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Problem: An overview of finding information on an experiment in caArray.
Topic: caArray Usage
Release: caArray 2.0 and above
Date entered:
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10/12/2011
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Solution
A caArray experiment captures as much relevant information about a real-world
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experiment
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as
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possible.
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This
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can
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include
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general
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information
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about
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the
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experiment,
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such
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as
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the
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experimental
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design
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and
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experimental
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factors,
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associated
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publications,
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protocols,
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array
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designs,
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quality
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control
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and
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data
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processing
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steps,
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or
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specific
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information
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about
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biological
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materials
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used
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in
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the
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experiment.
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Files
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containing
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data
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generated
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for
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an
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experiment
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can
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be
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uploaded,
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validated
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and
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imported
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into
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a
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caArray
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experiment.
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Once
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a
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user
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clicks
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on
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an
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experiment
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at
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the
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caArray
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web
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interface,
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five
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main
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menu
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items
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are
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presented
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for
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each
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experiment:
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Overview,
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Contacts,
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Annotations,
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Data,
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and
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Publications.
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- Overview:
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- This
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- page
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- highlights
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- several
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- key
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- characteristics
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- of
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- the
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- experiment.
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- The
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- information
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- on
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- the
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- "Overview"
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- page
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- either
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- comes
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- from
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- manual
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- data
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- entry
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- when
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- the
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- experiment
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- was
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- created
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- or
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- comes
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- from
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- the
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- loading
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- of
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- a
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- MAGE-TAB
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- IDF
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- file.
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- A
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- few
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- elements
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- are
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- worth
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- mentioning:
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- Experimental
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- Description:
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- a
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- detailed
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- description
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- of
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- the
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- experiment.
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- You
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- can
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- put
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- as
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- much
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- details
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- as
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- you
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- want
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- but
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- please
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- be
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- aware
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- that
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- it
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- is
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- just
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- one
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- single
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- paragraph.
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- Status:
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- either
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- "In
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- Progress"
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- (default)
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- or
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- "Locked"
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- (the
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- experiment
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- cannot
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- be
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- edited)
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- Array
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- Design:
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- this
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- represents
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- the
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- file(s)
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- describing
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- probes
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- on
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- the
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- corresponding
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- microarray
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- platform
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- Contact:
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- This
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- page
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- lists
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- users
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- who
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- are
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- the
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- Principal
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- Investigator(s)
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- or
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- the
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- contact
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- person(s)
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- for
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- this
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- experiment.
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- The
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- information
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- on
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- this
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- page
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- either
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- comes
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- from
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- manual
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- data
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- entry
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- when
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- the
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- experiment
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- was
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- created
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- or
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- comes
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- from
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- the
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- loading
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- of
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- a
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- MAGE-TAB
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- IDF
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- file.
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- Annotation:
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- This
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- collection
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- of
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- pages
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- gives
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- detailed
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- information
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- on
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- the
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- experiment
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- and
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- biomaterials
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- on
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- which
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- the
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- experiment
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- is
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- conducted.
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- It
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- has
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- seven
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- sub
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- menu
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- items
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- (tabs)
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- that
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- can
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- be
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- categorized
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- into
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- three
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- groups:
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- Experimental
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- Design
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- and
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- Experimental
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- Factors:
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- They
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- describe
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- the
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- experiment
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- mainly
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- using
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- a
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- controlled
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- vocabulary,
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- the
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- MGED
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- Ontology
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- (MO).
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- Non-MO
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- terms
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- can
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- be
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- added
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- as
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- well.
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- The
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- information
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- on
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- these
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- two
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- pages
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- either
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- comes
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- from
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- manual
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- data
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- entry
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- when
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- the
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- experiment
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- was
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- created
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- or
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- comes
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- from
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- the
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- loading
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- of
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- a
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- MAGE-TAB
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- IDF
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- file.
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- Sources,
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- Samples,
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- Extracts,
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- and
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- Labeled
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- Extracts:
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- They
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- are
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- biological
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- source
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- materials
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- (biomaterials)
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- specified
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- in
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- the
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- MAGE-TAB
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- format
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- (
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- ).
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- The
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- following
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- image
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- (from
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- the
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...
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- ),
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- describes
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- the
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- relationships
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- among
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- them:
In most cases the biomaterial information comes from the loading of a MAGE-TAB SDRF file. In the SDRF file a user gives proper labels for biomaterials and can also add additional columns describing the characteristics of each biomaterial according to the MAGE-TAB specification. On this set of pages, a user can track the linkage from source materials to labeled extract, then to the final hybridization on microarray chip.
- Hybridizations: This page captures information related to hybridizations on microarray chips. It establishes linkage between data files collected after hybridization and the corresponding labeled abstracts from which the data are derived. In most cases the hybridization information comes from the loading of a MAGE-TAB SDRF
file.Anchor _GoBack _GoBack
- Hybridizations: This page captures information related to hybridizations on microarray chips. It establishes linkage between data files collected after hybridization and the corresponding labeled abstracts from which the data are derived. In most cases the hybridization information comes from the loading of a MAGE-TAB SDRF
- Data: This collection of pages provides access to data loading, processing, and downloading.
- Data loading and processing: Data are first loaded into the "Manage Data" tab, typically using the MAGE-TAB format. Once they are processed (validated and imported, or classified as supplemental files), they are automatically removed from the "Manage Data" tab and moved to the "Imported Data" tab or the "Supplemental Files" tab.
- Data download: A user can download the whole dataset or any subset of data here. This page offers three download options:
- Download Experiment File Packages: it allows download of pre-packaged files.
- Download Selected Experiment Files: it allows download of a selected set of files.
- Export Experiment Annotation Packages: it allows the export of experiment annotation in either MAGE-TAB or GEO SOFT (some restrictions apply) format.
- Publications: This page lists all publications added by the experiment owner. The information on this page either comes from manual data entry or comes from the loading of a MAGE-TAB IDF file.
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