For some TARGET cases, additional clinical data are missing, and OCG is currently working with the GDC to populate those fields. Some “Recurrent Blood Derived Cancer-Bone Marrow” samples are currently incorrectly identified and users should identify these samples as sample_type_id of “04” in both the aliquot barcode and in the GDC’s sample.sample_type_id field.
TARGET Project Experimental Methods
On this page researchers can find detailed information describing how TARGET data was generated by genomic platform, including protocols for establishing high-quality nucleic acid samples.
*Note to users: Protocols are currently being added to this site, as a large portion of the data and metadata were recently released onto the TARGET Data Matrix. Please continue to check back in the coming weeks as updates are completed, and contact firstname.lastname@example.org with any questions.
TARGET Sample Naming
TARGET samples are named using a coding system specific to OCG characterization programs. Please use the OCG Sample Codes document to properly discern the metadata reiterated within the sample name. OCG-Project-Codes_Tissues-and-Samples_03-02-2021.pdf
Nucleic Acid Sample Processing
TARGET project teams use high-quality RNA and DNA from case-matched tumor and normal tissues to generate comprehensive genomics data. Below is a table outlining how each project team generated those samples.
|Column One||Sample Preparation Protocols|
|DNA/RNA Co-isolation with Qiagen AllPrep Kit (DNA/RNA) and mirVana (Total & Small RNAs)||AML , AML-IF , CCSK , RT , WT , OS , NBL (after 2013)|
|DNA Isolation with Qiagen QIAamp DNA Minikit||ALL P1 , ALL P2 , ALL MDLS|
|DNA Isolation with Qiagen Genomic-Tips||NBL (prior to 2013) , WT|
|RNA Isolation with Invitrogen TRIzol||ALL P1 , ALL P2 , ALL MDLS|
|RNA Isolation with Invitrogen TRIzol and Qiagen RNAeasy||NBL (prior to 2013)|