title: Normal Liver C0575KR1

city: Rehovot

first: Michal

last: Sheffer

address: Herzel

country: Israel

institute: Weizmann Institute of Science

description: Normal Liver C0575KR1 C0575KR1

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: data was summarized using PLIER algorithm

source_name: Tissue samples taken from colorectal cancer patients

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

value: Normal Liver

tag: scan date

tag: patient id

tag: included in analysis

value: No


title: Liver Metastasis C0667UR1

status: Public on Oct 02 2012

type: RNA

description: Liver Metastasis C0667UR1 C0667UR1

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: Liver Metastasis

tag: sample date

tag: age

tag: gender

value: M

tag: t

tag: n

tag: m

tag: group stage

value: IV

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: DOD

tag: fup interval

tag: recurrence

tag: recurrence interval

tag: microsattelite instability

value: MSS

tag: p53 mutation status

value: Wild-type

tag: anatomic location

value: Rectosigmoid


title: WT kidney, rep1

city: Cardiff

first: David

middle: Allan

last: Carter

state: Cardiff

address: Museum Avenue

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

description: Ex-vivo kidney

hyb_protocol: Following fragmentation, 20 µg of cRNA was hybridized for 18h at 45C on an Affymetrix rat RG_U34A GeneChip array. GeneChips were then washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.

data_processing: Data were analysed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Rattus norvegicus

source_name: WT kidney

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1oµg total RNA.

growth_protocol: Pups were kept on a 14:10 light:dark cycle, lights on 05.00h and sampled at 12.00h.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Kidneys were stored at -80C prior to RNA extraction

tag: strain background

value: Sprague-Dawley

tag: genotype/variation

value: wild type

value: 6 days postnatal

value: kidney

tag: sampling time

value: mid-day


title: Normal Colon C0667HR1_ez

description: Normal Colon C0667HR1_ez C0667HR1_ez

tag: tissue

value: Normal Colon

tag: scan date

tag: patient id

tag: included in analysis

value: Yes

tag: sample date


title: Normal Liver C0667KR1

description: Normal Liver C0667KR1 C0667KR1

tag: age

tag: gender

tag: t

tag: n

tag: m


title: Liver Metastasis C0575UR1

description: Liver Metastasis C0575UR1 C0575UR1


title: Normal Colon C0667HR1

description: Normal Colon C0667HR1 C0667HR1

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

tag: fup interval

tag: recurrence

tag: recurrence interval


title: Normal Colon c0487hr3

description: Normal Colon c0487hr3 c0487hr3

value: F

value: I

value: NED

tag: microsattelite instability

value: MSI-high

tag: p53 mutation status

tag: anatomic location

value: Ascending colon


title: Normal Colon C0575HR1

description: Normal Colon C0575HR1 C0575HR1

tag: tissue

tag: scan date


title: Primary Tumor C0667AR1

description: Primary Tumor C0667AR1 C0667AR1

value: Primary Tumor

tag: patient id

tag: included in analysis

value: M

value: IV


title: 4T1 cells harboring the empty pLKO.1puro lentiviral vector, biological rep3, Exp 1

status: Public on Oct 03 2012

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

hyb_protocol: Mouse Gene 1.0 ST arrays (Affymetrix) under standard conditions

scan_protocol: Affymetrix system

data_processing: Upon microarray hybridization, the raw data was normalized, filtered and analyzed with the Bioconductor software (www.bioconductor.com) using the Affy and Siggenes applications.

organism: Mus musculus

source_name: breast cancer cell line

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 μg/sample) to generated labeled cRNA probes according to the manufacturer’s instructions (Affymetrix).

growth_protocol: All cells were incubated at 37ºC with 5% CO2. 4T1 cells were cultured in Roswell Park Memorial Institute (RPMI) media supplemented with 10% fetal calf serum (FCS), penicillin (10 μg/ml), and streptomycin (100 μg/ml).

extract_protocol: Total cellular RNA was extracted from three independent exponential cultures of the appropriate cell lines using the RNAeasy kit (Qiagen)

treatment_protocol: Exponentially growing conditions

tag: cell line

tag: vector

value: empty pLKO.1puro lentiviral vector


title: Primary Tumor C0575A

description: Primary Tumor C0575A C0575A

value: No


title: Primary Tumor C0487AR3

description: Primary Tumor C0487AR3 C0487AR3

tag: sample date

tag: age

tag: gender

tag: t


title: Normal Colon C0415HR1

description: Normal Colon C0415HR1 C0415HR1

tag: n

tag: m

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: DOD

value: MSS

value: Wild-type

value: Rectosigmoid


title: Primary Tumor C0472AR1

description: Primary Tumor C0472AR1 C0472AR1

tag: fup interval

tag: recurrence

tag: recurrence interval

tag: microsattelite instability

value: Mutant

value: Cecum


title: Normal Liver C0415KR1

description: Normal Liver C0415KR1 C0415KR1

tag: tissue

value: Normal Liver

tag: scan date

tag: p53 mutation status

tag: anatomic location


title: Liver Metastasis C0415UR1

description: Liver Metastasis C0415UR1 C0415UR1

value: Liver Metastasis

tag: patient id

tag: included in analysis

value: F


title: Normal Liver C0472KR1

description: Normal Liver C0472KR1 C0472KR1

tag: sample date

tag: age

value: Yes


title: Normal Liver C0353KR1

description: Normal Liver C0353KR1 C0353KR1

tag: gender

tag: t


title: Primary Tumor C0334AR3

description: Primary Tumor C0334AR3 C0334AR3

tag: n

tag: m

value: II

value: NED

value: MSI-high


title: Primary Tumor C0353AR1

description: Primary Tumor C0353AR1 C0353AR1

value: Primary Tumor

value: M

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)


title: Liver Metastasis C0331UR1

description: Liver Metastasis C0331UR1 C0331UR1


title: Primary Tumor C0329AR1

description: Primary Tumor C0329AR1 C0329AR1

value: IV

tag: fup interval

tag: recurrence

value: Descending colon


title: Primary Tumor C0323AR1

description: Primary Tumor C0323AR1 C0323AR1

value: DOD

tag: recurrence interval

tag: microsattelite instability

value: Ascending colon


title: Normal Colon C0323H

description: Normal Colon C0323H C0323H

tag: tissue

value: Normal Colon

tag: scan date

value: Wild-type


title: Normal Liver C0331KR1

description: Normal Liver C0331KR1 C0331KR1

value: No


title: Normal Colon C0353HR1

description: Normal Colon C0353HR1 C0353HR1

value: MSS

tag: p53 mutation status

value: Mutant

tag: anatomic location

value: Rectosigmoid


title: Primary Tumor C0330AR3

description: Primary Tumor C0330AR3 C0330AR3

tag: patient id

tag: included in analysis

value: F


title: Primary Tumor C0312AR3

description: Primary Tumor C0312AR3 C0312AR3

value: Yes

tag: sample date

tag: age

value: III

value: DOC

value: Sigmoid colon


title: Liver Metastasis C0353UR1

description: Liver Metastasis C0353UR1 C0353UR1

value: Liver Metastasis

tag: gender

tag: t


title: Primary Tumor C0297AR1

description: Primary Tumor C0297AR1 C0297AR1

value: Primary Tumor

tag: n

tag: m

value: I

value: MSI-high


title: Polyp C0298BR3

description: Polyp C0298BR3 C0298BR3

value: Polyp

value: M

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: NED


title: Primary Tumor C0298AR3

description: Primary Tumor C0298AR3 C0298AR3

tag: fup interval

tag: recurrence


title: Normal Colon C0329HR1

description: Normal Colon C0329HR1 C0329HR1

value: Normal Colon

value: IV

value: DOD

tag: recurrence interval

tag: microsattelite instability

value: Descending colon


title: Primary Tumor C0295AR3

description: Primary Tumor C0295AR3 C0295AR3

tag: tissue

tag: scan date

value: DUN

value: No

value: Wild-type


title: Normal Colon C0297HR1

description: Normal Colon C0297HR1 C0297HR1

value: Yes

value: F

tag: p53 mutation status

value: Mutant

tag: anatomic location


title: Primary Tumor C0283AR3

description: Primary Tumor C0283AR3 C0283AR3

tag: patient id

tag: included in analysis

value: III


title: Normal Colon C03156H

description: Normal Colon C03156H C03156H

tag: sample date

tag: age

value: MSS

value: Sigmoid colon


title: Primary Tumor C0415AR1

description: Primary Tumor C0415AR1 C0415AR1

value: Primary Tumor

tag: gender

tag: t

value: Rectosigmoid


title: Primary Tumor C0285AR1

description: Primary Tumor C0285AR1 C0285AR1

value: M

tag: n

tag: m


title: Primary Tumor C0275AR3

description: Primary Tumor C0275AR3 C0275AR3

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: MSI-high

value: Cecum


title: Primary Tumor C0273A

description: Primary Tumor C0273A C0273A

value: NED

tag: fup interval

tag: recurrence


title: Polyp C0319BR3

description: Polyp C0319BR3 C0319BR3

value: Polyp


title: Liver Metastasis C0265UR1

description: Liver Metastasis C0265UR1 C0265UR1

value: Liver Metastasis


title: Normal Colon C0265HR1

description: Normal Colon C0265HR1 C0265HR1

value: Normal Colon


title: Liver Metastasis C0253UR1

description: Liver Metastasis C0253UR1 C0253UR1

value: No


title: Normal Liver C0265KR1

description: Normal Liver C0265KR1 C0265KR1

value: Normal Liver


title: Normal Colon C0251HR1

description: Normal Colon C0251HR1 C0251HR1

value: Yes


title: Normal Liver C0251KR1

description: Normal Liver C0251KR1 C0251KR1


title: Polyp C0252BR1

description: Polyp C0252BR1 C0252BR1


title: Primary Tumor C0225AR3

description: Primary Tumor C0225AR3 C0225AR3

value: DOD

tag: recurrence interval

tag: microsattelite instability

value: Wild-type

value: Rectum


title: Normal Colon C02308H

description: Normal Colon C02308H C02308H

tag: tissue

tag: scan date

value: F

value: IV

value: MSS

value: Mutant

value: Descending colon


title: Polyp C0224BR2

description: Polyp C0224BR2 C0224BR2


title: Primary Tumor C0193AR1

description: Primary Tumor C0193AR1 C0193AR1

value: Primary Tumor

value: M

value: MSI-high

tag: p53 mutation status

tag: anatomic location

value: Ascending colon


title: Primary Tumor C0186AR3

description: Primary Tumor C0186AR3 C0186AR3

tag: patient id

tag: included in analysis

value: Sigmoid colon


title: Primary Tumor C0203AR3

description: Primary Tumor C0203AR3 C0203AR3

tag: sample date

tag: age

value: II

value: NED


title: Primary Tumor C0192A

description: Primary Tumor C0192A C0192A

tag: gender

tag: t

value: I

value: DUN

value: No


title: Normal Colon C0198HR1

description: Normal Colon C0198HR1 C0198HR1

value: Normal Colon

value: Yes

tag: n

tag: m


title: Primary Tumor C0238AR3

description: Primary Tumor C0238AR3 C0238AR3

tag: group stage

value: III

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: DOC

value: Rectum


title: Primary Tumor C0210AR1

description: Primary Tumor C0210AR1 C0210AR1

value: F

tag: fup interval

tag: recurrence

value: Mutant

value: Cecum


title: Normal Colon C0193HR1

description: Normal Colon C0193HR1 C0193HR1

value: M

value: IV

value: DOD

tag: recurrence interval

tag: microsattelite instability

value: Wild-type


title: Primary Tumor C0181AR3

description: Primary Tumor C0181AR3 C0181AR3

tag: tissue

value: Primary Tumor

tag: scan date

value: II

value: MSS

value: Sigmoid colon


title: Primary Tumor C0221AR3

description: Primary Tumor C0221AR3 C0221AR3

value: NED

value: No

tag: p53 mutation status

tag: anatomic location


title: Normal Colon C0194HR1

description: Normal Colon C0194HR1 C0194HR1

value: Normal Colon

tag: patient id

tag: included in analysis

value: Yes

value: Ascending colon


title: Normal Colon C0180HR1

description: Normal Colon C0180HR1 C0180HR1

tag: sample date

tag: age

value: I

value: DUN


title: Primary Tumor C0194AR1

description: Primary Tumor C0194AR1 C0194AR1

tag: gender

tag: t

value: III

value: DOC

value: Mutant


title: Polyp C0210BR1

description: Polyp C0210BR1 C0210BR1

value: Polyp

value: F

tag: n

tag: m

value: MSI-high

value: Cecum


title: Primary Tumor C0257AR3

description: Primary Tumor C0257AR3 C0257AR3

value: Primary Tumor

value: M

tag: group stage

value: II

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)


