title: S0849-00147 D1 / R1

tag: tissue

tag: curative resection

tag: dukes

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

value: CRISC

tag: braf (v600e)

value: MT


title: PBMC Genomic DNA G00019

status: Public on Dec 31 2017

type: genomic

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto Scarborough

description: CFS Genomic DNA

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions

tag: Sex

value: female

tag: disease state

value: CFS


title: SAMPLE 80

type: RNA

city: Birmingham

first: John

middle: Kenneth

last: Colbourne

state: West Midlands

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description:
SAMPLE 80
Hybridized with SAMPLE 88 on the array

hyb_protocol: Labeled products were pooled to serve as a Master Mix for Array set. The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybrization master for a given source and biological replicate was applied to each of 12 subarrays with the appropriate Sample Tracking Control (STC) following protocols described in Lopez, J.A. and J.K. Colbourne. 2011. Dual-Labeled Expression Microarray Protocol for High-Throughput Genomic Investigations. CGB Technical Report 2011-02. doi:10.2506/cgbtr-201102.

scan_protocol: Axon GenePix 4200 Professional, 5 micron resolution.

data_processing: Raw signal intensity extract with NimbleScan 2.6 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.

molecule: total RNA

organism: Wyeomyia smithii

source_name: PBSD10 Replicate 1

label_protocol: DNA labeling using 1 O.D. CY-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA.

growth_protocol: The mosquitoes were maintained as diapausing larvae on an 8:16 light:dark cycle at 21°C and reared on a typical 18:6 light:dark cycle with a sinewave thermoperiod with a maximum temperature of 32°C and minimum temperature of 15°C which lagged the light cycle by 3 hours. Larvae were fed ad lib. a 4:1 mixture by volume of ground freeze-dried brine shrimp (San Franciso Bay Brand, 8239 Enterprise Drive, Neward, CA 94560, USA) and guinea pig chow (Geisler Guine Pig Chow, Sergeant’s Pet Care Products, 10077 S 134th St, Omaha, NE 68138, USA) once a week.  Adults were offered a continuous supply of organic (pesticide free)  raisins as a carbohydrate source.

extract_protocol: Tissue was homogenized using Trizol reagent (Invitrogen) and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

treatment_protocol: Short Day (SD) Day Sampling (ZT10)

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Day Sampling (ZT10)


title: SAMPLE 78

description:
SAMPLE 78
Hybridized with SAMPLE 32 on the array

source_name: PBSD10 Replicate 4


title: S0849-00138 D1 / R1

city: Belfast

first: Wendy

last: Allen

address: 97 Lisburn Road

department: Centre For Cancer Research and Cell Biology

institute: Queen's University Belfast

description: Gene expression data from fresh frozen colorectal cancer patient biopsy

hyb_protocol: Biotinylated cRNA targets were prepared from 3.0 mg of total RNA, according to the GeneChip Expression Analysis Technical Manual : One-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

scan_protocol: Scanner GeneChip 3000 ; Wavelength : 570 nm, size pixel: 1.56 µm ; each chip is scanned once;

data_processing: RMA normalisation (Bioconductor R makecdfenv and affy package) + ComBat (R sva package )

label: biotin

source_name: Fresh frozen colorectal cancer biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Samples stored at -80 C

extract_protocol: total RNA was extracted using Manual-Rneasy Mini (Qiagen)

treatment_protocol: Total RNA was performed according to the manufacturer's instructions.

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

value: Yes

tag: lvi

tag: tumour site

value: Rectum

tag: type of surgery

value: PROCECTOMY

value: C

tag: stage ii\iii

value: IIIA

tag: tstage

tag: nstage

tag: mstage

value: pMx

value: Moderate

value: Dead

tag: cms subgroup

tag: cris subgroup

value: CRISA

value: WT

tag: kras (codons 12, 13, 61)


title: S0849-00137 D1 / R1

tag: tissue

value: Female

value: Left Colon

value: Left colectomy

tag: curative resection

tag: dukes

value: B

value: IIA

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

tag: overall survival time

tag: progression-free survival time

tag: braf (v600e)

value: MT


title: S0849-00140 D1 / R1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

tag: type of surgery

tag: stage ii\iii


title: SAMPLE 79

description:
SAMPLE 79
Hybridized with SAMPLE 87 on the array

source_name: PBSD10 Replicate 2

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Day Sampling (ZT10)


title: SAMPLE 81

description:
SAMPLE 81
Hybridized with SAMPLE 33 & 60 on the array

source_name: PBSD22 Replicate 2

treatment_protocol: Short Day (SD) Night Sampling (ZT22)

value: Night Sampling (ZT22)


title: SAMPLE 75

description:
SAMPLE 75
Hybridized with SAMPLE 30 on the array


title: PBMC Genomic DNA G00151

description: CFS Genomic DNA

tag: disease state

value: CFS


title: SAMPLE 76

description:
SAMPLE 76
Hybridized with SAMPLE 85 on the array


title: S0849-00135 D1 / R1

tag: site

value: Yes

value: Right colon

value: Right Hemicolectomy

tag: curative resection

tag: dukes

value: IIB

tag: tstage

tag: nstage

tag: mstage

value: pMx

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

value: UNK

tag: cris subgroup

value: CRISA

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)


title: S0849-00141 D1 / R1

tag: tissue

value: colorectal cancer biopsy

value: Barcelona

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

tag: type of surgery

value: C

tag: stage ii\iii

value: IIIB

value: Alive

value: MT


title: S0849-00131 D1 / R1

tag: site

value: Female

value: Yes

value: Rectum

tag: curative resection

tag: dukes

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

value: Poor

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

value: CRISB


title: SAMPLE 77

description:
SAMPLE 77
Hybridized with SAMPLE 52 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Day Sampling (ZT10)


title: SAMPLE 73

description:
SAMPLE 73
Hybridized with SAMPLE 25 on the array

source_name: PBSD10 Replicate 3


title: SAMPLE 72

description:
SAMPLE 72
Hybridized with SAMPLE 48 on the array


title: S0849-00160 R1

value: colorectal cancer biopsy

value: SVH Dublin

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Sigmoid

tag: type of surgery

value: Laparoscopic left hemicolectomy

value: B

tag: stage ii\iii

value: IIA

value: Moderate

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)


title: S0849-00134 D1 / R1

tag: tissue

tag: site

value: Barcelona

value: Female

value: No

value: Rectum

value: Sigmoidectomy

tag: curative resection

tag: dukes

value: C

value: IIIB

tag: tstage

tag: nstage

tag: mstage

value: pMx

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

value: Yes

value: CRISA

value: MT


title: PBMC Genomic DNA G00052

description: CFS Genomic DNA

tag: Sex

value: female

tag: disease state

value: CFS


title: SAMPLE 74

description:
SAMPLE 74
Hybridized with SAMPLE 51 on the array

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Day Sampling (ZT10)


title: SAMPLE 71

description:
SAMPLE 71
Hybridized with SAMPLE 83 on the array

tag: tissue


title: S0849-00133 D1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

value: Right colon

tag: type of surgery

value: Right Hemicolectomy

value: B

tag: stage ii\iii

value: IIA

value: Moderate

value: Alive

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)


title: SAMPLE 70

description:
SAMPLE 70
Hybridized with SAMPLE 46 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

tag: population

tag: photoperiod

tag: sampling time


title: S0849-00132 D1 / R1

tag: site

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: Left Colon

value: Sigmoidectomy

tag: curative resection

tag: dukes

value: C

value: IIIB

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

tag: adjuvanttreatment

value: Yes

tag: status alive.dead

tag: recurrence

value: CRISB

value: MT


title: S0849-00130 D1 / R1

tag: tissue

value: colorectal cancer biopsy

value: Barcelona

value: Male

value: No

tag: lvi

tag: tumour site

tag: type of surgery

tag: stage ii\iii

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00136 D1 / R1

tag: site

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: Right colon

value: Right Hemicolectomy

tag: curative resection

tag: dukes

value: B

value: IIA

tag: tstage

tag: nstage

value: pMx

value: Moderate

value: Dead

value: UNK


title: SAMPLE 69

description:
SAMPLE 69
Hybridized with SAMPLE 26 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Day Sampling (ZT10)


title: S0849-00129 D1 / R1

value: colorectal cancer biopsy

value: Barcelona

value: Male

tag: lvi

tag: tumour site

value: Rectum

tag: type of surgery

value: Sigmoidectomy

tag: stage ii\iii

tag: mstage

tag: differentiation

value: Poor

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISA

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)


title: S0849-00128 D1 / R1

tag: tissue

tag: site

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: Yes

tag: evi

tag: curative resection

tag: dukes

value: C

value: IIIC

tag: tstage

tag: nstage

value: pMx

value: Moderate

value: No

value: CRISB

value: MT


title: S0849-00127 D1 / R1

tag: lvi

tag: tumour site

value: Right colon

tag: type of surgery

value: Right Hemicolectomy

value: B

tag: stage ii\iii

value: IIA

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

tag: overall survival time

value: CRISE


title: SAMPLE 68

description:
SAMPLE 68
Hybridized with SAMPLE 54 on the array

source_name: PBLD22 Replicate 2

treatment_protocol: Long Day (LD) Night Sampling (ZT22)

