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BARLEYEXPRESS QUICK START Step-by-step submission help BarleyExpress step-by-step
submission help page is designed to guide you through the submission
procedures to BarleyBase data base. If you read the
help page and still have problems, please contact BarleyBase
Curation team at barleybasewebmaster@iastate.edu
for more help. Basic submission steps in BarleyExpress 2. Login 4. Protocol submission
5. Experiment design
submission What are essential for making a submission ·
Your login information for existing user, or contact
information for new user to register. ·
You experimental Design ·
Your protocols ·
The raw data from Affymetrix MAS 5.0
Suite. *.DAT and *.CEL files are required for each hybridization. *.EXP and
*.CHP are recommended. ·
A browser with Sun JVM version xxxx
or above enabled. Step 1. Create an
account If this is your first submission to BarleyBase, please click the 'New User Register' link button in the login page. After clicking the button, you
will be presented with information entry fields to create a new login
account. Enter all the required fields marked by * and when finished,
click the 'Submit' button. The information will be used by the Curation team to contact you about your submission.
Please keep your password at a secure space, because this is the key to your
data. Step 2. Login If you have already created a login
account before, just enter your Login ID and Password in the boxes provided and
click the 'Login' button. If you have forgotten your password,
please click the Cannot remember your password?
link button. After clicking the button, enter your
e-mail address (as provided when creating the account) and we will send you
your password. Once you logged in, you can view all your account information.
The link “Experiment Management” and “Add/Edit your submissions, or Browse
experiments that you can access” would bring you to BarleyExpress.
Step 3. Select
submission type There are three operation types in BarleyExpress: Protocol submission, Experiment
submission and Browse experiment submission. You can submit five types of
protocols in Protocol submission:
The above
experiment submission steps can be finished sequentially in one submission
session. You may also suspend any time in the last two steps, and resume at
your convenient time later. When entering an experiment, you
must provide the protocols used in the experiment. You can browse existing
protocols in the database and link them to your experiment. If your protocols
are not listed, please submit it before starting the experiment submission. Only successful submissions will
receive a BarleyBase accession numbers. These are
unique identifiers assigned to each Experiment and Protocol entry in the BarleyBase database. You can browse your experiment
submissions in the BarleyBase, and also you can
update or edit your previous, unfinalized
submissions. For more information, please refer
to the relevant sections below Step 4. Protocol
submission Protocol is the documentation of the
set of steps taken during a procedure. Browse through existing Protocols that
have already submitted to the database. If the Protocols you are using are
not listed here, click the 'Protocol submission' page, choose the protocol
type that you would like to submit and provide the required information.
Please, see relevant sections below. Remember, you can choose to submit one
Protocol only. Once you have submitted your Protocols, you will be able to
link them to your experiment during the Experiment submission. If linked to
multiple Experiments, Protocols should be only submitted once. Extraction protocol is the documentation
of the set of steps taken to extract the nucleic acid from the sample. · Protocol
Name Provide a unique name that describes
your extraction protocol and help you differentiate it from others. E.g.: Trizol RNA isolation · Extracted
nucleic acid A drop down list of extract types is
provided. Select one of these to describe what you have extracted. E.g.: RNA If your extract is not on the list, please
specify a description in the text box provided. We may contact you for
further information. · Amplification A drop down list of amplification
methods is provided. Select one of these to describe your amplification. E.g.: RNA
Polymerase If your amplification method is not on the
list, please specify a description in the text box provided. We may contact
you for further information. · Protocol
resource Provide the resource of protocol
used in experiment. E.g.: Affymetrix manual. · Full protocol description Cut and paste the full protocol
description in the free text box provided. All the details, for example
