.
ArrayExpress & Atlas4
Components of a functional genomics experiment
• Array design information• Location of each element• Description of each element• Hybridization protocol
• Quantification matrix• Software specifications
• Sample source• Sample treatments• RNA extraction protocol• Labelling protocol
• Control array elements• Normalization method
• Image• Scanning protocol• Software specifications
ArrayArray
Normalized dataNormalized data
Raw dataRaw data
SampleSample SampleSample• Sample source• Sample treatments• Template preparation
LibraryLibrary
• Library preparation
ChipChip
• Cluster amplification
• Sequencing and imaging
Data analysisData analysis
• From images to sequences• Quality Control• Sequence alignment• Assembly• Specific steps depending on the application
Data analysisData analysis
Why do we need a database for functional genomics data?
ArrayExpress & Atlas6
E-MEXP-2451
Transcription profiling of grape berries during ripening
Grape berries undergo considerable physical and biochemical changes during the ripening process. Ripening is characterized by a number of changes, including the degradation of chlorophyll, an increase in berry deformability, a rapid increase in the level of hexoses in the berry vacuole, an increase in berry volume, the catabolism of organic acids, the development of skin colour, and the formation of compounds that influence flavour, aroma, and therefore, wine quality. The aim of this work is to identify differentially expressed genes during grape ripening by microarray and real-time PCR techniques. Using a custom array of new generation, we analysed the expression of 6000 grape genes from pre-veraison to full maturity, in Vitis vinifera cultivar Muscat of Hamburg, in two different years (2006 and 2007). Five time points per year and two biological replicates per stadium were considered. To reduced intra-plant and inter-plant biological variability, for each ripening stadium we collected around hundred berries from several bunch grapes of five plants of V. vinifera cv Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.
E-MEXP-2451
Transcription profiling of grape berries during ripening
Grape berries undergo considerable physical and biochemical changes during the ripening process. Ripening is characterized by a number of changes, including the degradation of chlorophyll, an increase in berry deformability, a rapid increase in the level of hexoses in the berry vacuole, an increase in berry volume, the catabolism of organic acids, the development of skin colour, and the formation of compounds that influence flavour, aroma, and therefore, wine quality. The aim of this work is to identify differentially expressed genes during grape ripening by microarray and real-time PCR techniques. Using a custom array of new generation, we analysed the expression of 6000 grape genes from pre-veraison to full maturity, in Vitis vinifera cultivar Muscat of Hamburg, in two different years (2006 and 2007). Five time points per year and two biological replicates per stadium were considered. To reduced intra-plant and inter-plant biological variability, for each ripening stadium we collected around hundred berries from several bunch grapes of five plants of V. vinifera cv Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.
Why do we need a database for functional genomics data?
ArrayExpress & Atlas7
ArrayExpresswww.ebi.ac.uk/arrayexpress/
Is a public repository for functional genomics data, mostly generated using microarray or high throughput sequencing (HTS) assays
Serves the scientific community as an archive for data supporting publications, together with GEO at NCBI and CIBEX at DDBJ
Provides easy access to well annotated microarray data in a structured and standardized format
Facilitates the sharing of microarray designs and experimental protocols
Based on FGED standards: MIAME checklist, MAGE-TAB format and MO Ontology.
MINSEQE checklist for HTS data (http://www.mged.org/minseqe/)
ArrayExpress8
Reporting standards
Data standardization efforts focus on answering 3 major questions:
1. What information do we need to capture?
2. What syntax (or file format) should we use to exchange data?
3. What semantics (or ontology) should we use to best describe its annotation?
ArrayExpress9
What information do we need to capture?MIAME checklist
Minimal Information About a Microarray Experiment
The 6 most critical elements contributing towards MIAME are:
