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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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Filter Cart

Viewable at the top right of NDA pages, the Filter Cart is a temporary holder for filters and data they select. Filters are added to the Workspace first, before being submitted to The Filter Cart. Data selected by filters in the Filter Cart can be added to a Data Package or an NDA Study from the Data Packaging Page, by clicking the 'Create Data Package / Add Data to Study' button.

The filter cart supports combining multiple filters together, and depending on filter type will use "AND" or "OR" when combining filters.

Multiple selections from the same filter type will result in those selections being applied with an ‘OR’ condition. For example, if you add an NDA Collection Filter with selections for both collections 2112 and 2563 to an empty Workspace, the subjects from NDA Collection 2112 ‘OR’ NDA Collection 2563 will be added to your Workspace even if a subject is in both NDA Collections. You can then add other NDA Collections to your Workspace which further extends the ‘OR’ condition.

If a different filter type is added to your Workspace, or a filter has already been submitted to the Filter Cart, the operation then performs a logical ‘AND’ operation. This means that given the subjects returned from the first filter, only those subjects that matched the first filter are returned by the second filter (i.e., subjects that satisfied both filters).

When combining other filters with the GUID filter, please note the GUID filter should be added last. Otherwise, preselected data may be lost. For example, a predefined filter from Featured Datasets may select a subset of data available for a subject. When combined with a GUID filter for the same subject, the filter cart will contain all data available from that subject, data structure, and dataset; this may be more data than was selected in the predefined filter for that subject. Again, you should add the GUID Filter as the last filter to your cart. This ensures 'AND' logic between filters and will limit results to the subjects, data structures, and datasets already included in your filter cart.

Note that only the subjects specific to your filter will be added to your Filter Cart and only on data shared with the research community. Other data for those same subjects may exist (i.e., within another NDA Collection, associated with a data structure that was not requested in the query, etc.). So, users should select ‘Find all Subjects Data’ to identify all data for those specific subjects.

Additional Tips:

  • You may query the data without an account, but to gain access you will need to create an NDA user account and apply for access. Most data access requires that you or your lab are sponsored by an NIH recognized institution with Federal Wide Assurance (FWA). Without access, you will not be able to obtain individual-level data.

Once you have selected data of interest you can:

  • Create a data package - This allows you to specify format for access/download
  • Assign to Study Cohort - Associate the data to an NDA Study allowing for a DOI to be generated and the data to be linked directly to a finding, publication, or data release.
  • Find All Subject Data - Depending on filter types being used, not all data associated with a subject will be selected. Data may be restricted by data structure, NDA Collection, or outcome variables (e.g., NDA Study). ‘Find All Data’ expands the filter criteria by replacing all filters in your Filter Cart with a single Query by GUID filter for all subjects selected by those filters.

Please Note:

  • When running a query, it may take a moment to populate the Filter Cart. Queries happen in the background so you can define other queries during this time.
  • When you add your first filter, all data associated with your query will be added to the Filter Cart (e.g., a Concept, an NDA Collection, a Data Structure/Element, etc.). As you add additional filters, they will also display in the Filter Cart. Only the name of filter will be shown in the Filter Cart, not the underlying structures.
  • Information about the contents of the Filter Cart can be seen by clicking "Edit”.
  • Once your results appear in the Filter Cart, you can create a data package or assign subjects to a study by selecting the 'Package/Assign to Study' option. You can also 'Edit' or 'Clear' filters.

Frequently Asked Questions

  • What is a Filter Cart?
    Viewable at the top right of NDA pages, the Filter Cart is a temporary holder of data identified by the user, through querying or browsing, as being of some potential interest. The Filter Cart is where you send the data from your Workspace after it has been filtered.
  • What do I do after filters are added to the Filter Cart?
    After filters are added to the Filter Cart, users have options to ‘Create a Package’ for download, ‘Associate to Study Cohort’, or ‘Find All Subject Data’. Selecting ‘Find All Subject Data’ identifies and pulls all data for the subjects into the Filter Cart. Choosing ‘Create a Package’ allows users to package and name their query information for download. Choosing ‘Associate to Study Cohort’ gives users the opportunity to choose the Study Cohort they wish to associate this data.
  • Are there limitations on the amount of data a user can download?

    NDA limits the rate at which individual users can transfer data out of Amazon Web Services (AWS) S3 Object storage to non-AWS internet addresses. All users have a download limit of 20 Terabytes. This limit applies to the volume of data an individual user can transfer within a 30-day window. Only downloads to non-AWS internet addresses will be counted against the limit.

  • How does Filter Cart Boolean logic work?

