title: Patient113-time5

type: protein

city: Lørenskog

first: Anne

middle: Hansen

last: Ree

address: Sykehusveien 25

department: Division of Medicine - Oncology

country: Norway

institute: Akershus University Hospital

description:
Sample name: LARC-RRP-113-5
Raw data file: 14340608_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

hyb_protocol: Hybridization of samples were done on glass chips, consisting of two sub-arrays that were pre-treated according to the manufactures instructions. The biotin labeled samples were diluted 1:20 and added onto the glass chips followed by ON incubation at 4C. The following day the glass slides were washed and incubated with a Cy3-conjugated streptavidin for two hours before they were washed again, dried and developed. See manufacturer´s manual for more, http://www.raybiotech.com/files/manual/Antibody-Array/AAH-BLG-1.pdf.

scan_protocol: The hybridized arrays were scanned for fluorescence using the Agilent scanner G2505C. The scans were obtained with photomultiplier tube (PMT) settings at 60% of maximal intensity.  Tiff images were made from these scans

data_processing:
The tiff images were segmented using GenePix 6.0, i.e. converted from image spots to numerical values of grey scale levels per spot. There is one  GenePix result file (gpr-file) per slide (or chip), and each slide consists of two arrays (samples), thus there are measurements from two samples in each gpr-file. The Slide block column in the sample annotation denotes whether this sample is hybridized to the first block (rows 1-1050 in gpr) or to the second block(rows 1051-2100 in gpr). The gpr-files were read into the R statistical environment using the limma-package. The F532 Median column was chosen as signal without background subtraction. About 10% of the measurements were judged as unreliable and removed. Data was normalized between arrays with global median normalization and print-batch normalized with the ComBat method without using covariates. See pre-process-script attached as supplementary file for details.
Replicate spots were averaged. Each sample´s values were adjusted to make a common median across samples, i.e global median normalization. Batch adjustment was performed with ComBat, with slide print batch as batch and no covariate. See pre-process-script attached as supplementary file (preprocess_geo.r) for details.

molecule: protein

source_name: serum

label_protocol: Serum extracted from peripheral blood were assayed on the RayBio Biotin Label-Based Human Antibody Array1 L Series 507 (Cat#AAH-BLG-1-4, RayBiotech Inc, Atlanta, GA, US) according to the manufactures protocol. In brief, 20 µl of the serum samples were diluted 1:5 in PBS and dialyzed over night (ON) at 4C. The following day the samples were labeled with biotin, dialyzed (ON at 4C) and stored at -80C until further processing.

extract_protocol: Serum samples.

tag: sampling point

tag: sampling date

tag: t stage

tag: n stage

tag: inclusion date

tag: date of local relapse

tag: date of metastatic disease

tag: censoring date

tag: trg score

tag: ypt stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: slide block

tag: hybridization order

tag: hybridization date

tag: barcode

tag: pmt

tag: slide print batch


title: Patient113-time1

status: Public on Apr 21 2016

description:
Sample name: LARC-RRP-113-1
Raw data file: 14340647_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

label: biotin

organism: Homo sapiens

tag: sampling point

tag: sampling date


title: Patient113-time4

description:
Sample name: LARC-RRP-113-4
Raw data file: 14340647_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: leukocyte_Beta_value_Sample15

type: genomic

city: University of Tampere

first: Laura

middle: Eeva Marketta

last: Kananen

state: Pirkanmaa

address: Biokatu 6

department: Department of Microbiology and immunology

country: Finland

institute: University of Tampere/School of Medicine

hyb_protocol: bisulphite-converted DNA was subjected to whole-genome amplification after which the DNA was enzymatically fragmented and hybridised to the Infinium HumanMethylation450 BeadChip

scan_protocol: The BeadChips were scanned with the Illumina iScan reader

data_processing: The data (N=187) was preprocessed as methylumiset object using R package wateRmelon(normalization&background correction with dasen; pfilter with default settings). Unspecific probes were excluded.  The batch effect of the Infinium chemistries was adjusted with BMIQ algorithm.    The final statistical analysis was made with N=184 samples because there were 3 samples with atypical low signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: leukocyte from fresh blood

label_protocol: Standard Illumina protocol using Cy5 and Cy3

growth_protocol: Fresh blood samples were collected to EDTA-tubes.

extract_protocol: DNA was extracted from leukocytes using theWizard Genomic DNA Purification Kit (Promega, Madison, WI, USA)

tag: age in 2011

tag: gender (1=woman; 0=man)

tag: cd8t cell proportion

tag: cd4t cell proportion

tag: nk cell proportion

tag: bcell cell proportion

tag: monocyte proportion

tag: granulocyte proportion


title: Patient107-time4

description:
Sample name: LARC-RRP-107-4
Raw data file: 14340594_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse

tag: date of metastatic disease

tag: censoring date

tag: trg score

tag: ypt stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: slide block

tag: hybridization order


title: Patient106-time2

description:
Sample name: LARC-RRP-106-2
Raw data file: 14340631_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date

tag: t stage

tag: n stage

tag: hybridization date

tag: barcode

tag: pmt

tag: slide print batch


title: leukocyte_Beta_value_Sample13

tag: age in 2011

tag: gender (1=woman; 0=man)

tag: cd8t cell proportion

tag: cd4t cell proportion

tag: nk cell proportion

tag: bcell cell proportion

tag: monocyte proportion

tag: granulocyte proportion


title: Patient106-time1

description:
Sample name: LARC-RRP-106-1
Raw data file: 14340634_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse

tag: date of metastatic disease

tag: censoring date

tag: trg score

tag: ypt stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: slide block

tag: hybridization order


title: Patient106-time4

description:
Sample name: LARC-RRP-106-4
Raw data file: 14340634_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date

