English

This sample attributes table contains sample IDs, subject IDs, histological type, IPS (Induced Pluripotent Stem Cell ) passage number, sample source, sequencing information (n=9 variables: analyte type, RNA integrity number, library prep kit, fragment size, sequencing type, strand, sequencing cycle number, sequencing platform, sequencing center which conducted sequencing), tumor status, days cells were differentiated into motor neurons, protocol, and cell markers .

5 forms  
pht006182
Description

pht006182

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

SAMPLE_ID

Data type

string

Alias
UMLS CUI [1,1]
C4684638
UMLS CUI [1,2]
C1299222
Subject ID
Description

SUBJECT_ID

Data type

text

Alias
UMLS CUI [1,1]
C2348585
Cell type samples were made from
Description

HISTOLOGICAL_TYPE

Data type

text

Alias
UMLS CUI [1,1]
C0449475
UMLS CUI [1,2]
C0370003
Induced Pluripotent Stem Cell line Passage number used for assay
Description

IPS_PASSAGE_NUMBER

Data type

text

Alias
UMLS CUI [1,1]
C2717959
UMLS CUI [1,2]
C0007600
UMLS CUI [1,3]
C5236382
UMLS CUI [1,4]
C1510438
How many days cells were differentiated into motor neurons
Description

IMN_DAYS_DIFFERENTIATION

Data type

text

Alias
UMLS CUI [1,1]
C1265611
UMLS CUI [1,2]
C0439228
UMLS CUI [1,3]
C0007634
UMLS CUI [1,4]
C2945687
UMLS CUI [1,5]
C0026609
Protocol used by Cedars-Sinai Stem Cell Core Facility
Description

PROTOCOL

Data type

string

Alias
UMLS CUI [1,1]
C2348563
UMLS CUI [1,2]
C1273517
UMLS CUI [1,3]
C1547538
Antibody markers used to classify induced Pluripotent Stem Cell lines or motor neuron cell lines
Description

CELL_MARKERS

Data type

text

Alias
UMLS CUI [1,1]
C0003241
UMLS CUI [1,2]
C0005516
UMLS CUI [1,3]
C0008902
UMLS CUI [1,4]
C2717959
UMLS CUI [1,5]
C0007600
UMLS CUI [2,1]
C0003241
UMLS CUI [2,2]
C0005516
UMLS CUI [2,3]
C0008902
UMLS CUI [2,4]
C0026609
UMLS CUI [2,5]
C0007600
Source Institution where samples originated
Description

SAMPLE_SOURCE

Data type

string

Alias
UMLS CUI [1,1]
C0449416
UMLS CUI [1,2]
C1301943
UMLS CUI [1,3]
C0370003
The analyte type of the sample (ex. DNA and RNA)
Description

ANALYTE_TYPE

Data type

string

Alias
UMLS CUI [1,1]
C0370003
UMLS CUI [1,2]
C4744818
RNA integrity number
Description

RIN_VALUE

Data type

text

Alias
UMLS CUI [1,1]
C0035668
UMLS CUI [1,2]
C1947912
UMLS CUI [1,3]
C0237753
Kit used to prepare the library for sequencing
Description

LIBRARY_PREP_KIT

Data type

string

Alias
UMLS CUI [1,1]
C2981406
UMLS CUI [1,2]
C1521827
UMLS CUI [1,3]
C0023621
UMLS CUI [1,4]
C1561491
The size of the actual fragments submitted for sequencing after library size-selection.
Description

FRAGMENT_SIZE

Data type

text

Measurement units
  • base pairs (bp)
Alias
UMLS CUI [1,1]
C0456389
UMLS CUI [1,2]
C1708096
UMLS CUI [1,3]
C1515023
UMLS CUI [1,4]
C1561491
UMLS CUI [1,5]
C0023621
UMLS CUI [1,6]
C4727200
base pairs (bp)
Defines the sequencing strategy. Paired-end sequences inserts in both directions, single-end sequences from one direction
Description

