Sample Attributes Data Dictionary

VARNAME VARDESC
EXTERNAL ONTOLOGY USED
SAMPLE_ID De-identified Sample Identifier  
ANALYTE_TYPE Analyte type (this is "RNA" for all our samples)  
IS_TUMOR Is Tumor present ?  
BIOPSY_ID Identifier to indicate the samples collected from the same biopsy  
SLICE_ID Identifier to indicate the samples collected from the same slice of the biopsy  
BODY_SITE Body site where where the biopsy was taken from  
FMAID Foundational Model of Anatomy Identifier for the body site where the biopsy is taken from Foundational Model of Anatomy
SURGEON Randomly assigned code for the surgeon who performed the biopsy  
SURGERY_YEAR Year of surgery  
BIOPSY_COMMENTS Additional comments (if any) from the surgeon who performed out the biopsy  
MULTI_LANES? Is the sample sequenced using multiple lanes of the sequencer ?  
MULTI_FLOWCELLS? Is the sample sequenced using multiple flowcells ?  
RNASEQ_GRP Identifier that groups the samples that were sequenced on the same flowcell  
SEQ_CENTER Sequencing center  
SEQUENCING_PLATFORM Sequencing platform  
HIGH_THROUGHPUT_SEQUENCER High throughput sequencer machine used for the sequencing
Experimental Factor Ontology
READ_LENGTH Read length of sequencing  
IS_PAIRED? Paired-end sequencing ?  
DEMULTIPLEXER Demultiplexer used  
SEQUENCING_DATE Sequencing date  
OPERATOR Randomly assigned code for the person who operated the sequencer  
RNASEQ_COMMENTS Additional comments (if any) on the sequencing of the sample  
C1_EXP_ID Identifier to group samples that were collected using the same Fluidigm C1 experiment (if applicable)  
C1_SAMPLE_LOAD Fresh/Frozen nuclei loaded on the Fluidigm C1 chip  
C1_CHIP Fluidigm C1 Chip information  
C1_ADDITIONAL_REAGENTS_ADDED
Additional reagents added besides the standard ones  
PROTOCOL_A_NAME Protocol A Name  
PROTOCOL_A_FILENAME Protocol A Filename  
PROTOCOL_B_NAME Protocol B Name (If applicable)  
PROTOCOL_B_FILENAME Protocol B Filename (If applicable)  
PROTOCOL_C_NAME Protocol C Name (If applicable)  
PROTOCOL_C_FILENAME Protocol C Filename (If applicable)  
HARVEST_METHOD Method used for harvesting the cells  
SAMPLE_HARVEST_BY Randomly assigned code for the person who harvested the cells  
SAMPLE_HARVEST_DATE Harvest date  
cDNA_BY Randomly assigned code for the person who prepared the cDNA  
cDNA_DATE cDNA preparation date  
LIBRARY_BY Randomly assigned code for the person who prepared the library for sequencing  
LIBRARY_DATE Library date  
HISTOLOGICAL TYPE Specifies the cell class. For instance neuron, cardiomyocyte, brown adipose tissue etc.  
CELL_SUBCLASS Specifies the cell sub-class. For instance: pyramidal, 5-HT, interneuron etc.  
SOURCE_TYPE What is the source of the cell. For instance "biopsy"  
SOURCE_UNIT Unit of source from where the sample material comes from. For instance "single cell".  
SOURCE_REGION Region of cell from where the input comes from. For instance "whole cell", "dendrite", "soma" etc.  
TREATMENT Any special treatment that the cell went through - such as TIVA  
HARVEST_QUANT Amount of RNA harvested  
INPUT_AMOUNT Input amount of RNA that goes in to library preparation  
BARCODE Unique sequence that is part of the Illumina barcode  
NUMBER_aRNA_AMPLIFICATION_ROUNDS Number of aRNA amplification rounds  
NUM_PCR_CYCLES_cDNA Number of PCR cycles used for cDNA preparation  
NUM_PCR_CYCLES_NEXTERA Number of PCR cycles used for Nextera (where applicable)  
IS_polyA_SELECTED Does the RNA go through poly(A) selection ?  
RIBOSOMAL_DEPLETION_KIT Ribosomal depletion kit used (if any)  
ADDITIONAL_SAMPLE_COMMENTS
Additional sample comments (if any)  
SPIKE_IN_TYPE
SpikeIn Type (if it is used)  
SPIKE_IN_DILUTION
SpikeIn Dilution (if it is used)