    The Filter Cart currently employs basic AND/OR Boolean logic. A single filter may contain multiple selections for that filter type, e.g., a single NDA Study filter might contain NDA Study 1 and NDA Study 2. A subject that is in EITHER 1 OR 2 will be returned. Adding multiple filters to the cart, regardless of type, will AND the result of each filter. If NDA Study 1 and NDA Study 2 are added as individual filters, data for a subject will only be selected if the subject is included in BOTH 1 AND 2.

    When combining other filters with the GUID filter, please note the GUID filter should be added last. Otherwise, preselected data may be lost. For example, a predefined filter from Featured Datasets may select a subset of data available for a subject. When combined with a GUID filter for the same subject, the filter cart will contain all data available from that subject, data structure, and dataset; this may be more data than was selected in the predefined filter for that subject. Again, you should add the GUID Filter as the last filter to your cart. This ensures 'AND' logic between filters and will limit results to the subjects, data structures, and datasets already included in your filter cart.

Glossary

  • Workspace
    The Workspace within the General Query Tool is a holding area where you can review your pending filters prior to adding them to Filter Cart. Therefore, the first step in accessing data is to select one or more items and move it into the Workspace.
  • Filter Cart
    Viewable at the top right of NDA pages, the Filter Cart is a temporary holder of data identified by the user through querying or browsing as being of some potential interest. The Filter Cart adds data using an AND condition. The opportunity to further refine data to determine what will be downloaded or sent to a miNDAR is available on the Data Packaging Page, the next step after the Filter Cart. Subsequent access to data is restricted by User Permission or Privilege; however Filter Cart use is not.
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ChIP Sequencing