tag: t stage

tag: n stage

tag: hybridization date

tag: barcode

tag: pmt

tag: slide print batch


title: Patient107-time2

description:
Sample name: LARC-RRP-107-2
Raw data file: 14340595_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: Patient100-time5

description:
Sample name: LARC-RRP-100-5
Raw data file: 14340636_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date


title: leukocyte_Beta_value_Sample6

tag: age in 2011

tag: gender (1=woman; 0=man)

tag: cd8t cell proportion

tag: cd4t cell proportion

tag: nk cell proportion

tag: bcell cell proportion

tag: monocyte proportion

tag: granulocyte proportion


title: leukocyte_Beta_value_Sample9


title: leukocyte_Beta_value_Sample8


title: leukocyte_Beta_value_Sample34


title: leukocyte_Beta_value_Sample7


title: leukocyte_Beta_value_Sample33


title: Patient100-time4

description:
Sample name: LARC-RRP-100-4
Raw data file: 14340637_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date

tag: t stage

tag: n stage

tag: trg score

tag: ypt stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: slide block

tag: hybridization order


title: Patient100-time1

description:
Sample name: LARC-RRP-100-1
Raw data file: 14340637_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse

tag: date of metastatic disease

tag: censoring date

tag: hybridization date

tag: barcode

tag: pmt

tag: slide print batch


title: Patient097-time5

description:
Sample name: LARC-RRP-097-5
Raw data file: 14340626_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient097-time4

description:
Sample name: LARC-RRP-097-4
Raw data file: 14340625_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: Patient096-time2

description:
Sample name: LARC-RRP-096-2
Raw data file: 14340546_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient097-time2

description:
Sample name: LARC-RRP-097-2
Raw data file: 14340626_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient096-time5

description:
Sample name: LARC-RRP-096-5
Raw data file: 14340544_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: slide block

tag: hybridization order


title: Patient097-time1

description:
Sample name: LARC-RRP-097-1
Raw data file: 14340625_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: leukocyte_Beta_value_Sample11

tag: age in 2011

tag: gender (1=woman; 0=man)

tag: cd8t cell proportion

tag: cd4t cell proportion

tag: nk cell proportion

tag: bcell cell proportion

tag: monocyte proportion

tag: granulocyte proportion


title: Patient096-time1

description:
Sample name: LARC-RRP-096-1
Raw data file: 14340544_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date

tag: t stage

tag: n stage

tag: date of metastatic disease

tag: censoring date

tag: hybridization date

tag: barcode

tag: pmt

tag: slide print batch


title: Patient094-time4

description:
Sample name: LARC-RRP-094-4
Raw data file: 14340458_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse

tag: trg score

tag: ypt stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: slide block

tag: hybridization order


title: Patient094-time5

description:
Sample name: LARC-RRP-094-5
Raw data file: 14340459_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient093-time1

description:
Sample name: LARC-RRP-093-1
Raw data file: 14340460_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage

value: X


title: Patient093-time4

description:
Sample name: LARC-RRP-093-4
Raw data file: 14340460_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date


title: Patient092-time5

description:
Sample name: LARC-RRP-092-5
Raw data file: 14341350_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: hybridization date

tag: barcode


title: Patient094-time1

description:
Sample name: LARC-RRP-094-1
Raw data file: 14340458_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: pmt

tag: slide print batch


title: Patient092-time4

description:
Sample name: LARC-RRP-092-4
Raw data file: 14341349_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: Patient093-time2

description:
Sample name: LARC-RRP-093-2
Raw data file: 14340461_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient092-time1

description:
Sample name: LARC-RRP-092-1
Raw data file: 14341349_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient094-time2

description:
Sample name: LARC-RRP-094-2
Raw data file: 14340459_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: slide block

tag: hybridization order


title: Patient089-time2

description:
Sample name: LARC-RRP-089-2
Raw data file: 14340455_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date


title: Patient089-time4

description:
Sample name: LARC-RRP-089-4
Raw data file: 14340453_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: leukocyte_Beta_value_Sample4

tag: age in 2011

tag: gender (1=woman; 0=man)

tag: cd8t cell proportion

tag: cd4t cell proportion

tag: nk cell proportion

tag: bcell cell proportion

tag: monocyte proportion

tag: granulocyte proportion


title: leukocyte_Beta_value_Sample2


title: Patient088-time5

description:
Sample name: LARC-RRP-088-5
Raw data file: 14340464_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse

tag: date of metastatic disease

tag: censoring date

tag: trg score

tag: ypt stage

tag: hybridization date

tag: barcode

tag: pmt

tag: slide print batch


title: Patient089-time1

description:
Sample name: LARC-RRP-089-1
Raw data file: 14340453_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date

tag: t stage

tag: n stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: slide block

tag: hybridization order


title: leukocyte_Beta_value_Sample3

tag: age in 2011

tag: gender (1=woman; 0=man)

tag: cd8t cell proportion

tag: cd4t cell proportion

tag: nk cell proportion

tag: bcell cell proportion

tag: monocyte proportion

tag: granulocyte proportion


title: Patient088-time4

description:
Sample name: LARC-RRP-088-4
Raw data file: 14340463_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse

tag: date of metastatic disease

tag: censoring date

tag: trg score

tag: ypt stage

tag: hybridization date

tag: barcode

tag: pmt

tag: slide print batch


title: Patient088-time1

description:
Sample name: LARC-RRP-088-1
Raw data file: 14340463_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date

tag: t stage

tag: n stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: slide block

tag: hybridization order


title: Patient092-time2

description:
Sample name: LARC-RRP-092-2
Raw data file: 14341350_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: Patient088-time2

description:
Sample name: LARC-RRP-088-2
Raw data file: 14340464_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient086-time4

description:
Sample name: LARC-RRP-086-4
Raw data file: 14340576_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: trg score