title: Primary Tumor C0234AR3

description: Primary Tumor C0234AR3 C0234AR3

value: IV

value: DOD

tag: fup interval

tag: recurrence

value: Wild-type

value: Rectum


title: Polyp, high grade C0210CR1

description: Polyp, high grade C0210CR1 C0210CR1

value: Polyp, high grade

value: Yes

value: No

tag: recurrence interval

tag: microsattelite instability


title: Primary Tumor C0198AR1

description: Primary Tumor C0198AR1 C0198AR1

tag: tissue

tag: scan date

value: I

value: DUN

value: MSS

value: Sigmoid colon


title: Primary Tumor C0180AR1

description: Primary Tumor C0180AR1 C0180AR1

tag: p53 mutation status

tag: anatomic location


title: Primary Tumor C0200AR3

description: Primary Tumor C0200AR3 C0200AR3

tag: patient id

tag: included in analysis

value: Mutant

value: Descending colon


title: Polyp C0177BR2

description: Polyp C0177BR2 C0177BR2

value: Polyp


title: Normal Colon C0172HR1

description: Normal Colon C0172HR1 C0172HR1

value: Normal Colon

tag: sample date

tag: age

value: F


title: Normal Liver C0253KR1

description: Normal Liver C0253KR1 C0253KR1

value: Normal Liver


title: Primary Tumor C0178AR1

description: Primary Tumor C0178AR1 C0178AR1

value: Primary Tumor

tag: gender

value: M

tag: t

value: III

value: Cecum


title: Primary Tumor C0168AR3

description: Primary Tumor C0168AR3 C0168AR3

tag: n

tag: m

value: IV

value: DOD

value: MSI-high

value: Wild-type


title: Primary Tumor C0159AR3

description: Primary Tumor C0159AR3 C0159AR3

value: Yes

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)


title: Primary Tumor C0154AR1

description: Primary Tumor C0154AR1 C0154AR1

value: II

value: NED

tag: fup interval

tag: recurrence

value: No

value: MSS


title: Primary Tumor C0155AR3

description: Primary Tumor C0155AR3 C0155AR3

tag: recurrence interval

tag: microsattelite instability

value: Transverse colon


title: Primary Tumor C0171AR1

description: Primary Tumor C0171AR1 C0171AR1

tag: tissue

tag: scan date

value: I

value: Sigmoid colon


title: Primary Tumor C0157AR1

description: Primary Tumor C0157AR1 C0157AR1

value: DUN

tag: p53 mutation status

value: Mutant

tag: anatomic location

value: Ascending colon


title: Primary Tumor C0149AR3

description: Primary Tumor C0149AR3 C0149AR3

value: Primary Tumor

tag: patient id

tag: included in analysis

value: M

value: Rectum


title: Primary Tumor C0156AR1

description: Primary Tumor C0156AR1 C0156AR1

tag: sample date

tag: age

value: Rectosigmoid


title: Liver Metastasis C0141UR3

description: Liver Metastasis C0141UR3 C0141UR3

value: Liver Metastasis


title: Primary Tumor C0147AR3

description: Primary Tumor C0147AR3 C0147AR3

tag: gender

value: F

tag: t


title: Primary Tumor C0170AR1

description: Primary Tumor C0170AR1 C0170AR1

value: Yes

tag: n

tag: m

value: DOD


title: Normal Colon C0157H

description: Normal Colon C0157H C0157H

value: Normal Colon

tag: group stage

value: II

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)


title: Liver Metastasis C0139UR1

description: Liver Metastasis C0139UR1 C0139UR1

value: No


title: Normal Colon C0147HR1

description: Normal Colon C0147HR1 C0147HR1

value: NED

tag: fup interval

tag: recurrence

value: MSS


title: Primary Tumor C0140AR3

description: Primary Tumor C0140AR3 C0140AR3

tag: recurrence interval

tag: microsattelite instability

value: MSI-high

value: Wild-type

value: Cecum


title: Normal Liver C0139KR2

description: Normal Liver C0139KR2 C0139KR2

tag: tissue

value: Normal Liver

tag: scan date


title: Primary Tumor C0172AR1

description: Primary Tumor C0172AR1 C0172AR1

value: Primary Tumor

value: DUN

tag: p53 mutation status

value: Mutant

tag: anatomic location

value: Descending colon


title: Primary Tumor C0151AR1

description: Primary Tumor C0151AR1 C0151AR1

tag: patient id

tag: included in analysis

value: III


title: Liver Metastasis C0152UR3

description: Liver Metastasis C0152UR3 C0152UR3

value: Liver Metastasis


title: Liver Metastasis C0145UR3

description: Liver Metastasis C0145UR3 C0145UR3


title: Normal Colon C0158H

description: Normal Colon C0158H C0158H

value: Yes

tag: sample date

tag: age

value: M

value: AUN

value: Rectosigmoid


title: Primary Tumor C0153AR1

description: Primary Tumor C0153AR1 C0153AR1

tag: gender

value: F

tag: t

value: DOD


title: Normal Liver C0139KR1

description: Normal Liver C0139KR1 C0139KR1

value: No


title: Primary Tumor C0158AR1

description: Primary Tumor C0158AR1 C0158AR1

tag: n

tag: m

value: MSS


title: Normal Colon C0137HR1

description: Normal Colon C0137HR1 C0137HR1

value: Normal Colon

tag: group stage

value: II

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: DOC

value: Sigmoid colon


title: Normal Colon C0153HR1

description: Normal Colon C0153HR1 C0153HR1

tag: fup interval

tag: recurrence


title: Primary Tumor C0124AR3

description: Primary Tumor C0124AR3 C0124AR3

value: Primary Tumor

value: IV

tag: recurrence interval

tag: microsattelite instability


title: Normal Colon C0134HR1

description: Normal Colon C0134HR1 C0134HR1

tag: tissue

tag: scan date

value: I

value: MSI-high

value: Wild-type

value: Ascending colon


title: Normal Liver C0136KR1

description: Normal Liver C0136KR1 C0136KR1

value: Normal Liver

value: AWD

value: MSI-low

tag: p53 mutation status

value: Mutant

tag: anatomic location


title: Normal Colon C0136HR1

description: Normal Colon C0136HR1 C0136HR1

tag: patient id

tag: included in analysis

value: Yes

value: F


title: Primary Tumor C0127AR3

description: Primary Tumor C0127AR3 C0127AR3

tag: sample date

tag: age

value: NED

value: No

value: MSS

value: Rectosigmoid


title: Primary Tumor C0137AR1

description: Primary Tumor C0137AR1 C0137AR1

tag: gender

tag: t

value: II

value: DOC

value: Sigmoid colon


title: Primary Tumor C0147AR1

description: Primary Tumor C0147AR1 C0147AR1

value: Primary Tumor

tag: n

tag: m


title: Normal Colon C0117HR1

description: Normal Colon C0117HR1 C0117HR1

value: Normal Colon

value: M

tag: group stage

value: IV

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: DOD

value: Cecum


title: Primary Tumor C0115AR3

description: Primary Tumor C0115AR3 C0115AR3

tag: fup interval

tag: recurrence

value: MSI-low


title: Primary Tumor C0130AR3

description: Primary Tumor C0130AR3 C0130AR3

value: I

value: DUN

tag: recurrence interval

tag: microsattelite instability

value: MSI-high

value: Mutant

value: Rectum


title: Primary Tumor C0105A

description: Primary Tumor C0105A C0105A

tag: tissue

tag: scan date

value: Yes

value: F

value: NED

value: No

value: Wild-type


title: Primary Tumor C0134AR1

description: Primary Tumor C0134AR1 C0134AR1

value: Primary Tumor

value: AUN

tag: p53 mutation status

tag: anatomic location

value: Ascending colon


title: Primary Tumor C0125AR3

description: Primary Tumor C0125AR3 C0125AR3

tag: patient id

tag: included in analysis

value: M

value: III

value: MSS


title: Primary Tumor C0112AR1

description: Primary Tumor C0112AR1 C0112AR1

tag: sample date

tag: age

value: II

value: DOC

value: MSI-low

value: Sigmoid colon


title: Primary Tumor C0122AR3

description: Primary Tumor C0122AR3 C0122AR3

tag: gender

tag: t

value: IV

value: DOD


title: Primary Tumor C0136AR1

description: Primary Tumor C0136AR1 C0136AR1

value: Yes

tag: n

tag: m

value: AWD

value: Mutant


title: Liver Metastasis C0136UR1

description: Liver Metastasis C0136UR1 C0136UR1

value: Liver Metastasis

value: No

value: F

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)


title: Polyp C0128BR1

description: Polyp C0128BR1 C0128BR1

value: Polyp

value: DUN

tag: fup interval

tag: recurrence

value: Descending colon


title: Normal Colon C0114HR1

description: Normal Colon C0114HR1 C0114HR1

value: Normal Colon

value: III

tag: recurrence interval

tag: microsattelite instability

value: Cecum


title: Primary Tumor C0111AR1

description: Primary Tumor C0111AR1 C0111AR1

tag: tissue

value: Primary Tumor

tag: scan date

value: M

value: II

value: NED

value: Transverse colon


title: Primary Tumor C0101AR3

description: Primary Tumor C0101AR3 C0101AR3

value: Yes

value: IV

value: MSS

tag: p53 mutation status

tag: anatomic location

value: Sigmoid colon


title: Primary Tumor C0114AR1

description: Primary Tumor C0114AR1 C0114AR1

tag: patient id

tag: included in analysis

value: DOD

value: Mutant


title: Primary Tumor C0123AR3

description: Primary Tumor C0123AR3 C0123AR3

tag: sample date

tag: age

value: F

value: No

value: Ascending colon


title: Primary Tumor C0117AR1

description: Primary Tumor C0117AR1 C0117AR1

tag: gender

tag: t


title: Primary Tumor C0081AR3

description: Primary Tumor C0081AR3 C0081AR3

tag: n

tag: m


title: Normal Colon C0123HR1

description: Normal Colon C0123HR1 C0123HR1

value: Normal Colon

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)