1. Essential sample annotation including experimental factors and their values (e.g. compound and dose)
2. Experimental design including sample data relationships (e.g. which raw data file relates to which sample, ….)
3. Sufficient array annotation (e.g. gene identifiers, genomic coordinates, probe sequences or array catalog number)
4. Essential laboratory and data processing protocols (e.g. normalization method used)
5. Raw data for each hybridization (e.g. CEL or GPR files)
6. Final normalized data for the set of hybridizations in the experiment
ArrayExpress10
What information do we need to capture? MINSEQE checklist
Minimal Information about a high-throughput Nucleotide SEQuencing Experiment
The proposed guidelines for MINSEQE are (still work in progress):
1. General information about the experiment
2. Essential sample annotation including experimental factors and their values (e.g. compound and dose)
3. Experimental design including sample data relationships (e.g. which raw data file relates to which sample, ….)
4. Essential experimental and data processing protocols
5. Sequence read data with quality scores, raw intensities and processing parameters for the instrument
6. Final processed data for the set of assays in the experiment
ArrayExpress11
MAGE-TAB is a simple spreadsheet format that uses a number of different files to capture information about a microarray experiment:
IDF Investigation Description Format file, contains top-level information about the experiment including title, description, submitter contact details and protocols.
SDRF Sample and Data Relationship Format file contains the relationships between samples and arrays, as well as sample properties and experimental factors, as provided by the data submitter.
ADF Array Design Format file, describes the design of an array, i. e. the sequence located at each feature on the array and annotation of the sequences.
Data files Raw and processed data files. The ‘raw’ data files are the files produced by the microarray image analysis software, such as CEL files for Affymetrix or GPR files from GenePix.
The processed data file is a ‘data matrix’ file containing processed values, as provided by the data submitter.
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What syntax (or file format) should we use to exchange data?
What semantics (or ontology) should we use to best describe its annotation?
Ontology, which is a formal specification of terms in a particular subject area and the relations among them.
Its purpose is to provide a basic, stable and unambiguous description of such terms and relations in order to avoid improper and inconsistent use of the terminology pertaining to a given domain.
ArrayExpress13
Experimental factor ontology (EFO)http://www.ebi.ac.uk/efo
Application focused ontology modeling experimental factors (EFs) in AE
Developed to:
Consistent curation – ensure that curators use same vocabulary
Query support (e.g, query for 'cancer' and get also ‘leukemia')
EFs are transformed into an ontological representation, forming classes and relationships between those classes
EFO terms map to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology
ArrayExpress14
ArrayExpress & Atlas15
What semantics (or ontology) should we use to best describe its annotation?
ArrayExpress16
ArrayExpress – two databases
ArrayExpress – two databases
ArrayExpress18
ArrayExpress Archive
22281
ArrayExpress & Atlas19
...and counting...and counting
How much data in AE Archive?
ArrayExpress20
ArrayExpress21
Archive by species
ArrayExpress22
Browsing the AE Archive
Browsing the AE ArchiveSpecies
investigatedSpecies
investigatedCurated title of
experimentCurated title of
experiment
The date when the data released
The date when the data released
AE unique experiment ID
AE unique experiment ID
ArrayExpress23
Raw sequencing data available in
ENA
Raw sequencing data available in
ENA
The list of experiments retrieved can be printed, saved as Tab-delimited format or exported to Excel or as RSS feed
The list of experiments retrieved can be printed, saved as Tab-delimited format or exported to Excel or as RSS feed
The total number of experiments and assay retrieved
The total number of experiments and assay retrieved
The direct link to raw and processed data. An icon indicates that this type of data is available.
The direct link to raw and processed data. An icon indicates that this type of data is available.