tag: ypt stage


title: Patient086-time1

description:
Sample name: LARC-RRP-086-1
Raw data file: 14340576_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: Patient086-time2

description:
Sample name: LARC-RRP-086-2
Raw data file: 14340577_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: pmt

tag: slide print batch


title: Patient089-time5

description:
Sample name: LARC-RRP-089-5
Raw data file: 14340455_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient084-time5

description:
Sample name: LARC-RRP-084-5
Raw data file: 14340628_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: Patient084-time4

description:
Sample name: LARC-RRP-084-4
Raw data file: 14340627_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: leukocyte_Beta_value_Sample1

tag: age in 2011

tag: gender (1=woman; 0=man)

tag: cd8t cell proportion

tag: cd4t cell proportion

tag: nk cell proportion

tag: bcell cell proportion

tag: monocyte proportion

tag: granulocyte proportion


title: Patient081-time2

description:
Sample name: LARC-RRP-081-2
Raw data file: 14340600_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse

tag: date of metastatic disease

tag: censoring date

tag: trg score

tag: ypt stage

tag: slide block

tag: hybridization order

tag: hybridization date

tag: barcode


title: Patient079-time4

description:
Sample name: LARC-RRP-079-4
Raw data file: 14341356_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date

tag: t stage

tag: n stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: pmt

tag: slide print batch


title: Patient081-time1

description:
Sample name: LARC-RRP-081-1
Raw data file: 14340601_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: Patient079-time1

description:
Sample name: LARC-RRP-079-1
Raw data file: 14341356_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient084-time1

description:
Sample name: LARC-RRP-084-1
Raw data file: 14340627_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient084-time2

description:
Sample name: LARC-RRP-084-2
Raw data file: 14340628_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: slide block

tag: hybridization order


title: leukocyte_Beta_value_Sample5

tag: age in 2011

tag: gender (1=woman; 0=man)

tag: cd8t cell proportion

tag: cd4t cell proportion

tag: nk cell proportion

tag: bcell cell proportion

tag: monocyte proportion

tag: granulocyte proportion


title: Patient078-time4

description:
Sample name: LARC-RRP-078-4
Raw data file: 14340473_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date

tag: t stage

tag: n stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: hybridization date

tag: barcode

tag: pmt

tag: slide print batch


title: Patient078-time5

description:
Sample name: LARC-RRP-078-5
Raw data file: 14340474_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse

tag: date of metastatic disease

tag: censoring date

tag: trg score

tag: ypt stage

tag: slide block

tag: hybridization order


title: Patient077-time5

description:
Sample name: LARC-RRP-077-5
Raw data file: 14341353_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient078-time1

description:
Sample name: LARC-RRP-078-1
Raw data file: 14340473_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage


title: Patient077-time1

description:
Sample name: LARC-RRP-077-1
Raw data file: 14341353_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient077-time2

description:
Sample name: LARC-RRP-077-2
Raw data file: 14341354_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: Patient079-time2

description:
Sample name: LARC-RRP-079-2
Raw data file: 14341354_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: pmt

tag: slide print batch


title: Patient081-time4

description:
Sample name: LARC-RRP-081-4
Raw data file: 14340601_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: Patient076-time5

description:
Sample name: LARC-RRP-076-5
Raw data file: 14340585_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date


title: Patient076-time4

description:
Sample name: LARC-RRP-076-4
Raw data file: 14340583_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: trg score

tag: ypt stage


title: Patient075-time5

description:
Sample name: LARC-RRP-075-5
Raw data file: 14340604_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: slide block

tag: hybridization order


title: Patient076-time1

description:
Sample name: LARC-RRP-076-1
Raw data file: 14340583_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date


title: Patient075-time2

description:
Sample name: LARC-RRP-075-2
Raw data file: 14340603_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: Patient074-time4

description:
Sample name: LARC-RRP-074-4
Raw data file: 14340567_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient074-time5

description:
Sample name: LARC-RRP-074-5
Raw data file: 14340568_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: hybridization date

tag: barcode


title: Patient073-time5

description:
Sample name: LARC-RRP-073-5
Raw data file: 14340472_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: pmt

tag: slide print batch


title: Patient074-time1

description:
Sample name: LARC-RRP-074-1
Raw data file: 14340567_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: Patient074-time2

description:
Sample name: LARC-RRP-074-2
Raw data file: 14340568_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient075-time1

description:
Sample name: LARC-RRP-075-1
Raw data file: 14340604_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient073-time2

description:
Sample name: LARC-RRP-073-2
Raw data file: 14340472_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: slide block

tag: hybridization order


title: Patient073-time4

description:
Sample name: LARC-RRP-073-4
Raw data file: 14340471_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient073-time1

description:
Sample name: LARC-RRP-073-1
Raw data file: 14340471_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage


title: Patient072-time5

description:
Sample name: LARC-RRP-072-5
Raw data file: 14340536_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient072-time4

description:
Sample name: LARC-RRP-072-4
Raw data file: 14340535_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: hybridization date

tag: barcode


title: Patient072-time2

description:
Sample name: LARC-RRP-072-2
Raw data file: 14340536_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: pmt

tag: slide print batch


title: Patient070-time4

description:
Sample name: LARC-RRP-070-4
Raw data file: 14340648_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: Patient070-time5

description:
Sample name: LARC-RRP-070-5
Raw data file: 14340649_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date


title: Patient072-time1

description:
Sample name: LARC-RRP-072-1
Raw data file: 14340535_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient071-time2

description:
Sample name: LARC-RRP-071-2
Raw data file: 14340461_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: slide block

tag: hybridization order


title: Patient071-time1

description:
Sample name: LARC-RRP-071-1
Raw data file: 14340462_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date


title: Patient076-time2

description:
Sample name: LARC-RRP-076-2
Raw data file: 14340585_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage


