org.nmdp.ngs.sra.xsd.SRA.experiment.xsd Maven / Gradle / Ivy
Impementation of lookup table between Sample Pool member and identified read_group_tags for a given
READ_LABEL
Assignment of read_group_tag to decoded read
Label a sample within a scope of the pool
Proportion of this sample (in percent) that was included in sample pool.
The SAMPLE_DESCRIPTOR specifies how to decode the individual reads
of interest from the monolithic spot sequence. The spot descriptor contains aspects
of the experimental design, platform, and processing information. There will be two
methods of specification: one will be an index into a table of typical decodings,
the other being an exact specification.
Identifies a list of group/pool/multiplex sample members. This implies that
this sample record is a group, pool, or multiplex, but is continues to receive
its own accession and can be referenced by an experiment. By default if
no match to any of the listed members can be determined, then the default
sampel reference is used.
The LIBRARY_DESCRIPTOR specifies the origin of the material being
sequenced and any treatments that the material might have undergone that affect the
sequencing result. This specification is needed even if the platform does not
require a library construction step per se.
The submitter's name for this library.
Sequencing technique intended for this library.
Whole Genome Sequencing - random sequencing of the
whole genome (see pubmed 10731132 for details)
Whole Genome Amplification followed by random
sequencing. (see pubmed 1631067,8962113 for details)
Random sequencing of exonic regions selected from
the genome. (see pubmed 20111037 for details)
Random sequencing of whole transcriptome, also
known as Whole Transcriptome Shotgun Sequencing, or WTSS). (see
pubmed 18611170 for details)
Micro RNA sequencing strategy designed to capture
post-transcriptional RNA elements and include non-coding
functional elements. (see pubmed 21787409 for details)
Capture of other non-coding RNA types, including
post-translation modification types such as snRNA (small nuclear
RNA) or snoRNA (small nucleolar RNA), or expression regulation
types such as siRNA (small interfering RNA) or piRNA/piwi/RNA
(piwi-interacting RNA).
Random sequencing of a whole chromosome or other
replicon isolated from a genome.
Genomic clone based (hierarchical) sequencing.
Shotgun of pooled clones (usually BACs and
Fosmids).
Sequencing of overlapping or distinct PCR or
RT-PCR products. For example, metagenomic community profiling
using SSU rRNA .
Clone end (5', 3', or both) sequencing.
Sequencing intended to finish (close) gaps in
existing coverage.
chromatin immunoprecipitation.
following MNase digestion.
Sequencing of hypersensitive sites, or segments
of open chromatin that are more readily cleaved by DNaseI.
MethylC-seq. Sequencing following treatment of DNA
with bisulfite to convert cytosine residues to uracil depending
on methylation status.
Single pass sequencing of cDNA templates
Full-length sequencing of cDNA templates
Concatenated Tag Sequencing
Methylation-Sensitive Restriction Enzyme
Sequencing.
Methylated DNA Immunoprecipitation Sequencing.
Methyl CpG Binding Domain Sequencing.
Quantitatively determine fitness of bacterial
genes based on how many times a purposely seeded transposon gets
inserted into each gene of a colony after some time.
CGHub special request: Independent experiment to
re-evaluate putative variants.
Formaldehyde Assisted Isolation of Regulatory
Elements
Systematic Evolution of Ligands by EXponential
enrichment
Direct sequencing of RNA immunoprecipitates
(includes CLIP-Seq, HITS-CLIP and PAR-CLIP).
Direct sequencing of proximity-ligated chromatin
immunoprecipitates.
Library strategy not listed.
The LIBRARY_SOURCE specifies the type of source material that is being sequenced.
Genomic DNA (includes PCR products from genomic DNA).
Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).
Mixed material from metagenome.
Transcription products from community targets
Synthetic DNA.
Viral RNA.
Other, unspecified, or unknown library source material.
Method used to enrich the target in the sequence library
preparation
No selection or random selection.
Target selection and enrichment via PCR.
Source material was selected by randomly generated primers.
Selection by reverse transcription PCR.