Loaded in Atlas flagLoaded in Atlas flag
Number of assays
Number of assays
ArrayExpress24
Browsing the AE Archive
Experimental factor ontology (EFO)Example:
ArrayExpress25
carcinomacarcinoma
acinar cell carcinoma
adrenocortical carcinoma
bladder carcinoma
breast carcinoma
cervical carcinoma
esophageal carcinoma
follicular thyroid carcinoma
hepatocellular carcinoma
pancreatic carcinoma
papillary thyroid carcinoma
renal carcinoma
signet ring cell carcinoma
uterine carcinoma
adenocarcinoma
adenoid cystic carcinoma
endometrioid carcinoma
gastric carcinoma
hereditary leiomyomatosis and renal cell cancer
hypopharyngeal carcinoma
acinar cell carcinoma
adrenocortical carcinoma
bladder carcinoma
breast carcinoma
cervical carcinoma
esophageal carcinoma
follicular thyroid carcinoma
hepatocellular carcinoma
pancreatic carcinoma
papillary thyroid carcinoma
renal carcinoma
signet ring cell carcinoma
uterine carcinoma
adenocarcinoma
adenoid cystic carcinoma
endometrioid carcinoma
gastric carcinoma
hereditary leiomyomatosis and renal cell cancer
hypopharyngeal carcinoma
Searching AE ArchiveSimple query - EFO
ArrayExpress26
•Matches to exact terms are highlighted in yellow•Matches to child terms in the EFO are highlighted in pink
Searching AE ArchiveSimple query
Search across all fields:• AE accession number e.g. E-MEXP-568 • Secondary accession numbers e.g. GEO series accession
GSE5389 • Experiment name • Submitter's experiment description • Sample attributes, experimental factor and values, including
species (e.g. GeneticModification, Mus musculus, DREB2C over-expression)
• Publication title, authors and journal name, PubMed ID
Synonyms for terms are always included in searches e.g. 'human' and 'Homo sapiens’
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AE Archive query output
• Matches to exact terms are highlighted in yellow
AE Archive – experiment view
ArrayExpress29
MIAME or MINSEQE scores show how much the experiment is standard compliant
MIAME or MINSEQE scores show how much the experiment is standard compliant
Experimental factor(s) and its values
Experimental factor(s) and its values
Link to files available.
This varies between sequencing and microarray data. For
microarray experiments you also have array design file.
Link to files available.
This varies between sequencing and microarray data. For
microarray experiments you also have array design file.
AE Archive – SDRF file
ArrayExpress30
SDRF file – sample & data relationship
ArrayExpress31
AE Archive – ADF file
ArrayExpress32
AE Archive – all files
ArrayExpress33
ArrayExpress34
AE Archive – all files
Searching AE ArchiveAdvanced query
Combine search terms• Enter two or more keywords in the search box with the operators AND,
OR or NOT. AND is the default search term; a search for kidney cancer will return hits with a match to ‘kidney' AND ‘cancer’
• Search terms of more than one word must be entered inside quotes otherwise only the first word will be searched for. E.g. “kidney cancer”
Specify fields for searches• Particular fields for searching can also be specified in the format
of fieldname:value
ArrayExpress35
Searching AE ArchiveAdvanced query - fieldnames
ArrayExpress36
Field name Searches Example
accession Experiment primary or secondary accession accession:E-MEXP-568
array Array design accession or name array:AFFY-2 OR array:Agilent*
ef Experimental factor, the name of the main variables in an experiment.
ef:celltype OR ef:compound
efv Experimental factor value. Has EFO expansion. efv:fibroblast
expdesign Experiment design type expdesign:”dose response”
exptype Experiment type. Has EFO expansion. exptype:RNA-seq
gxa Presence in the Gene Expression Atlas. Only value is gxa:true.
ef:compound AND gxa:true
pmid PubMed identifier pmid:16553887
sa Sample attribute values. Has EFO expansion. sa:wild_type
species Species of the samples. Has EFO expansion. species:”homo sapiens” AND ef:cellline
Searching AE ArchiveAdvanced query
ArrayExpress37
Filter What is filtered
assaycount:[x TO y] filter on the number of of assays where x <= y and both values are between 0 and 99,999 (inclusive) . To count excluding the values given use curly brackets e.g. assaycount:{1 TO 5} will find experiments with 2-4 assays. Single numbers may also be given e.g. assaycount:10 will find experiments with 10 assays.
