Main Content

Biospecimen Entity Field Information

Term Category CDE Required?
consent type Case --- Optional
days to consent Case --- Optional
days to lost to followup Case 6154721 Optional
disease type Case 6161017 Required
index date Case 6154722 Optional
lost to followup Case 6161018 Optional
primary site Case 6161019 Required
biospecimen anatomic site Sample 4742851 Optional
biospecimen laterality Sample 8028966 Optional
catalog reference Sample --- Optional
current weight Sample 5432606 Optional
days to collection Sample 3008340 Optional
days to sample procurement Sample --- Optional
diagnosis pathologically confirmed Sample 15115494 Optional
distance normal to tumor Sample 3088708 Optional
distributor reference Sample --- Optional
freezing method Sample 5432607 Optional
growth rate Sample --- Optional
initial weight Sample 5432605 Optional
intermediate dimension Sample --- Optional
longest dimension Sample 5432602 Optional
method of sample procurement Sample --- Optional
passage count Sample --- Optional
pathology report uuid Sample --- Optional
preservation method Sample 5432521 Required
sample ordinal Sample --- Optional
sample type Sample 3111302 Optional
shortest dimension Sample 5432603 Optional
specimen type Sample C70713 Required
time between clamping and freezing Sample 5432611 Optional
time between excision and freezing Sample 5432612 Optional
tissue collection type Sample --- Optional
tissue type Sample 5432687 Required
tumor code id Sample --- Optional
tumor descriptor Sample 3288124 Required
creation datetime Portion 5432592 Optional
is ffpe Portion 4170557 Optional
portion number Portion 5432711 Optional
weight Portion 5432593 Optional
a260 a280 ratio Analyte 15113234 Optional
amount Analyte --- Optional
analyte quantity Analyte --- Optional
analyte type Analyte 15063661 Required
analyte volume Analyte 15248383 Optional
concentration Analyte 5432594 Optional
dna integrity number Analyte C183240 Optional
experimental protocol type Analyte --- Optional
normal tumor genotype snp match Analyte 4588156 Optional
ribosomal rna 28s 16s ratio Analyte --- Optional
ribosomal rna 28s 18s ratio Analyte --- Optional
rna integrity number Analyte C63637 Optional
spectrophotometer method Analyte 3008378 Optional
well number Analyte 5432613 Optional
aliquot quantity Aliquot 15745091 Optional
aliquot volume Aliquot 15745088 Optional
amount Aliquot --- Optional
analyte type Aliquot 15063661 Optional
concentration Aliquot 5432594 Optional
no matched normal low pass wgs Aliquot --- Optional
no matched normal targeted sequencing Aliquot --- Optional
no matched normal wgs Aliquot --- Optional
no matched normal wxs Aliquot --- Optional
selected normal low pass wgs Aliquot --- Optional
selected normal targeted sequencing Aliquot --- Optional
selected normal wgs Aliquot --- Optional
selected normal wxs Aliquot --- Optional
source center Aliquot --- Optional
adapter name Read group --- Optional
adapter sequence Read group --- Optional
base caller name Read group --- Optional
base caller version Read group --- Optional
chipseq antibody Read group --- Optional
chipseq target Read group --- Optional
days to sequencing Read group --- Optional
experiment name Read group --- Required
flow cell barcode Read group --- Optional
fragment maximum length Read group --- Optional
fragment mean length Read group --- Optional
fragment minimum length Read group --- Optional
fragment standard deviation length Read group --- Optional
fragmentation enzyme Read group --- Optional
includes spike ins Read group --- Optional
instrument model Read group 5432604 Optional
is paired end Read group --- Required
lane number Read group --- Optional
library name Read group --- Required
library preparation kit catalog number Read group --- Optional
library preparation kit name Read group --- Optional
library preparation kit vendor Read group --- Optional
library preparation kit version Read group --- Optional
library selection Read group --- Required
library strand Read group --- Optional
library strategy Read group --- Required
multiplex barcode Read group --- Optional
number expect cells Read group --- Optional
platform Read group --- Required
read group name Read group --- Required
read length Read group --- Required
rin Read group 5278775 Optional
sequencing center Read group --- Required
sequencing date Read group --- Optional
single cell library Read group --- Optional
size selection range Read group --- Optional
spike ins concentration Read group --- Optional
spike ins fasta Read group --- Optional
target capture kit Read group --- Required
target capture kit catalog number Read group --- Optional
target capture kit name Read group --- Optional
target capture kit target region Read group --- Optional
target capture kit vendor Read group --- Optional
target capture kit version Read group --- Optional
to trim adapter sequence Read group --- Optional
bone marrow malignant cells Slide --- Optional
number proliferating cells Slide 5432636 Optional
percent eosinophil infiltration Slide 2897700 Optional
percent follicular component Slide --- Optional
percent granulocyte infiltration Slide 2897705 Optional
percent inflam infiltration Slide 2897695 Optional
percent lymphocyte infiltration Slide 2897710 Optional
percent monocyte infiltration Slide 5455535 Optional
percent necrosis Slide 2841237 Optional
percent neutrophil infiltration Slide 2841267 Optional
percent normal cells Slide 2841233 Optional
percent rhabdoid features Slide 6790120 Optional
percent sarcomatoid features Slide 2429786 Optional
percent stromal cells Slide 2841241 Optional
percent tumor cells Slide 5432686 Optional
percent tumor nuclei Slide 2841225 Optional
prostatic chips positive count Slide --- Optional
prostatic chips total count Slide --- Optional
prostatic involvement percent Slide --- Optional
section location Slide --- Required
tissue microarray coordinates Slide --- Optional