enzyme used, must be provided. E.g.: Work in
hood. Wear safety glasses when working with TRIzol
and chloroform. Preheat the Trizol to 60oC for at
least 1 hr. Once you have entered the Extraction
protocol information click the 'Submit' button. Labeling protocol is the documentation of
the set of steps taken to label the nucleic acid extracted from the sample. · Protocol
Name Provide a unique name that describes
your labeling protocol and help you differentiate it from others. E.g.:
Cleanup of Double-Stranded cDNA The labeling protocol name will be
used to help you during the submission procedures. If you incur in any problem during the
submission and need to contact us, please reference the labeling protocol
name and your name in the subject line of your e-mail. · Amount
of nucleic acid labeled Provide the amount of nucleic acid
labeled and specify the unit. E.g.: 5 ug · Label
used Specify he name of the label used to
label the nucleic acid extracted from the sample. A drop down list of label types is
provided. Select one of these to describe the one you used to label your
nucleic acid. E.g.: Biotin · Amplification A drop down list of amplification
methods is provided. Select one of these to describe your amplification. E.g.: RNA
Polymerase
· Protocol
resource Provide the resource of protocol
used in experiment. E.g.: Affymetrix manual. · Full
protocol description Submit the details of the label
incorporation method in the free text box provided. E.g.: In vitro
transcription by using double-stranded cDNA as a
template in the presence of biotinylated UTP and
CTP, using an ENZO BioArray HighYield
RNA Transcript Labeling Kit (Affymetrix, Santa
Clara, CA, and ENZO Diagnostics, Farmingdale, NY) according to the
manufacturer’s instructions Once you have entered the Labeling
protocol information click the 'Submit' button. Hybridization protocol is the
documentation of the set of steps taken to hybridize the labeled extract to
the array. · Protocol
name Provide a unique name that describes
your hybridization protocol and help you differentiate it from others. E.g.:
Eukaryotic Target Hybridization The hybridization protocol name will be
used to help you during the submission procedures. If you incur in any
problem during the submission and need to contact us, please reference the
hybridization protocol name and your name in the subject line of your e-mail. · Hybridization
chamber type A drop down list of hybridization chamber
types is provided. Select one of these to describe your hybridization
chamber. · Quantity
of the labeled extract used Specify the quantity of the labeled
extract used in the hybridization procedure. · Duration Specify the time length of the
hybridization. · Hybridization
volume Specify the total volume of the hybridization.
· Temperature Specify the temperature of the
hybridization. · Protocol
resource Provide the resource of protocol
used in experiment. E.g.: Affymetrix manual. · Full
protocol description Submit the details of the hybridization method
in the free text box provided. Once you have entered the Hybridization
protocol information click the 'Submit' button. Scanning protocol is the documentation of
the set of steps taken to scan the hybridized array. · Protocol
name Provide a unique name that describes
your scanning protocol and help you differentiate it from others. E.g.:
Probe Array Scan The scanning protocol name will be used to
help you during the submission procedures. If you incur in any problem during
the submission and need to contact us, please reference the scanning protocol
name or ID and your name in the subject line of your e-mail. · Scanner
type A drop down list of scanner types is
provided. Select one of these to describe your scanner. · Scanning
software A drop down list of scanning software is
provided. Select one of these to describe your software. · Protocol
resource Provide the resource of protocol
used in experiment. E.g.: Affymetrix manual. · Full
protocol description Submit the details of the scanning method
in the free text box provided. Once you have entered the Scanning
protocol information click the 'Submit' button.
·
Protocol name Provide a unique name that describes
your procedure and help you differentiate it from others. E.g.: Affy- Eukaryotic Array
Washing and Staining The procedure name will be used to help
you during the submission procedures. If you incur in any problem during the
submission and need to contact us, please reference the scanning protocol
name or ID and your name in the subject line of your e-mail. · Instrument A drop down list of instrument is
provided. Select one of these to describe your instrument. · Software A drop down list of software is provided.