efcount:[x TO y] filter on the number of experimental factors
samplecount:[x TO y] filter on the number of samples
sacount:[x TO y] filter on the number of sample attribute categories
rawcount:[x TO y] filter on the number of raw files
fgemcount:[x TO y] filter on the number of final gene expression matrix (processed data) files
miamescore:[x TO y] filter on the MIAME compliance score (maximum score is 5)
date:yyyy-mm-dd filter by release date•date:2009-12-01 - will search for experiments released on 1st of Dec 2009 •date:2009* - will search for experiments released in 2009•date:[2008-01-01 2008-05-31] - will search for experiments released between 1st of Jan and end of May 2008
Filtering experiments by counts of a particular attribute• Experiments fulfilling certain count criteria can also be searched for e.g. having
more than 10 assays (hybridizations)
ArrayExpress & Atlas38
Searching AE ArchiveAdvanced query – Examples
Exercise 1
ArrayExpress39
ArrayExpress40
ArrayExpress – two databases
ArrayExpress41
The criteria we use for selecting experiments for inclusion in the Atlas are as follows:
• Array designs relating to experiment must be provided to enable re-annotation using Ensembl or Uniprot (or have the potential for this to be done)
• High MIAME scores • Experiment must have 6 or more hybridizations • Sufficient replication and large sample size• EF and EFV must be well annotated• Adequate sample annotation must be provided • Processed data must be provided or raw data which can be
renormalized must be available
Gene Expression AtlasExperiment selection criteria
ArrayExpress42
New meta-analytical tool for searching gene expression profiles across experiments in AE
Data is taken as normalized by the submitter
Gene-wise linear models (limma) and t-statistics are applied to calculate the strength of genes’ differential expression across conditions across experiments
The result is a two-dimensional matrix where rows correspond to genes and columns correspond to conditions, rather than samples.
The matrix entries are p-values together with a sign, indicating the significance and direction of differential expression
Gene Expression AtlasAtlas construction
ArrayExpress43
Gene Expression AtlasAtlas construction
Gene Expression AtlasAtlas construction
ArrayExpress45
Gene Expression Atlas
ArrayExpress46
Atlas home pagehttp://www.ebi.ac.uk/gxa/
Query for genesQuery for genes
Query for conditionsQuery for conditionsRestrict query by direction of differential expression
Restrict query by direction of differential expression
The ‘advanced query’ option allows building more complex queries
The ‘advanced query’ option allows building more complex queries
ArrayExpress47
Atlas home pageThe ‘Genes’ search box
ArrayExpress48
Atlas home pageThe ‘Conditions’ search box
ArrayExpress49
Atlas home pageA single gene query
Atlas gene summary page
ArrayExpress50
ArrayExpress & Atlas51
Atlas home pageA ‘Conditions’ only query
ArrayExpress52
Atlas heatmap view
Atlas list view
Click the ‘expression profile’ link to view the experiment page
Click the ‘expression profile’ link to view the experiment page
ArrayExpress53
Atlas data download
ArrayExpress54
ArrayExpress55
Atlas experiment page
Box plot showing differential expression of Mt2,Agxt2l1 and Insig2 across the growth conditions studied. Data is available for 3 separate array probes.
Box plot showing differential expression of Mt2,Agxt2l1 and Insig2 across the growth conditions studied. Data is available for 3 separate array probes.
Search for a specific gene, experimental factor or expression level (up/down)
Search for a specific gene, experimental factor or expression level (up/down)
ArrayExpress & Atlas56
Atlas experiment page – HTS data
ArrayExpress57
Atlas gene-condition query
ArrayExpress58
Atlas query refining
ArrayExpress59
Atlas gene-condition query
ArrayExpress60
Atlas query refining
ArrayExpress61
Atlas query refining
ArrayExpress62
Exercises 2 & 3
ArrayExpress63
Data submission to AE
ArrayExpress64
Data submission to AEwww.ebi.ac.uk/microarray/submissions.html
MIAMExpress- Overview
• MIAMExpress is a web based tool for submitting microarray data and microarray designs to the ArrayExpress database
• MIAMExpress can be used for experiments up to 50 hybridizations in size
ArrayExpress & Atlas65
Array design (custom)Array design (custom) Experiment Experiment ProtocolProtocol
MIAMExpress- Getting Started
ArrayExpress & Atlas66
MIAMExpress- Protocol Submission
ArrayExpress & Atlas67
Change the automatically generated protocol name to something meaningful like Sanger Lab Growth Protocol
Change the automatically generated protocol name to something meaningful like Sanger Lab Growth Protocol
MIAMExpress- Experiment Submission
ArrayExpress & Atlas68
Experiment description Samples Extracts
Labeledextracts Hybs
Upload raw and norm data
Upload combined data files
Batchloader interface where you fill in your
experiment information in a spreadsheet-like
format
Batchloader interface where you fill in your
experiment information in a spreadsheet-like
format
Web page interface in which a series of
web forms are filled out.