title: Patient070-time2

description:
Sample name: LARC-RRP-070-2
Raw data file: 14340649_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient107-time1

description:
Sample name: LARC-RRP-107-1
Raw data file: 14340594_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: Patient071-time5

description:
Sample name: LARC-RRP-071-5
Raw data file: 14340462_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: pmt

tag: slide print batch


title: Patient069-time5

description:
Sample name: LARC-RRP-069-5
Raw data file: 14340669_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: Patient070-time1

description:
Sample name: LARC-RRP-070-1
Raw data file: 14340648_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient069-time2

description:
Sample name: LARC-RRP-069-2
Raw data file: 14340669_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient069-time4

description:
Sample name: LARC-RRP-069-4
Raw data file: 14340668_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: slide block

tag: hybridization order


title: Patient067-time2

description:
Sample name: LARC-RRP-067-2
Raw data file: 14340563_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date


title: Patient066-time5

description:
Sample name: LARC-RRP-066-5
Raw data file: 14340597_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: Patient066-time2

description:
Sample name: LARC-RRP-066-2
Raw data file: 14340595_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient069-time1

description:
Sample name: LARC-RRP-069-1
Raw data file: 14340668_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: Patient067-time5

description:
Sample name: LARC-RRP-067-5
Raw data file: 14340563_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: pmt

tag: slide print batch


title: Patient065-time2

description:
Sample name: LARC-RRP-065-2
Raw data file: 14340659_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: Patient066-time1

description:
Sample name: LARC-RRP-066-1
Raw data file: 14340597_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient065-time1

description:
Sample name: LARC-RRP-065-1
Raw data file: 14340658_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient067-time1

description:
Sample name: LARC-RRP-067-1
Raw data file: 14340557_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: slide block

tag: hybridization order


title: Patient065-time5

description:
Sample name: LARC-RRP-065-5
Raw data file: 14340659_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient064-time5

description:
Sample name: LARC-RRP-064-5
Raw data file: 14340532_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: Patient064-time4

description:
Sample name: LARC-RRP-064-4
Raw data file: 14340530_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient064-time2

description:
Sample name: LARC-RRP-064-2
Raw data file: 14340532_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: Patient064-time1

description:
Sample name: LARC-RRP-064-1
Raw data file: 14340530_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: pmt

tag: slide print batch


title: Patient067-time4

description:
Sample name: LARC-RRP-067-4
Raw data file: 14340557_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: Patient062-time4

description:
Sample name: LARC-RRP-062-4
Raw data file: 14340540_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date


title: Patient062-time5

description:
Sample name: LARC-RRP-062-5
Raw data file: 14340541_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: trg score

tag: ypt stage


title: Patient060-time1

description:
Sample name: LARC-RRP-060-1
Raw data file: 14340475_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: slide block

tag: hybridization order


title: Patient062-time2

description:
Sample name: LARC-RRP-062-2
Raw data file: 14340541_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date


title: Patient065-time4

description:
Sample name: LARC-RRP-065-4
Raw data file: 14340658_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: Patient059-time4

description:
Sample name: LARC-RRP-059-4
Raw data file: 14340607_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient062-time1

description:
Sample name: LARC-RRP-062-1
Raw data file: 14340540_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: Patient060-time5

description:
Sample name: LARC-RRP-060-5
Raw data file: 14340474_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: pmt

tag: slide print batch


title: Patient060-time4

description:
Sample name: LARC-RRP-060-4
Raw data file: 14340475_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: Patient059-time2

description:
Sample name: LARC-RRP-059-2
Raw data file: 14340608_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient057-time2

description:
Sample name: LARC-RRP-057-2
Raw data file: 14341367_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient057-time5

description:
Sample name: LARC-RRP-057-5
Raw data file: 14341367_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: slide block

tag: hybridization order


title: Patient058-time5

description:
Sample name: LARC-RRP-058-5
Raw data file: 14340655_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient058-time1

description:
Sample name: LARC-RRP-058-1
Raw data file: 14340654_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage


title: Patient058-time4

description:
Sample name: LARC-RRP-058-4
Raw data file: 14340654_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient059-time1

description:
Sample name: LARC-RRP-059-1
Raw data file: 14340607_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: Patient055-time5

description:
Sample name: LARC-RRP-055-5
Raw data file: 14340651_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: pmt

tag: slide print batch


title: Patient058-time2

description:
Sample name: LARC-RRP-058-2
Raw data file: 14340655_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: Patient055-time2

description:
Sample name: LARC-RRP-055-2
Raw data file: 14340651_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient057-time4

description:
Sample name: LARC-RRP-057-4
Raw data file: 14341365_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: trg score

tag: ypt stage


title: Patient055-time4

description:
Sample name: LARC-RRP-055-4
Raw data file: 14340650_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: slide block

tag: hybridization order


title: Patient055-time1

description:
Sample name: LARC-RRP-055-1
Raw data file: 14340650_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date


title: Patient054-time4

description:
Sample name: LARC-RRP-054-4
Raw data file: 14340450_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: Patient054-time1

description:
Sample name: LARC-RRP-054-1
Raw data file: 14340450_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient053-time4

description:
Sample name: LARC-RRP-053-4
Raw data file: 14340663_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: hybridization date

tag: barcode


title: Patient053-time5

description:
Sample name: LARC-RRP-053-5
Raw data file: 14340664_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: pmt

tag: slide print batch


title: Patient053-time1

description:
Sample name: LARC-RRP-053-1
Raw data file: 14340663_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: Patient054-time2

description:
Sample name: LARC-RRP-054-2
Raw data file: 14340451_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient052-time4

description:
Sample name: LARC-RRP-052-4
Raw data file: 14340528_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: trg score

