Englisch

This sample attributes table includes body site where sample was extracted, analyte type, histological type, tumor status, genotyping and sequencing centers, manufacturer and kit information (n=7 variables; laser capture, RNA measurement, ribosomal depletion, library prep, and sequencing platform), RNA total, concentration, volume, and mass, sequencing chemistry and read length.

5 Formulare  
pht003424
Beschreibung

pht003424

Alias
UMLS CUI [1,1]
C3846158
De-identified Sample ID
Beschreibung

SAMPLE_ID

Datentyp

string

Alias
UMLS CUI [1,1]
C4684638
UMLS CUI [1,2]
C1299222
Body site where sample was collected
Beschreibung

BODY_SITE

Datentyp

string

Alias
UMLS CUI [1,1]
C0449705
Analyte Type
Beschreibung

ANALYTE_TYPE

Datentyp

string

Alias
UMLS CUI [1,1]
C4744818
Tumor status
Beschreibung

IS_TUMOR

Datentyp

text

Alias
UMLS CUI [1,1]
C0475752
Cell or tissue type or subtype of sample
Beschreibung

HISTOLOGICAL_TYPE

Datentyp

string

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0007634
UMLS CUI [1,3]
C0332307
UMLS CUI [2,1]
C2347026
UMLS CUI [2,2]
C0007634
UMLS CUI [2,3]
C0449560
UMLS CUI [3,1]
C1292533
UMLS CUI [3,2]
C0332307
UMLS CUI [4,1]
C1292533
UMLS CUI [4,2]
C0449560
Name of the center which conducted genotyping
Beschreibung

GENOTYPING_CENTER

Datentyp

text

Alias
UMLS CUI [1,1]
C0683939
UMLS CUI [1,2]
C1285573
Laser Capture Microdissection manufacturer and system
Beschreibung

LCM_PLATFORM

Datentyp

string

Alias
UMLS CUI [1,1]
C1113652
UMLS CUI [1,2]
C0947322
UMLS CUI [1,3]
C0449913
Kit utilized to extract RNA from the mircodissected cells
Beschreibung

RNA_EXTRACTION_KIT

Datentyp

string

Alias
UMLS CUI [1,1]
C3688883
UMLS CUI [1,2]
C0042153
UMLS CUI [1,3]
C3839010
UMLS CUI [1,4]
C0598304
UMLS CUI [1,5]
C0007634
Manufacturer and product name
Beschreibung

RNA_MEASUREMENT_DEVICE

Datentyp

string

Alias
UMLS CUI [1,1]
C0947322
UMLS CUI [1,2]
C2708250
Kit utilized for the quantitation of RNA
Beschreibung

RNA_MEASUREMENT_KIT

Datentyp

string

Alias
UMLS CUI [1,1]
C0812225
UMLS CUI [1,2]
C0042153
UMLS CUI [1,3]
C0920624
UMLS CUI [1,4]
C0035668
Total amount of RNA extracted from all microdissected cells
Beschreibung

TOTAL_RNA_FROM_LCM

Datentyp

float

Maßeinheiten
  • micrograms
Alias
UMLS CUI [1,1]
C0439810
UMLS CUI [1,2]
C1264637
UMLS CUI [1,3]
C0035668
UMLS CUI [1,4]
C0185115
UMLS CUI [1,5]
C0598304
UMLS CUI [1,6]
C0007634
micrograms
RNA concentration following extraction
Beschreibung

RNA_CONCENTRATION

Datentyp

float

Maßeinheiten
  • micrograms/microliter
Alias
UMLS CUI [1,1]
C1446561
UMLS CUI [1,2]
C0035668
UMLS CUI [1,3]
C0231290
UMLS CUI [1,4]
C0185115
micrograms/microliter
Amount of RNA solution used for sequencing
Beschreibung

RNA_VOLUME_USED_FOR_RNA-Seq

Datentyp

float

Maßeinheiten
  • microliters
Alias
UMLS CUI [1,1]
C1264637
UMLS CUI [1,2]
C0035668
UMLS CUI [1,3]
C0037633
UMLS CUI [1,4]
C0042153
UMLS CUI [1,5]
C1561491
microliters
Amount of RNA used for sequencing
Beschreibung