title: Primary Tumor C0113AR3

description: Primary Tumor C0113AR3 C0113AR3

value: I

tag: fup interval

tag: recurrence

value: Rectum


title: Primary Tumor C0104AR3

description: Primary Tumor C0104AR3 C0104AR3

value: Primary Tumor

tag: recurrence interval

tag: microsattelite instability

value: Wild-type


title: Normal Colon C0111HR1

description: Normal Colon C0111HR1 C0111HR1

tag: tissue

tag: scan date

value: M

value: II

value: MSI-low


title: Polyp C0047BR1

description: Polyp C0047BR1 C0047BR1

value: Polyp

value: Yes


title: Polyp C0020BR1

description: Polyp C0020BR1 C0020BR1


title: Primary Tumor A8528AR3

description: Primary Tumor A8528AR3 A8528AR3

value: III

value: DUN

value: MSS

tag: p53 mutation status

tag: anatomic location

value: Cecum


title: Liver Metastasis C0068UR3

description: Liver Metastasis C0068UR3 C0068UR3

value: Liver Metastasis

tag: patient id

tag: included in analysis


title: Polyp A9369BR3

description: Polyp A9369BR3 A9369BR3


title: Liver Metastasis C0059UR3

description: Liver Metastasis C0059UR3 C0059UR3


title: Polyp A6143BR3

description: Polyp A6143BR3 A6143BR3


title: Liver Metastasis A5960UR4

description: Liver Metastasis A5960UR4 A5960UR4

value: No


title: Primary Tumor A6275AR3

description: Primary Tumor A6275AR3 A6275AR3

tag: sample date

tag: age

value: F

value: MSI-high


title: Primary Tumor A6141AR

description: Primary Tumor A6141AR A6141AR

tag: gender

tag: t

value: NED

value: Transverse colon


title: Polyp A8528BR3

description: Polyp A8528BR3 A8528BR3

tag: n

tag: m


title: Primary Tumor A5627AR3

description: Primary Tumor A5627AR3 A5627AR3

value: Primary Tumor

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: Sigmoid colon


title: Polyp A5627BR3

description: Polyp A5627BR3 A5627BR3

value: M

tag: fup interval

tag: recurrence


title: Primary Tumor A7366AR3

description: Primary Tumor A7366AR3 A7366AR3

value: II

tag: recurrence interval

tag: microsattelite instability


title: Primary Tumor C0128AR3

description: Primary Tumor C0128AR3 C0128AR3

tag: tissue

tag: scan date

value: Mutant

value: Descending colon


title: Liver Metastasis C0072UR3

description: Liver Metastasis C0072UR3 C0072UR3

value: Yes


title: Polyp C0035BR1

description: Polyp C0035BR1 C0035BR1

value: Polyp


title: Liver Metastasis C0075UR3

description: Liver Metastasis C0075UR3 C0075UR3


title: Liver Metastasis A5607UR4

description: Liver Metastasis A5607UR4 A5607UR4


title: Polyp A8457BR3

description: Polyp A8457BR3 A8457BR3


title: Polyp A5153BR3

description: Polyp A5153BR3 A5153BR3


title: Liver Metastasis C0045UR3

description: Liver Metastasis C0045UR3 C0045UR3


title: Primary Tumor A8307AR4

description: Primary Tumor A8307AR4 A8307AR4

value: IV

tag: p53 mutation status

tag: anatomic location


title: Liver Metastasis C0056UR3

description: Liver Metastasis C0056UR3 C0056UR3

tag: patient id

tag: included in analysis


title: Microadenoma A5135DR2

description: Microadenoma A5135DR2 A5135DR2

value: Microadenoma

tag: sample date

tag: age

value: Ascending colon


title: Polyp A5790BR3

description: Polyp A5790BR3 A5790BR3


title: Polyp A5790BR3_2

description: Polyp A5790BR3_2 A5790BR3_2


title: Normal Colon A5153HR

description: Normal Colon A5153HR A5153HR

value: Normal Colon


title: Primary Tumor A5465AR3

description: Primary Tumor A5465AR3 A5465AR3

tag: gender

tag: t

value: III

value: No

value: MSS

value: Splenic Flexure


title: Primary Tumor A5320AR3

description: Primary Tumor A5320AR3 A5320AR3

value: F

tag: n

tag: m

value: NED


title: Primary Tumor A5135AR2

description: Primary Tumor A5135AR2 A5135AR2

value: Primary Tumor

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)


title: Polyp A5086BR4

description: Polyp A5086BR4 A5086BR4


title: Primary Tumor A4902AR3

description: Primary Tumor A4902AR3 A4902AR3

value: M

tag: fup interval

tag: recurrence

value: Rectosigmoid


title: Primary Tumor A4902AR2

description: Primary Tumor A4902AR2 A4902AR2

tag: recurrence interval

tag: microsattelite instability


title: Microadenoma A4902DR2

description: Microadenoma A4902DR2 A4902DR2

tag: tissue

tag: scan date


title: Primary Tumor A4779AR3

description: Primary Tumor A4779AR3 A4779AR3

value: II

value: DUN

tag: p53 mutation status

tag: anatomic location

value: Cecum


title: Primary Tumor A4947AR4

description: Primary Tumor A4947AR4 A4947AR4

tag: patient id

tag: included in analysis

value: Yes

value: MSI-low

value: Wild-type

value: Sigmoid colon


title: Primary Tumor A4792AR4

description: Primary Tumor A4792AR4 A4792AR4

tag: sample date

tag: age

value: Hepatic Flexure


title: Polyp A4410BR3_ren

description: Polyp A4410BR3_ren A4410BR3_ren

value: Polyp


title: Liver Metastasis A4756UR4

description: Liver Metastasis A4756UR4 A4756UR4

value: Liver Metastasis

value: No


title: Normal Colon A4410HR2

description: Normal Colon A4410HR2 A4410HR2

value: Normal Colon


title: Primary Tumor A4342AR4

description: Primary Tumor A4342AR4 A4342AR4

tag: gender

tag: t

value: III


title: Liver Metastasis A3684UR4

description: Liver Metastasis A3684UR4 A3684UR4


title: Liver Metastasis A4396UR4

description: Liver Metastasis A4396UR4 A4396UR4


title: Primary Tumor A4248AR4

description: Primary Tumor A4248AR4 A4248AR4

value: F

tag: n

tag: m

value: NED

value: MSI-high

value: Descending colon


title: Polyp A4410BR3

description: Polyp A4410BR3 A4410BR3


title: Primary Tumor A3536AR4

description: Primary Tumor A3536AR4 A3536AR4

value: Primary Tumor

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)