Select one of these to describe your software. · Protocol
resource Provide the resource of protocol
used in experiment. E.g.: Affymetrix manual. · Full
protocol description Submit the details of the washing and
staining method in used in your experiment. Once you have entered the Washing and
staining procedure information click the 'Submit' button. Step
5. Experiment submission Remember, if you have planned to enter an
Experiment, you MUST also provide
the Protocols to complete the submission!! New or pending experimental submission If during the experiment submission your
need to suspend the procedure, the information you have entered will be saved
for you (even if you logoff). When login again you can edit/update or copy
experiment submission (s). In order to view or update a pending submission,
click an ‘Overview’ button at the rightmost side, or select from
‘View/Edit/Add submissions’ at the left-side of your “Browse experiment in BarleyBase” page and click corresponding link
buttons. If you want to start a new
experiment submission, just click the 'Submit new experiment' link button. ·
Experiment name Provide a unique name that describes
your experiment submission and help you differentiate it from others. E.g.: Barley
treated with powdery mildew. The submission name will be used for
tracking your submission. If you incur in any problem during the submission and
need to contact us, please reference the submission name and your name in the
subject line of your e-mail. · Experiment
type Experiment type is a controlled
vocabulary that classifies the experiment. A drop down list of experimental
design types is provided. Select one or more of these to describe your
experiment. E.g.:
Temperature shock and Dose response For further information on the
Experiment types, see this MGED Ontology link. If your experiment type is not on the
list, please specify a description in the text box provided. We may contact
you for further information. · Experimental
factors Experimental factor is a parameter
or a condition tested in the experiment. A drop down list of experimental
factors is provided. Select one or more of these factors to describe your
experiment. E.g.:
Compound and Age If your experimental factor is not
on the list, please specify a description in the text box provided. We may
contact you for further information. For further information on the
experimental factors, see this MGED Ontology link. · Experiment
description Briefly describe your experiment in
the text box provided. E.g.: This
experiment was conducted to elucidate the molecular mechanisms of incompatible
and compatible barley-powdery mildew interactions. We used two isolates of Blumeria graminis sp. hordei to inoculate 3 barley near
isogonics lines with Mla1, Mla6 and Mla13 resistance specificities.
Reciprocal inoculations generated 6 genotype-isolate combinations. Each
experimental flat contained six rows of 10 – 15 seven day old (ten cm)
seedlings of a particular genotype, with the six rows randomly assigned for
harvest at the 6 time points 0, 8, 16, 20, 24, and 32 hours after inoculation
(hai). Inoculation was performed by tipping the
flats at 45° and dusting the plants with a high density of fresh conidiospores. This procedure was repeated from the
opposite angle to ensure complete coverage. Inoculated plants were maintained
in two separate growth chambers corresponding to the two pathogen isolates.
Rows of plants were harvested at the assigned times and flash frozen in
liquid nitrogen. Thus the design is equivalent to a standard split-split-plot
design (see, e.g., Chapter 14 of Kuehl, 2000).
Replications play the role of blocks, isolate is the whole-plot factor,
genotype is the split-plot factor, and time is the split-split-plot factor. Once you have entered the
Experimental design information click the 'Submit' button. ·
Number of level of an experiment factor
·
Number of level of an experiment factor Each experiment factor has
multiple levels which describe how the factor was varied in the experiment.
For example, the levels of the factor 'gender' are male and female. The
levels of the factor 'time' may be 0 minutes after infection, 30 minutes
after infection, 60 minutes after infection, 90 minutes after infection, and
120 minutes after infection For each treatment factor, specify the names of
each level considered in the experiment.