SEQ_TYPE

Data type

text

Alias
UMLS CUI [1,1]
C0679199
UMLS CUI [1,2]
C1561491
UMLS CUI [2,1]
C4725720
UMLS CUI [3,1]
C0205171
UMLS CUI [3,2]
C0444930
UMLS CUI [3,3]
C1561491
Defines if a particular strand is sequenced
Description

STRAND

Data type

text

Alias
UMLS CUI [1,1]
C1561491
UMLS CUI [1,2]
C5239603
UMLS CUI [1,3]
C1704973
Number of sequencing cycles used
Description

SEQ_CYCLE_NUMBER

Data type

string

Alias
UMLS CUI [1,1]
C1265611
UMLS CUI [1,2]
C1294197
UMLS CUI [1,3]
C1511572
Company and instrument model used for sequencing
Description

SEQ_PLATFORM

Data type

string

Alias
UMLS CUI [1,1]
C0683757
UMLS CUI [1,2]
C0348000
UMLS CUI [1,3]
C1561491
Name of the center which conducted sequencing
Description

SEQUENCING_CENTER

Data type

text

Alias
UMLS CUI [1,1]
C1301943
UMLS CUI [1,2]
C0565990
UMLS CUI [1,3]
C1561491
The tumor status of the sample
Description

IS_TUMOR

Data type

string

Alias
UMLS CUI [1,1]
C0475752
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Similar models

This sample attributes table contains sample IDs, subject IDs, histological type, IPS (Induced Pluripotent Stem Cell ) passage number, sample source, sequencing information (n=9 variables: analyte type, RNA integrity number, library prep kit, fragment size, sequencing type, strand, sequencing cycle number, sequencing platform, sequencing center which conducted sequencing), tumor status, days cells were differentiated into motor neurons, protocol, and cell markers .