Hypo-methylated partial restriction digest
Methyl Filtrated
Selection for less repetitive (and more gene rich)
sequence through Cot filtration (CF) or other fractionation
techniques based on DNA kinetics.
Physical selection of size appropriate targets.
Methylation Spanning Linking Library
PolyA selection or enrichment for messenger RNA
(mRNA). complementary DNA.
Chromatin immunoprecipitation
Micrococcal Nuclease (MNase) digestion
Deoxyribonuclease (MNase) digestion
Selection by hybridization in array or solution.
Reproducible genomic subsets, often generated by restriction fragment size selection,
containing a manageable number of loci to facilitate re-sampling.
DNA fractionation using restriction enzymes.
Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C).
Enrichment by methyl-CpG binding domain.
Cap-analysis gene expression.
Rapid Amplification of cDNA Ends.
Multiple Displacement Amplification, a non-PCR based DNA amplification technique
that amplifies a minute quantifies of DNA to levels suitable for genomic analysis.
Targeted sequence capture protocol covering an arbitrary set of nonrepetitive
genomics targets. An example is capture bisulfite sequencing using padlock probes (BSPP).
Other library enrichment, screening, or selection process.
Library enrichment, screening, or selection is not specified.
LIBRARY_LAYOUT specifies whether to expect single, paired, or other configuration of reads.
In the case of paired reads, information about the relative distance and orientation is specified.
Reads are unpaired (usual case).
Names the gene(s) or locus(loci) or other genomic feature(s) targeted by the sequence.
Reference to an archived primer or
probe set. Example: dbProbe
Bacterial small subunit ribosomal RNA, a locus used for
phylogenetic studies of bacteria and as a target for random target PCR in
environmental biodiversity screening.
Eukaryotic small subunit ribosomal RNA, a locus used for
phylogenetic studies of eukaryotes and as a target for random target PCR in
environmental biodiversity screening.
RuBisCO large subunit : ribulose-1,5-bisphosphate
carboxylase/oxygenase large subunit, a locus used for phylogenetic studies
of plants.
Maturase K gene, a locus used for phylogenetic studies of
plants.
Mitochondrial cytochrome c oxidase 1 gene, a locus used for
phylogenetic studies of animals
Internal transcribed spacers 1 and 2 plus 5.8S rRNA region,
a locus used for phylogenetic studies of fungi.
All exonic regions of the genome.
Other locus, please describe.
Submitter supplied description of alternate locus and auxiliary
information.
The optional pooling strategy indicates how the library or libraries are organized if multiple samples are involved.
Free form text describing the protocol by which the sequencing library was constructed.
Goal and setup of the individual library.
Pick a sample to associate this experiment with. The sample may be an individual or a pool,
depending on how it is specified.
The LIBRARY_DESCRIPTOR specifies the origin of the material being sequenced and any
treatments that the material might have undergone that affect the sequencing result. This specification is
needed even if the platform does not require a library construction step per se.
The SPOT_DESCRIPTOR specifies how to decode the individual reads of interest from the
monolithic spot sequence. The spot descriptor contains aspects of the experimental design, platform, and
processing information. There will be two methods of specification: one will be an index into a table of
typical decodings, the other being an exact specification. This construct is needed for loading data and for
interpreting the loaded runs. It can be omitted if the loader can infer read layout (from multiple input
files or from one input files).
An Experiment specifies of what will be sequenced and how the sequencing will be performed.
It does not contain results.
An Experiment is composed of a design, a platform selection, and processing parameters.
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.
The STUDY_REF descriptor establishes the relationship of the experiment to the parent
study. This can either be the accession of an existing archived study record, or
a reference to a new study record in the same submission (which does not yet have an
accession).
The PLATFORM record selects which sequencing platform and platform-specific runtime parameters.
This will be determined by the Center.
Links to resources related to this experiment or experiment set (publication, datasets, online databases).
Properties and attributes of the experiment. These can be entered as free-form
tag-value pairs.
An EXPERMENT_SET is a container for a set of experiments and a common namespace.