BarleyExpress is using UploadApplet for
upload batch data files. To get the UploadApplet
working, you need the latest Java Virtual Machine. You can download Sun JVM. You can also view uploaded files for an experiment. Select data file prefix from the drop down
list for a replicate in a treatment. Provide detailed information on the sample
(s) (biomaterial) used in your experiment. · Sample name Provide a unique name or ID that
describes your sample (biomaterial) and help you differentiate it from
others. E.g.:
Barley_Mla6_Bgh_isolate_5874_0hai The sample name will be used to help you
during the submission procedures. If you incur in any problem during the
submission and need to contact us, please reference the sample name or ID and
your name in the subject line of your e-mail. · Organism The genus and the species (and
subspecies) of the organism from which the sample (biomaterial) is derived
[MGED Ontology definition]. A drop down list of organism names
is provided. Select one of these to describe your sample. E.g.: Barley · Sample provider
The resource (company, hospital,
contact name or geographical location) used to purchase or obtain the cells,
animals, or tissues (biomaterial) [MGED Ontology definition]. Specify details
in the text box provided. E.g.: · Sample
type The form in which the original
sample (biomaterial before any treatment) is provided [MGED Ontology
Definition]. A drop down list of sample types is
provided. Select one of these to describe your sample. If your sample type is not on the
list, please specify a name in the text box provided. We may contact you for
further information. For further information on sample types,
see this MGED Ontology link. · Developmental
stage The developmental stage of the
organism's life cycle during which the sample (biomaterial) was extracted
[MGED Ontology definition]. A drop down list of developmental
stages is provided. Select one of these to describe your organism. If your
developmental stage is not on the list, please specify a name in the text box
provided. E.g.:
Seedling stage We may contact you for further
information. If the developmental stage field is
not applicable to you, select the n/a option or leave blank the free text box
provided. For further information on the
developmental stage, see this MGED Ontology link. · Age The time period elapsed since an
identifiable time point in the life cycle of an organism. (If a developmental
stage is specified, the identifiable time point would be the beginning of
that stage. Otherwise the identifiable time point must be specified in the
'Time point' section below) [MGED Ontology Definition] Specify the age or the age range in
the text box provided. Age should be numeric, please choose the correct
units. E.g.: Min
7 Max 9 E.g.:
weeks If the age field is not applicable
to you, select the n/a option or leave blank the free text box provided. For further information on the age, see
this MGED Ontology link. · Individual
identifier Identifier or number or bar-code of
the individual organism culture or cell used from which the sample
(biomaterial) was derived. For patients, the identifier must be approved by
Institutional Review Boards (IRB, review and monitor biomedical research
involving human subjects) or appropriate body [MGED Ontology Definition] Specify an identifier in the text
box provided. E.g.:
Barley-00732 · Individual genetic
trait or genotype The genotype of the individual
organism from which the biomaterial was derived. Individual genetic
characteristics include polymorphisms, disease alleles, and haplotypes. [MGED Ontology Definition]. Specify the genotype of the individual
organism in the text box provided. For further information on the age, see
this MGED Ontology link. · Separation
technique The technique used to separate tissues or
cells from a heterogeneous sample. A drop down list of separation techniques
is provided. Select one or more to describe your separation. If the
separation technique you used is not on the list, please specify a name in
the text box provided. We may contact you for further information. If the
separation technique field is not applicable to you, select the n/a option or
leave blank the free text box provided. · Cell
type or target cell type Cell type (source of the nucleic
acid) used in the experiment and the target cell type is the cell of primary
interest. The sample (biomaterial) may be derived from a mixed population of
cells although only one cell type is of interest [MGED Ontology Definition].
Specify the cell type or the cell type of primary interest in the text box
provided. E.g.: Hepatocytes We may contact you for further
information. For further information on cell type, see
this MGED Ontology link. For further information on target cell type, see
this MGED Ontology link. · In
vivo or in vitro treatment The source organism has been
undergone some in vivo treatment or the sample source has undergone treatment
outside of the organism.The treatment is effected
by a defined chemical, biological, or physical agent or compound [MGED
Ontology Definition]. A drop down list of treatment applications is provided.
Select one or to describe your treatment. E.g.: in
vivo If your treatment application is not on
the list, please specify a name in the text box provided. We may contact you
for further information. · Treatment
application type The type of manipulation applied to
the sample (biomaterial) for the purposes of generating one of the variables
under study [MGED Ontology Definition]. A drop down list of treatment types
is provided. Select one to describe your treatment. E.g.:
Compound
If your treatment type is not on the
list, please specify a name in the text box provided. We may contact you for
further information. E.g.:
Vehicle (methyl cellulose) In order to describe the treatment to your
sample use the Sample treatment protocol page. For more details see ' Sample
treatment protocol' section. Once you have entered all the above
information for the sample description, click the 'Submit' button. |