tag: ypt stage


title: Patient051-time5

description:
Sample name: LARC-RRP-051-5
Raw data file: 14340556_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: slide block

tag: hybridization order


title: Patient052-time1

description:
Sample name: LARC-RRP-052-1
Raw data file: 14340528_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date


title: Patient052-time2

description:
Sample name: LARC-RRP-052-2
Raw data file: 14340529_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage


title: Patient054-time5

description:
Sample name: LARC-RRP-054-5
Raw data file: 14340451_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient051-time2

description:
Sample name: LARC-RRP-051-2
Raw data file: 14340556_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: Patient051-time1

description:
Sample name: LARC-RRP-051-1
Raw data file: 14340555_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: pmt

tag: slide print batch


title: Patient048-time4

description:
Sample name: LARC-RRP-048-4
Raw data file: 14340565_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: Patient048-time5

description:
Sample name: LARC-RRP-048-5
Raw data file: 14340566_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date


title: Patient050-time2

description:
Sample name: LARC-RRP-050-2
Raw data file: 14340554_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient057-time1

description:
Sample name: LARC-RRP-057-1
Raw data file: 14341365_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: slide block

tag: hybridization order


title: Patient050-time4

description:
Sample name: LARC-RRP-050-4
Raw data file: 14340553_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient050-time1

description:
Sample name: LARC-RRP-050-1
Raw data file: 14340553_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage


title: Patient048-time2

description:
Sample name: LARC-RRP-048-2
Raw data file: 14340566_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient051-time4

description:
Sample name: LARC-RRP-051-4
Raw data file: 14340555_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: hybridization date

tag: barcode


title: Patient047-time5

description:
Sample name: LARC-RRP-047-5
Raw data file: 14340547_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: pmt

tag: slide print batch


title: Patient048-time1

description:
Sample name: LARC-RRP-048-1
Raw data file: 14340565_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: Patient047-time2

description:
Sample name: LARC-RRP-047-2
Raw data file: 14340546_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date


title: Patient047-time1

description:
Sample name: LARC-RRP-047-1
Raw data file: 14340547_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient052-time5

description:
Sample name: LARC-RRP-052-5
Raw data file: 14340529_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: slide block

tag: hybridization order


title: Patient045-time4

description:
Sample name: LARC-RRP-045-4
Raw data file: 14341359_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient045-time5

description:
Sample name: LARC-RRP-045-5
Raw data file: 14341360_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: Patient045-time1

description:
Sample name: LARC-RRP-045-1
Raw data file: 14341359_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient050-time5

description:
Sample name: LARC-RRP-050-5
Raw data file: 14340554_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: hybridization date

tag: barcode


title: Patient044-time5

description:
Sample name: LARC-RRP-044-5
Raw data file: 14340470_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: pmt

tag: slide print batch


title: Patient043-time4

description:
Sample name: LARC-RRP-043-4
Raw data file: 14340605_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: Patient043-time2

description:
Sample name: LARC-RRP-043-2
Raw data file: 14340606_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient044-time2

description:
Sample name: LARC-RRP-044-2
Raw data file: 14340468_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: trg score

tag: ypt stage


title: Patient044-time1

description:
Sample name: LARC-RRP-044-1
Raw data file: 14340470_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: slide block

tag: hybridization order


title: Patient043-time5

description:
Sample name: LARC-RRP-043-5
Raw data file: 14340606_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient042-time4

description:
Sample name: LARC-RRP-042-4
Raw data file: 14340551_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: Patient042-time5

description:
Sample name: LARC-RRP-042-5
Raw data file: 14340552_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient043-time1

description:
Sample name: LARC-RRP-043-1
Raw data file: 14340605_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: Patient042-time2

description:
Sample name: LARC-RRP-042-2
Raw data file: 14340552_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: pmt

tag: slide print batch


title: Patient041-time5

description:
Sample name: LARC-RRP-041-5
Raw data file: 14340534_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: Patient042-time1

description:
Sample name: LARC-RRP-042-1
Raw data file: 14340551_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient036-time1

description:
Sample name: LARC-RRP-036-1
Raw data file: 14340635_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient041-time2

description:
Sample name: LARC-RRP-041-2
Raw data file: 14340534_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: slide block

tag: hybridization order


title: Patient036-time4

description:
Sample name: LARC-RRP-036-4
Raw data file: 14340635_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient045-time2

description:
Sample name: LARC-RRP-045-2
Raw data file: 14341360_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage


title: Patient037-time1

description:
Sample name: LARC-RRP-037-1
Raw data file: 14340656_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient036-time2

description:
Sample name: LARC-RRP-036-2
Raw data file: 14340636_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: Patient037-time4

description:
Sample name: LARC-RRP-037-4
Raw data file: 14340656_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: pmt

tag: slide print batch


title: Patient037-time2

description:
Sample name: LARC-RRP-037-2
Raw data file: 14340657_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: Patient041-time4

description:
Sample name: LARC-RRP-041-4
Raw data file: 14340533_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date


title: Patient041-time1

description:
Sample name: LARC-RRP-041-1
Raw data file: 14340533_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient037-time5

description:
Sample name: LARC-RRP-037-5
Raw data file: 14340657_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: slide block

tag: hybridization order


title: Patient035-time4

description:
Sample name: LARC-RRP-035-4
Raw data file: 14340598_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date


title: Patient033-time5

description:
Sample name: LARC-RRP-033-5
Raw data file: 14340468_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage


title: Patient033-time1

description:
Sample name: LARC-RRP-033-1
Raw data file: 14340467_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: M31_SUPA

city: London

first: Catarina

last: Samora

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: The Francis Crick Institute

description:
total DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized in buffer containing SSPE, TritonX-100, denatured salmon sperm DNA and biotin-labelled control oligonucleotide, oligo B2. Samples were denatured at 95ºC for 10 minutes before being hybridized to the arrays for 16 hours at 42C in a GeneChip Hybridization Oven 640.