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Night Sampling (ZT22)


title: S0849-00163 R1

value: colorectal cancer biopsy

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: Sigmoid

value: Open Anterior Resection

tag: curative resection

tag: dukes

tag: tstage

tag: nstage

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)


title: S0849-00124 R1

tag: tissue

value: Barcelona

value: No

tag: lvi

value: Yes

tag: tumour site

value: Left Colon

tag: type of surgery

value: Sigmoidectomy

value: C

tag: stage ii\iii

value: IIIB

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

tag: overall survival time

value: CRISD

value: MT


title: SAMPLE 65

description:
SAMPLE 65
Hybridized with SAMPLE 22 on the array

source_name: PBLD22 Replicate 3

tag: Sex

value: female

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Night Sampling (ZT22)


title: SAMPLE 63

description:
SAMPLE 63
Hybridized with SAMPLE 49 on the array

source_name: PBLD22 Replicate 4


title: S0849-00124 D1 / R1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: Right colon

value: Right Hemicolectomy

tag: curative resection

tag: dukes

tag: tstage

tag: nstage

value: pMx

value: Poor

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISA

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)


title: S0849-00122 R1

tag: tissue

value: Florence

tag: lvi

tag: tumour site

value: sigma

tag: type of surgery

value: left hemicolectomy

value: B

tag: stage ii\iii

value: IIA

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

value: No

tag: status alive.dead

value: Dead

tag: recurrence

tag: overall survival time

value: CRISD


title: SAMPLE 66

description:
SAMPLE 66
Hybridized with SAMPLE 86 on the array

source_name: PBLD22 Replicate 1

tag: Sex

value: female

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Night Sampling (ZT22)


title: SAMPLE 64

description:
SAMPLE 64
Hybridized with SAMPLE 21 on the array


title: SAMPLE 61

description:
SAMPLE 61
Hybridized with SAMPLE 47 on the array


title: SAMPLE 59

description:
SAMPLE 59
Hybridized with SAMPLE 15 on the array


title: SAMPLE 58

description:
SAMPLE 58
Hybridized with SAMPLE 45 on the array


title: SAMPLE 62

description:
SAMPLE 62
Hybridized with SAMPLE 82 on the array


title: SAMPLE 67

description:
SAMPLE 67
Hybridized with SAMPLE 84 on the array


title: SAMPLE 60

description:
SAMPLE 60
Hybridized with SAMPLE 81 on the array


title: S0849-00123 R1

description: Gene expression data from fresh frozen colorectal cancer patient biopsy

value: colorectal cancer biopsy

tag: site

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: right colon

value: subtotal colectomy (left right)

tag: curative resection

tag: dukes

value: C

value: IIIB

tag: tstage

tag: nstage

value: Moderate + colloid expression

value: Yes

value: Alive

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISA

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00139 D1 / R1

tag: tissue

value: Barcelona

value: Female

value: No

tag: lvi

tag: tumour site

value: Rectum

tag: type of surgery

value: PROCECTOMY

tag: stage ii\iii

value: IIIC

tag: mstage

tag: differentiation

value: Poor

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

tag: overall survival time

value: UNK

value: CRISB

value: WT

value: MT


title: S0849-00119 R1

value: colorectal cancer biopsy

tag: site

value: Florence

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: rectum

value: RAR

tag: curative resection

tag: dukes

value: B

value: IIA

tag: tstage

tag: nstage

value: adenoca. Colloid express

value: Dead


title: S0849-00115 R1

tag: tissue

value: Female

tag: lvi

tag: tumour site

value: colon

tag: type of surgery

value: intestinal resection

value: C

tag: stage ii\iii

value: IIIB

value: Moderate

value: Yes

value: Alive

value: No

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISD

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00120 R1

value: colorectal cancer biopsy

tag: site

value: Florence

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

value: right colon

value: right hemicolectomy

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

tag: overall survival time

value: CRISA

value: WT

value: MT


title: S0849-00121 R1

tag: tissue

value: Male

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: rectum

tag: type of surgery

value: left hemicolectomy RAR

tag: curative resection

tag: dukes

tag: tstage

tag: nstage

value: UNK

value: CRISC


title: S0849-00114 R1

tag: site

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

value: Colon

value: Intestinal resection

value: B

tag: stage ii\iii

value: IIA

value: Moderate

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00110 R1

tag: tissue

value: colorectal cancer biopsy

value: Female

tag: positive lymph nodes

tag: evi

tag: lvi

value: rectum intraperitoneal

value: RAR

tag: mstage

tag: differentiation

value: colloid

tag: adjuvanttreatment

value: Yes

tag: status alive.dead

value: Alive

tag: recurrence

value: No

tag: overall survival time


title: S0849-00113 R1

tag: site

value: Florence

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

value: X

tag: tumour site

tag: type of surgery

tag: curative resection

tag: dukes

tag: tstage

tag: nstage

value: WT

value: MT


title: SAMPLE 55

description:
SAMPLE 55
Hybridized with SAMPLE 10 on the array

source_name: PBLD10 Replicate 2

treatment_protocol: Long Day (LD) Day Sampling (ZT10)

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Day Sampling (ZT10)


title: SAMPLE 53

description:
SAMPLE 53
Hybridized with SAMPLE 9 on the array

source_name: PBLD10 Replicate 4


title: S0849-00126 D1 / R1

value: colorectal cancer biopsy

value: Barcelona

tag: positive lymph nodes

tag: evi

tag: lvi

value: Right colon

value: Right Hemicolectomy

value: C

tag: stage ii\iii

value: IIIB

tag: mstage

value: pMx

tag: differentiation

value: Well

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISE

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: SAMPLE 57

description:
SAMPLE 57
Hybridized with SAMPLE 14 on the array

tag: Sex

tag: developmental stage

tag: tissue

tag: population

tag: photoperiod

value: Night Sampling (ZT22)


title: S0849-00109 R1

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

value: Yes

tag: tumour site

value: Caecum

tag: type of surgery

value: Right hemicolectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

value: IIIA

tag: tstage

tag: nstage

value: Moderate

value: WT

value: MT


title: S0849-00111 R1

tag: tissue

value: colorectal cancer biopsy

value: Florence

value: Male

value: Rectum

value: Anterior Resection

value: C

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: SAMPLE 51

description:
SAMPLE 51
Hybridized with SAMPLE 74 on the array

source_name: PBLD10 Replicate 3

tag: Sex

value: female

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Day Sampling (ZT10)


title: S0849-00108 R1

tag: tissue

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

value: Ascending colon

tag: type of surgery

value: Right hemicolectomy

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

value: Alive

value: CRISD


title: SAMPLE 52

description:
SAMPLE 52
Hybridized with SAMPLE 77 on the array

tag: Sex

tag: developmental stage

tag: population

tag: photoperiod


title: NoRecurrence_Endom Cancer_8_matched4

city: Paris

first: Céline

last: Méhats

address: 24 rue du Faubourg St jacques

country: France

institute: Inserm

hyb_protocol: Following fragmentation, mirRNA targets were hybridized for 20 hr at 48C on mirRNA-40 Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were preprocessed and analyzing using Partek Genomic Suite and the customed cdf brain Array V21 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/mirbasef.asp) with mirID as identifiers.

source_name: Endometrium cancer

label_protocol: After validation of the RNA quality with Bioanalyzer 2100, 1 µg of total RNA was biotin labelled following the FlashTag Biotin HSR RNA labelling kit (Affymetrix).

extract_protocol: Total RNA was extracted using the miRNeasy FFPE Kit (Qiagen, Courtaboeuf, France), according to the manufacturer's instructions.

tag: recurrence

value: Recurrence -

tag: sample origin

value: FPPE section


title: S0849-00104 R1

tag: tissue

value: colorectal cancer biopsy

tag: site

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

value: Caecum

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISA

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)


title: SAMPLE 46

description:
SAMPLE 46
Hybridized with SAMPLE 70 on the array

source_name: PBLD10 Replicate 1

tag: Sex

value: female

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Day Sampling (ZT10)


title: SAMPLE 45

description:
SAMPLE 45
Hybridized with SAMPLE 58 on the array

tag: tissue


title: SAMPLE 48

description:
SAMPLE 48
Hybridized with SAMPLE 72 on the array


title: SAMPLE 56

description:
SAMPLE 56
Hybridized with SAMPLE 12 on the array


title: SAMPLE 49

description:
SAMPLE 49
Hybridized with SAMPLE 63 on the array


title: S0849-00103 R1

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

value: Yes

tag: tumour site

value: Upper rectum

tag: type of surgery

value: Laparoscopic Anterior Resection

tag: curative resection

tag: dukes

value: C

tag: stage ii\iii

value: IIIB

tag: tstage

tag: nstage

tag: recurrence


title: SAMPLE 54

description:
SAMPLE 54
Hybridized with SAMPLE 68 on the array

tag: Sex

tag: developmental stage

tag: population

tag: photoperiod

tag: sampling time


title: S0849-00107 R1

tag: tissue

value: colorectal cancer biopsy

tag: site

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

value: Sigmoid

value: Sigmoid colectomy

value: B

value: IIA

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00106 R1

value: Female

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Caecum

tag: type of surgery

value: Laparoscopic right hemicolectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

tag: tstage

tag: nstage

value: Poor

tag: recurrence

value: UNK

value: CRISA

value: WT


title: S0849-00101 R1

tag: tissue

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

value: No

value: Ascending colon

value: Open right hemicolectomy

value: C

value: IIIA

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: overall survival time

value: CRISE

value: MT


title: S0849-00105 R1

value: colorectal cancer biopsy

value: Female

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Transverse colon

tag: type of surgery

value: B

value: IIA

value: Well

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: SAMPLE 47

description:
SAMPLE 47
Hybridized with SAMPLE 61 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Day Sampling (ZT10)