title: Polyp A3443BR4

description: Polyp A3443BR4 A3443BR4


title: Liver Metastasis A3203UR4

description: Liver Metastasis A3203UR4 A3203UR4


title: Polyp A4177BR3

description: Polyp A4177BR3 A4177BR3


title: Liver Metastasis A3622UR4

description: Liver Metastasis A3622UR4 A3622UR4


title: Liver Metastasis A2561UR4

description: Liver Metastasis A2561UR4 A2561UR4


title: Primary Tumor A2434AR3

description: Primary Tumor A2434AR3 A2434AR3

value: M

value: IV

value: DOD

tag: fup interval

tag: recurrence

value: MSS

value: Mutant


title: Primary Tumor A2715AR3

description: Primary Tumor A2715AR3 A2715AR3

value: Yes

tag: recurrence interval

tag: microsattelite instability

value: Rectum


title: Liver Metastasis A4674UR4

description: Liver Metastasis A4674UR4 A4674UR4

tag: tissue

tag: scan date


title: Normal Colon A4779HR2

description: Normal Colon A4779HR2 A4779HR2

value: II

value: DUN

tag: p53 mutation status

tag: anatomic location

value: Cecum


title: Primary Tumor A2367AR4

description: Primary Tumor A2367AR4 A2367AR4

tag: patient id

tag: included in analysis

value: Ascending colon


title: Primary Tumor A2226AR4

description: Primary Tumor A2226AR4 A2226AR4

tag: sample date

tag: age

value: No

value: Transverse colon


title: Polyp A1853BR3

description: Polyp A1853BR3 A1853BR3

value: Polyp


title: Normal Colon a2191hr

description: Normal Colon a2191hr a2191hr

value: Normal Colon


title: Primary Tumor A1644AR4

description: Primary Tumor A1644AR4 A1644AR4

tag: gender

tag: t

value: MSI-low

value: Sigmoid colon


title: Primary Tumor A0319AR4

description: Primary Tumor A0319AR4 A0319AR4

value: Primary Tumor

value: F

tag: n

tag: m


title: Primary Tumor A1516AR4

description: Primary Tumor A1516AR4 A1516AR4

value: M

tag: group stage

value: III

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: MSI-high


title: Primary Tumor A0702AR4

description: Primary Tumor A0702AR4 A0702AR4

value: Yes

value: IV

value: DOD

tag: fup interval

tag: recurrence

value: Descending colon


title: Normal Colon A1327HR2

description: Normal Colon A1327HR2 A1327HR2


title: Liver Metastasis A1288UR4

description: Liver Metastasis A1288UR4 A1288UR4

value: Liver Metastasis


title: Normal Colon A1853HR2

description: Normal Colon A1853HR2 A1853HR2


title: Primary Tumor A1716AR4

description: Primary Tumor A1716AR4 A1716AR4

value: II

value: NED

tag: recurrence interval

tag: microsattelite instability

value: Wild-type

value: Ascending colon


title: Liver Metastasis 80649UR4

description: Liver Metastasis 80649UR4 80649UR4

tag: tissue

tag: scan date


title: Liver Metastasis 79744UR4

description: Liver Metastasis 79744UR4 79744UR4

value: No


title: Primary Tumor 15329AR3

description: Primary Tumor 15329AR3 15329AR3

value: MSI-low

tag: p53 mutation status

tag: anatomic location

value: Cecum


title: Lung Metastasis 14938VR1

description: Lung Metastasis 14938VR1 14938VR1

value: Lung Metastasis

tag: patient id

tag: included in analysis


title: Polyp A1327BR3

description: Polyp A1327BR3 A1327BR3

value: Polyp


title: Lung Metastasis 14756VR1

description: Lung Metastasis 14756VR1 14756VR1


title: Primary Tumor A5135AR2_ez

description: Primary Tumor A5135AR2_ez A5135AR2_ez

value: Primary Tumor

tag: sample date

tag: age

value: M


title: Polyp A0022BR4

description: Polyp A0022BR4 A0022BR4


title: Lung Metastasis 14756VR1_ez

description: Lung Metastasis 14756VR1_ez 14756VR1_ez


title: Primary Tumor 14475AR3

description: Primary Tumor 14475AR3 14475AR3

tag: gender

value: F

tag: t

value: MSS


title: Primary Tumor 12847AR3

description: Primary Tumor 12847AR3 12847AR3

value: Yes

tag: n

tag: m

value: I

value: DOC

value: Sigmoid colon


title: Liver Metastasis A1423UR4

description: Liver Metastasis A1423UR4 A1423UR4

value: Liver Metastasis


title: Primary Tumor 12355AR3

description: Primary Tumor 12355AR3 12355AR3

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: DUN

value: Rectosigmoid


title: Primary Tumor 12292AR3

description: Primary Tumor 12292AR3 12292AR3

value: IV

value: DOD

tag: fup interval

tag: recurrence


title: Lung Metastasis 12285VR1

description: Lung Metastasis 12285VR1 12285VR1


title: Primary Tumor 13357AR3

description: Primary Tumor 13357AR3 13357AR3

value: II

value: No

tag: recurrence interval

tag: microsattelite instability

value: MSI-high

value: Wild-type

value: Descending colon


title: Primary Tumor 13321AR3

description: Primary Tumor 13321AR3 13321AR3

tag: tissue

value: Primary Tumor

tag: scan date

value: M


title: Lung Metastasis 11190VR1

description: Lung Metastasis 11190VR1 11190VR1

value: Lung Metastasis


title: Primary Tumor 12297AR3

description: Primary Tumor 12297AR3 12297AR3

value: Yes

value: NED

value: MSS

tag: p53 mutation status

tag: anatomic location

value: Splenic Flexure


title: Lung Metastasis 11670VR1

description: Lung Metastasis 11670VR1 11670VR1

tag: patient id

tag: included in analysis


title: Lung Metastasis 13279VR1

description: Lung Metastasis 13279VR1 13279VR1


title: Normal Lung 12051MR1

description: Normal Lung 12051MR1 12051MR1

value: Normal Lung


title: Lung Metastasis 12051VR1

description: Lung Metastasis 12051VR1 12051VR1


title: Normal Lung 13279MR1

description: Normal Lung 13279MR1 13279MR1


title: Lung Metastasis 10258VR1

description: Lung Metastasis 10258VR1 10258VR1


title: Primary Tumor 12237AR3

description: Primary Tumor 12237AR3 12237AR3

tag: sample date

tag: age

value: F

value: Mutant

value: Transverse colon


title: Primary Tumor 10630AR3

description: Primary Tumor 10630AR3 10630AR3

tag: gender

tag: t

value: I


title: Primary Tumor 11325AR3

description: Primary Tumor 11325AR3 11325AR3

tag: n

tag: m

value: II

value: Rectosigmoid


title: Lung Metastasis 11185VR1

description: Lung Metastasis 11185VR1 11185VR1


title: Primary Tumor 10264AR3

description: Primary Tumor 10264AR3 10264AR3

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: No

value: Ascending colon


title: Primary Tumor 10216AR3

description: Primary Tumor 10216AR3 10216AR3

tag: fup interval

tag: recurrence

value: Wild-type

value: Sigmoid colon


title: Polyp 10078BR1

description: Polyp 10078BR1 10078BR1

value: Polyp


title: Primary Tumor 10194AR2

description: Primary Tumor 10194AR2 10194AR2

value: Primary Tumor

value: M

value: IV

value: DOD

tag: recurrence interval

tag: microsattelite instability


title: Liver Metastasis 09518UR2

description: Liver Metastasis 09518UR2 09518UR2

tag: tissue

value: Liver Metastasis

tag: scan date

value: Yes


title: Primary Tumor 09468AR2

description: Primary Tumor 09468AR2 09468AR2

value: F

value: MSS

tag: p53 mutation status

tag: anatomic location


title: Primary Tumor 09728AR2

description: Primary Tumor 09728AR2 09728AR2

tag: patient id

tag: included in analysis

value: NED

value: Cecum


title: Primary Tumor 10368AR3

description: Primary Tumor 10368AR3 10368AR3

tag: sample date

tag: age


title: Primary Tumor 11718AR3

description: Primary Tumor 11718AR3 11718AR3

tag: gender

tag: t


title: Polyp 09518BR3

description: Polyp 09518BR3 09518BR3


title: Polyp 09728BR2

description: Polyp 09728BR2 09728BR2

tag: n

tag: m

value: II


title: Primary Tumor 10512AR3

description: Primary Tumor 10512AR3 10512AR3

tag: group stage

value: I

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: Mutant


title: Primary Tumor 09811AR2

description: Primary Tumor 09811AR2 09811AR2

tag: fup interval

tag: recurrence

value: Descending colon


title: Primary Tumor 09420AR2

description: Primary Tumor 09420AR2 09420AR2

value: AWD

tag: recurrence interval

tag: microsattelite instability

value: Rectum


title: Primary Tumor 09394AR2

description: Primary Tumor 09394AR2 09394AR2

tag: tissue

tag: scan date

value: III

value: No

value: Sigmoid colon


title: Polyp 09446BR2

description: Polyp 09446BR2 09446BR2

value: Polyp


title: Primary Tumor 09054AR2

description: Primary Tumor 09054AR2 09054AR2

value: Primary Tumor

tag: p53 mutation status

tag: anatomic location


title: Primary Tumor 09297AR2

description: Primary Tumor 09297AR2 09297AR2

tag: patient id

tag: included in analysis

value: IV

value: DOD

value: MSI-low


title: Polyp 08568BR1

description: Polyp 08568BR1 08568BR1

value: Yes


title: Primary Tumor 09077AR2

description: Primary Tumor 09077AR2 09077AR2

tag: sample date

tag: age

value: M

value: DUN

value: MSS


title: Primary Tumor 09185AR2

description: Primary Tumor 09185AR2 09185AR2

tag: gender

tag: t

value: II

value: NED

value: MSI-high

value: Wild-type

value: Transverse colon


title: Primary Tumor 08792AR2

description: Primary Tumor 08792AR2 08792AR2

value: F

tag: n

tag: m

value: III


title: Primary Tumor 08029AR2

description: Primary Tumor 08029AR2 08029AR2

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: No

value: Mutant

value: Rectosigmoid


title: Primary Tumor 09343AR2

description: Primary Tumor 09343AR2 09343AR2

value: Primary Tumor

tag: fup interval

tag: recurrence

value: Cecum


title: Lung Metastasis 08088VR1

description: Lung Metastasis 08088VR1 08088VR1

value: Lung Metastasis


title: Primary Tumor 08061AR2

description: Primary Tumor 08061AR2 08061AR2

value: Yes

value: I

tag: recurrence interval

tag: microsattelite instability

value: Sigmoid colon


title: Normal Lung 08088MR1

description: Normal Lung 08088MR1 08088MR1

tag: tissue

value: Normal Lung

tag: scan date


title: Polyp 08070BR1

description: Polyp 08070BR1 08070BR1

value: Polyp


title: Primary Tumor 08018AR2

description: Primary Tumor 08018AR2 08018AR2

value: M

value: IV

value: DOD

value: MSS

tag: p53 mutation status

tag: anatomic location

value: Ascending colon


title: Primary Tumor 07930AR2

description: Primary Tumor 07930AR2 07930AR2

tag: patient id

tag: included in analysis

value: F


title: Primary Tumor 07721AR2

description: Primary Tumor 07721AR2 07721AR2

tag: sample date

tag: age

value: III


title: Primary Tumor 07427AR2

description: Primary Tumor 07427AR2 07427AR2

tag: gender

tag: t

value: Wild-type

value: Descending colon


title: Primary Tumor 07145AR2

description: Primary Tumor 07145AR2 07145AR2

value: Primary Tumor

tag: n

tag: m

value: NED

value: No

value: MSI-low

value: Mutant


title: Polyp 07392BR2

description: Polyp 07392BR2 07392BR2

value: Yes


title: Primary Tumor 07973AR2

description: Primary Tumor 07973AR2 07973AR2

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: Rectosigmoid


title: Primary Tumor 07576AR2

description: Primary Tumor 07576AR2 07576AR2

value: II

tag: fup interval

tag: recurrence

value: Cecum


title: Primary Tumor 06840AR2

description: Primary Tumor 06840AR2 06840AR2

value: M

tag: recurrence interval

tag: microsattelite instability


title: Lung Metastasis 06764VR1

description: Lung Metastasis 06764VR1 06764VR1

tag: tissue

value: Lung Metastasis

tag: scan date


title: Polyp 07677BR1

description: Polyp 07677BR1 07677BR1

value: Polyp


title: Primary Tumor 06997AR3

description: Primary Tumor 06997AR3 06997AR3

tag: p53 mutation status

tag: anatomic location


title: Primary Tumor 07632AR2

description: Primary Tumor 07632AR2 07632AR2

tag: patient id

tag: included in analysis

value: MSS

value: Transverse colon


title: Primary Tumor 08168AR2

description: Primary Tumor 08168AR2 08168AR2

tag: sample date

tag: age

value: Sigmoid colon


title: Primary Tumor 07061AR2

description: Primary Tumor 07061AR2 07061AR2

tag: gender

value: F

tag: t

value: III


title: Primary Tumor 06706AR2

description: Primary Tumor 06706AR2 06706AR2

value: Primary Tumor

tag: n

tag: m

value: Descending colon


title: Primary Tumor 07662AR2

description: Primary Tumor 07662AR2 07662AR2

tag: group stage

value: IV

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: DOD


title: Normal Colon 06657HR3

description: Normal Colon 06657HR3 06657HR3

value: Normal Colon

value: NED

tag: fup interval

tag: recurrence

value: MSI-low

value: Mutant


title: Lung Metastasis 07445VR1

description: Lung Metastasis 07445VR1 07445VR1

value: No


title: Polyp 06572BR1

description: Polyp 06572BR1 06572BR1

value: Yes


title: Lung Metastasis 06432VR1

description: Lung Metastasis 06432VR1 06432VR1

value: Lung Metastasis


title: Primary Tumor 06657AR2

description: Primary Tumor 06657AR2 06657AR2

tag: recurrence interval

tag: microsattelite instability


title: Primary Tumor 05885AR2

description: Primary Tumor 05885AR2 05885AR2

tag: tissue

tag: scan date

value: Ascending colon


title: Primary Tumor 06220AR2

description: Primary Tumor 06220AR2 06220AR2

value: M

value: MSS

tag: p53 mutation status

value: Wild-type

tag: anatomic location


title: Primary Tumor 06051AR2

description: Primary Tumor 06051AR2 06051AR2

tag: patient id

tag: included in analysis

value: F

value: II

value: Cecum


title: Primary Tumor 06265AR2

description: Primary Tumor 06265AR2 06265AR2

value: Primary Tumor

tag: sample date

tag: age

value: DUN

value: Sigmoid colon


title: Normal Lung 06764MR3

description: Normal Lung 06764MR3 06764MR3

value: Normal Lung


title: Primary Tumor 05839AR2

description: Primary Tumor 05839AR2 05839AR2

tag: gender

tag: t

value: IV

value: DOD


title: Lung Metastasis 05969VR1

description: Lung Metastasis 05969VR1 05969VR1


title: Normal Colon 05786hr3

description: Normal Colon 05786hr3 05786hr3

value: Normal Colon

tag: n

tag: m


title: Primary Tumor 06314AR2

description: Primary Tumor 06314AR2 06314AR2

tag: group stage

value: I

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: NED

value: No

value: Rectum


title: Primary Tumor 05786AR2

description: Primary Tumor 05786AR2 05786AR2

value: Yes

value: M

tag: fup interval

tag: recurrence

value: Ascending colon


title: Primary Tumor 05629AR4

description: Primary Tumor 05629AR4 05629AR4

tag: recurrence interval

tag: microsattelite instability

value: MSI-high

value: Wild-type


title: Primary Tumor 05708AR2

description: Primary Tumor 05708AR2 05708AR2

tag: tissue

tag: scan date

value: F

value: MSS

value: Mutant


title: Polyp 04809BR1

description: Polyp 04809BR1 04809BR1

value: Polyp


title: Primary Tumor 05025AR4

description: Primary Tumor 05025AR4 05025AR4

value: Primary Tumor

tag: p53 mutation status

tag: anatomic location


title: Polyp 05479BR1

description: Polyp 05479BR1 05479BR1

tag: patient id

tag: included in analysis


title: Primary Tumor 05334AR4

description: Primary Tumor 05334AR4 05334AR4

tag: sample date

tag: age

value: III

value: DUN

value: MSI-low

value: Cecum


title: Polyp 05192BR1

description: Polyp 05192BR1 05192BR1


title: Normal Colon 04494HR4

description: Normal Colon 04494HR4 04494HR4

value: Normal Colon

tag: gender

tag: t

value: IV

value: DOD

value: Sigmoid colon


title: Primary Tumor 05424AR4

description: Primary Tumor 05424AR4 05424AR4

value: Yes

value: M

tag: n

tag: m

value: Transverse colon


title: Primary Tumor 04276AR2

description: Primary Tumor 04276AR2 04276AR2

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: NED

value: No

value: Ascending colon


title: Primary Tumor 04549AR4

description: Primary Tumor 04549AR4 04549AR4

tag: fup interval

tag: recurrence

value: MSS

value: Mutant


title: Normal Lung 04222MR1

description: Normal Lung 04222MR1 04222MR1

value: Normal Lung


title: Normal Colon 04800hr4

description: Normal Colon 04800hr4 04800hr4

value: F

value: III

tag: recurrence interval

tag: microsattelite instability


title: Normal Colon 03753HR3

description: Normal Colon 03753HR3 03753HR3

tag: tissue

tag: scan date

value: I

value: MSI-high

value: Wild-type


title: Normal Colon 04549HR4

description: Normal Colon 04549HR4 04549HR4

value: Normal Colon

value: IV

tag: p53 mutation status

tag: anatomic location

value: Cecum


title: Primary Tumor 03777AR2

description: Primary Tumor 03777AR2 03777AR2

value: Primary Tumor

tag: patient id

tag: included in analysis

value: Yes

value: DOD

value: Rectosigmoid


title: Polyp 04449BR4

description: Polyp 04449BR4 04449BR4

value: Polyp


title: Normal Colon 04176HR3

description: Normal Colon 04176HR3 04176HR3

tag: sample date

tag: age

value: Descending colon


title: Normal Colon 03862HR2

description: Normal Colon 03862HR2 03862HR2

tag: gender

value: M

tag: t

value: MSS

value: Transverse colon


title: Primary Tumor 04388AR2

description: Primary Tumor 04388AR2 04388AR2

value: F

tag: n

tag: m

value: NED

value: No

value: Mutant


title: Primary Tumor 04176AR2

description: Primary Tumor 04176AR2 04176AR2

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: Wild-type


title: Normal Colon 04276HR2

description: Normal Colon 04276HR2 04276HR2

value: Normal Colon

value: III

tag: fup interval

tag: recurrence

value: Ascending colon


title: Lung Metastasis 03820VR1

description: Lung Metastasis 03820VR1 03820VR1

value: Lung Metastasis


title: Lung Metastasis 04222VR1

description: Lung Metastasis 04222VR1 04222VR1

value: Yes


title: Primary Tumor 04494AR4

description: Primary Tumor 04494AR4 04494AR4

value: Primary Tumor

value: IV

value: DOD

tag: recurrence interval

tag: microsattelite instability

value: Sigmoid colon


title: Primary Tumor 03862AR2

description: Primary Tumor 03862AR2 03862AR2

tag: tissue

tag: scan date

value: M


title: Primary Tumor 04800AR4

description: Primary Tumor 04800AR4 04800AR4

value: MSS

tag: p53 mutation status

tag: anatomic location


title: Primary Tumor 03753AR1

description: Primary Tumor 03753AR1 03753AR1

tag: patient id

tag: included in analysis

value: I

value: MSI-high

value: Cecum


title: Normal Colon 03706HR2

description: Normal Colon 03706HR2 03706HR2

tag: sample date

tag: age

value: Descending colon


title: Primary Tumor 03752AR1

description: Primary Tumor 03752AR1 03752AR1

tag: gender

tag: t

value: NED

value: No

value: Mutant

value: Rectosigmoid


title: Normal Colon 03637HR2

description: Normal Colon 03637HR2 03637HR2

value: Normal Colon

value: F

tag: n

tag: m


title: Primary Tumor 03706AR2

description: Primary Tumor 03706AR2 03706AR2

value: Yes

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)