5 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
pht006182
C3846158 (UMLS CUI [1,1])
SAMPLE_ID
Item
De-identified Sample ID
string
C4684638 (UMLS CUI [1,1])
C1299222 (UMLS CUI [1,2])
SUBJECT_ID
Item
Subject ID
text
C2348585 (UMLS CUI [1,1])
Item
Cell type samples were made from
text
C0449475 (UMLS CUI [1,1])
C0370003 (UMLS CUI [1,2])
HISTOLOGICAL_TYPE
Code List
Cell type samples were made from
CL Item
induced Pluripotent Stem Cell (iPSC)
IPS_PASSAGE_NUMBER
Item
Induced Pluripotent Stem Cell line Passage number used for assay
text
C2717959 (UMLS CUI [1,1])
C0007600 (UMLS CUI [1,2])
C5236382 (UMLS CUI [1,3])
C1510438 (UMLS CUI [1,4])
Item
How many days cells were differentiated into motor neurons
text
C1265611 (UMLS CUI [1,1])
C0439228 (UMLS CUI [1,2])
C0007634 (UMLS CUI [1,3])
C2945687 (UMLS CUI [1,4])
C0026609 (UMLS CUI [1,5])
IMN_DAYS_DIFFERENTIATION
Code List
How many days cells were differentiated into motor neurons
CL Item
motor neurons gnerated from induced pluripotent stem cells (iMN)
PROTOCOL
Item
Protocol used by Cedars-Sinai Stem Cell Core Facility
string
C2348563 (UMLS CUI [1,1])
C1273517 (UMLS CUI [1,2])
C1547538 (UMLS CUI [1,3])
Item
Antibody markers used to classify induced Pluripotent Stem Cell lines or motor neuron cell lines
text
C0003241 (UMLS CUI [1,1])
C0005516 (UMLS CUI [1,2])
C0008902 (UMLS CUI [1,3])
C2717959 (UMLS CUI [1,4])
C0007600 (UMLS CUI [1,5])
C0003241 (UMLS CUI [2,1])
C0005516 (UMLS CUI [2,2])
C0008902 (UMLS CUI [2,3])
C0026609 (UMLS CUI [2,4])
C0007600 (UMLS CUI [2,5])
CELL_MARKERS
Code List
Antibody markers used to classify induced Pluripotent Stem Cell lines or motor neuron cell lines
CL Item
Alkaline Phosphatase (A)
CL Item
ISL1 (ISL1)
CL Item
KLF4 (K)
CL Item
Lin28 (L)
CL Item
Nanog (N)
CL Item
NKX6-2 (NKX62)
CL Item
Oct4 (O)
CL Item
Sox2 (S)
CL Item
SMI-32 (SMI32)
CL Item
SSEA4 (SS)
CL Item
Tra-1-60 (T60)
CL Item
Tra-1-81 (T81)
CL Item
TuJ-1 (TUJ1)
SAMPLE_SOURCE
Item
Source Institution where samples originated
string
C0449416 (UMLS CUI [1,1])
C1301943 (UMLS CUI [1,2])
C0370003 (UMLS CUI [1,3])
ANALYTE_TYPE
Item
The analyte type of the sample (ex. DNA and RNA)
string
C0370003 (UMLS CUI [1,1])
C4744818 (UMLS CUI [1,2])
Item
RNA integrity number
text
C0035668 (UMLS CUI [1,1])
C1947912 (UMLS CUI [1,2])
C0237753 (UMLS CUI [1,3])
RIN_VALUE
Code List
RNA integrity number
CL Item
Not applicable (NA)
C1272460 (UMLS CUI [1,1])
LIBRARY_PREP_KIT
Item
Kit used to prepare the library for sequencing
string
C2981406 (UMLS CUI [1,1])
C1521827 (UMLS CUI [1,2])
C0023621 (UMLS CUI [1,3])
C1561491 (UMLS CUI [1,4])
FRAGMENT_SIZE
Item
The size of the actual fragments submitted for sequencing after library size-selection.
text
C0456389 (UMLS CUI [1,1])
C1708096 (UMLS CUI [1,2])
C1515023 (UMLS CUI [1,3])
C1561491 (UMLS CUI [1,4])
C0023621 (UMLS CUI [1,5])
C4727200 (UMLS CUI [1,6])
Item
Defines the sequencing strategy. Paired-end sequences inserts in both directions, single-end sequences from one direction
text
C0679199 (UMLS CUI [1,1])
C1561491 (UMLS CUI [1,2])
C4725720 (UMLS CUI [2,1])
C0205171 (UMLS CUI [3,1])
C0444930 (UMLS CUI [3,2])
C1561491 (UMLS CUI [3,3])
SEQ_TYPE
Code List
Defines the sequencing strategy. Paired-end sequences inserts in both directions, single-end sequences from one direction
CL Item
Paired-End (PE)
CL Item
Single-End (SE)
Item
Defines if a particular strand is sequenced
text
C1561491 (UMLS CUI [1,1])
C5239603 (UMLS CUI [1,2])
C1704973 (UMLS CUI [1,3])
STRAND
Code List
Defines if a particular strand is sequenced
CL Item
Not applicable (NA)
C1272460 (UMLS CUI [1,1])
CL Item
nonstranded (NS)
CL Item
Stranded (S)
SEQ_CYCLE_NUMBER
Item
Number of sequencing cycles used
string
C1265611 (UMLS CUI [1,1])
C1294197 (UMLS CUI [1,2])
C1511572 (UMLS CUI [1,3])
SEQ_PLATFORM
Item
Company and instrument model used for sequencing
string
C0683757 (UMLS CUI [1,1])
C0348000 (UMLS CUI [1,2])
C1561491 (UMLS CUI [1,3])
Item
Name of the center which conducted sequencing
text
C1301943 (UMLS CUI [1,1])
C0565990 (UMLS CUI [1,2])
C1561491 (UMLS CUI [1,3])
SEQUENCING_CENTER
Code List
Name of the center which conducted sequencing
CL Item
UCI Genomics High-Throughput Facility (UCI GHTF)
IS_TUMOR
Item
The tumor status of the sample
string
C0475752 (UMLS CUI [1,1])
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