title: S0849-00102 R1

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

value: No

value: Yes

value: Sigmoid

value: Laparoscopic Anterior Resection

tag: curative resection

tag: dukes

tag: stage ii\iii

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

tag: overall survival time

value: CRISC

value: WT


title: NoRecurrence_Endom Cancer_7_matched4

value: Recurrence -

tag: sample origin

value: FPPE section


title: SAMPLE 44

description:
SAMPLE 44
Hybridized with SAMPLE 32 on the array

source_name: KCSD22 Replicate 4

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Night Sampling (ZT22)


title: S0849-00100 R1

value: colorectal cancer biopsy

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Transverse colon

tag: type of surgery

value: Open right hemicolectomy

tag: curative resection

tag: dukes

value: B

value: IIA

value: Alive

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISA

tag: braf (v600e)

tag: kras (codons 12, 13, 61)

value: MT


title: NoRecurrence_Endom Cancer_5_matched3

tag: recurrence

tag: sample origin


title: NoRecurrence_Endom Cancer_6_matched3


title: NoRecurrence_Endom Cancer_4_matched2


title: NoRecurrence_Endom Cancer_3_matched2


title: NoRecurrence_Endom Cancer_2_matched1


title: Recurrence_Endom Cancer_7

value: Recurrence +


title: NoRecurrence_Endom Cancer_1_matched1

value: Recurrence -


title: S0849-00096 R1

tag: tissue

tag: site

tag: age diagnosis

value: Female

value: No

value: Rectosigmoid

value: Laparoscopic assisted High Anterior Resection

value: C

tag: stage ii\iii

value: IIIB

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

value: Yes

tag: status alive.dead

tag: overall survival time

value: CRISC

value: WT


title: Recurrence_Endom Cancer_5

value: FPPE section


title: Recurrence_Endom Cancer_6


title: S0849-00097 R1

value: colorectal cancer biopsy

value: SVH Dublin

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Transverse colon

tag: type of surgery

value: Open transverse colectomy

tag: curative resection

tag: dukes

value: B

value: IIA

value: Well

tag: progression-free survival time

tag: cms subgroup


title: S0849-00095 R1

tag: tissue

tag: site

tag: age diagnosis

value: No

value: Ascending colon

value: Open right hemicolectomy

tag: stage ii\iii

tag: tstage

tag: nstage

value: Alive

tag: recurrence

tag: cris subgroup

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00099 R1

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

value: Rectosigmoid

value: Open Anterior Resection

value: C

value: IIIB

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: overall survival time

value: MT


title: SAMPLE 39

description:
SAMPLE 39
Hybridized with SAMPLE 20 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Night Sampling (ZT22)


title: SAMPLE 43

description:
SAMPLE 43
Hybridized with SAMPLE 86 on the array

source_name: KCSD22 Replicate 1


title: SAMPLE 38

description:
SAMPLE 38
Hybridized with SAMPLE 26 on the array


title: Recurrence_Endom Cancer_4

tag: recurrence

value: Recurrence +

tag: sample origin

value: FPPE section


title: S0849-00092 R1

description: Gene expression data from fresh frozen colorectal cancer patient biopsy

value: colorectal cancer biopsy

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

value: No

value: Yes

tag: tumour site

value: Ascending colon

tag: type of surgery

value: Open right hemicolectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

value: IIIC

tag: tstage

tag: nstage

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISA

tag: braf (v600e)

tag: kras (codons 12, 13, 61)

value: WT


title: S0849-00090 R1

tag: tissue

value: Male

tag: positive lymph nodes

tag: evi

tag: lvi

value: Sigmoid

value: Open Anterior Resection

value: C

value: IIIB

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

tag: overall survival time

value: CRISD


title: SAMPLE 41

description:
SAMPLE 41
Hybridized with SAMPLE 82 on the array

source_name: KCSD22 Replicate 3

tag: Sex

value: female

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Night Sampling (ZT22)


title: SAMPLE 34

description:
SAMPLE 34
Hybridized with SAMPLE 25 on the array


title: SAMPLE 37

description:
SAMPLE 37
Hybridized with SAMPLE 19 on the array


title: SAMPLE 35

description:
SAMPLE 35
Hybridized with SAMPLE 16 on the array


title: S0849-00094 R1

value: colorectal cancer biopsy

tag: site

value: SVH Dublin

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

value: No

tag: tumour site

value: Rectum

tag: type of surgery

value: Laparoscopic Anterior Resection

tag: curative resection

tag: dukes

tag: stage ii\iii

tag: tstage

tag: nstage

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)


title: S0849-00098 R1

tag: tissue

tag: positive lymph nodes

tag: evi

tag: lvi

value: Sigmoid

value: Laparoscopic sigmoid colectomy

value: C

value: IIIB

tag: mstage

tag: differentiation

tag: adjuvanttreatment

value: Yes

tag: status alive.dead

tag: recurrence

tag: overall survival time

value: WT

tag: kras (codons 12, 13, 61)

value: MT


title: Recurrence_Endom Cancer_3

value: Recurrence +

tag: sample origin

value: FPPE section


title: S0849-00091 R1

tag: site

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: tumour site

value: Ascending colon

tag: type of surgery

value: Laparoscopic right hemicolectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

tag: tstage

tag: nstage

value: Moderate

value: Dead

value: CRISA


title: SAMPLE 42

description:
SAMPLE 42
Hybridized with SAMPLE 84 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Night Sampling (ZT22)


title: SAMPLE 33

description:
SAMPLE 33
Hybridized with SAMPLE 81 on the array

source_name: KCSD22 Replicate 2


title: S0849-00088 R1

source_name: Fresh frozen colorectal cancer biopsy

value: colorectal cancer biopsy

tag: site

value: SVH Dublin

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

value: Laparoscopic sub-total colectomy

value: C

value: IIIB

tag: mstage

tag: differentiation

tag: adjuvanttreatment

value: Yes

tag: status alive.dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: Recurrence_Endom Cancer_2

value: Recurrence +

tag: sample origin

value: FPPE section


title: NoRecurrence_Endom Cancer_14_matched7

value: Recurrence -


title: S0849-00089 R1

tag: tissue

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

value: Extensive

tag: tumour site

value: Sigmoid

tag: type of surgery

value: Laparoscopic Anterior Resection

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

value: Moderate

value: Alive

value: CRISD

value: WT

value: MT


title: NoRecurrence_Endom Cancer_13_matched7

tag: recurrence


title: Recurrence_Endom Cancer_1


title: SAMPLE 36

description:
SAMPLE 36
Hybridized with SAMPLE 17 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time

value: Night Sampling (ZT22)


title: SAMPLE 40

description:
SAMPLE 40
Hybridized with SAMPLE 30 on the array

tag: tissue


title: S0849-00086 R1

value: colorectal cancer biopsy

tag: site

value: SVH Dublin

tag: age diagnosis

value: Female

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

value: Rectum

value: Open Anterior Resection

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: SAMPLE 32

description:
SAMPLE 32
Hybridized with SAMPLE 44 & 78 on the array

source_name: KCSD10 Replicate 4

tag: Sex

tag: developmental stage

tag: population

tag: photoperiod

tag: sampling time

value: Day Sampling (ZT10)


title: SAMPLE 29

description:
SAMPLE 29
Hybridized with SAMPLE 5 on the array

source_name: KCSD10 Replicate 2

tag: tissue


title: NoRecurrence_Endom Cancer_12_matched6

tag: recurrence

value: Recurrence -

tag: sample origin

value: FPPE section


title: S0849-00084 R1

tag: site

value: Florence

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Caecum

tag: type of surgery

value: Right hemicolectomy

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

value: Moderate

value: Yes

value: Dead

value: CRISA

value: WT

value: MT


title: NoRecurrence_Endom Cancer_10_matched5

tag: recurrence

tag: sample origin


title: NoRecurrence_Endom Cancer_9_matched5


title: SAMPLE 31

description:
SAMPLE 31
Hybridized with SAMPLE 7 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Short Day (SD)

tag: sampling time


title: S0849-00083 R1

value: colorectal cancer biopsy

tag: site

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Left colon

value: Left hemicolectomy

tag: adjuvanttreatment

value: No

tag: status alive.dead

value: Alive

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISD

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00085 R1

tag: tissue

value: Florence

tag: type of surgery

value: UK

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

value: Moderate

tag: recurrence

value: UNK


title: NoRecurrence_Endom Cancer_11_matched6

value: Recurrence -

tag: sample origin

value: FPPE section


title: SAMPLE 50

description:
SAMPLE 50
Hybridized with SAMPLE 6 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: PB from New Jersey, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Day Sampling (ZT10)


title: SAMPLE 28

description:
SAMPLE 28
Hybridized with SAMPLE 4 on the array

source_name: KCSD10 Replicate 1

value: KC from Maine, USA

value: Short Day (SD)


title: SAMPLE 26

description:
SAMPLE 26
Hybridized with SAMPLE 69 & 38 on the array


title: SAMPLE 25

description:
SAMPLE 25
Hybridized with SAMPLE 34 & 73 on the array

source_name: KCSD10 Replicate 3


title: S0849-00081 R1

value: colorectal cancer biopsy

tag: site

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: colon

value: colon resection

tag: adjuvanttreatment

value: No

tag: status alive.dead

value: Dead

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)