Web page interface in which a series of
web forms are filled out.
MIAMExpress-Batch Upload Tool
ArrayExpress & Atlas69
Experiment description Samples Extracts
Labeledextracts Hybs
Upload raw and norm data
Upload combined data files
HELPHELP
MIAMExpress-Batch Upload Tool
ArrayExpress & Atlas70
Click multiply to create as many rows as you need. Hint: If you complete all the values in the first row prior to this it will save you time
Click multiply to create as many rows as you need. Hint: If you complete all the values in the first row prior to this it will save you time
ToolbarToolbar
Cross document functionalityCross document functionality
MIAMExpress-Batch Upload Tool
ArrayExpress & Atlas71
Labeledextracts
Double click and select one or more samples per extract
Double click and select one or more samples per extract
MIAMExpress-Batch Upload Tool
ArrayExpress & Atlas72
HybsUpload raw and
norm data
Use the folder icon to select the required data files
Use the folder icon to select the required data files
Affymetrix users submit the .CEL file here (and .EXP if available). For all other submissions the raw data must be a single .txt or .gpr file.
Affymetrix users submit the .CEL file here (and .EXP if available). For all other submissions the raw data must be a single .txt or .gpr file.
MIAMExpress-Batch Upload Tool
ArrayExpress & Atlas73
HybsUpload raw and
norm dataUpload combined
data files
If you are supplying a Final Gene Expression Data File you must supply a transformation protocol
If you are supplying a Final Gene Expression Data File you must supply a transformation protocol
MIAMExpress-Data File Formats for Submission
• Submitted normalized data files must contain data from a single hybridization only. If your normalization procedure creates a file containing data from all your hybs then you can submit this as a final gene expression matrix (FGEM).
• A normalization protocol should be submitted along with your normalized data files-be precise when describing how the data was calculated
• A final gene expression matrix (FGEM) or combined data file is a file containing data from several hybridizations.
• The creation of your FGEM must be described in your transformation protocol.
• The format of the FGEM is as follows:• each line corresponds to an array element • each column corresponds to your calculated value
ArrayExpress & Atlas74
Array Submission- Background
• An array design describes how a microarray was manufactured, what was printed/synthesized at each position on the array and what biological sequences these represent.
• If the array design has already been submitted to ArrayExpress, you do not need to re-submit it.
• If you have used a custom array design you will need to submit the array design as an Array Design Format (ADF) file
• After submitting an array design you can immediately continue with your experiment submission
• The ADF file can be created in any spreadsheet application but must be saved as a tab delimited text file.
ArrayExpress & Atlas75
MIAMExpress-Array Submission
ArrayExpress & Atlas76
Enter some general information about your array
Enter some general information about your array
Checker- This tool will check for errors in the format and content of an ADF file.
Checker- This tool will check for errors in the format and content of an ADF file.
MIAMExpress-Array Submission
ArrayExpress & Atlas77
Location and name of each reporter (probe) on the array
Annotation such as the nucleotide sequence or database accession associated with the reporter e.g. RefSeq
Type of reporter (cDNA, oligonucleotide, RNA, DNA etc) that is present
Group of reporter - which are the control and which are the experimental reporters
Optional additional information - this can be used to show that several reporters are associated with the same gene for example, or add a comment about a reporter.
control_biosequence - for example a spike
control_buffer - buffer spotted on the array
control_empty - nothing spotted on the array
control_genomic_DNA - e.g. salmon sperm DNA
control_label - landing lights
control_reporter_size - size standard
control_spike_calibration - spike at varying concentrations
control_unknown_type
MAGE-TAB Example: IDF
ArrayExpress & Atlas78
MAGE-TAB Example: SDRF
ArrayExpress & Atlas79
MAGE-TAB Example: SDRF
ArrayExpress & Atlas80
MAGE-TAB Submission
ArrayExpress & Atlas81
Submitter is directed to either submit an experiment or download a template to the desktop
Submitter is directed to either submit an experiment or download a template to the desktop
Ontology LinkOntology Link
Indicate submission typeIndicate submission type
MAGE-TAB Submission
ArrayExpress & Atlas82
What happens after submission?
• Email confirmation• Curation• The curation team will review your submission and will
email you with any questions.• Possible reopening for editing
• We will send you an accession number when all the required information has been provided.