scan_protocol: The washing and scanning protocol (FlexMidi_euk2v3_450), provided by Affymetrix, was performed automatically on a GeneChip Fluidics Station 450. Arrays were scanned using the GeneChip Scanner 3000 7G, and primary analysis of tiling chip data was performed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Signal intensities between the ChIP and supernatant samples were normalized across all probe sets. Changes and change p-values were called as detailed in the Affymetrix Statistical Algorithms Reference Guide (http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf). Probe sets and changes were averaged within adjacent 100 bp windows for graphical depiction. DETECTION P-VALUE = Reliability of raw signal intensity, VALUE=Normalized signal intensity against SUPernatant fraction.

organism: Saccharomyces cerevisiae

source_name: input DNA from yeast cells

label_protocol: 10 ng of amplified DNA was digested with DNase I and end-labeled using biotin-N6-ddATP using terminal transferase TdT (Roche, 400 U/µl) and Biotin-N6-ddATP (Enzo Life Sciences).

growth_protocol: Cells were grown in YP + Raffinose to an OD600 of 0.3. Cells were then arrested in G1 by adding alpha-factor to a final concentration of 0.05mg/ml during 2h. Cells were released and treated as described in the individual samples.

extract_protocol: Chromatin Immunoprecipitation followed by hybridization to a high-density oligonucleotide microarray (ChIP on chip) were performed as previously described (Katou et al. 2003; Lengronne et al. 2004; Lengronne et al. 2006). Briefly, cross-linked cells were disrupted using a Multi-Beads Shocker, and whole cell extracts were sonicated to obtain 400-600 bp genomic DNA fragments. Chromatin immunoprecipitation (ChIP) was performed with anti-PK monoclonal antibody (clone SV5-Pk1, Serotec) coupled to protein A Dynabeads. Immunoprecipates were eluted and incubated overnight at 65ºC to reverse the cross-link. An aliquot of the supernatant fraction of the immunoprecipitation was treated in parallel to provide a whole genome DNA sample for comparison. The ChIP and supernatant samples were then incubated with proteinase K, extracted twice with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RNaseA. The DNA was purified, concentrated by ethanol precipitation and amplified by PCR after random priming.

treatment_protocol: Cells were cross-linked with 1% Formaldehyde for 30 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 10 minutes.

tag: sample type

value: input


title: M39_IPB

description:
Cells were synchronised by alpha-factor block and release into nocodazole-containing medium for 2 hours at 25C and shifted to 37C for an extra hour and galactose was added for a further hour
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04

source_name: ChIP DNA from yeast cells

tag: strain

tag: genotype/variation

value: MATa, SCC1-Pk9::TRP1

tag: antibody

value: anti-Pk Clone V5 vendor:Serotec

value: IP


title: M40_IPB

description:
Cells were synchronised by alpha factor arrest and release into nocodazole-containing medium for 2 hours at 25C
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04

value: MATa T7 promoter-GAL2, SCC1-PK3::HIS3


title: M39_IPC

description:
Cells were synchronised by alpha-factor block and release into nocodazole-containing medium for 2 hours at 25C and shifted to 37C for an extra hour
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04


title: M41_IPB

value: MATa T7 promoter-GAL2, SCC1-PK3::HIS3, ADH1 promoter-NLS-T7 polymerase::TRP1


title: Patient032-time5

description:
Sample name: LARC-RRP-032-5
Raw data file: 14340653_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse

tag: hybridization date

tag: barcode

tag: pmt

tag: slide print batch


title: Patient032-time4

description:
Sample name: LARC-RRP-032-4
Raw data file: 14340652_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date

tag: trg score

tag: ypt stage

tag: slide block

tag: hybridization order


title: M39_IPA

description:
Cells were synchronised by alpha-factor block and release into nocodazole-containing medium for 2 hours at 25C
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04


title: Patient032-time2

description:
Sample name: LARC-RRP-032-2
Raw data file: 14340653_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date

tag: t stage

tag: n stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient032-time1

description:
Sample name: LARC-RRP-032-1
Raw data file: 14340652_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: M34_IPA

tag: strain

tag: genotype/variation

value: MATa rat1-1 SCC1-Pk9::TRP1

tag: antibody

tag: sample type


title: M34_IPB


title: M34_IPC


title: Patient034-time4

description:
Sample name: LARC-RRP-034-4
Raw data file: 14340622_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date

tag: hybridization date

tag: barcode

tag: pmt

tag: slide print batch


title: Patient035-time1

description:
Sample name: LARC-RRP-035-1
Raw data file: 14340598_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date

tag: trg score

tag: ypt stage

tag: slide block

tag: hybridization order


title: Patient035-time2

description:
Sample name: LARC-RRP-035-2
Raw data file: 14340600_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage

tag: inclusion date

tag: date of local relapse

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient034-time1

description:
Sample name: LARC-RRP-034-1
Raw data file: 14340622_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient034-time2

description:
Sample name: LARC-RRP-034-2
Raw data file: 14340623_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: M37_IPD

description:
Cells were synchronised by alpha factor arrest and release into nocodazole-containing medium for 2 hours at 25C and galactose was added for an extra hour
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04

tag: strain

tag: genotype/variation

value: MATa wpl1_delta::kanR, SCC1-myc9::TRP1, LEU2::tetR-GFP, URA3::TetOs

tag: antibody

value: anti-myc Clone 9E10

tag: sample type


title: M37_IPC


title: M46_IPB

description:
Cells were synchronised by alpha factor arrest and release into nocodazole for 1.5 hours in YP-Raffinose at 25C. Cells were then shifted to 37C for 1 hour. Now galactose was added for 1 hour
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04