title: Primary Tumor 03657AR2

description: Primary Tumor 03657AR2 03657AR2

value: Primary Tumor

value: III

tag: fup interval

tag: recurrence

value: Transverse colon


title: Primary Tumor 03637AR2

description: Primary Tumor 03637AR2 03637AR2

value: IV

value: DOD

tag: recurrence interval

tag: microsattelite instability


title: Polyp 03637BR2

description: Polyp 03637BR2 03637BR2

tag: tissue

value: Polyp

tag: scan date

value: MSS


title: Normal Colon 03777hr3

description: Normal Colon 03777hr3 03777hr3

tag: p53 mutation status

tag: anatomic location


title: Primary Tumor 03393AR1

description: Primary Tumor 03393AR1 03393AR1

tag: patient id

tag: included in analysis

value: I

value: Rectum


title: Primary Tumor 03519AR2

description: Primary Tumor 03519AR2 03519AR2

tag: sample date

tag: age

value: M

value: Ascending colon


title: Polyp 03598BR2

description: Polyp 03598BR2 03598BR2


title: Primary Tumor 03465AR3

description: Primary Tumor 03465AR3 03465AR3

tag: gender

tag: t

value: II

value: NED

value: No

value: MSI-high

value: Descending colon


title: Normal Colon 03023HR1

description: Normal Colon 03023HR1 03023HR1

value: Normal Colon

value: Yes

value: F

tag: n

tag: m

value: Wild-type

value: Sigmoid colon


title: Primary Tumor 03283AR1

description: Primary Tumor 03283AR1 03283AR1

value: Primary Tumor

tag: group stage

value: III

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: DOD

value: Mutant


title: Primary Tumor 03156AR1

description: Primary Tumor 03156AR1 03156AR1

value: I

tag: fup interval

tag: recurrence

value: MSS


title: Lung Metastasis 03358VR1

description: Lung Metastasis 03358VR1 03358VR1

value: Lung Metastasis


title: Normal Colon 03657HR2

description: Normal Colon 03657HR2 03657HR2

tag: recurrence interval

tag: microsattelite instability

value: Transverse colon


title: Primary Tumor 03531AR2

description: Primary Tumor 03531AR2 03531AR2

tag: tissue

tag: scan date

value: M

value: IV


title: Normal Colon 02815HR1

description: Normal Colon 02815HR1 02815HR1

tag: p53 mutation status

tag: anatomic location


title: Normal Colon 03519HR2

description: Normal Colon 03519HR2 03519HR2

tag: patient id

tag: included in analysis

value: Ascending colon


title: Primary Tumor 02815AR1

description: Primary Tumor 02815AR1 02815AR1

tag: sample date

tag: age


title: Primary Tumor 02832AR1

description: Primary Tumor 02832AR1 02832AR1

tag: gender

tag: t


title: Polyp 03393BR1

description: Polyp 03393BR1 03393BR1

value: Polyp

tag: n

tag: m

value: NED

value: No

value: Rectum


title: Normal Colon 03598HR2

description: Normal Colon 03598HR2 03598HR2

value: Normal Colon

value: Yes


title: Primary Tumor 02779AR1

description: Primary Tumor 02779AR1 02779AR1

value: Primary Tumor

value: F

tag: group stage

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: Wild-type

value: Rectosigmoid


title: Polyp 02779BR1

description: Polyp 02779BR1 02779BR1

value: I

tag: fup interval

tag: recurrence


title: Polyp 02679BR1

description: Polyp 02679BR1 02679BR1

value: III

value: DUN

tag: recurrence interval

tag: microsattelite instability

value: MSS

value: Sigmoid colon


title: Primary Tumor 02500AR1

description: Primary Tumor 02500AR1 02500AR1

tag: tissue

tag: scan date

value: M


title: Primary Tumor 02308AR1

description: Primary Tumor 02308AR1 02308AR1

value: IV

value: DOD

tag: p53 mutation status

value: Mutant

tag: anatomic location

value: Descending colon


title: Primary Tumor 03023AR1

description: Primary Tumor 03023AR1 03023AR1

tag: patient id

tag: included in analysis


title: Primary Tumor 02679AR1

description: Primary Tumor 02679AR1 02679AR1

tag: sample date

tag: age

value: No


title: Polyp 01984BR1

description: Polyp 01984BR1 01984BR1

value: Polyp


title: Primary Tumor 03401AR1

description: Primary Tumor 03401AR1 03401AR1

value: Yes

tag: gender

tag: t

value: MSI-low

value: Cecum


title: Polyp 02663BR1

description: Polyp 02663BR1 02663BR1


title: Primary Tumor 00990AR1

description: Primary Tumor 00990AR1 00990AR1

value: Primary Tumor

tag: n

tag: m


title: Normal Colon 02184HR2

description: Normal Colon 02184HR2 02184HR2

value: Normal Colon

value: F

tag: group stage

value: II

tag: fup status (ned,  no evidence of disease, awd, alive with disease, aun, alive unknown, dod, dead of disease, doc, dead of other cause, dun, dead, cause unknown)

value: NED

value: Wild-type


title: Liver Metastasis 00947UR1

description: Liver Metastasis 00947UR1 00947UR1

value: Liver Metastasis


title: Primary Tumor 02184AR2

description: Primary Tumor 02184AR2 02184AR2

tag: fup interval

tag: recurrence

value: MSS

value: Sigmoid colon


title: Primary Tumor 07925AR2

description: Primary Tumor 07925AR2 07925AR2

value: M

value: IV

value: DOD

tag: recurrence interval

tag: microsattelite instability

value: MSI-high

value: Transverse colon


title: Normal Lung 01720MR1

description: Normal Lung 01720MR1 01720MR1

tag: tissue

value: Normal Lung

tag: scan date

value: No


title: Lung Metastasis 02050VR1

description: Lung Metastasis 02050VR1 02050VR1

value: Lung Metastasis


title: Liver Metastasis 00852UR1

description: Liver Metastasis 00852UR1 00852UR1

value: Yes


title: Liver Metastasis 00838UR1_ez

description: Liver Metastasis 00838UR1_ez 00838UR1_ez


title: Primary Tumor 02189AR1

description: Primary Tumor 02189AR1 02189AR1

value: Primary Tumor

value: III

value: DUN

tag: p53 mutation status

value: Mutant

tag: anatomic location

value: Rectosigmoid


title: Liver Metastasis 00823UR1

description: Liver Metastasis 00823UR1 00823UR1

value: Liver Metastasis

tag: patient id

tag: included in analysis


title: Normal Liver 00871KR3

description: Normal Liver 00871KR3 00871KR3

value: Normal Liver


title: Liver Metastasis 00838UR1

description: Liver Metastasis 00838UR1 00838UR1


title: Normal Lung 02050MR1

description: Normal Lung 02050MR1 02050MR1


title: Lung Metastasis 01720VR1

description: Lung Metastasis 01720VR1 01720VR1


title: Normal Colon 02189HR1

description: Normal Colon 02189HR1 02189HR1

value: Normal Colon

tag: sample date

tag: age

value: MSS


title: Primary Tumor 00620AR1

description: Primary Tumor 00620AR1 00620AR1

tag: gender

value: F

tag: t

value: IV

value: Ascending colon


title: Polyp 00888BR1

description: Polyp 00888BR1 00888BR1

value: Polyp


title: Liver Metastasis 00823UR1_ez

description: Liver Metastasis 00823UR1_ez 00823UR1_ez


title: Liver Metastasis 00485UR1_ez

description: Liver Metastasis 00485UR1_ez 00485UR1_ez


title: Liver Metastasis 00485UR2

description: Liver Metastasis 00485UR2 00485UR2


title: Liver Metastasis 00464UR1

description: Liver Metastasis 00464UR1 00464UR1


title: Liver Metastasis 00823UR2

description: Liver Metastasis 00823UR2 00823UR2


title: Liver Metastasis 00838UR2

description: Liver Metastasis 00838UR2 00838UR2


title: Liver Metastasis 00450UR1_ez

description: Liver Metastasis 00450UR1_ez 00450UR1_ez


title: Liver Metastasis 00450UR2

description: Liver Metastasis 00450UR2 00450UR2


title: Liver Metastasis 00450UR1

description: Liver Metastasis 00450UR1 00450UR1


title: Polyp 00300BR2

description: Polyp 00300BR2 00300BR2


title: 22Rv1 Docetaxel resistant 2

city: New York

first: Josep

last: Domingo-Domenech

state: New York

address: Annenberg Building, Room 24-16

department: Pathology

country: USA

institute: Mount Sinai School of Medicine

description:
22Rv1-DR 2
Gene expression data from 22Rv1 Docetaxel-resistant cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix Human U133 Plus 2.0 or Affymetrix Human U133A 2.0 arrays.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite, MicroDB, and Data Mining tool software (Affymetrix). Quantile normalization and RMA summarization were used to obtain probeset level expression.

source_name: 22Rv1 Docetaxel-resistant cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Parental Docetaxel-sensitive and resistant cells were grown with RPMI supplemented with 10% FBS alone or under exposure to Docetaxel, respectively, before harvesting total RNA.

tag: cell line

tag: cell type

value: prostate cancer cells

tag: phenotype

value: docetaxel resistant


title: 22Rv1 parental sensitive 2

description:
22Rv1 2
Gene expression data from 22Rv1 parental Docetaxel-sensitive cells.

value: docetaxel sensitive


title: DU145 Docetaxel resistant 1

description:
DU145-DR 1
Gene expression data from DU145 Docetaxel-resistant cells.

source_name: DU145 Docetaxel-resistant cells


title: DU145 parental sensitive 2

description:
DU145 2
Gene expression data from DU145 parental Docetaxel-sensitive cells.


title: 22Rv1 parental sensitive 1

description:
22Rv1 1
Gene expression data from 22Rv1 parental Docetaxel-sensitive cells.


title: Ncoa3 shRNA knockdown, Day 4, biological replicate 2

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: Biological Ncoa3 knockdown replicate 2

hyb_protocol: 1.5 ug of cRNA were hybridized to Illumina MouseWG-6 v2.0 expression beadchip for 18 hr at 58°C in an Ilumina hybridization oven.

scan_protocol: The Illumina MouseWG-6 v2.0 expression beadchip were washed and stained with streptavidin-Cy3 before scanning using an Illumina Bead Reader.

data_processing: The data were analyzed using Bead Array suite software. Rank invariant normalization method was chosen to obtain the signal intensity.

source_name: E14 mouse embryonic stem cells (ESCs)

label_protocol: Biotinylated cRNA were prepared from 500 ng of total RNA according to the standard protocol (Illumina TotalPrep RNA Amplification Kit, Instruction Manual, Catalog AMIL1791).

growth_protocol: Feeder-free E14 mouse ESCs were cultured on 0.1% gelatin in Dulbecco’s modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon). All cells were kept at 37C with 5% CO2.

extract_protocol: Total RNA was extracted using Buffer RLT (Qiagen) and purified with RNeasy minikit (Qiagen).

treatment_protocol: Transfection of Esrrb shRNA plasmid was performed using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions

tag: treatment

value: Ncoa3 shRNA (targeting Ncoa3 transcript) transfected E14 mouse embryonic stem cells


title: Liver Metastasis 00485UR1

description: Liver Metastasis 00485UR1 00485UR1

value: No


title: Scrambled shRNA knockdown, Day 4, biological replicate 3

description: Biological control knockdown replicate 3

value: Control scrambled sequence shRNA transfected E14 mouse embryonic stem cells


title: Ncoa3 shRNA knockdown, Day 4, biological replicate 3

description: Biological Ncoa3 knockdown replicate 3


title: Ncoa3 shRNA knockdown, Day 4, biological replicate 1

description: Biological Ncoa3 knockdown replicate 1


title: Scrambled shRNA knockdown, Day 4, biological replicate 2

description: Biological control knockdown replicate 2


title: 22Rv1 Docetaxel resistant 1

description:
22Rv1-DR 1
Gene expression data from 22Rv1 Docetaxel-resistant cells.


title: DU145 parental sensitive 1

description:
DU145 1
Gene expression data from DU145 parental Docetaxel-sensitive cells.


title: DU145 Docetaxel resistant 2

description:
DU145-DR 2
Gene expression data from DU145 Docetaxel-resistant cells.


title: Scrambled shRNA knockdown, Day 4, biological replicate 1

description: Biological control knockdown replicate 1


title: Transgenic (antisense OsDDM1) plant Replicate 2 vs. Control "Nipponbare" plant Replicate 2

city: Tsukuba

first: Naoki

last: Kishimoto

state: Ibaraki

address: 2-1-2 Kannondai

department: Agrogenomics Research Center

country: Japan

institute: National Institute of Agrobiological Sciences

description: Control biological replicate 2 vs. Transgenic biological replicate 2 (the dye-swap experiment)