• We will load your experiment into ArrayExpress and provide you with a reviewer login for viewing the data before it is made public.
ArrayExpress & Atlas83
Submission of High-throughput sequencing gene expression data
ArrayExpress & Atlas84
Source Name Material Type Term Source REF Characteristics[Organism] Characteristics[Sex] Characteristics[StrainOrLine] Protocol REFfinch 1 whole_organism MGED Ontology Geospiza fortis male Pinta EXTRACTIONfinch 2 whole_organism MGED Ontology Geospiza fortis male Pinta EXTRACTIONfinch 3 whole_organism MGED Ontology Geospiza fortis male Marchesa EXTRACTIONfinch 4 whole_organism MGED Ontology Geospiza fortis male Marchesa EXTRACTIONfinch 5 whole_organism MGED Ontology Geospiza fortis male Santiago EXTRACTIONfinch 6 whole_organism MGED Ontology Geospiza fortis male Santiago EXTRACTIONfinch 7 whole_organism MGED Ontology Geospiza fortis male Floreana EXTRACTIONfinch 8 whole_organism MGED Ontology Geospiza fortis male Floreana EXTRACTIONfinch 9 whole_organism MGED Ontology Geospiza fortis male Pinzon EXTRACTIONfinch 10 whole_organism MGED Ontology Geospiza fortis male Pinzon EXTRACTION
MAGE-TAB Example: SDRF
ArrayExpress & Atlas86
MAGE-TAB Example: SDRF
What needs to be included in the Spreadsheet?• Include Assay Name and Technology Type columns
• Raw files must go in the Array Data File column
• A sequencing protocol must be provided.• The sequencing protocol should have a performer- this is used as the run center name. • This protocol must have a Protocol Hardware value saying which sequencing instrument was
used (e.g. 454 GS, Illumina Genome Analyzer, AB SOLiD System• Reference this in the Protocol REF column before the Assay Name column.
• These 4 extra Comment[] columns should be added after Extract Name to provide information about how the library was prepared
• 1. Comment[LIBRARY_LAYOUT] - Specifies whether to expect single or paired reads . The column should contain one of the following: SINGLE or PAIRED
• 2. Comment[LIBRARY_SOURCE] - Specifies the type of source material that is being sequenced. The column should contain one of the following: TRANSCRIPTOMIC, METAGENOMIC, SYNTHETIC, VIRAL RNA, OTHER *
• 3. Comment[LIBRARY_STRATEGY] - Sequencing technique intended for the library. The column should contain one of the following: WGS, WCS, WXS, CLONE, CLONEEND, POOLCLONE, FINISHING, AMPLICON, RNA-Seq, EST, FL-cDNA, CTS, ChIP-Seq, MNase-Seq, DNase-Hypersensitivity, Bisulfite-Seq, MRE-Seq, MeDIP-Seq, MBD-Seq, OTHER *
• 4. Comment[LIBRARY_SELECTION] - Method was used to select and/or enrich the material being sequenced. The column should contain one of the following: RANDOM, PCR, RANDOM PCR, RT-PCR, cDNA, CAGE, RACE, ChIP, MNase DNAse, HMPR, MF, MSLL, 5-methylcytidine antibody, MBD2 protein methyl-CpG binding domain, Hybrid Selection, Reduced Representation, Restriction Digest, size fractionation, CF-S, CF-M, CF-H, CF-T, other, unspecified *
ArrayExpress & Atlas87
Submissions- Key Point
Don’t be afraid to ask
ArrayExpress & Atlas88
Summary: ArrayExpress
Search by experiment
Search by keywordSearch by keyword
Link to sample properties and
experiment design
Link to sample properties and
experiment design
View experimentView experiment
Search by gene across experiments
Browse results summaryBrowse results summary
Search by gene name,
species and experimental condition
Search by gene name,
species and experimental condition
View expression
under different conditions and
profiles
View expression
under different conditions and
profiles
ArrayExpress90
AcknowledgementsArrayExpress/Atlas training is funded by the European Commission under SLING, grant agreement number 226073 (Integrating Activity) within
Research Infrastructures Action of the FP7 Capacities Specific Programme.