value: MT


title: SAMPLE 24

description:
SAMPLE 24
Hybridized with SAMPLE 11 on the array

source_name: KCLD22 Replicate 3

tag: Sex

value: female

tag: developmental stage

tag: tissue

tag: population

tag: photoperiod

tag: sampling time

value: Night Sampling (ZT22)


title: SAMPLE 30

description:
SAMPLE 30
Hybridized with SAMPLE 40 & 75 on the array

value: larvae

value: whole larvae


title: S0849-00078 D1 / R1

description: Gene expression data from fresh frozen colorectal cancer patient biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: Yes

value: Right colon

tag: type of surgery

value: Right Hemicolectomy

tag: curative resection

tag: dukes

value: C

tag: stage ii\iii

value: IIIC

tag: tstage

tag: nstage

tag: mstage

value: pMx

tag: differentiation

value: Moderate

value: Alive

tag: recurrence

value: CRISE


title: S0849-00080 R1

tag: tissue

value: colorectal cancer biopsy

value: Florence

value: Female

tag: lvi

tag: tumour site

value: Transverse/left colon

value: Subtotal hemicolectomy (transverse left)

value: IIIB

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00076 D1 / R1

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

value: Sigmoid

tag: type of surgery

value: Sigmoidectomy- bladder-prostate

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIC

value: CRISD


title: S0849-00077 D1 / R1

tag: tissue

tag: lvi

value: Yes

tag: tumour site

value: Left Colon

value: Extended right hemicolectomy

value: C

tag: tstage

tag: nstage

tag: mstage

value: pMx

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

value: CRISA

value: WT

value: MT


title: S0849-00082 R1

value: colorectal cancer biopsy

tag: site

value: Florence

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

value: left colon/cecum

value: left hemicolectomy/cecum

value: IIA

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: SAMPLE 22

description:
SAMPLE 22
Hybridized with SAMPLE 65 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Night Sampling (ZT22)


title: S0849-00074 D1 / R1

value: Barcelona

tag: positive lymph nodes

value: No

tag: evi

value: Yes

tag: lvi

tag: tumour site

value: Sigmoid

tag: type of surgery

value: Sigmoidectomy

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

tag: tstage

tag: nstage

tag: mstage

value: pMx

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

value: CRISE


title: SAMPLE 20

description:
SAMPLE 20
Hybridized with SAMPLE 39 on the array

source_name: KCLD22 Replicate 4

tag: Sex

tag: developmental stage

tag: tissue

tag: population

tag: photoperiod


title: SAMPLE 27

description:
SAMPLE 27
Hybridized with SAMPLE 3 on the array

value: Short Day (SD)

tag: sampling time

value: Day Sampling (ZT10)


title: SAMPLE 19

description:
SAMPLE 19
Hybridized with SAMPLE 37 on the array

value: female

value: larvae


title: SAMPLE 21

description:
SAMPLE 21
Hybridized with SAMPLE 64 on the array

source_name: KCLD22 Replicate 1

value: whole larvae

value: KC from Maine, USA


title: SAMPLE 17

description:
SAMPLE 17
Hybridized with SAMPLE 36 on the array

source_name: KCLD22 Replicate 2

value: Long Day (LD)

value: Night Sampling (ZT22)


title: S0849-00071 D1 / R1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

value: Right colon

tag: type of surgery

value: Right Hemicolectomy

value: C

value: IIIC

value: Poor

value: Alive

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISA

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00069 D1 / R1_V

tag: tissue

value: Female

value: Yes

tag: curative resection

tag: dukes

tag: stage ii\iii

tag: tstage

tag: nstage

tag: mstage

value: pMx

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

value: CRISD

value: MT

value: WT


title: SAMPLE 14

description:
SAMPLE 14
Hybridized with SAMPLE 57 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Night Sampling (ZT22)


title: SAMPLE 16

description:
SAMPLE 16
Hybridized with SAMPLE 35 on the array


title: S0849-00070 D1 / R1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: No

tag: lvi

tag: tumour site

value: Left Colon

tag: type of surgery

value: colectomy

value: C

value: IIIB

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISB

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: SAMPLE 9

description:
SAMPLE 9
Hybridized with SAMPLE 53 on the array

source_name: KCLD10 Replicate 4

tag: Sex

tag: developmental stage

tag: tissue

tag: population

tag: photoperiod

value: Day Sampling (ZT10)


title: S0849-00068 D1 / R1

tag: site

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

value: Yes

value: Left colectomy

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

value: CRISC

value: WT

value: MT


title: S0849-00066 D1 / R1

tag: tissue

value: colorectal cancer biopsy

value: Barcelona

value: Male

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Sigmoid

tag: type of surgery

value: Sigmoidectomy

value: IIIC

value: pMx

value: Poor

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISE

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00072 D1 / R1

tag: site

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

value: No

value: Yes

value: Right colon

value: Right Hemicolectomy

tag: curative resection

tag: dukes

value: C

tag: stage ii\iii

value: IIIB

tag: tstage

tag: nstage

tag: mstage


title: S0849-00073 D1 / R1

tag: tissue

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

tag: type of surgery

value: B

value: IIC

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

value: WT


title: S0849-00064 R1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISB

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00062 D1 / R1

tag: tissue

tag: positive lymph nodes

tag: evi

tag: lvi

value: Left Colon

value: Sigmoidectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

value: IIIC

tag: tstage

tag: nstage

tag: mstage

value: Moderate

value: MT


title: S0849-00058 D1

tag: site

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

value: No

tag: tumour site

tag: type of surgery

value: IIA

value: pMx

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

value: CRISD


title: SAMPLE 6

description:
SAMPLE 6
Hybridized with SAMPLE 50 on the array

source_name: KCLD10 Replicate 1

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Day Sampling (ZT10)


title: S0849-00067 D1 / R1

value: colorectal cancer biopsy

value: Barcelona

value: Female

tag: positive lymph nodes

tag: evi

tag: lvi

value: Yes

value: Sigmoid

tag: curative resection

tag: dukes

value: C

tag: stage ii\iii

tag: tstage

tag: nstage

tag: mstage

value: Poor

value: Alive

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: SAMPLE 13

description:
SAMPLE 13
Hybridized with SAMPLE 1 on the array

tag: Sex

tag: developmental stage

tag: tissue

tag: population

tag: photoperiod

value: Night Sampling (ZT22)


title: SAMPLE 11

description:
SAMPLE 11
Hybridized with SAMPLE 24 on the array

source_name: KCLD10 Replicate 3

tag: sampling time


title: SAMPLE 12

description:
SAMPLE 12
Hybridized with SAMPLE 56 on the array


title: S0849-00061 D1 / R1

tag: site

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: No

tag: lvi

tag: tumour site

value: Right colon

tag: type of surgery

value: Right Hemicolectomy

tag: curative resection

tag: dukes

value: B

value: IIB

value: pMx

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence


title: SAMPLE 23

description:
SAMPLE 23
Hybridized with SAMPLE 8 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Long Day (LD)


title: cTnT+ 2

first: Peter

last: Zandstra

address: 160 College Street, University of Toronto

department: Institute of Biomaterials and Biomedical Engineering

institute: University of Toronto

description: RMA expression value was derived from the TAC software; core-gene analysis

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Data analysis and statistical evaluations were performed using R (v3.3.1) Bioconductor suite to extract, normalize, and summarize gene expression data
RMA

organism: Mus musculus

source_name: embryonic stem cells

label_protocol: standard Affymetrix protocol

growth_protocol: Mouse embryonic stem cells were differentiated to cardiac progenitors and sorted for Flk1+Pdgfra+ and Flk1+Pdgfra- sub-populations. The Flk1+Pdgfra+ sub-population was subsequently cultured and differentiated further into cTnT+ cardiomyocytes.

extract_protocol: Lysate was procesed by the Centre for Applied Genomics (Toronto, Canada)

treatment_protocol: Cells were lysed using RLT lysis buffer (Qiagen) and frozen at -80C

tag: cell line


title: S0849-00075 D1 / R1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: Yes

value: C

tag: stage ii\iii

value: IIIC

tag: tstage

tag: nstage

tag: mstage

value: Poor

value: Dead

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

value: UNK

tag: cris subgroup

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)

value: MT


title: S0849-00063 D1 / R1

tag: tissue

value: Male

tag: evi

value: No

tag: lvi

tag: tumour site

value: Left Colon

tag: type of surgery

value: Sigmoidectomy

tag: curative resection

tag: dukes

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

value: CRISB


title: SAMPLE 4

description:
SAMPLE 4
Hybridized with SAMPLE 28 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Day Sampling (ZT10)


title: SAMPLE 3

description:
SAMPLE 3
Hybridized with SAMPLE 27 on the array


title: S0849-00056 D1

description: Gene expression data from fresh frozen colorectal cancer patient biopsy

