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New Illumina GA sample tracking fields and incoming sample sheets #18

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Use specs laid out by David, Dan, Charlie, lab

DNA/RNA

- subtype
    - DNA
    - mRNA
    - total RNA
    - cDNA
        - random primed
        - oligoDT
    - mtDNA
    - chip DNA
    - chromatin IP
    - GDNA
    - WDNA
    - Restriction digested
        - restriction enzyme (drop down or free text?)
    - PCR fragments
    - bisulfite converted/bis-DNA/bc-DNA
- concentration
- method for determining concentration
- unit type (drop down) 
    - (A) whole blood
    - (A) buffy
    - (B) blood clot
    - (C) uL
    - (C) mL
    - (C) perafin block
- amount/container type (dependent on unit type selected)
    - (A) container type
    - (B) serum tube type
    - (C) amount
- tissue
    - blood
    - saliva
    - unknown
- source
    - case
    - control
    - unkown

Original issue reported on code.google.com by dmagli...@gmail.com on 7 Apr 2011 at 8:30

GoogleCodeExporter commented 8 years ago

Original comment by dmagli...@gmail.com on 7 Apr 2011 at 8:34

GoogleCodeExporter commented 8 years ago 
These were ones I had thought of independently (I had them as Issue 12), some 
are overlapping.  Also, the one above doesn't have anything about non-human 
samples.  And why is Charles not included on this ticket?

- Sample name
- Sample external unique identifier (optional)
- Organism (human, mouse, D. melanogaster, etc.)
- Genome assembly to align to (pulldown menu, hg18, mm9, etc.). Required.
- sex
- Material submitted (pulldown - RNA, cDNA, unenriched gDNA, ChIP enriched DNA, 
Other enriched DNA)
- Volume submitted (required). ______ (float). ______ units (pulldown mL, etc.)
- Concentration of material submitted (required). ______ (float) units 
(pulldown uM, etc.)
- Fragmentation of material submitted (pulldown - None, bioruptor, covaris, 
other)
- Size selection of material submitted (leave empty if none). Lower length 
(int) ______, Higher length (int) _______
- Sequencing adapters added before submission (pulldown - None, Illumina SE 
v.4, Illumina PE v. 4, Illumina PE v.4 index #1, etc.)
- Sequence contains 5' barcode (checkbox). Length of 5' barcode _____ (int) bp
- Desired sequencing (see recommended guidelines): (Pulldown: Let EC decide, 
GAII 36bp SE, GAII 101bp SE, etc.)
- Number of sequence reads desired (Optional, see guidelines): Number (int)_____

Also, the following information is required for TCGA (not necessarily on 
submission sheet, but must get into Geneus)

3.4     Sample Metadata
For open SRA submissions, the submitter must create or reference a SRA
sample or BioSample (SRS).
For protected SRA submissions, the submitter must reference an
existing BioSample record (SRS). Reference can be made to the
submitted sample name with refcenter set to the original repository
short name. Submitters should NOT create these records.
Open SRA samples or Biosamples have diverse attributes and information content.
Protected SRA samples are exported from dbGaP and make visible a
standard subset of attributes, including at the time of this writing:
Title – Brief yet unique headline returned with the record as part of
a search result. Identifiers – SRS accession, dbGaP sample accession
Organism – Target organism {human} Original_repository – Namespace for
sample set {TCGA} Submitted_sample_id – Sample name {TCGA aliquot id}
Submitted_subject_id – Subject name {TCGA subject id, substring of the
aliquot id} Sex – {male, female, unknown} Sample_type – Project
specific sample type {TCGA: normal, primary tumor, etc} Is_tumor –
{0,1} Histological_type – Sample diagnosis {TCGA: Serous
Cystadenocarcinoma, etc}
Analyte_type – {DNA, RNA, etc} Study_name – Short name for the parent
study {TCGA} Description – Free form text describing the sample. Links
– Includes link to parent dbGaP authorized access study homepage
An example of a TCGA record that has this information:
http://www.ncbi.nlm.nih.gov/biosample/limits?term=TCGA-13-0725-01A-01D-0359-05

3.5     Library Metadata
Each library mentioned in the BAM will map to a new or existing SRA
experiment. The SRA experiment contains the following data:
Experiment title – The title string that will be presented to users of
the public archive when this record is retrieved in a search result.
Please limit this string to 80 characters. Experiment description –
Description of the library and its sequencing. Library Name –
Controlled vocabulary of terms describing overall strategy of the
library. Library Strategy – Controlled vocabulary of terms describing
overall strategy of the library. Terms used by TCGA include {WGS,
WXS*, RNA-Seq*}.i
Library Source – Controlled vocabulary of terms describing starting
material from the sample. Terms used by TCGA include {GENOMIC,
TRANSCRIPTOMIC*}. Library Selection method – Controlled vocabulary of
terms describing selection or reduction method use in library
construction. Terms used by TCGA include {Random, Hybrid Selection}.
Library Layout – Specification of the layout: fragment/paired, and if
paired, the nominal insert size and standard deviation.
Library Protocol description – Description of the library construction
protocol, or reference to a standard protocol. Targeted loci* - Set of
loci to be selected for sequencing {16S RNA, exome} and associated
probes.
Platform – Controlled vocabulary of platform type {Illumina, LS454,
AB_SOLID, CompleteGenomics} Instrument model – Controlled vocabulary
of instrument models {Illumina Genome Analyzer II, etc} Expected
sequence length – Number of raw bases or color space calls expected
for the read (includes both mate pairs and all technical portions).
Sequence processing software and version – Name and version of
sequencing processing software used.

Original comment by benb...@gmail.com on 10 Apr 2011 at 2:59

GoogleCodeExporter commented 8 years ago 
We also need a "external sample ID" and "external study ID".  This pair of 
identifiers can uniquely identify any sample in the NCCC clinical study 
databases.

Original comment by benb...@gmail.com on 10 May 2011 at 7:45

GoogleCodeExporter commented 8 years ago 
- added External Sample ID (text field, not required)
- added External Study ID (text field, not required)

Original comment by dmagli...@gmail.com on 13 May 2011 at 11:19

GoogleCodeExporter commented 8 years ago 
Previous added as property of all sample types.

Original comment by dmagli...@gmail.com on 13 May 2011 at 11:21

GoogleCodeExporter commented 8 years ago 
- added Test/Control (drop down with case, control, unknown as options; applied 
to all sample types)

Original comment by dmagli...@gmail.com on 14 May 2011 at 12:00

GoogleCodeExporter commented 8 years ago 
To be reworked by/in conjunction with Janice.

Original comment by dmagli...@gmail.com on 6 Feb 2012 at 7:46

GoogleCodeExporter commented 8 years ago 
Issue 12 has been merged into this issue.

Original comment by zack...@gmail.com on 7 Aug 2012 at 8:09

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 7 Aug 2012 at 8:11