value: MATa scc2-4, SCC1-Pk9::TRP1, LEU2::GAL1 promoter-SCC1-HA3

value: anti-myc Clone 9E10 anti-HA Clone 12CA5


title: Patient033-time4

description:
Sample name: LARC-RRP-033-4
Raw data file: 14340467_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date

tag: trg score

tag: ypt stage

tag: pmt

tag: slide print batch


title: M37_IPB

value: MATa SCC1-myc9::TRP1


title: Patient031-time4

description:
Sample name: LARC-RRP-031-4
Raw data file: 14340578_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage

tag: inclusion date

tag: date of local relapse

tag: slide block

tag: hybridization order


title: Patient031-time5

description:
Sample name: LARC-RRP-031-5
Raw data file: 14340577_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: hybridization date

tag: barcode


title: M37_IPA

description:
Cells were synchronised by alpha factor arrest and release into nocodazole-containing medium for 2 hours at 25C
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04

tag: strain

tag: genotype/variation

tag: antibody

tag: sample type


title: Patient031-time1

description:
Sample name: LARC-RRP-031-1
Raw data file: 14340578_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date

tag: trg score

tag: ypt stage

tag: pmt

tag: slide print batch


title: M36_IPE

description:
Cells were synchronised by alpha factor arrest and release into nocodazole-containing medium for 2 hours at 25C and galactose was added for a further 15min
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04

value: MATa smc1R58A::LEU2, smc3R58A::TRP1, SCC1-Pk3::HIS3


title: M36_IPD


title: M46_IPD

description:
As M46_IPB but 30 minutes after cells were filtered, washed and resuspended in YNB-Raffinose medium lacking amino acids at 37C
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04


title: Patient030-time4

description:
Sample name: LARC-RRP-030-4
Raw data file: 14341357_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage

tag: inclusion date

tag: date of local relapse

tag: slide block

tag: hybridization order


title: Patient030-time5

description:
Sample name: LARC-RRP-030-5
Raw data file: 14341358_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: hybridization date

tag: barcode


title: Patient030-time2

description:
Sample name: LARC-RRP-030-2
Raw data file: 14341358_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date


title: M36_IPB

tag: strain

tag: genotype/variation

value: MATa SCC1-Pk3::HIS3

tag: antibody

tag: sample type


title: Patient030-time1

description:
Sample name: LARC-RRP-030-1
Raw data file: 14341357_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage

tag: trg score

tag: ypt stage

tag: pmt

tag: slide print batch


title: M36_IPA


title: M9_IPE

description:
Cells were synchronised by alpha factor arrest and release into nocodazole-containing medium for 1 hour at 25C, then shifted to 35C for 1 additional hour and galactose was added for an additional hour
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
S_cerevisiaeF_4x

value: MATa, SCC1-Pk9::TRP1 scc2-4


title: M10_IPA

description:
Cells were synchronised by alpha factor arrest and release into nocodazole-containing medium for 1 hour at 25C, then shifted to 35C for 1 additional hour
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
S_cerevisiaeF_4x


title: Patient029-time5

description:
Sample name: LARC-RRP-029-5
Raw data file: 14340582_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse

tag: date of metastatic disease

tag: censoring date

tag: slide block

tag: hybridization order


title: M9_IPD


title: Patient029-time4

description:
Sample name: LARC-RRP-029-4
Raw data file: 14340581_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: hybridization date

tag: barcode


title: Patient028-time4

description:
Sample name: LARC-RRP-028-4
Raw data file: 14340537_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: M10_IPB

tag: strain

tag: genotype/variation

tag: antibody

tag: sample type


title: Patient028-time5

description:
Sample name: LARC-RRP-028-5
Raw data file: 14340539_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse

tag: trg score

tag: ypt stage

tag: pmt

tag: slide print batch


title: Patient027-time4

description:
Sample name: LARC-RRP-027-4
Raw data file: 14341361_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date

tag: date of metastatic disease

tag: censoring date

tag: slide block

tag: hybridization order


title: Patient027-time5

description:
Sample name: LARC-RRP-027-5
Raw data file: 14341362_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: hybridization date

tag: barcode


title: Patient027-time2

description:
Sample name: LARC-RRP-027-2
Raw data file: 14341362_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse


title: Patient028-time2

description:
Sample name: LARC-RRP-028-2
Raw data file: 14340539_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient028-time1

description:
Sample name: LARC-RRP-028-1
Raw data file: 14340537_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: pmt

tag: slide print batch


title: Patient027-time1

description:
Sample name: LARC-RRP-027-1
Raw data file: 14341361_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date


title: Patient026-time1

description:
Sample name: LARC-RRP-026-1
Raw data file: 14340602_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient026-time4

description:
Sample name: LARC-RRP-026-4
Raw data file: 14340602_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: slide block

tag: hybridization order


title: Patient029-time2

description:
Sample name: LARC-RRP-029-2
Raw data file: 14340582_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage


title: Patient024-time4

description:
Sample name: LARC-RRP-024-4
Raw data file: 14340673_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: M9_IPB

tag: strain

tag: genotype/variation

tag: antibody

tag: sample type


title: M9_IPA


title: Patient024-time1

description:
Sample name: LARC-RRP-024-1
Raw data file: 14340673_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: date of local relapse

tag: trg score

tag: ypt stage

tag: hybridization date

tag: barcode


title: Patient023-time5

description:
Sample name: LARC-RRP-023-5
Raw data file: 14340592_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: sampling date

tag: date of metastatic disease

tag: censoring date

tag: pmt

tag: slide print batch


title: Patient023-time4

description:
Sample name: LARC-RRP-023-4
Raw data file: 14340593_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: slide block

tag: hybridization order


title: Patient022-time4

description:
Sample name: LARC-RRP-022-4
Raw data file: 14340591_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: Patient022-time5