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: Sigmoid

value: C

tag: stage ii\iii

value: IIIB

tag: tstage

tag: nstage

tag: mstage

value: pMx

value: Poor

value: Yes

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISD

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: SAMPLE 8

description:
SAMPLE 8
Hybridized with SAMPLE 23 on the array

tag: Sex

tag: developmental stage

tag: tissue

tag: population

tag: photoperiod


title: cTnT+ 3

tag: cell line


title: SAMPLE 10

description:
SAMPLE 10
Hybridized with SAMPLE 55 on the array

source_name: KCLD10 Replicate 2

tag: sampling time


title: SAMPLE 5

description:
SAMPLE 5
Hybridized with SAMPLE 29 on the array


title: S0849-00059 D1 / R1

tag: site

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

tag: type of surgery

value: Sigmoidectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

value: IIIC

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

value: WT

value: MT


title: cTnT+ 1

tag: cell line


title: Flk1+ 2


title: S0849-00057 D1

tag: tissue

tag: site

value: Left Colon

value: Left colectomy

value: B

value: IIC

tag: tstage

tag: nstage

tag: mstage

value: Moderate

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: SAMPLE 7

description:
SAMPLE 7
Hybridized with SAMPLE 31 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Day Sampling (ZT10)


title: Flk1+ 3

tag: cell line


title: SAMPLE 1

description:
SAMPLE 1
Hybridized with SAMPLE 13 on the array

tag: tissue


title: S0849-00054 D1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

value: Right colon

tag: type of surgery

value: Right Hemicolectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

value: IIA

value: pMx

tag: differentiation

value: Poor

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

value: CRISB


title: S0849-00042 D1

tag: tissue

value: Male

value: Sigmoid

value: Sigmoidectomy

value: B

tag: tstage

tag: nstage

tag: mstage

value: Moderate

value: Yes

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)

value: MT


title: S0849-00041 D1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

tag: type of surgery

tag: curative resection

value: C

value: IIIB

value: Alive


title: SAMPLE 18

description:
SAMPLE 18
Hybridized with SAMPLE 2 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Night Sampling (ZT22)


title: S0849-00043 D1

value: Male

value: Sigmoid

value: Sigmoidectomy

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

tag: mstage

value: pMx

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00055 D1

tag: tissue

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

value: Right colon

tag: type of surgery

value: Right Hemicolectomy

tag: curative resection

value: Well

value: CRISA

value: WT

value: MT


title: S0849-00053 D1

value: Left Colon

tag: dukes

tag: stage ii\iii

value: IIC

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

tag: overall survival time

value: UNK

value: CRISD


title: SAMPLE 2

description:
SAMPLE 2
Hybridized with SAMPLE 18 on the array

tag: Sex

value: female

tag: developmental stage

value: larvae

tag: tissue

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Day Sampling (ZT10)


title: KC replicate 2.2

description: Nimblegen Wyeomyia smithii custom Expression Array 12x135k (All Probes)

data_processing: Raw signal intensity extract with NimbleScan 2.6 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data. .txt files contain the quantile-normalized data also available in the sample data tables.

source_name: Total RNA from northern obligate non-biters (KC)

value: adult

value: Head

tag: strain

value: WI

value: northern obligate non-biters


title: S0849-00039 D1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: No

tag: evi

tag: lvi

tag: tumour site

value: Sigmoid

tag: type of surgery

value: Sigmoidectomy

tag: curative resection

tag: dukes

value: B

value: IIA

value: pMx

value: Moderate

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISB

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)


title: S0849-00035 D1

tag: tissue

value: Yes

value: Right colon

value: Right Hemicolectomy

value: C

tag: stage ii\iii

value: IIIC

tag: tstage

tag: nstage

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

tag: overall survival time

value: CRISC

value: MT


title: S0849-00033 D1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

tag: type of surgery

value: Colectomy

tag: curative resection

value: No


title: S0849-00032 D1

tag: tissue

value: Sigmoid

value: Sigmoidectomy

tag: dukes

tag: stage ii\iii

tag: tstage

tag: nstage

value: pMx

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: KC replicate 3.2

tag: Sex

value: female

tag: developmental stage

value: adult

value: Head

tag: strain

value: WI

tag: population

value: northern obligate non-biters


title: KC replicate 4.2


title: Flk1+Pdgfra+ 3

tag: cell line


title: Flk1+ 1


title: Flk1+Pdgfra+ 2


title: WIOB replicate 4.2

source_name: Total RNA from biting individuals in the WI line selected for biting (WIOB)

value: biters in base population


title: WIOB replicate 1.2


title: WIOB replicate 3.2


title: KC replicate 1.2


title: KC replicate 4.1


title: S0849-00040 D1

tag: site

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

tag: positive lymph nodes

value: Yes

tag: evi

tag: lvi

tag: tumour site

value: Right colon

tag: type of surgery

value: Right Hemicolectomy

value: B

value: IIA

tag: mstage

tag: differentiation

value: Poor

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

tag: overall survival time

value: CRISB

value: WT


title: WIOB replicate 3.1

tag: Sex

tag: developmental stage

tag: tissue

tag: strain

tag: population


title: KC replicate 1.1


title: S0849-00029 D1

value: colorectal cancer biopsy

tag: site

value: Barcelona

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: curative resection

tag: dukes

value: C

tag: stage ii\iii

value: IIIC

tag: tstage

tag: nstage

value: pMx

value: No

value: Dead

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

value: MT

tag: kras (codons 12, 13, 61)


title: KC replicate 2.1

tag: Sex

value: female

tag: developmental stage

value: adult

tag: tissue

value: Head

value: WI

value: northern obligate non-biters


title: S0849-00037 D1

tag: site

value: Male

tag: positive lymph nodes

tag: evi

tag: lvi

value: Yes

tag: tumour site

value: Right colon

tag: type of surgery

value: colectomy

value: B

value: IIC

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

tag: overall survival time

value: UNK

value: CRISC


title: KC replicate 3.1

tag: strain

tag: population


title: S0849-00023 R1

value: colorectal cancer biopsy

value: Aberdeen

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

value: No

value: Sigmoid

value: Sigmoid colectomy

tag: curative resection

tag: dukes

value: C

tag: stage ii\iii

value: IIIB

tag: tstage

tag: nstage

value: pMx

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)


title: S0849-00021 R1

tag: tissue

tag: site

value: Female

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

tag: type of surgery

value: Left hemicolectomy

value: IIA

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

value: MT


title: WIOB replicate 2.1

tag: Sex

value: female

tag: developmental stage

value: adult

value: Head

tag: strain

value: WI

tag: population

value: biters in base population


title: S0849-00024 R1

value: colorectal cancer biopsy

value: Aberdeen

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

value: No

value: Hepatic flexure

value: Right hemicolectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

tag: tstage

tag: nstage

value: Moderate

value: Yes

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISD

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00034 D1

tag: tissue

tag: site

value: Barcelona

value: Female

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Sigmoid

tag: type of surgery

value: Sigmoidectomy

value: C

value: IIIB

tag: mstage

value: pMx

tag: differentiation

value: Well

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

value: WT


title: WIOB replicate 2.2

tag: Sex

value: female

tag: developmental stage

value: adult

value: Head

tag: strain

value: WI

tag: population

value: biters in base population


title: S0849-00020 R1

value: colorectal cancer biopsy

value: Aberdeen

tag: age diagnosis

tag: gender

value: Male

tag: total number of lymph nodes excised

value: No

value: Sigmoid colectomy

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

value: Moderate

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISA

tag: braf (v600e)

tag: kras (codons 12, 13, 61)

value: MT


title: WIOB replicate 4.1

tag: Sex

tag: developmental stage

tag: tissue


title: S0849-00027 R1

tag: site

tag: age diagnosis

value: Female

tag: positive lymph nodes

tag: evi

value: Yes

tag: lvi

tag: tumour site

value: Recto-sigmoid

tag: type of surgery

value: C

value: IIIB

tag: mstage

value: pMx

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

value: CRISE


title: SAMPLE 15

description:
SAMPLE 15
Hybridized with SAMPLE 59 on the array

value: female

value: larvae

value: whole larvae

tag: population

value: KC from Maine, USA

tag: photoperiod

value: Long Day (LD)

tag: sampling time

value: Night Sampling (ZT22)


title: S0849-00017 R1

value: colorectal cancer biopsy

value: Aberdeen

tag: gender

value: Male

tag: total number of lymph nodes excised

value: No

value: Sigmoid

value: Sigmoid colectomy

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

value: Moderate

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISC

tag: braf (v600e)

value: WT

tag: kras (codons 12, 13, 61)


title: S0849-00016 R1

tag: tissue

tag: site

tag: age diagnosis

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

tag: type of surgery

tag: mstage

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

value: UNK

value: MT


title: WI replicate 1.2

source_name: Total RNA from non-biters in the base population (WI)

tag: Sex

value: female

tag: developmental stage

value: adult

value: Head

tag: strain

value: WI

tag: population

value: non-biters in base population


title: Flk1+Pdgfra+ 1

tag: cell line


title: S0849-00015 R1

source_name: Fresh frozen colorectal cancer biopsy

tag: tissue

value: colorectal cancer biopsy

tag: site

value: Aberdeen

tag: gender

value: Female

tag: total number of lymph nodes excised

tag: curative resection

tag: dukes

value: C

tag: stage ii\iii

value: IIIB

tag: tstage

tag: nstage

value: pMx

value: Dead

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISA

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: S0849-00022 R1

tag: age diagnosis

value: Male

tag: positive lymph nodes

tag: evi

value: No

tag: lvi

tag: tumour site

value: Sigmoid

tag: type of surgery

value: Sigmoid colectomy

value: B

value: IIA

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

value: CRISC

value: WT


title: WI replicate 1.1

tag: Sex

value: female

tag: developmental stage

value: adult

tag: tissue

value: Head

tag: strain

value: WI

tag: population

value: non-biters in base population


title: S0849-00019 R1

value: colorectal cancer biopsy

tag: site

value: Aberdeen

tag: gender

value: Female

tag: total number of lymph nodes excised

value: Hepatic flexure

value: Ext right hemicolectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

tag: tstage

tag: nstage

value: pMx

value: Yes

value: Alive

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISE

tag: braf (v600e)