0 Shared Subjects

Metadata information about Chromatin immunoprecipitation with sequencing (ChIP-seq) experiment/project. ChIP-seq identifies genome-wide DNA binding sites for transcription factors and other proteins.
Omics
Omics
05/23/2022
chip_seq01
05/26/2022
View Change History
01
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*
src_subject_id String 20 Required Subject ID how it's defined in lab/project
interview_date Date Required Date on which the interview/genetic test/sampling/imaging/biospecimen was completed. MM/DD/YYYY
interview_age Integer Required Age in months at the time of the interview/test/sampling/imaging. 0 :: 1260 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.
sex String 20 Required Sex of subject at birth M;F; O; NR M = Male; F = Female; O=Other; NR = Not reported
experiment_id Integer Required ID for the Experiment/settings/run
cellid String 4,000 Recommended Unique identifier of cells
samplesubtype Integer Recommended Subtype of sample, whether it is cells, nuclei, or bulk 1::3 1=Cell; 2=Nucleus; 3=Bulk
libraryid String 4,000 Recommended Library ID as provided by the lab
gen_software String 4,000 Recommended Name of the software used on sequencing platform
softwareversion String 4,000 Recommended Version number of the software used
referenceset Integer Recommended A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data 1::5; -99 1=1000 Genomes phase 3; 2=GRCh38; 3=GRCh37; 4=MMUL1.0; 5=HRC; -99=Other
otherreferenceset String 4,000 Recommended A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data
librarybatch String 4,000 Recommended Batch library was prepared in
sequencingbatch String 4,000 Recommended Batch library was sequenced in
libraryselection Integer Recommended The general strategy by which the library was prepared 1::37; -88; -99 1=Random; 2=PCR Random PCR; 3=RT-PCR; 4=HMPR; 5=MF; 6=repeat fractionation; 7=size fractionation; 8=MSLL; 9=cDNA; 10=cDNA random priming; 11=cDNA oligo-dT; 12=PolyA; 13=Oligo-dT; 14=Inverse rRNA; 15=ChIP; 16=MNase; 17=DNase; 18=Hybrid selection; 19=Reduced representation; 20=Restriction digest; 21=5-methylcytidine antibody; 22=MBD2 protein methyl-CpG binding domain; 23=CAGE; 24=RACE; 25=MDA; 26=padlock probes capture method; 27=cell hashing; 28=DHA library construction; 29=EndItDNAEndRepairKit; 30=KapaHyperPrep; 31=IncRNAenrichment; 32=MULTIseq; 33=PCR-free; 34=rRNA depletion; 35=SPLITseq; 36=STARRseq; 37=SureCell; -99=Other; -88=Unspecified
libraryconstructionprotocol Integer Recommended Method used to construct the sequence library 1::30; -99 1=SMART-seq; 2=SMART-seq2; 3=SMART-seq3; 4=SMART-seq4; 5=STRT-seq; 6=STRT-seq-C1; 7=STRT-seq-2i; 8=Quartz-seq; 9=Quartz-seq2; 10=CEL-seq; 11=CEL-seq2; 12=10x Chromium Single Cell 3' V3 FeatureBarcoding; 13=10x Chromium Single Cell 3' V2 and V3 GE; 14=10x Chromium Single Cell 3' V1 GE; 15=10x Chromium Single Cell 5' VDJ; 16=10x Chromium Single Cell 5' GE; 17=SureCell 3' WTA for ddSEQ; 18=MARS-seq / MARS-seq2.0; SCRB-seq / mcSCRB-seq; 18=Drop-seq / Seq-Well; 19=scifi-RNA-seq; 20=Microwell-seq; 21=BD Rhapsody; 22=sci-RNA-seq3; 23=sci-RNA-seq; 24=Seq-Well S3; 25=Tang 2009; 26=SPLiT-seq; 27=inDrop; 28=NEBNext; 29=NexteraXT; 30=Omni-ATAC; -99=Other
otherlibraryconstructprotocol String 4,000 Recommended Other type of library construction protocol not listed otherlibraryconstructionprotocol
librarysource Integer Recommended The type of source material that is being sequenced 1; 2; -99 1=Genomic; 2=Genomic single cell; -99=Other
otherlibrarysource String 4,000 Recommended Other library source not listed
readlength Float Recommended The length of the read
librarylayout Integer Recommended If the library is paired-end or single-end 1; 2 1=Single; 2=Paired-end
totalreads Integer Recommended Total number of sequencing reads from a library
numbercells Integer Recommended Number of cells or nuclei sequenced
readstrandorigin Integer Recommended The strand from which the read originates in a strand-specific protocol 1; 2 1=Forward; 2=Reverse
isstranded Integer Recommended Whether or not the library is stranded. 0; 1 0=No; 1=Yes
assaytarget Integer Recommended Target of the assay 1::103; -99 1=ARID1B; 2=ARID3A; 3=ARNT; 4=ASCL1; 5=ASH1L; 6=ASH2L; 7=ATF7; 8=BCL11A; 9=BHLHE40; 10=BHLHE41; 11=BMI1; 12=BRCA1; 13=BRD4; 14=CC2D1A; 15=CHD4; 16=CLOCKCREB1; 17=CREM; 18=CTCF; 19=DEAF1; 20=DPF2; 21=EED; 22=EGR1; 23=EHMT2; 24=E2F1; 25=EWSR1; 26=EZH2; 27=FOXK2; 28=FOXP1GABPB1; 29=GATA4; 30=GATAD2A; 31=GATAD2B; 32=GMEB1; 33=H3K27ac; 34=H3K27me3; 35=H3K36me3; 36=H3K4me1; 37=H3K4me3; 38=H3K9ac; 39=H3K9me3; 40=HCFC1; 41=HNRNPK; 42=IE_V1-V3; 43=Input; 44=KAT2B; 45=KDM4A; 46=KLF16; 47=KLF5; 48=MAZ; 49=MEF2A; 50=MEIS2; 51=MITF; 52=NCOA2; 53=NCOR1; 54=NEUROD1; 55=NFIB; 56=NFIC; 57=NONO; 58=NR2F1; 59=NRF1; 60=NR2F2; 61=NR3C1; 62=OLIG2; 63=PKNOX1; 64=Pol2; 65=RAD21; 66=RB1; 67=RELB; 68=REST; 69=SATB2; 70=SIN3A; 71=SIN3B; 72=SIRT1; 73=SIX4; 74=SKIL; 75=SMARCA5; 76=SMC3; 77=SOX8; 78=P1; 79=SP4; 80=SRF; 81=SREBP2; 82=TAF1; 83=TBR1; 84=TCF12; 85=TCF7L2; 86=TDP43; 87=TRIM28; 88=YBX1; 89=YBX3; 90=YY1; 91=ZBTB7B; 92=ZEB1; 93=ZEB2; 94=ZFP91; 95=ZHX1; 96=ZKSCAN1; 97=ZNF143; 98=ZNF207; 99=ZNF24; 100=ZNF318; 101=ZNF384; 102=ZNF407; 103=ZNF592; -99=Other
otherassaytarget String 4,000 Recommended Other assay target
antibody String 4,000 Recommended Name of the antibody used in the assay
gen_vendor String 4,000 Recommended Commercial or institutional source of a component used in an assay
catalognumber String 4,000 Recommended The identifier assigned to a product, usually in the list of products published by a reseller or manufacturer
lotnumber String 4,000 Recommended A distinctive alpha-numeric identification code assigned by the manufacturer or distributor to a specific quantity of manufactured material or product within a batch
antibodyamount Float Recommended Amount of antibody used for an assay
antibodyamountunits String 4,000 Recommended Units of measure for the amount of antibody used for an assay
chromatinamount Float Recommended Amount of chromatin used for an assay
chromatinamountunits String 4,000 Recommended Units of measure for the amount of chromatin used for an assay
data_file1 File 255 Recommended Data file 1
data_file1_type String 300 Recommended type of data file 1
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.