experiment_IlluminaPaired.xml

<?xml version='1.0' encoding='UTF-8'?>
<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_6/SRA.experiment.xsd">
  <EXPERIMENT alias="TODO: Submitter designated name for the 'Experiment'. The name must be unique within the submission account." center_name="TODO: The center name (its acronym) of the submitter's account" broker_name="TODO: The center name (its acronym) of the broker if applicable, if not, remove this attribute (broker_name)">
    <TITLE>TODO: Short text that can be used to call out experiment records in searches or in displays. This element is technically optional but should be used for all new records.</TITLE>    <!-- Optional block -->
    <STUDY_REF refname="TODO: Identifies the parent study (that encompasses this experiment) by name within the namespace defined by attribute 'Study_refCenter'." refcenter="TODO: Acronym of the center name used to submit the referenced study."/>
    <DESIGN>
      <DESIGN_DESCRIPTION>TODO: Goal and setup of the individual library including how the library was constructed</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="TODO: Accession ID of the Sample associated with this experiment."/>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>TODO: The submitter's name for this library.</LIBRARY_NAME>     <!-- Optional block -->
        <LIBRARY_STRATEGY>TODO: Sequencing technique intended for this library. Must be value from Controlled vocabulary (description in parenthesis):
              WGS	(Random sequencing of the whole genome)
              WGA	(whole genome amplification to replace some instances of RANDOM)
              WXS	(Random sequencing of exonic regions selected from the genome)
              RNA-Seq	(Random sequencing of whole transcriptome)
              ssRNA-seq	
              miRNA-Seq	(for micro RNA and other small non-coding RNA sequencing)
              ncRNA-Seq	(Non-coding RNA)
              FL-cDNA	(Full-length sequencing of cDNA templates)
              EST	(Single pass sequencing of cDNA templates)
              Hi-C
              ATAC-seq
              WCS	(Random sequencing of a whole chromosome or other replicon isolated from a genome)
              RAD-Seq	
              CLONE	(Genomic clone based (hierarchical) sequencing)
              POOLCLONE	(Shotgun of pooled clones (usually BACs and Fosmids))
              AMPLICON	(Sequencing of overlapping or distinct PCR or RT-PCR products)
              CLONEEND	(Clone end (5', 3', or both) sequencing)
              FINISHING	(Sequencing intended to finish (close) gaps in existing coverage)
              ChIP-Seq	(Direct sequencing of chromatin immunoprecipitates)
              MNase-Seq	(Direct sequencing following MNase digestion)
              DNase-Hypersensitivity	(Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI)
              Bisulfite-Seq	(Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status)
              CTS	(Concatenated Tag Sequencing)
              MRE-Seq	(Methylation-Sensitive Restriction Enzyme Sequencing strategy)
              MeDIP-Seq	(Methylated DNA Immunoprecipitation Sequencing strategy)
              MBD-Seq	(Direct sequencing of methylated fractions sequencing strategy)
              Tn-Seq	(for gene fitness determination through transposon seeding)
              VALIDATION
              FAIRE-seq	(Formaldehyde-Assisted Isolation of Regulatory Elements) 
              SELEX	(Systematic Evolution of Ligands by EXponential enrichment (SELEX) is an in vitro strategy to analyze RNA sequences that perform an activity of interest, most commonly high affinity binding to a ligand)
              RIP-Seq	(Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLI))
              ChIA-PET	(Direct sequencing of proximity-ligated chromatin immunoprecipitates)
              Synthetic-Long-Read
              Targeted-Capture
              Tethered Chromatin Conformation Capture
              NOMe-Seq
              ChM-Seq
              GBS
              OTHER	(Library strategy not listed)</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>TODO: Specifies the type of source material that is being sequenced. Must be value from Controlled vocabulary (description in parenthesis):
              GENOMIC	(Genomic DNA (includes PCR products from genomic DNA))
              GENOMIC SINGLE CELL
              TRANSCRIPTOMIC	(Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries))
              TRANSCRIPTOMIC SINGLE CELL
              METAGENOMIC	(Mixed material from metagenome)
              METATRANSCRIPTOMIC	(Transcription products from community targets)
              SYNTHETIC	(Synthetic DNA)
              VIRAL RNA	(Viral RNA)
              OTHER	(Other, unspecified, or unknown library source material)
</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>TODO: Method used to enrich the target in the sequence library preparation. Must be value from Controlled vocabulary (description in parenthesis):
              RANDOM	(Random selection by shearing or other method)
              PCR	(Source material was selected by designed primers)
              RANDOM PCR	(Source material was selected by randomly generated primers)
              RT-PCR	(Source material was selected by reverse transcription PCR)
              HMPR	(Hypo-methylated partial restriction digest)
              MF	(Methyl Filtrated)
              repeat fractionation	(replaces: CF-S, CF-M, CF-H, CF-T)
              size fractionation
              MSLL	(Methylation Spanning Linking Library)
              cDNA	(complementary DNA)
              cDNA_randomPriming
              cDNA_oligo_dT
              PolyA
              Oligo-dT
              Inverse rRNA
              Inverse rRNA selection
              ChIP	(Chromatin immunoprecipitation)
              ChIP-Seq
              MNase	(Micrococcal Nuclease (MNase) digestion)
              DNase	(Deoxyribonuclease (MNase) digestion)
              Hybrid Selection	(Selection by hybridization in array or solution)
              Reduced Representation	(Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling)
              Restriction Digest	(DNA fractionation using restriction enzymes)