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2505B, software G2565BA

data_processing: Data was analyzed by Fearure Extraction software (version 9.1, Agilent)

organism: Oryza sativa

source_name: Young leaves of an antisense OsDDM1 plant

label_protocol: Low RNA inout Lineat Amplification/Labeling Lit (Agilent)

growth_protocol:
The transgenic line “1-17” harboring an antisense construct derived from a rice DDM1a EST clone, C30395_1A (the 5’ end sequence: AU062733), was produced as follows: A sequence of the EST clone (2 kb) was used for the antisense construction and inserted downstream of the 35S promoter of cauliflower mosaic virus in pBI101 binary vector in the antisense orientation with standard cloning techniques; The antisense construct was introduced into Agrobacterium tumefaciens (strain LBA4404); The transfected A. tumefaciens was allowed to infect primary callus derived from scutellum tissue and transgenic lines were generated according to an Agrobacterium-mediated transformation method of rice (Plant Molecular Biology Reporter 15 (1), 1997); The line 1-17 is a few generation descendant from a T0 plant [T0 plant: a plant regenerated from transformed calli].  Transgenic plants 1-17A and 1-17C are sibling individuals in the line 1-17.
Plants were raised in green house for about 2 months in a room of greenhouse.

extract_protocol: Total RNA was extracted from young leaves by using Trizol (Invitrogen).

treatment_protocol: Young leaves were sampled before the boot stage. Cut leaves were frozen using liquid nitrogen immediately after sampling.

tag: genotype/variation

value: an antisense OsDDM1 line "1-17"

tag: cultivar

value: Nipponbare

tag: individual id

value: young leaves

source_name: "Nipponbare" young leaves

value: cultiva "Nipponbare"

tag: indivisual id


title: Transgenic (antisense OsDDM1) plant Replicate 1 vs. Control "Nipponbare" plant Replicate 1

description: Control biological replicate 1 vs. Transgenic biological replicate 1 (the dye-swap experiment)

tag: tissue


title: PVG 48h Control

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: PVG ASCs with PBS control for 48h

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: PVG 48h Control

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: ASCs from 3 LEW and 3 PVG rats of 8-week age and separated ASCs from each individual into four conditions, 24h and 48h control, 24h and 48h with 1 μg/ml LPS stimulation.

tag: strains

value: Piebald Virol Glaxo

value: adipose-derived mesenchymal stem cells (ASCs)


title: PVG 48h LPS

description: PVG ASCs with 1 μg/ml LPS treatment for 48h

source_name: PVG 48h LPS


title: LEW 24h LPS

description: LEW ASCs with 1 μg/ml LPS treatment for 24h

source_name: LEW 24h LPS

value: Lewis/Jms


title: PVG 24h Control

description: PVG ASCs with PBS control for 24h

source_name: PVG 24h Control


title: Control "Nipponbare" plant Replicate 2 vs. Transgenic (antisense OsDDM1) plant Replicate 2

description: Control biological replicate 2 vs. Transgenic biological replicate 2.

value: wildtype


title: PVG 24h LPS

description: PVG ASCs with 1 μg/ml LPS treatment for 24h

source_name: PVG 24h LPS


title: LEW 48h LPS

description: LEW ASCs with 1 μg/ml LPS treatment for 48h

source_name: LEW 48h LPS


title: Control "Nipponbare" plant Replicate 1 vs. Transgenic (antisense OsDDM1) plant Replicate 1

description: Control biological replicate 1 vs. Transgenic biological replicate 1.


title: Rac2-/- Macrophages- Normoxia 5

city: San Diego

first: Lei

last: Bao

state: CA

address: 3855 Health Sciences Drive

department: Cancer Center

institute: UCSD

hyb_protocol: RNA was hybridized to Affymetrix Mouse Genome 1.0 ST array using affymetryx instruction manual. The hybridization cocktail containing fragmented and labeled RNA, hybridization mix and hybridization controls were heated at  95°C for 5 min, and was allowed to hybridize for 16 hrs.

scan_protocol: Scanning was performed on Affymetryx gene chip scanner 7G

data_processing: bioconductor/RMA

source_name: Rac2-/- Macrophages grown on MCSF

label_protocol: Invitro  transcription was performed to label RNA, using IVT mastermix according to Affimetryx instructions.This reaction mixture was incubated for 16 hrs at 40°C using the program for IVT.

growth_protocol: Bone marrow-derived macrophages were generated by flushing the bone marrow cavity with culture media (RPMI, Invitrogen, Rockville, MD). Following centrifugation at 1500 rpm, resuspended cells were lysed in red blood cell lysis buffer (0.155 M ammonium chloride, 0.01 M potassium bicarbonate, and 0.1 M EDTA) and kept at room temperature for 5 min. Following centrifugation, cells were resuspended in macrophage medium (RPMI) supplemented with 20% fetal bovine serum, 1% penicillin/streptomycin. Fibroblasts were allowed to adhere for 4 h at 37 °C, and the nonadherent cells were transferred to another flask. This step was repeated after overnight incubation at 37 °C and were allowed to grow on RPMI media containing 20% FBS and 50 ng/ml M-CSF. On day 8, most of the adhering cells are macrophages (>80% MAC1-positive cells and 100% phagocytic activity via FcγRII/III).

extract_protocol: Total RNA was isolated from bone marrow derived macrophages using the Qiagen RNAeasy kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. 100ng of RNA is used for labelling. RNA integrity was checked for all the samples and they have RIN no. between 8-9.

treatment_protocol: Macrophages were kept under normoxic conditions 16% O2, 37°C for 8 days. No treatment was provided they were used as such for RNA isolation.

value: Bone marrow derived macrophages

value: male

tag: strain

value: grown on MCSF for 7 days


title: WT- Macrophages- Normoxia 3

source_name: WT Macrophages grown on MCSF

value: WT mice


title: WT- Macrophages- Normoxia 4


title: Rac2-/- Macrophages- Normoxia 4


title: Rac2-/- Macrophages- Normoxia 1


title: RPE/choroid Aged Cfh-/- rep1

city: Copenhagen

first: Carsten

last: Faber

address: Blegdamsvej 3

department: Fac. of Health Science, ISIM

country: Denmark

institute: University of Copenhagen

description: SAMPLE 29

hyb_protocol: Standard protocol

scan_protocol: Standard protocol

data_processing: Expression Console 1.1 (Affymetrix)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: TRIzol reagent followed by RNeasy mini spin columns and DNase I treatment.

tag: strain background

value: Cfh-/-

tag: age group

value: aged

value: retinal pigment epithelium (RPE)/choroid


title: RPE/choroid Aged WT rep4

description: SAMPLE 28

value: WT


title: WT- Macrophages- Normoxia 2


title: LEW 24h Control

description: LEW ASCs with PBS control for 24h

source_name: LEW 24h Control


title: RPE/choroid Aged Cfh-/- rep4

description: SAMPLE 32


title: Rac2-/- Macrophages- Normoxia 2


title: LEW 48h Control

description: LEW ASCs with PBS control for 48h

source_name: LEW 48h Control


title: RPE/choroid Aged Cfh-/- rep3

description: SAMPLE 31


title: WT- Macrophages- Normoxia 5


title: Rac2-/- Macrophages- Normoxia 3


title: RPE/choroid Aged Cfh-/- rep2

description: SAMPLE 30


title: WT- Macrophages- Normoxia 1


title: RPE/choroid Aged WT rep1

description: SAMPLE 25


title: RPE/choroid Aged WT rep2

description: SAMPLE 26


title: RPE/choroid Young Cfh-/- rep2

description: SAMPLE 22

value: young


title: RPE/choroid Young WT rep3

description: SAMPLE 19


title: RPE/choroid Young Cfh-/- rep1

description: SAMPLE 21


title: RPE/choroid Aged WT rep3

description: SAMPLE 27


title: RPE/choroid Young WT rep1

description: SAMPLE 17


title: NR Aged Cfh-/- rep3

description: SAMPLE 15

value: neuroretina


title: NR Aged Cfh-/- rep4

description: SAMPLE 16


title: NR Aged Cfh-/- rep2

description: SAMPLE 14


title: RPE/choroid Young Cfh-/- rep4

description: SAMPLE 24


title: NR Young Cfh-/- rep1

description: SAMPLE 5


title: RPE/choroid Young WT rep2

description: SAMPLE 18


title: NR Aged WT rep2

description: SAMPLE 10


title: RPE/choroid Young WT rep4

description: SAMPLE 20


title: RPE/choroid Young Cfh-/- rep3

description: SAMPLE 23


title: NR Young Cfh-/- rep3

description: SAMPLE 7


title: NR Aged WT rep1

description: SAMPLE 9


title: NR Aged Cfh-/- rep1

description: SAMPLE 13


title: NR Young WT rep3

description: SAMPLE 3


title: NR Young Cfh-/- rep4

description: SAMPLE 8


title: NR Aged WT rep3

description: SAMPLE 11


title: NR Young Cfh-/- rep2

description: SAMPLE 6


title: NR Aged WT rep4

description: SAMPLE 12


title: NR Young WT rep1

description: SAMPLE 1


title: NR Young WT rep2

description: SAMPLE 2


title: CRC904

city: Boston

first: Levi

last: Waldron

state: MA

address: 655 Huntington Avenue

department: Biostatistics

institute: Harvard School of Publich Health

hyb_protocol: Standard Illumina DASL hybridization protocol

scan_protocol: Standard Illumina DASL scanning protocol

data_processing: Processed data were log2-transformed then quantile normalized using the lumi Bioconductor package.  Probes not present (p<0.01) in at least 10% of samples, and samples not passing quality control, were eliminated prior to quantile normalization, so are shown as null.

source_name: FFPE tissue sample (FFPE-preserved CRC tumor)

label_protocol: Refer to the Illumina beadarray Assay System Manual.

extract_protocol: Using formalin-fixed, paraffin-embedded CRC tissues, total RNA was extracted using TRIzol (Invitrogen).

tag: tumor id

tag: tumor location

value: colon

tag: sample age

tag: rna (ng/ul)