tag: kras (codons 12, 13, 61)


title: WI replicate 3.2

tag: Sex

tag: developmental stage

tag: tissue


title: S0849-00026 R1

tag: site

tag: age diagnosis

value: Male

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Transverse colon

tag: type of surgery

value: Extended right hemicolectomy

value: C

value: IIIC

tag: mstage

tag: differentiation

value: Poor

tag: adjuvanttreatment

value: No

tag: status alive.dead

value: Dead

tag: recurrence

value: UNK

value: CRISA


title: S0849-00005 R1

value: colorectal cancer biopsy

value: Aberdeen

tag: gender

tag: total number of lymph nodes excised

value: Sigmoid

value: Sigmoid colectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

value: IIIA

tag: tstage

tag: nstage

value: Moderate

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)

value: WT

value: MT


title: WI replicate 4.2

tag: Sex

value: female

tag: developmental stage

value: adult

tag: tissue

value: Head

tag: strain

value: WI

tag: population

value: non-biters in base population


title: WI replicate 4.1


title: WIOB replicate 1.1

value: biters in base population


title: S0849-00004 R1

tag: site

tag: age diagnosis

tag: gender

value: Female

tag: positive lymph nodes

tag: evi

value: No

tag: lvi

tag: tumour site

value: Asc colon

tag: type of surgery

value: Right hemicolectomy

value: C

value: IIIB

tag: mstage

value: pMx

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

value: Dead

tag: recurrence

value: Yes

value: CRISD

tag: kras (codons 12, 13, 61)


title: WI replicate 3.1

tag: Sex

tag: developmental stage

tag: tissue


title: S0849-00018 R1

value: colorectal cancer biopsy

tag: site

value: Aberdeen

value: Male

tag: total number of lymph nodes excised

value: Distal

tag: curative resection

tag: dukes

value: B

tag: stage ii\iii

value: IIA

tag: tstage

tag: nstage

value: Moderate

value: Alive

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISE

tag: braf (v600e)

value: WT


title: U937_BRYO1_1hr_rep4

status: Public on Dec 30 2017

city: Bethesda

first: Noemi

last: Kedei

state: MD

address: 37 Convent drive 4048

department: NCI

country: USA

institute: NIH

hyb_protocol: Four replicates of each group were hybridized to Affymetrix mouse (human) Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45oC, 60 RPM for 16 hrs. Washing and staining were performed on Affymetrix Fluidics Station 450.

scan_protocol: The slides were scanned on Affymetrix GeneChip scanner 3000.  Data were collected using Affymetrix AGCC software.

data_processing:
data were processed withPartek® Genomics Suite 6.5; exon-level processing steps: pre-background adjustement for GC content, RMA background correction, quantile normalization, log base 2 transformation, probesets summarization with mean; gene-level expression values were obtained with the mean method.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

label_protocol: 100 ng of RNA was reverse transcribed and amplified using Ambion WT expression kit following manufacturer’s suggested protocol.  Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

growth_protocol: LNCaP and U937 cells were grown in RPMI-1640 supplemented with 10% FBS and 2 mM L-glutamine. 800,000 LNCaP cells (in 3 ml medium) and 600,000 U937 cells (in 4 ml medium) were plated onto 6 cm dishes and treated 48 hours after plating.

extract_protocol: Total RNA was extracted using Trizol. RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >9).

treatment_protocol: Cells were treated with 100 nM PMA, 100 nM Bryostatin 1 or 0.1 % DMSO for 1 and 6 hours.

tag: cell line

tag: cell type

value: Human leukemic monocyte lymphoma cell line

tag: treated with

value: bryostatin 1

tag: treatment time


title: U937_PMA_1hr_rep4

value: PMA


title: WI replicate 2.2

tag: Sex

value: female

tag: developmental stage

value: adult

tag: tissue

value: Head

tag: strain

value: WI

tag: population

value: non-biters in base population


title: U937_BRYO1_6hr_rep4


title: WI replicate 2.1


title: U937_BRYO1_1hr_rep3


title: S0849-00014 R1

value: colorectal cancer biopsy

tag: site

value: Aberdeen

tag: age diagnosis

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

value: No

tag: lvi

tag: tumour site

value: Hepatic flexure

tag: type of surgery

value: Right hemicolectomy

tag: curative resection

tag: dukes

tag: stage ii\iii

tag: mstage

value: pMx

tag: differentiation

tag: adjuvanttreatment

tag: status alive.dead

tag: recurrence

value: CRISB

value: MT

tag: kras (codons 12, 13, 61)


title: S0849-00012 R1

tag: tissue

tag: site

tag: age diagnosis

value: Female

value: Caecum

value: B

value: IIA

tag: tstage

tag: nstage

value: Poor

value: Alive

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISA

tag: braf (v600e)

value: WT


title: S0849-00002 R1

tag: gender

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Asc colon

tag: type of surgery

tag: curative resection

tag: dukes

tag: stage ii\iii

value: IIB

value: Moderate

value: Dead

value: CRISE


title: S0849-00009 R1

tag: tissue

value: colorectal cancer biopsy

tag: site

value: Aberdeen

tag: age diagnosis

value: No

value: Right hemicolectomy

value: C

value: IIIB

tag: tstage

tag: mstage

tag: differentiation

tag: adjuvanttreatment

value: Yes

tag: status alive.dead

tag: recurrence

value: CRISD

tag: kras (codons 12, 13, 61)


title: U937_PMA_6hr_rep4

tag: cell line

tag: cell type

value: Human leukemic monocyte lymphoma cell line

tag: treated with

value: PMA

tag: treatment time


title: U937_DMSO_6hr_rep2

value: DMSO


title: U937_PMA_1hr_rep3


title: U937_DMSO_1hr_rep4


title: S0849-00011 R1

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Sigmoid

tag: type of surgery

value: Sigmoid colectomy

tag: curative resection

value: B

value: IIA

tag: nstage

value: pMx

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

value: CRISA

tag: braf (v600e)

value: WT

value: MT


title: U937_BRYO1_1hr_rep2

tag: cell line

tag: cell type

value: bryostatin 1


title: S0849-00013 R1

tag: tissue

value: colorectal cancer biopsy

tag: site

value: Aberdeen

tag: age diagnosis

value: No

value: Rectum

value: Anterior resection

tag: dukes

tag: stage ii\iii

tag: tstage

tag: mstage

tag: differentiation

value: Moderate

tag: adjuvanttreatment

tag: status alive.dead

value: Alive

tag: recurrence

tag: kras (codons 12, 13, 61)


title: U937_DMSO_6hr_rep4

value: Human leukemic monocyte lymphoma cell line

tag: treated with

value: DMSO

tag: treatment time


title: U937_BRYO1_6hr_rep3


title: U937_PMA_6hr_rep3

value: PMA


title: S0849-00010 R1

tag: gender

value: Male

tag: total number of lymph nodes excised

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

value: Asc colon

tag: type of surgery

value: Right hemicolectomy

tag: curative resection

value: C

value: IIIB

tag: nstage

value: Dead

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

value: UNK

tag: cris subgroup

value: CRISB

tag: braf (v600e)


title: U937_BRYO1_6hr_rep2

tag: cell line

tag: cell type

value: bryostatin 1


title: U937_DMSO_6hr_rep3

tag: treated with

tag: treatment time


title: S0849-00001 R1_V

tag: tissue

value: colorectal cancer biopsy

tag: site

value: Aberdeen

tag: age diagnosis

tag: gender

value: Female

tag: total number of lymph nodes excised

value: No

value: Sigmoid

value: Sigmoid colectomy

tag: dukes

value: B

tag: stage ii\iii

value: IIB

tag: tstage

tag: mstage

value: pMx

tag: differentiation

tag: adjuvanttreatment

value: Yes

tag: status alive.dead

tag: recurrence

value: CRISD

value: WT

tag: kras (codons 12, 13, 61)

value: MT


title: U937_DMSO_1hr_rep3

tag: cell line

tag: cell type

value: Human leukemic monocyte lymphoma cell line

value: DMSO


title: U937_BRYO1_1hr_rep1

tag: treated with

tag: treatment time


title: U937_DMSO_6hr_rep1


title: LNCaP_BRYO1_6hr_rep4

value: LNCaP

value: Human prostate adenocarcinoma cell line


title: LNCaP_DMSO_6hr_rep4


title: LNCaP_PMA_6hr_rep4

value: PMA


title: U937_DMSO_1hr_rep2


title: U937_PMA_6hr_rep1


title: U937_DMSO_1hr_rep1


title: LNCaP_BRYO1_1hr_rep4

value: bryostatin 1


title: LNCaP_PMA_6hr_rep3


title: S0849-00003 R1

tag: tissue

value: colorectal cancer biopsy

tag: site

value: Aberdeen

value: Female

tag: positive lymph nodes

tag: evi

tag: lvi

tag: tumour site

tag: type of surgery

tag: curative resection

value: IIA

tag: nstage

value: Moderate

value: Alive

tag: overall survival time

tag: progression-free survival time

tag: cms subgroup

tag: cris subgroup

tag: braf (v600e)


title: U937_PMA_1hr_rep1

tag: cell line

tag: cell type


title: LNCaP_BRYO1_1hr_rep2

tag: treated with

tag: treatment time


title: LNCaP_BRYO1_1hr_rep3


title: LNCaP_DMSO_6hr_rep3


title: U937_PMA_1hr_rep2


title: LNCaP_DMSO_6hr_rep1


title: U937_BRYO1_6hr_rep1


title: LNCaP_PMA_6hr_rep2


title: LNCaP_BRYO1_6hr_rep2


title: LNCaP_BRYO1_6hr_rep3


title: LNCaP_BRYO1_6hr_rep1


title: LNCaP_PMA_1hr_rep1


title: U937_Merle23_8h_rep3

data_processing:
Data were processed withPartek® Genomics Suite 6.5; exon-level processing steps: pre-background adjustement for GC content, RMA background correction, quantile normalization, log base 2 transformation, probesets summarization with mean; gene-level expression values were obtained with the mean method.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

treatment_protocol: Cells were treated with 100 nM PMA, 100 nM Bryostatin 1, 1000 nM Merle 23 or 0.1 % DMSO for 6 hours (LNCaP) or for 8 hours (U937).