              5-methylcytidine antibody	(Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C))
              MBD2 protein methyl-CpG binding domain	(Enrichment by methyl-CpG binding domain)
              CAGE	(Cap-analysis gene expression)
              RACE	(Rapid Amplification of cDNA Ends)
              MDA	(Multiple displacement amplification)
              padlock probes capture method	(to be used in conjuction with Bisulfite-Seq)
              other	(Other library enrichment, screening, or selection process)
              unspecified	(Library enrichment, screening, or selection is not specified)</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="TODO: The nominal length (e.g. 390) is the average distance between the paired reads in base pair." NOMINAL_SDEV="TODO: The nominal sdev refers to the standard deviation (e.g. '50.22') of paired-end library average internal insert sizes."/>
        </LIBRARY_LAYOUT>
        <TARGETED_LOCI>   <!-- Optional block -->
          <LOCUS locus_name="TODO: Names the gene(s) or locus(loci) or other genomic feature(s) targeted by the sequence. Choose from:               
              16S rRNA
              18S rRNA
              28S rRNA
              RBCL
              matK
              COX1
              ITS1-5.8S-ITS2
              exome
              other" description="TODO: Description of alternate locus and/or auxiliary information. "/>
          <!-- If you want to provide several loci, repeat <LOCUS> here as many times as needed. -->
        </TARGETED_LOCI>
        <LIBRARY_CONSTRUCTION_PROTOCOL>TODO: Free form text describing the protocol by which the sequencing library was constructed</LIBRARY_CONSTRUCTION_PROTOCOL>   <!-- Optional block -->
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>   <!-- Optional block -->
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>TODO: Number of base/color calls, cycles, or flows per spot (e.g. 102)
          (raw sequence length or flow length including all application and technical tags and mate pairs, but not including gap lengths). This value will be platform dependent, library dependent, and possibly run dependent. Variable length platforms will still have a constant flow/cycle length.</SPOT_LENGTH>
          <READ_SPEC>
            <READ_INDEX>TODO: READ_INDEX starts at 0 and is incrementally increased for each sequential read spec within a spot descriptor. </READ_INDEX>
            <READ_LABEL>TODO: A label to name this tag (e.g. "F", "R", "Forward_read"…). Can be used to determine read name.  </READ_LABEL>
            <READ_CLASS>TODO: the class of the read, either 'Application Read' or 'Technical Read'.</READ_CLASS>
            <READ_TYPE>TODO: The type of read. Choose one of the following terms: 'Forward', 'Reverse', 'Adapter', 'Primer', 'Linker', 'BarCode', 'Other'.</READ_TYPE>
            <RELATIVE_ORDER follows_read_index="TODO: Optionally specify the read index that precedes this read. The read is located beginning at the offset or cycle relative to another read. This choice is appropriate for example when specifying a read that follows a variable length expected sequence(s)."/>
            <BASE_COORD>TODO: The location (coordinates) of the read. Start in terms of base count (1 is beginning of spot)</BASE_COORD>
            <EXPECTED_BASECALL_TABLE default_length="TODO: Specify whether the spot should have a default length (e.g. '7') for this tag if the expected base cannot be matched.">
              <BASECALL min_match="TODO: Minimum number of matches to trigger identification. " max_mismatch="TODO: Maximum number of mismatches for identification" match_edge="TODO: Where the match should occur. Changes the rules on how min_match and max_mismatch are counted.">TODO: Basecall itself (e.g. "AAGGTGC")</BASECALL>
            </EXPECTED_BASECALL_TABLE>
          </READ_SPEC>
          <!-- If you want to provide several read specifications, repeat <READ_SPEC> here as many times as needed. -->
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>TODO: Illumina is 4-channel flowgram with 1-to-1 mapping between basecalls and flows. Choose which sequencing platform and platform-specific runtime parameters were used from the following list: 
            Illumina Genome Analyzer
            Illumina Genome Analyzer II
            Illumina Genome Analyzer IIx
            Illumina HiSeq 2500
            Illumina HiSeq 2000
            Illumina HiSeq 1000
            Illumina MiSeq
            Illumina HiScanSQ
            unspecified</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
    <PROCESSING>    <!-- Optional block -->
      <PIPELINE>
        <PIPE_SECTION>
          <STEP_INDEX>TODO: Lexically ordered value (e.g. '1', '2'…) that allows for the pipe section to be hierarchically ordered.</STEP_INDEX>
          <PREV_STEP_INDEX>TODO: Step index of the previous step in the workflow (e.g. '1', '2'…). If this is the first pipe section, use 'N/A'.</PREV_STEP_INDEX>
          <PROGRAM>TODO: Name of the program or process for primary analysis (e.g. 'Rig Software'). This may include a test or condition that leads to branching in the workflow.</PROGRAM>
          <VERSION>TODO: Version of the program or process for primary analysis (e.g. '2.3.306')</VERSION>
          <NOTES>TODO: Notes about the program or process for primary analysis (e.g. 'Image Analysis 1.3.4 - set birghtness to 30%')</NOTES>
        </PIPE_SECTION>
        <!-- If you want to provide several pipe sections, repeat <PIPE_SECTION> here as many times as needed. -->
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>   <!-- Optional block -->
      <EXPERIMENT_ATTRIBUTE>
        <TAG>TODO: Name of the custom attribute.</TAG>
        <VALUE>TODO: Value of the custom attribute.</VALUE>
        <UNITS>TODO: Optional scientific units.</UNITS>
      </EXPERIMENT_ATTRIBUTE>
      <!-- If you want to provide several pipe sections, repeat <EXPERIMENT_ATTRIBUTE> (with at least TAG and VALUE) here as many times as needed. -->
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
  <!--  If you are submitting more than one Experiment, replicate the block <EXPERIMENT> here, 
          as many times as necessary.  -->
</EXPERIMENT_SET>