value: E

tag: plate


title: CRC926

value: F


title: CRC893

value: rectum

value: D


title: NR Young WT rep4

description: SAMPLE 4


title: CRC1020

value: G


title: CRC981

value: C


title: CRC923


title: CRC886

value: H


title: CRC969


title: CRC1014


title: CRC870


title: CRC958


title: CRC983


title: CRC957

value: B


title: CRC1016


title: CRC980


title: CRC1011


title: CRC1007


title: CRC1009


title: CRC885


title: CRC1010


title: CRC1000


title: CRC971


title: CRC1015


title: CRC996


title: CRC1003


title: CRC984


title: CRC972


title: CRC959


title: CRC1013


title: CRC1002


title: CRC1004


title: CRC1005


title: CRC1038


title: CRC1024


title: CRC1001


title: CRC880


title: CRC997


title: CRC973


title: CRC999


title: CRC998


title: CRC1026


title: CRC960


title: CRC1006


title: CRC995


title: CRC994


title: CRC1008


title: CRC1012


title: CRC968


title: CRC956


title: CRC954


title: CRC953


title: CRC955


title: CRC985


title: CRC951


title: CRC991


title: CRC992


title: CRC949


title: CRC950


title: CRC970


title: CRC947


title: CRC943


title: CRC961


title: CRC986


title: CRC878


title: CRC944


title: CRC946


title: CRC1022


title: CRC942


title: CRC945


title: CRC948


title: CRC938


title: CRC976


title: CRC941


title: CRC940


title: CRC937


title: CRC877


title: CRC933


title: CRC988


title: CRC987


title: CRC939


title: CRC934


title: CRC936


title: CRC1023


title: CRC982


title: CRC990


title: CRC935


title: CRC989


title: CRC929


title: CRC928


title: CRC922


title: CRC927


title: CRC978


title: CRC975


title: CRC979


title: CRC977


title: CRC931


title: CRC930


title: CRC925


title: CRC875


title: CRC924


title: CRC921


title: CRC974


title: CRC919


title: CRC920


title: CRC917


title: CRC918


title: CRC913


title: CRC915


title: CRC916


title: CRC914


title: CRC873


title: CRC906


title: CRC963


title: CRC912


title: CRC908


title: CRC965


title: CRC911


title: CRC907


title: CRC910


title: CRC966


title: CRC1019

value: A


title: CRC909


title: CRC901


title: CRC905


title: CRC903


title: CRC962


title: CRC1018


title: CRC871


title: CRC967


title: CRC902


title: CRC1017


title: CRC1021


title: CRC896


title: CRC897


title: CRC952


title: CRC891


title: CRC895


title: CRC892


title: CRC819


title: CRC842


title: CRC899


title: CRC826


title: CRC890


title: CRC790


title: CRC889


title: CRC847


title: CRC855


title: CRC825


title: CRC810


title: CRC841


title: CRC818


title: CRC866


title: CRC848


title: CRC780


title: CRC894


title: CRC811


title: CRC861


title: CRC862


title: CRC797


title: CRC803


title: CRC834


title: CRC789


title: CRC860


title: CRC796


title: CRC869


title: CRC854


title: CRC840


title: CRC824


title: CRC777


title: CRC809


title: CRC816


title: CRC839


title: CRC794


title: CRC802


title: CRC817


title: CRC823


title: CRC788


title: CRC778


title: CRC846


title: CRC853


title: CRC865


title: CRC795


title: CRC776


title: CRC787


title: CRC801


title: CRC859


title: CRC807


title: CRC845


title: CRC808


title: CRC867


title: CRC852


title: CRC835


title: CRC815


title: CRC800


title: CRC830


title: CRC793


title: CRC844


title: CRC781


title: CRC858


title: CRC786


title: CRC838


title: CRC822


title: CRC851


title: CRC814


title: CRC806


title: CRC828


title: CRC850


title: CRC832


title: CRC857


title: CRC785


title: CRC837


title: CRC799


title: CRC843


title: CRC805


title: CRC813


title: CRC775


title: CRC774


title: CRC784


title: CRC868


title: CRC833


title: CRC836


title: CRC792


title: CRC812


title: CRC820


title: CRC856


title: CRC821


title: CRC791


title: CRC827


title: CRC849


title: CRC783


title: CRC773


title: CRC761


title: CRC715


title: CRC760


title: CRC754


title: CRC804


title: CRC772


title: CRC726


title: CRC700


title: CRC680


title: CRC708


title: CRC900


title: CRC737


title: CRC729


title: CRC687


title: CRC771


title: CRC763


title: CRC898


title: CRC699


title: CRC748


title: CRC798


title: CRC679


title: CRC721


title: CRC753


title: CRC686


title: CRC770


title: CRC714


title: CRC758


title: CRC743


title: CRC706


title: CRC707


title: CRC713


title: CRC736


title: CRC720


title: CRC831


title: CRC692


title: CRC752


title: CRC769


title: CRC698


title: CRC678


title: CRC747


title: CRC691


title: CRC685


title: CRC751


title: CRC768


title: CRC745


title: CRC719


title: CRC677


title: CRC705


title: CRC742


title: CRC762


title: CRC746


title: CRC697


title: CRC723


title: CRC741


title: CRC735


title: CRC712


title: CRC725


title: CRC724


title: CRC765


title: CRC728


title: CRC684


title: CRC782


title: CRC696


title: CRC757


title: CRC703


title: CRC676


title: CRC718


title: CRC704


title: CRC711


title: CRC740


title: CRC695


title: CRC683


title: CRC675


title: CRC739


title: CRC733


title: CRC727


title: CRC717


title: CRC694


title: CRC764


title: CRC689


title: CRC710


title: CRC767


title: CRC750


title: CRC702


title: CRC734


title: CRC682


title: CRC749


title: CRC744


title: CRC829


title: CRC766


title: CRC652


title: CRC681


title: CRC716


title: CRC701


title: CRC709


title: CRC732


title: CRC688


title: CRC738


title: CRC693


title: CRC673


title: CRC756


title: CRC641


title: CRC598


title: CRC613


title: CRC634


title: CRC659


title: CRC670


title: CRC863


title: CRC606


title: CRC658


title: CRC864


title: CRC666


title: CRC584


title: CRC605


title: CRC625


title: CRC647


title: CRC640


title: CRC597


title: CRC657


title: CRC651


title: CRC633


title: CRC583


title: CRC646


title: CRC612


title: CRC592


title: CRC591


title: CRC665


title: CRC617


title: CRC664


title: CRC632


title: CRC667


title: CRC624


title: CRC604


title: CRC639


title: CRC590


title: CRC611


title: CRC645


title: CRC618


title: CRC581


title: CRC631


title: CRC603


title: CRC582


title: CRC623


title: CRC638


title: CRC630


title: CRC650


title: CRC589


title: CRC663


title: CRC637


title: CRC656


title: CRC622


title: CRC596


title: CRC672


title: CRC602


title: CRC610


title: CRC616


title: CRC662


title: CRC588


title: CRC643


title: CRC671


title: CRC644


title: CRC690


title: CRC655


title: CRC668


title: CRC661


title: CRC580


title: CRC609


title: CRC601


title: CRC649


title: CRC579


title: CRC629


title: CRC587


title: CRC621


title: CRC669


title: CRC779


title: CRC595


title: CRC620


title: CRC608


title: CRC594


title: CRC628


title: CRC578


title: CRC600


title: CRC636


title: CRC586


title: CRC660


title: CRC648


title: CRC642


title: CRC635


title: CRC653


title: CRC599


title: CRC593


title: CRC619


title: CRC627


title: CRC537


title: CRC575


title: CRC506


title: CRC615


title: CRC551


title: CRC577


title: CRC511


title: CRC614


title: CRC564


title: CRC545


title: CRC755


title: CRC585


title: CRC530


title: CRC544


title: CRC500


title: CRC607


title: CRC493


title: CRC487


title: CRC558


title: CRC559


title: CRC536


title: CRC510


title: CRC505


title: CRC529


title: CRC568


title: CRC557


title: CRC543


title: CRC492


title: CRC572


title: CRC522


title: CRC499


title: CRC504


title: CRC549


title: CRC556


title: CRC527


title: CRC528


title: CRC562


title: CRC498


title: CRC486


title: CRC542


title: CRC574


title: CRC517


title: CRC516


title: CRC514


title: CRC491


title: CRC519


title: CRC566


title: CRC521


title: CRC485


title: CRC563


title: CRC567


title: CRC535


title: CRC576


title: CRC555


title: CRC484


title: CRC509


title: CRC525


title: CRC515


title: CRC571


title: CRC548


title: CRC490


title: CRC497


title: CRC496


title: CRC565


title: CRC508


title: CRC483


title: CRC526


title: CRC503


title: CRC512


title: CRC540


title: CRC553


title: CRC541


title: CRC533


title: CRC524


title: CRC554


title: CRC561


title: CRC573


title: CRC570


title: CRC502


title: CRC539


title: CRC547


title: CRC532


title: CRC520


title: CRC501


title: CRC482


title: CRC495


title: CRC569


title: CRC552


title: CRC538


title: CRC523


title: CRC481


title: CRC441


title: CRC414


title: CRC470


title: CRC489


title: CRC401


title: CRC480


title: CRC421


title: CRC469


title: CRC408


title: CRC518


title: CRC455


title: CRC546


title: CRC494


title: CRC507


title: CRC531


title: CRC463


title: CRC560


title: CRC479


title: CRC488


title: CRC464


title: CRC448


title: CRC393


title: CRC472


title: CRC447


title: CRC454


title: CRC395


title: CRC413


title: CRC471


title: CRC440


title: CRC430


title: CRC429


title: CRC446


title: CRC478


title: CRC392


title: CRC450


title: CRC439


title: CRC477


title: CRC386


title: CRC459


title: CRC412


title: CRC452


title: CRC424


title: CRC420


title: CRC427


title: CRC468


title: CRC399


title: CRC436


title: CRC461


title: CRC425


title: CRC407


title: CRC462


title: CRC419


title: CRC453


title: CRC467


title: CRC451


title: CRC391


title: CRC428


title: CRC460


title: CRC406


title: CRC435


title: CRC513


title: CRC431


title: CRC405


title: CRC418


title: CRC426


title: CRC445


title: CRC476


title: CRC444


title: CRC423


title: CRC398


title: CRC475


title: CRC416


title: CRC389


title: CRC466


title: CRC443


title: CRC457


title: CRC404


title: CRC433


title: CRC473


title: CRC438


title: CRC411


title: CRC390


title: CRC397


title: CRC400


title: CRC449


title: CRC434


title: CRC417


title: CRC410


title: CRC388


title: CRC474


title: CRC465


title: CRC403


title: CRC442


title: CRC355


title: CRC315


title: CRC432


title: CRC437


title: CRC402


title: CRC387


title: CRC422


title: CRC731


title: CRC362


title: CRC409


title: CRC415


title: CRC335


title: CRC369


title: CRC383


title: CRC394


title: CRC328


title: CRC123


title: CRC456


title: CRC458


title: CRC304


title: CRC377


title: CRC730


title: CRC341


title: CRC307


title: CRC340


title: CRC117


title: CRC327


title: CRC354


title: CRC722


title: CRC368


title: CRC306


title: CRC360


title: CRC359


title: CRC385


title: CRC326


title: CRC292


title: CRC334


title: CRC299


title: CRC384


title: CRC375


title: CRC116


title: CRC314


title: CRC380


title: CRC99


title: CRC367


title: CRC333


title: CRC361


title: CRC353


title: CRC366


title: CRC318


title: CRC346


title: CRC305


title: CRC95


title: CRC374


title: CRC313


title: CRC382


title: CRC325


title: CRC298


title: CRC324


title: CRC381


title: CRC357


title: CRC291


title: CRC323


title: CRC330


title: CRC338


title: CRC312


title: CRC303


title: CRC396


title: CRC347


title: CRC344


title: CRC310


title: CRC351


title: CRC358


title: CRC331


title: CRC373


title: CRC365


title: CRC352


title: CRC364


title: CRC285


title: CRC332


title: CRC317


title: CRC372


title: CRC348


title: CRC337


title: CRC343


title: CRC345


title: CRC309


title: CRC370


title: CRC302


title: CRC371


title: CRC321


title: CRC295


title: CRC349


title: CRC363


title: CRC322


title: CRC336


title: CRC301


title: CRC356


title: CRC297


title: CRC279


title: CRC300


title: CRC296


title: CRC197


title: CRC288


title: CRC241


title: CRC259


title: CRC376


title: CRC267


title: CRC208


title: CRC378


title: CRC350


title: CRC205


title: CRC182


title: CRC379


title: CRC308


title: CRC189


title: CRC250


title: CRC329


title: CRC316


title: CRC278


title: CRC266


title: CRC249


title: CRC252


title: CRC204


title: CRC240


title: CRC196


title: CRC294


title: CRC195


title: CRC276


title: CRC286


title: CRC248


title: CRC181


title: CRC287


title: CRC258


title: CRC264


title: CRC203


title: CRC243


title: CRC277


title: CRC180


title: CRC265


title: CRC207


title: CRC270


title: CRC239


title: CRC311


title: CRC293


title: CRC188


title: CRC256


title: CRC242


title: CRC202


title: CRC238


title: CRC201


title: CRC247


title: CRC194


title: CRC193


title: CRC255


title: CRC320


title: CRC284


title: CRC206


title: CRC275


title: CRC179


title: CRC187


title: CRC235


title: CRC271


title: CRC237


title: CRC246


title: CRC186


title: CRC283


title: CRC262


title: CRC319


title: CRC254


title: CRC200


title: CRC263


title: CRC274


title: CRC185


title: CRC342


title: CRC236


title: CRC245


title: CRC290


title: CRC178


title: CRC192


title: CRC269


title: CRC177


title: CRC184


title: CRC260


title: CRC253


title: CRC280


title: CRC191


title: CRC281


title: CRC234


title: CRC273


title: CRC257


title: CRC244


title: CRC272


title: CRC251


title: CRC198


title: CRC190


title: CRC261


title: CRC226


title: CRC268


title: CRC289


title: CRC183


title: CRC199


title: CRC231


title: CRC174


title: CRC233


title: CRC158


title: CRC217


title: CRC151


title: CRC166


title: CRC143


title: CRC114


title: CRC173


title: CRC225


title: CRC150


title: CRC157


title: CRC104


title: CRC124


title: CRC110


title: CRC142


title: CRC164


title: CRC141