RNA_MASS_USED_FOR_RNA-Seq

Datentyp

float

Maßeinheiten
  • micrograms
Alias
UMLS CUI [1,1]
C1264637
UMLS CUI [1,2]
C0035668
UMLS CUI [1,3]
C0042153
UMLS CUI [1,4]
C1561491
micrograms
Kit utilized to deplete 5S, 5.8S, 18S and 28S ribosomal RNA from total RNA
Beschreibung

RIBOSOMAL_DEPLETION

Datentyp

string

Alias
UMLS CUI [1,1]
C0812225
UMLS CUI [1,2]
C0042153
UMLS CUI [1,3]
C0333668
UMLS CUI [1,4]
C0035707
UMLS CUI [1,5]
C0035706
UMLS CUI [1,6]
C0035703
UMLS CUI [1,7]
C0035705
UMLS CUI [1,8]
C5235881
Kit used to convert full set of RNA transcripts into a cDNA library
Beschreibung

LIBRARY_PREP

Datentyp

string

Alias
UMLS CUI [1,1]
C0812225
UMLS CUI [1,2]
C0042153
UMLS CUI [1,3]
C0439836
UMLS CUI [1,4]
C0035668
UMLS CUI [1,5]
C1519595
UMLS CUI [1,6]
C0751608
Manufacturer and technology version
Beschreibung

SEQUENCING_PLATFORM

Datentyp

string

Alias
UMLS CUI [1,1]
C0947322
UMLS CUI [1,2]
C0039421
UMLS CUI [1,3]
C0333052
RNA-Seq sequences the transcriptome
Beschreibung

SEQUENCING_CHEMISTRY

Datentyp

string

Alias
UMLS CUI [1,1]
C4760607
UMLS CUI [1,2]
C4086963
Length of fragment sequenced
Beschreibung

READ_LENGTH

Datentyp

text

Alias
UMLS CUI [1,1]
C1444754
UMLS CUI [1,2]
C1708096
UMLS CUI [1,3]
C1561491
Name of the center which conducted sequencing
Beschreibung

SEQUENCING_CENTER

Datentyp

string

Alias
UMLS CUI [1,1]
C0683939
UMLS CUI [1,2]
C1561491
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Ähnliche Modelle

This sample attributes table includes body site where sample was extracted, analyte type, histological type, tumor status, genotyping and sequencing centers, manufacturer and kit information (n=7 variables; laser capture, RNA measurement, ribosomal depletion, library prep, and sequencing platform), RNA total, concentration, volume, and mass, sequencing chemistry and read length.