value: 8 hours


title: U937_Merle23_8h_rep2


title: LNCaP_DMSO_6hr_rep2


title: LNCaP_PMA_1hr_rep3


title: LNCaP_BRYO1_1hr_rep1


title: U937_Bryostatin1_8h_rep5


title: U937_Bryostatin1_8h_rep3


title: U937_Merle23_8h_rep1


title: LNCaP_DMSO_1hr_rep3


title: U937_PMA_8h_rep1


title: U937_DMSO_8h_rep4


title: U937_PMA_8h_rep4


title: U937_Bryostatin1_8h_rep1


title: U937_PMA_8h_rep2


title: U937_Bryostatin1_8h_rep2


title: LNCaP_DMSO_1hr_rep2


title: U937_DMSO_8h_rep2


title: U937_DMSO_8h_rep1


title: LNCaP_PMA_6hr_rep1


title: U937_Bryostatin1_8h_rep4


title: U937_PMA_8h_rep5


title: LNCaP_Merle23_6h_rep4

value: 6 hours


title: LNCaP_DMSO_1hr_rep1


title: U937_DMSO_8h_rep5


title: U937_Merle23_8h_rep5


title: LNCaP_PMA_1hr_rep2


title: LNCaP_PMA_1hr_rep4


title: LNCaP_Bryostatin1_6h_rep2


title: LNCaP_PMA_6h_rep3


title: U937_PMA_8h_rep3


title: LNCaP_Merle23_6h_rep5


title: LNCaP_PMA_6h_rep4


title: LNCaP_Bryostatin1_6h_rep1


title: LNCaP_Bryostatin1_6h_rep4


title: LNCaP_DMSO_6h_rep3


title: LNCaP_Merle23_6h_rep1


title: LNCaP_Bryostatin1_6h_rep5


title: U937_DMSO_8h_rep3


title: X6_8Gy_4H

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

country: Japan

institute: Kanazawa University

description: Gene expression of MIAPaCa-2 cells after Proton irradiationin 8Gy

hyb_protocol: The prepared target complementary RNA was hybridized to DNA microarray plate by using the Whole Human Genome Microarray kit, 4x44K (Agilent Technologies).

scan_protocol: Agilent Technologies Scanner G2505B was used for the microarray scan, together with the Feature Extraction Software Version 10.5.1.1

data_processing:
Analysis of the obtained gene expression was performed by using BRB array tool (NCI, http://linus.nci.nih.gov/BRB-ArrayTools.html ) as well as by using MetaCore software (GeneGo, Carlsbad, CA).
Normalized signal intensity is processed relatively to reference array (Median array as reference). Intensity filter thresholded at a minimum value of 10. Replicate spots were averaged within an array. Genes were excluded if missing values exceeded 50% between arrays and if a minimum fold change was not met (Less than 20% of expression data values have at least a 1.5-fold change in either direction from the gene's median value). Multiple probes sets were reduced to one per gene symbol by using the most variable probe set measured by IQR across arrays.

source_name: MIAPaCa-2 cells Proton 8Gy

label_protocol: Isolated RNA was amplified and labeled with Cy3 by using the Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA).

extract_protocol: RNA was isolated from the cells by using RNA isolation kit (RNeasy MiniKit, Qiagen, Heidelberg, Germany). Gene expression analysis was performed by using DNA microarray.

value: Pancreas carcinoma


title: LNCaP_Merle23_6h_rep3


title: LNCaP_DMSO_6h_rep1


title: LNCaP_PMA_6h_rep1


title: X2_8Gy_4H


title: LNCaP_PMA_6h_rep5


title: U937_PMA_6hr_rep2


title: LNCaP_DMSO_6h_rep4


title: LNCaP_Bryostatin1_6h_rep3


title: LNCaP_DMSO_6h_rep2


title: LNCaP_PMA_6h_rep2


title: LNCaP_Merle23_6h_rep2


title: U937_Merle23_8h_rep4


title: LNCaP_DMSO_6h_rep5


title: X9_8Gy_4H


title: X2_0Gy_2

description: Gene expression of MIAPaCa-2 cells not re-irradiated

source_name: MIAPaCa-2 cells not re-irradiated


title: X1_8Gy_4H


title: X6_0Gy_2


title: X9_0Gy_2


title: P5_8Gy_4H


title: P4_8Gy_4H


title: X1_0Gy_2


title: P1_8Gy_4H


title: 32.MIAPaCa Proton 2Gy 3h

description: Gene expression of MIAPaCa-2 cells after 3hr of 2Gy Proton irradiationin

source_name: MIAPaCa-2 cells Proton 2Gy 3h


title: 38.MIAPaCa Proton 2Gy 12h

description: Gene expression of MIAPaCa-2 cells after 12hr of 2Gy Proton irradiationin

source_name: MIAPaCa-2 cells Proton 2Gy 12h


title: P3_8Gy_4H


title: 40.MIAPaCa Proton 8Gy 12h

description: Gene expression of MIAPaCa-2 cells after 12hr of 8Gy Proton irradiationin

source_name: MIAPaCa-2 cells Proton 8Gy 12h


title: P3_0Gy_2


title: P1_0Gy


title: 10.MIAPaCa X-ray 8Gy 12h

description: Gene expression of MIAPaCa-2 cells after 12hr of 8Gy X-ray irradiationin

source_name: MIAPaCa-2 cells X-ray 8Gy 12h


title: P5_0Gy_2


title: P2_0Gy_2


title: X9_0Gy

description: Gene expression of MIAPaCa-2 cells after X-ray irradiationin 8Gy

source_name: MIAPaCa-2 cells X-ray 8Gy


title: P5_0Gy


title: P2_8Gy_4H


title: P1_0Gy_2


title: X1_0Gy


title: P4_0Gy


title: X2_0Gy


title: P2_0Gy


title: 8.MIAPaCa X-ray 2Gy 12h

description: Gene expression of MIAPaCa-2 cells after 12hr of 2Gy X-ray irradiationin

source_name: MIAPaCa-2 cells X-ray 2Gy 12h


title: 34.MIAPaCa Proton 8Gy 3h

description: Gene expression of MIAPaCa-2 cells after 3hr of 8Gy Proton irradiationin

source_name: MIAPaCa-2 cells Proton 8Gy 3h


title: P3_0Gy


title: X6_0Gy


title: 4.MIAPaCa X-ray 8Gy 3h

description: Gene expression of MIAPaCa-2 cells after 3hr of 8Gy X-ray irradiationin

source_name: MIAPaCa-2 cells X-ray 8Gy 3h


title: P4_0Gy_2


title: POLR2A_plasmid Oxfored Nanopore sequencing barcode06_T5

type: SRA

city: Taipei

first: Trees-Juen

last: Chuang

address: 128, Academia Road, Sec. 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academic Sinica

description: total RNA with rRNA

library_source: transcriptomic

data_processing:
Genes expression (FPKM) of H9 ESC RNA-seq was analyzed using TopHat,Cufflinks. genome build : hg19; gene annotation version: ensembl 75
Genes expression (RPKM) of O6 ESC RNA-seq was analyzed using TopHat,Cufflinks. genome build : rheMac3; gene annotation version: ensembl 75
HeLa ONT reads were clipped the barcode using fastx_clipper in the FASTX-toolkit. The clipped ONT reads were aligned using BWA MEM -x ont2d to the human genome (hg19). Gene expression for ONT was analyzed using custom scripts. For the targeted sample event, the number of reads overlapping with its exons was counted normalized to total number of reads in a sample and reported as Reads Per Event per 10,000 reads (RPE10K).
POLR2A plasmid ONT reads were trimmed off the barcodes using Porechop (v0.2.3). The clipped ONT reads were aligned using BWA MEM -x ont2d to the human genome (hg19). Gene expression for ONT was analyzed using custom scripts. For the targeted sample event, the number of reads overlapping with its targeted resgions  was counted normalized to total number of reads in a sample and reported as Reads Per Event per 10,000 reads (RPE10K).