title: CRC149


title: CRC224


title: CRC165


title: CRC214


title: CRC122


title: CRC230


title: CRC172


title: CRC156


title: CRC135


title: CRC215


title: CRC112


title: CRC113


title: CRC229


title: CRC105


title: CRC126


title: CRC103


title: CRC220


title: CRC232


title: CRC223


title: CRC111


title: CRC171


title: CRC176


title: CRC163


title: CRC140


title: CRC148


title: CRC134


title: CRC109


title: CRC228


title: CRC102


title: CRC222


title: CRC121


title: CRC147


title: CRC162


title: CRC120


title: CRC133


title: CRC155


title: CRC170


title: CRC212


title: CRC211


title: CRC216


title: CRC161


title: CRC130


title: CRC131


title: CRC175


title: CRC169


title: CRC139


title: CRC221


title: CRC132


title: CRC154


title: CRC146


title: CRC119


title: CRC108


title: CRC138


title: CRC219


title: CRC129


title: CRC210


title: CRC160


title: CRC168


title: CRC107


title: CRC128


title: CRC209


title: CRC218


title: CRC106


title: CRC227


title: CRC152


title: CRC144


title: CRC137


title: CRC125


title: CRC86


title: CRC213


title: CRC115


title: CRC159


title: CRC94


title: CRC118


title: CRC145


title: CRC63


title: CRC136


title: CRC127


title: CRC74


title: CRC101


title: CRC153


title: CRC167


title: CRC36


title: CRC59


title: CRC39


title: CRC78


title: CRC49


title: CRC8


title: CRC16


title: CRC24


title: CRC93


title: CRC58


title: CRC23


title: CRC60


title: CRC46


title: CRC35


title: CRC7


title: CRC85


title: CRC76


title: CRC34


title: CRC56


title: CRC67


title: CRC69


title: CRC84


title: CRC92


title: CRC28


title: CRC15


title: CRC57


title: CRC77


title: CRC22


title: CRC25


title: CRC45


title: CRC6


title: CRC91


title: CRC73


title: CRC14


title: CRC44


title: CRC55


title: CRC66


title: CRC83


title: CRC5


title: CRC32


title: CRC100


title: CRC54


title: CRC90


title: CRC21


title: CRC31


title: CRC26


title: CRC4


title: CRC65


title: CRC43


title: CRC48


title: CRC52


title: CRC47


title: CRC98


title: CRC72


title: CRC12


title: CRC81


title: CRC82


title: CRC89


title: CRC64


title: CRC53


title: CRC20


title: CRC71


title: CRC42


title: CRC13


title: CRC11


title: CRC19


title: CRC97


title: CRC30


title: CRC3


title: CRC18


title: CRC87


title: CRC27


title: CRC79


title: CRC80


title: CRC10


title: CRC38


title: CRC61


title: CRC62


title: CRC2


title: CRC68


title: CRC75


title: CRC51


title: CRC96


title: CRC70


title: CRC1


title: CRC40


title: CRC50


title: CRC41


title: CRC17


title: CRC29


title: CRC9


title: 5511977013_E

city: Herston

first: Amy

middle: McCart

last: Reed

state: Queensland

address: Royal Brisbane & Women's Hospital Campus

department: UQ Centre for Clinical Research

country: Australia

institute: University of Queensland

description: replicate 1

hyb_protocol: Refer to the Illumina beadarray Assay System Manual.

data_processing: Processed data were log2-transformed then quantile normalized using the lumi Bioconductor package.

source_name: lymph node metastasis

extract_protocol: Using formalin-fixed, paraffin-embedded HCC tissues, total RNA was extracted using Roche High Pure FFPE Kit.

value: WL13 LN

value: LobLN

value: AUG-10 A

value: FFPE tissue sample

value: no


title: 5511977013_C

description: replicate 2

scan_protocol: Refer to the Illumina beadarray Assay System Manual.

source_name: positive control

value: positive (10A)


title: 5511977013_G

description: replicate 1


title: 5511977013_F

description: replicate 1


title: 5511977013_D

description: replicate 1

value: ML30 LN


title: 5511977013_H

description: replicate 1

value: WL04 LN


title: 5511977013_B

description: replicate 2

value: WL93 LN


title: 5511977013_A

description: replicate 2

value: WL113 LN


title: 5505171020_E

description: replicate 2


title: 5505171021_F

description: replicate 1


title: 5505171021_A

description: replicate 1


title: 5505171021_E

description: replicate 1


title: 5505171020_F

description: replicate 1

value: WL100 LN


title: 5505171020_D

description: replicate 1

value: WL177 LN


title: 5505171019_G

description: replicate 2


title: 5505171019_F

description: replicate 1

value: WL172 LN


title: 5505171021_B

description: replicate 1


title: 5505171020_C

description: replicate 1


title: 5505171020_B

description: replicate 3


title: 5505171020_G

description: replicate 1


title: 5505171019_B

description: replicate 2


title: 5505171011_G

description: replicate 2

source_name: negative control

value: Negative


title: 5505171011_H

description: replicate 1


title: 5505171021_C

description: replicate 1


title: 5505171020_H

description: replicate 3


title: 5505171021_G

description: replicate 1


title: 5505171021_H

description: replicate 2

value: ML37 LN


title: 5505171019_C

description: replicate 1

value: WL95 LN


title: 5505171021_D

description: replicate 1


title: 5505171019_E

description: replicate 1


title: 5505171019_D

description: replicate 1

value: WL121 LN


title: 5505171019_A

description: replicate 1

value: ML45 LN


title: 5505171020_A

description: replicate 1

value: LobLN


title: 5505171019_H

description: replicate 1

value: WL179 LN

value: AUG-10 A


title: 5505171011_F

description: replicate 1

value: ML18 LN

value: FFPE tissue sample

value: no


title: 5505171011_E

description: replicate 1


title: 5505171011_D

description: replicate 2

value: WL11 LN


title: 5505171011_B

description: replicate 2


title: 5505171010_E

description: replicate 1


title: 5505171010_D

description: replicate 1

value: WL84 LN


title: 5505171010_H

description: replicate 1

value: WL10 LN


title: 5505171010_C

description: replicate 1

value: WL15 LN


title: WT1-cy3_ccpA1-cy5

type: genomic

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description:
Raw data file: WT1-cy3_ccpA1-cy5.gpr
Biological replicate 1 of 3.

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix Pro 6 dual-channel laser scanner

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

molecule: genomic DNA

organism: Clostridioides difficile

source_name: strain C630E grown 6h in TYG (reference)

label_protocol: DNA samples were labelled using the Bioprime plus array CGH indirect genomic labeling system (invitrogen)

growth_protocol: C.difficile strains were grown for 6 hours in TYG medium.

extract_protocol: Formaldehyde 1% 10min, Glycine 400mM, Centrifugation, IP buffer, Sonication, Immunoprecipitation using ccpA antibodies and Pan mouse immunoglobulin G magnetic beads, proteinase K, DNA purification kit.

value: wild type

tag: chip antibody

value: anti-ccpA antibody (made in-house)

source_name: ccpA mutant grown 6h in TYG (test)

value: ccpA mutant


title: 5505171011_A

description: replicate 1


title: 5505171010_F

description: replicate 1


title: 5505171010_A

description: replicate 2


title: 5505171010_B

description: replicate 1

value: WL178 LN


title: WT2-cy3_ccpA2-cy5

description:
Raw data file: WT2-cy3_ccpA2-cy5.gpr
Biological replicate 2 of 3.

source_name: strain JIR8094 (CD630E) grown 6h in TYG (reference)


title: 5505171010_G

description: replicate 1

value: WL166 LN


title: WT3-cy5_ccpA3-cy3

description:
Raw data file: WT3-cy5_ccpA3-cy3.gpr
Biological replicate 3 of 3.


title: 5505171011_C

description: replicate 1

value: WL129 LN


title: 5505171009_G

description: replicate 1


title: 5505171009_H

description: replicate 1


title: 5505171009_F

description: replicate 1

value: WL93 LN


title: 5505171009_D

description: replicate 2

value: ML14 LN

value: LobLN


title: 5505171009_C

description: replicate 1

value: AUG-10 A


title: CRC88

value: rectum

value: B


title: 5505171008_H

description: replicate 1

value: FFPE tissue sample

value: no


title: 5505171009_B

description: replicate 1

value: ML36 LN


title: 5826611032_J

description: replicate 1

source_name: primary breast tumor

value: MCF7 heat

value: Feb Trial

value: yes


title: 5826611032_K

description: replicate 1

source_name: pooled breast positive control

value: PR POOL HEAT


title: 5826611032_I

description: replicate 1


title: 5505171009_A

description: replicate 1


title: 5826611032_G

description: replicate 1

value: BR POOL HEAT


title: 5505171009_E

description: replicate 1


title: 5826611032_L

description: replicate 1


title: 5826611032_H

description: replicate 1


title: 5505171008_G

description: replicate 1

value: WL174 LN


title: 5826611032_E

description: replicate 1

value: PR POOL


title: 5505171008_D

description: replicate 1

value: WL165 LN


title: 5826611032_C

description: replicate 1

value: Negative


title: 5505171008_A

description: replicate 1

value: ML39 LN


title: 5505171008_C

description: replicate 1

value: WL183 LN

value: LobLN


title: 5505171008_E

description: replicate 1

value: AUG-10 A


title: 5505171008_F

description: replicate 1

value: WL131 LN


title: 5826611032_A

description: replicate 1

value: BR POOL

value: FFPE tissue sample


title: 5826611032_B

description: replicate 1

value: MCF7 intact

value: no


title: 5826611032_F

description: replicate 1

value: MCF7 FFPE

value: Feb Trial


title: 5505171007_H

description: replicate 1

value: positive (10A)


title: 5505171008_B

description: replicate 1

value: WL111 LN


title: 5826611009_J

description: replicate 2

value: PR POOL HEAT

value: yes


title: 5826611009_L

description: replicate 2


title: 5505171007_E

description: replicate 1


title: 5505171007_F

description: replicate 1

value: WL14 LN


title: 5505171007_G

description: replicate 1


title: 5826611009_I

description: replicate 2

value: MCF7 heat


title: 5826611009_D

description: replicate 2

value: BR POOL HEAT


title: 5505171007_D

description: replicate 1


title: 5826611009_H

description: replicate 2


title: 5505171007_B

description: replicate 2


title: 5826611009_F

description: replicate 2


title: 5826611009_K

description: replicate 2


title: 5826611009_C

description: replicate 2


title: 5826611009_E

description: replicate 2

value: PR POOL


title: 5826611009_G

description: replicate 2


title: 5826611032_D

description: replicate 1


title: 5505171007_A

description: replicate 1

value: ML76 LN

value: LobLN


title: 5505171006_H

description: replicate 1

value: AUG-10 A


title: 5505171006_G

description: replicate 1


title: 5655639060_L

description: replicate 2

value: Dec Trial


title: 5505171006_E

description: replicate 1

value: FFPE tissue sample


title: 5826611009_A

description: replicate 2

value: Negative


title: 5505171006_D

description: replicate 1

value: WL176 LN

value: no


title: 5826611009_B

description: replicate 2

value: MCF7 intact

value: Feb Trial


title: 5505171006_C

description: replicate 1


title: 5655639060_J

description: replicate 2


title: 5505171006_A

description: replicate 1

value: WL11 LN


title: 5655639060_I

description: replicate 2


title: 5655639060_G

description: replicate 2


title: 5505171003_H

description: replicate 1

value: WL189 LN


title: 5505171003_G

description: replicate 1

value: WL113 LN


title: 5655639060_B

description: replicate 1


title: 5655639060_K

description: replicate 3


title: 5655639060_F

description: replicate 2


title: 5505171006_B

description: replicate 1

value: WL90 LN


title: 5505171003_F

description: replicate 1

value: WL87 LN


title: 5505171003_E

description: replicate 1


title: 5655639060_C

description: replicate 2


title: 5655639060_E

description: replicate 2


title: 5505171003_D

description: replicate 1

value: WL32 LN


title: 5655508058_L

description: replicate 2


title: 5655639060_D

description: replicate 1


title: 5655639060_A

description: replicate 1


title: 5505171003_A

description: replicate 2

value: ML60 LN


title: 5505171006_F

description: replicate 1

value: WL110 LN


title: 5655639060_H

description: replicate 1


title: 5655508058_I

description: replicate 2


title: 5505171002_H

description: replicate 1

value: LobLN


title: 5655508058_K

description: replicate 2


title: 5505171002_F

description: replicate 1

value: AUG-10 A


title: 5505171003_B

description: replicate 1


title: 5141777059_G

description: replicate 1

source_name: lung

value: 8 G (lung)

value: Autopsy

value: AUG-10 B


title: 5505171002_A

description: replicate 1

value: ML37 LN

value: FFPE tissue sample


title: 5655508058_B

description: replicate 1

value: Dec Trial

value: no


title: 5505171003_C

description: replicate 1


title: 5655508058_E

description: replicate 1


title: 5655508058_D

description: replicate 1


title: 5505171002_D

description: replicate 1


title: 5505171002_G

description: replicate 1

value: WL126 LN


title: 5505171002_E

description: replicate 1


title: 5655508058_H

description: replicate 1


title: 5655508058_G

description: replicate 1


title: 5655508058_J

description: replicate 2


title: 5505171002_B

description: replicate 1


title: 5505171002_C

description: replicate 1


title: 5141777059_H

description: replicate 1

source_name: liver

value: 10 D 2 (liver)


title: 5141777059_E

description: replicate 2

value: Negative


title: 5141777059_F

description: replicate 2


title: 5141777059_D

description: replicate 2

value: 10 D 1 (liver)