5 Formulare
Name
Typ
Description | Question | Decode (Coded Value)
Datentyp
Alias
Item Group
pht003424
C3846158 (UMLS CUI [1,1])
SAMPLE_ID
Item
De-identified Sample ID
string
C4684638 (UMLS CUI [1,1])
C1299222 (UMLS CUI [1,2])
BODY_SITE
Item
Body site where sample was collected
string
C0449705 (UMLS CUI [1,1])
ANALYTE_TYPE
Item
Analyte Type
string
C4744818 (UMLS CUI [1,1])
Item
Tumor status
text
C0475752 (UMLS CUI [1,1])
IS_TUMOR
Code List
Tumor status
CL Item
Is not a tumor (N)
CL Item
Is Tumor (Y)
HISTOLOGICAL_TYPE
Item
Cell or tissue type or subtype of sample
string
C2347026 (UMLS CUI [1,1])
C0007634 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C2347026 (UMLS CUI [2,1])
C0007634 (UMLS CUI [2,2])
C0449560 (UMLS CUI [2,3])
C1292533 (UMLS CUI [3,1])
C0332307 (UMLS CUI [3,2])
C1292533 (UMLS CUI [4,1])
C0449560 (UMLS CUI [4,2])
Item
Name of the center which conducted genotyping
text
C0683939 (UMLS CUI [1,1])
C1285573 (UMLS CUI [1,2])
GENOTYPING_CENTER
Code List
Name of the center which conducted genotyping
CL Item
Not applicable (NA)
C1272460 (UMLS CUI [1,1])
LCM_PLATFORM
Item
Laser Capture Microdissection manufacturer and system
string
C1113652 (UMLS CUI [1,1])
C0947322 (UMLS CUI [1,2])
C0449913 (UMLS CUI [1,3])
RNA_EXTRACTION_KIT
Item
Kit utilized to extract RNA from the mircodissected cells
string
C3688883 (UMLS CUI [1,1])
C0042153 (UMLS CUI [1,2])
C3839010 (UMLS CUI [1,3])
C0598304 (UMLS CUI [1,4])
C0007634 (UMLS CUI [1,5])
RNA_MEASUREMENT_DEVICE
Item
Manufacturer and product name
string
C0947322 (UMLS CUI [1,1])
C2708250 (UMLS CUI [1,2])
RNA_MEASUREMENT_KIT
Item
Kit utilized for the quantitation of RNA
string
C0812225 (UMLS CUI [1,1])
C0042153 (UMLS CUI [1,2])
C0920624 (UMLS CUI [1,3])
C0035668 (UMLS CUI [1,4])
TOTAL_RNA_FROM_LCM
Item
Total amount of RNA extracted from all microdissected cells
float
C0439810 (UMLS CUI [1,1])
C1264637 (UMLS CUI [1,2])
C0035668 (UMLS CUI [1,3])
C0185115 (UMLS CUI [1,4])
C0598304 (UMLS CUI [1,5])
C0007634 (UMLS CUI [1,6])
RNA_CONCENTRATION
Item
RNA concentration following extraction
float
C1446561 (UMLS CUI [1,1])
C0035668 (UMLS CUI [1,2])
C0231290 (UMLS CUI [1,3])
C0185115 (UMLS CUI [1,4])
RNA_VOLUME_USED_FOR_RNA-Seq
Item
Amount of RNA solution used for sequencing
float
C1264637 (UMLS CUI [1,1])
C0035668 (UMLS CUI [1,2])
C0037633 (UMLS CUI [1,3])
C0042153 (UMLS CUI [1,4])
C1561491 (UMLS CUI [1,5])
RNA_MASS_USED_FOR_RNA-Seq
Item
Amount of RNA used for sequencing
float
C1264637 (UMLS CUI [1,1])
C0035668 (UMLS CUI [1,2])
C0042153 (UMLS CUI [1,3])
C1561491 (UMLS CUI [1,4])
RIBOSOMAL_DEPLETION
Item
Kit utilized to deplete 5S, 5.8S, 18S and 28S ribosomal RNA from total RNA
string
C0812225 (UMLS CUI [1,1])
C0042153 (UMLS CUI [1,2])
C0333668 (UMLS CUI [1,3])
C0035707 (UMLS CUI [1,4])
C0035706 (UMLS CUI [1,5])
C0035703 (UMLS CUI [1,6])
C0035705 (UMLS CUI [1,7])
C5235881 (UMLS CUI [1,8])
LIBRARY_PREP
Item
Kit used to convert full set of RNA transcripts into a cDNA library
string
C0812225 (UMLS CUI [1,1])
C0042153 (UMLS CUI [1,2])
C0439836 (UMLS CUI [1,3])
C0035668 (UMLS CUI [1,4])
C1519595 (UMLS CUI [1,5])
C0751608 (UMLS CUI [1,6])
SEQUENCING_PLATFORM
Item
Manufacturer and technology version
string
C0947322 (UMLS CUI [1,1])
C0039421 (UMLS CUI [1,2])
C0333052 (UMLS CUI [1,3])
SEQUENCING_CHEMISTRY
Item
RNA-Seq sequences the transcriptome
string
C4760607 (UMLS CUI [1,1])
C4086963 (UMLS CUI [1,2])
READ_LENGTH
Item
Length of fragment sequenced
text
C1444754 (UMLS CUI [1,1])
C1708096 (UMLS CUI [1,2])
C1561491 (UMLS CUI [1,3])
SEQUENCING_CENTER
Item
Name of the center which conducted sequencing
string
C0683939 (UMLS CUI [1,1])
C1561491 (UMLS CUI [1,2])
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