source_name: POLR2A plasmid ONT

extract_protocol:
The plasmids of wild-type and a series of Alu deletion constructs for the    POLR2A transcription segments (exons 9 and 10) cloned into pZW1 were    directly obtained from Prof. Ling-Ling Chen (Chinese Academy of Sciences,    China). We examine whether deletions of inverted *Alu* repeats (IR*Alu*s)    can simultaneously affect *POLR2A* tsRNA and *POLR2A* circRNA. The EV    plasmid was wild-type, and T1-T7 were seven different IR*Alu* deletion    constructs (please see our article Figure 4F).
Library for Nanopore sequencing was constructed using Ligation sequencing Kit 1D (SKQ-LSK108) and Native barcoding kit (EXP-NBD103) following Oxford Nanopore Technologies (ONT) protocol.                                 barcode1: AAGAAAGTTGTCGGTGTCTTTGTG;   barcode2: TCGATTCCGTTTGTAGTCGTCTGT;  barcode3: GAGTCTTGTGTCCCAGTTACCAGG;  barcode4: TTCGGATTCTATCGTGTTTCCCTA;  barcode5: CTTGTCCAGGGTTTGTGTAACCTT;  barcode6: TTCTCGCAAAGGCAGAAAGTAGTC;  barcode 7: GTGTTACCGTGGGAATGAATCCTT; barcode 8: TTCAGGGAACAAACCAAGTTACGT
Oxford Nanopore amplicon

tag: barcode

value: TTCTCGCAAAGGCAGAAAGTAGTC


title: POLR2A_plasmid Oxfored Nanopore sequencing barcode07_T6

description: total RNA with rRNA

value: GTGTTACCGTGGGAATGAATCCTT


title: POLR2A_plasmid Oxfored Nanopore sequencing barcode05_T4

description: total RNA with rRNA

value: CTTGTCCAGGGTTTGTGTAACCTT


title: POLR2A_plasmid Oxfored Nanopore sequencing barcode02_T1

description: total RNA with rRNA

value: TCGATTCCGTTTGTAGTCGTCTGT


title: POLR2A_plasmid Oxfored Nanopore sequencing barcoe01_EV

description: total RNA with rRNA

value: AAGAAAGTTGTCGGTGTCTTTGTG


title: H3K27me2me3_N6228_tert_CACACATC_120117

status: Public on Dec 29 2017

city: Eugene

first: Eric

last: Selker

state: Oregon

address: 1370 Franklin Blvd.

department: Biology

institute: University of Oregon

library_source: genomic

data_processing:
To make ChIPseq enrichment files for display in Integrative Genomics Viewer (IGV, Robinson et al, 2011, Nat. Biotechnol.), reads were mapped with bowtie2 to the nc12-fixed genome (Galazka et al., 2016) using default parameters, and reads were converted to .bam files, sorted, and indexed.  The .bam files (and the corresponding .bai index files) were counted with the "Count" command of igvtools, using the mean window function and 200bp windows.  Output file was a .tdf file, displayable on IGV.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 25 -200bp (.tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV). The bcf files were produced from bam files (mapped to the Neurospora crassa assembly 12 Fixed by samtools), and report enrichment values.

organism: Neurospora crassa

source_name: germinated conidia

growth_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC.

extract_protocol: ChIP-seq: Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP.  Tissue added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and was disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 2uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A or Protein G slurry (agarose or magnetic beads) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the QIAquick PCR purification kit  and eluted in 30 μl of water.  Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the Illumina Tru-Seq kits A and B (Illumina, IP-202-1012 and IP-202-1024) according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 10 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

tag: tissue

value: germinated conidia

tag: chip antibody

value: H3K27me2me3 (ActiveMotif; cat# 39535)


title: POLR2A_plasmid Oxfored Nanopore sequencing barcode08_T7

description: total RNA with rRNA

value: TTCAGGGAACAAACCAAGTTACGT


title: hT-ALL#1_thoracic_vertebrae

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

hyb_protocol: GeneChip® HumanGene2.0ST (Affymetrix) are hybridized at 45°C for 17 hours

scan_protocol: After overnight hybridization, Chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V19 was used for annotation.

source_name: hT-ALL isolated from mouse thoracic vertebrae

label_protocol: 200 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled

growth_protocol: human (h)T-ALL cells from children patients were transplanted in immunodeficient mice. When more than 90% of hT-ALL were detected in femur BM, mice were sacrified and hT-ALL cells were isolated from thorax and tail bone marrow. (respectively thoracic or tail vertebrae).

extract_protocol: total RNA was extracted from hT-ALL according RNAqueous's protocol (Thermo Fisher Scientific)

treatment_protocol: Mouse vertebrae were crushed, BM cells were labelled with anti human CD45-PE antibody (eBioscience) and human CD45+ leukemic cells were purified by immuno-magnetic strategy with anti-PE antibody coated on microbeads (from Miltenyi Biotech). Purified hT-ALL were spun down/washed with PBS and lysed in RNAqueous lysis buffer (Thermo Fisher Scientific).

value: hT-ALL

tag: strain

value: NSG

tag: source

value: thorax vertebrae (adipocyte poor) bone marrow


title: hT-ALL#10_thoracic_vertebrae


title: hT-ALL#3_tail_vertebrae

source_name: hT-ALL isolated from mouse tail vertebrae

value: tail vertebrae (adipocyte rich) bone marrow


title: hT-ALL#1_tail_vertebrae


title: hT-ALL#3_thoracic_vertebrae


title: POLR2A_plasmid Oxfored Nanopore sequencing barcode03_T2

description: total RNA with rRNA

value: GAGTCTTGTGTCCCAGTTACCAGG


title: hT-ALL#10_tail_vertebrae


title: POLR2A_plasmid Oxfored Nanopore sequencing barcode04_T3

description: total RNA with rRNA

value: TTCGGATTCTATCGTGTTTCCCTA


title: 2.MIAPaCa X-ray 2Gy 3h

description: Gene expression of MIAPaCa-2 cells after 3hr of 2Gy X-ray irradiationin

source_name: MIAPaCa-2 cells X-ray 2Gy 3h


title: 1.MIAPaCa(Cell)Control

description: Gene expression of non-irradiated control cells

source_name: MIAPaCa-2 cells (Cell)Control


title: MM001_Mouse_1_Mock_Day_4_1-27-2017

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

source_name: Mouse lung cells, Mock-inoculated, 4 day, bioreplicate 1

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

extract_protocol:
MERSCOV004.0P
plaque assay protocol: MERSCOV005.0P

treatment_protocol: MERSCOV004.0P: Cells were infected with a multiplicity of infection of 3 PFU.

value: Mouse lung cells

tag: time

tag: virus

value: Mock


title: MM001_Mouse_3_Mock_Day_2_1-25-2017

source_name: Mouse lung cells, Mock-inoculated, 2 day, bioreplicate 3


title: MM001_Mouse_2_Mock_Day_2_1-25-2017

source_name: Mouse lung cells, Mock-inoculated, 2 day, bioreplicate 2


title: MM001_Mouse_2_Mock_Day_7_1-30-2017

source_name: Mouse lung cells, Mock-inoculated, 7 day, bioreplicate 2


title: MM001_Mouse_3_Mock_Day_4_1-27-2017

source_name: Mouse lung cells, Mock-inoculated, 4 day, bioreplicate 3


title: MM001_Mouse_3_Mock_Day_7_1-30-2017

source_name: Mouse lung cells, Mock-inoculated, 7 day, bioreplicate 3


title: MM001_Mouse_2_Mock_Day_4_1-27-2017

source_name: Mouse lung cells, Mock-inoculated, 4 day, bioreplicate 2


title: MM001_Mouse_4_Mock_Day_2_1-25-2017

source_name: Mouse lung cells, Mock-inoculated, 2 day, bioreplicate 4


title: MM001_Mouse_4_MERS_10e6_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 7 day, bioreplicate 4


title: MM001_Mouse_1_Mock_Day_7_1-30-2017

source_name: Mouse lung cells, Mock-inoculated, 7 day, bioreplicate 1


title: MM001_Mouse_1_Mock_Day_2_1-25-2017

source_name: Mouse lung cells, Mock-inoculated, 2 day, bioreplicate 1


title: MM001_Mouse_2_MERS_10e6_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 7 day, bioreplicate 2


title: MM001_Mouse_1_MERS_10e6_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 2 day, bioreplicate 1


title: MM001_Mouse_4_MERS_10e6_Day_4_1-27-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 4 day, bioreplicate 4


title: MM001_Mouse_3_MERS_10e6_Day_4_1-27-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 4 day, bioreplicate 3


title: MM001_Mouse_2_MERS_10e6_Day_4_1-27-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 4 day, bioreplicate 2


title: MM001_Mouse_3_MERS_10e6_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 7 day, bioreplicate 3


title: MM001_Mouse_1_MERS_10e6_Day_4_1-27-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 4 day, bioreplicate 1


title: MM001_Mouse_4_MERS_10e6_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 2 day, bioreplicate 4


title: MM001_Mouse_3_MERS_10e6_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 2 day, bioreplicate 3


title: MM001_Mouse_1_MERS_10e6_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 7 day, bioreplicate 1


title: MM001_Mouse_3_MERS_10e5_Day_4_1-27-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 4 day, bioreplicate 3


title: MM001_Mouse_3_MERS_10e5_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 7 day, bioreplicate 3


title: MM001_Mouse_1_MERS_10e5_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 7 day, bioreplicate 1


title: MM001_Mouse_2_MERS_10e6_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e6 dose, 2 day, bioreplicate 2


title: MM001_Mouse_4_MERS_10e5_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 7 day, bioreplicate 4


title: MM001_Mouse_2_MERS_10e5_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 7 day, bioreplicate 2