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This is a U.S. Government computer system, which may be accessed and used only for authorized Government business by authorized personnel. Unauthorized access or use of this computer system may subject violators to criminal, civil, and/or administrative action. All information on this computer system may be intercepted, recorded, read, copied, and disclosed by and to authorized personnel for official purposes, including criminal investigations. Such information includes sensitive data encrypted to comply with confidentiality and privacy requirements. Access or use of this computer system by any person, whether authorized or unauthorized, constitutes consent to these terms. There is no right of privacy in this system.

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Genomics Sample

63,463 Shared Subjects

Genomics sample data
Omics
Omics
06/08/2011
genomics_sample03
03/12/2024
View Change History
03
Definition
Submission Template
Query Element Name Data Type Size Required Description Value Range Notes Aliases
subjectkey GUID Required The NDAR Global Unique Identifier (GUID) for research subject NDAR*
Query experiment_id Integer Required ID for the Experiment/settings/run genom_experiment_id
src_subject_id String 20 Required Subject ID how it's defined in lab/project
interview_age Integer Required Age in months at the time of the interview/test/sampling/imaging. 0::1440 Age is rounded to chronological month. If the research participant is 15-days-old at time of interview, the appropriate value would be 0 months. If the participant is 16-days-old, the value would be 1 month.
interview_date Date Required Date on which the interview/genetic test/sampling/imaging/biospecimen was completed. MM/DD/YYYY
Query sample_description String 3,500 Required Sample description: tissue type, i.e. blood, saliva, brain etc. whole blood; saliva; brain; urine; serum; plasma; CSF; IPS; Fibroblast; Neuronal Progenitor; skin biopsy; temporal cortex; lymphoblastoid cell line; unknown; semen; frontal cortex; parietal cortex; basal ganglia; Placenta; hair; occipital visual cortex; cerebellum; spleen; stool; muscle; kidney; liver; heart; cord blood; nasal swab; DNA; RNA; breastmilk; buccal; oral cells; rectal swab; cervicovaginal swab genom_sample_description
sample_id_original String 100 Required Original, user-defined Sample ID genom_sample_id_original
Query organism String 50 Required Organism genom_organism
Query sample_amount Float Required Sample amount genom_sample_amount
Query sample_unit String 50 Required Measurement unit for Sample genom_sample_unit
data_code String 100 Recommended Comments about experiment details
Query data_file1_type String 300 Required type of data file 1 genom_data_file1_type
data_file1 File 255 Required Data file 1 genom_data_file1
data_file2_type String 100 Recommended data file 2 type/description
data_file2 File 255 Recommended data file 2
data_file3 File 255 Recommended Data file 3
Query data_file3_type String 100 Recommended Data file 3 type
data_file4 File 255 Recommended Data file 4
Query data_file4_type String 100 Recommended Data file 4 type
Query storage_protocol String 255 Required Description of Storage Protocol genom_storage_protocol
Query data_file_location String 50 Required dbGaP; NDAR; NIMH Genetics; AGRE; Sfari; Proteomics DB name genom_data_file_location
Query biorepository String 100 Required Sample provider: i.e. NIMH_Genetics; ATP; Correil genom_biorepository
patient_id_biorepository String 100 Required Biorepository Patient ID genom_patient_id_biorepository
sample_id_biorepository String 100 Required Biorepository Sample ID genom_sample_id_biorepository
cell_id_original String 100 Recommended Original, user-defined cell line ID
cell_id_biorepository String 100 Recommended Biorepository cell line ID
comments_misc String 4,000 Recommended Miscellaneous comments on study, interview, methodology relevant to this form data
Query site String 101 Recommended Site Study Site
Query rat280 Float Recommended Ratio of absorbance at 260nm and 280nm
Query rat230 Float Recommended Ratio of absorbance at 260nm and 230nm
Query gqn Float Recommended genomic DNA quality number
seq_batch Date Recommended Sequencing batch: Date sent to sequencing facility
eventname String 60 Recommended The event name for which the data was collected
sex String 20 Required Sex of subject at birth M;F; O; NR M = Male; F = Female; O=Other; NR = Not reported gender
assay_marker String 255 Recommended Antibody used against histone protein in order to immuno-precipitate the chromatin
flowcell_given_to_core String 255 Recommended Flowcell identifier
flowcell_2 String 255 Recommended CMC_HBCC-specific flowcell identifier
flowcell_name String 255 Recommended flowcell identifier
flowcell_name_2 String 255 Recommended CMC_HBCC-specific flowcell name
flowcell_lane_a String 255 Recommended Flowcell lane
flowcell_lane_b String 255 Recommended Flowcell lane
flowcell_id String 255 Recommended Flowcell identifier multiple flowcells separated by ::
lane_id String 255 Recommended Flowcell lane identifier
array_chip_platform String 255 Recommended Name of genotyping array chip used
array_chip_version String 255 Recommended Version of genotyping array chip used
brain_rin Float Recommended RNA integrity number
rine Float Recommended RIN equivalent (RINe) value for assigning integrity values to RNA
source_tissue String 255 Recommended Brain tissue used to isolate the DNA/RNA i.e. ACC; DLPFC; CER; dACC; STG; Dura; Hippo; Caudate; Olfactory mucosa cells anterior cingulate cortex (ACC); dorsal anterior cingulate cortex (dACC); dorsolateral prefrontal cortex (DLPFC); cerebellum (CER); superior temporal gyrus (STG); Dura mater (Dura); Hippocampus (Hippo); Caudate nucleus (Caudate); Olfactory mucosa cells
sample_prep_batch String 255 Recommended Sample preparation batch OR DNA/RNA Isolation batch OR experimental batch
total_rna_dna Float Recommended Total RNA (micrograms) OR Total DNA (micrograms)
library_prep_batch String 255 Recommended Sequencing library batch
ribozero_batch String 255 Recommended Ribozero treatment batch
sequencing_batch String 255 Recommended Sequencing batch
flowcell_batch String 255 Recommended Multiplex batch
inventory_code String 50 Recommended Paxgene RNA tube inventory code
chipwell_id String 101 Recommended Chipwell barcode
timepoint_label String 50 Recommended Timepoint/visit label
fetal_age Integer Recommended Age of the fetus (i.e., gestational age) in days 0::322
fetal_age_type Integer Recommended Type of gestational age used for fetal_age 1;2 1 = Postovulatory gestational age, defined as days since the last ovulation, expected term of 266 days; 2 = Postmenstrual gestational age, days since the last menstrual period, expected term of 280 days
genotyping_chip_type String 4,000 Recommended Chip type used for genotyping
Data Structure

This page displays the data structure defined for the measure identified in the title and structure short name. The table below displays a list of data elements in this structure (also called variables) and the following information:

  • Element Name: This is the standard element name
  • Data Type: Which type of data this element is, e.g. String, Float, File location.
  • Size: If applicable, the character limit of this element
  • Required: This column displays whether the element is Required for valid submissions, Recommended for valid submissions, Conditional on other elements, or Optional
  • Description: A basic description
  • Value Range: Which values can appear validly in this element (case sensitive for strings)
  • Notes: Expanded description or notes on coding of values
  • Aliases: A list of currently supported Aliases (alternate element names)
  • For valid elements with shared data, on the far left is a Filter button you can use to view a summary of shared data for that element and apply a query filter to your Cart based on selected value ranges

At the top of this page you can also:

  • Use the search bar to filter the elements displayed. This will not filter on the Size of Required columns
  • Download a copy of this definition in CSV format
  • Download a blank CSV submission template prepopulated with the correct structure header rows ready to fill with subject records and upload

Please email the The NDA Help Desk with any questions.

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