description:
Sample name: LARC-RRP-022-5
Raw data file: 14340592_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient029-time1

description:
Sample name: LARC-RRP-029-1
Raw data file: 14340581_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: hybridization date

tag: barcode


title: Patient022-time1

description:
Sample name: LARC-RRP-022-1
Raw data file: 14340591_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date


title: Patient021-time1

description:
Sample name: LARC-RRP-021-1
Raw data file: 14340569_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: censoring date


title: Patient021-time5

description:
Sample name: LARC-RRP-021-5
Raw data file: 14340571_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: pmt

tag: slide print batch


title: Patient021-time2

description:
Sample name: LARC-RRP-021-2
Raw data file: 14340571_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: n stage


title: Patient026-time5

description:
Sample name: LARC-RRP-026-5
Raw data file: 14340603_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient024-time5

description:
Sample name: LARC-RRP-024-5
Raw data file: 14340672_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: slide block

tag: hybridization order


title: Patient019-time4

description:
Sample name: LARC-RRP-019-4
Raw data file: 14340671_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: Patient023-time1

description:
Sample name: LARC-RRP-023-1
Raw data file: 14340593_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: trg score

tag: ypt stage


title: Patient021-time4

description:
Sample name: LARC-RRP-021-4
Raw data file: 14340569_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: hybridization date

tag: barcode


title: Patient019-time2

description:
Sample name: LARC-RRP-019-2
Raw data file: 14340672_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date


title: Patient018-time4

description:
Sample name: LARC-RRP-018-4
Raw data file: 14340629_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: censoring date


title: Patient019-time1

description:
Sample name: LARC-RRP-019-1
Raw data file: 14340671_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: pmt

tag: slide print batch


title: Patient017-time5

description:
Sample name: LARC-RRP-017-5
Raw data file: 14341364_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage


title: Patient018-time2

description:
Sample name: LARC-RRP-018-2
Raw data file: 14340631_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypn stage

tag: ctcae grade diarrhea at crt completion


title: Patient018-time1

description:
Sample name: LARC-RRP-018-1
Raw data file: 14340629_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: slide block

tag: hybridization order


title: Patient017-time4

description:
Sample name: LARC-RRP-017-4
Raw data file: 14341363_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: date of local relapse


title: PE (C07_11)

type: RNA

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

description: Neonatal rat coardiomyocytes

hyb_protocol: Hybridization of 5.5ug labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual

scan_protocol: Washing and staining of the arrays was done on a Affymetrix 450 fluidics stations using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual. Arrays where then scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual

data_processing: The data where normalized using RMA normalization strategies using the MADMAX analysis pipeline pmid:21778530

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: PE

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 500ng of total RNA without rRNA reduction

growth_protocol: NRVCs were grown in DMEM , 5% FCS and pen-strep, NRCVs serum starved in DMEM, after 24 hours NRCVs were  stimulated, washed and RNA was isolated

extract_protocol: Total RNA was isolated from treated NRVCs

treatment_protocol: 50 uM PE ( phenylephrine) or 10nM IGF1 (insulin-like growth factor 1)

tag: strain

value: Sprague Dawley

tag: cell type

value: neonatal rat ventricular cardiomyocytes (NRVCs)

tag: agent

value: PE


title: Control (G05_07)

description: Neonatal rat coardiomyocytes

source_name: Control

value: control


title: Control (D05_04)

description: Neonatal rat coardiomyocytes


title: PE (H05_08)

description: Neonatal rat coardiomyocytes


title: IGF1 (C05_03)

description: Neonatal rat coardiomyocytes


title: IGF1 (A07_09)

description: Neonatal rat coardiomyocytes


title: oral mucosa fibroblasts-derived iPSCs rep1

city: Tokushima

first: Keiko

last: Miyoshi

address: 3-18-15 Kuramoto-cho

department: Department of Molecular Biology

country: Japan

institute: The University of Tokushima Graduate School, Institute of Health Biosciences

description: oral mucosa fibroblasts (OF2)-derived iPSCs, clone 2-30

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 80μl of hyb solution to each array, then tape holes. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuGene-1_0-st-v1.r3.pgf
meta-probeset file: HuGene-1_0-st-v1.r3.mps

source_name: oral mucosa fibroblasts-derived iPSCs

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: hOFs and hDFs were cultured in  DMEM or EMEM supplemented with 10% serum, respectively. hOF-iPSCs were cultured in Primate ES medium (Reprocell) suplemented with 5ng/ml bFGF.

extract_protocol: Total RNA was isolated using TRI Reagent (Molecular Research Center) according to the manufacturer’s instructions, with additional ethanol precipitation. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: Not applicable

tag: age

tag: gender

value: M

value: oral mucosa fibroblasts-derived iPSCs


title: Patient017-time2

description:
Sample name: LARC-RRP-017-2
Raw data file: 14341364_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: sampling date

tag: date of metastatic disease

tag: trg score

tag: ypt stage

tag: hybridization date

tag: barcode


title: dermal fibroblasts rep3

description: dermal fibroblasts

source_name: dermal fibroblasts

value: dermal fibroblasts


title: IGF1 (F05_06)

description: Neonatal rat coardiomyocytes


title: oral mucosa fibroblasts-derived iPSCs rep2

description: oral mucosa fibroblasts (OF3B)-derived iPSCs, clone 3-4


title: Control (A05_01)

description: Neonatal rat coardiomyocytes


title: dermal fibroblasts rep2

description: dermal fibroblasts

value: F


title: PE (E05_05)

description: Neonatal rat coardiomyocytes


title: Patient016-time5

description:
Sample name: LARC-RRP-016-5
Raw data file: 14340550_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: n stage

tag: censoring date

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: pmt

tag: slide print batch


title: IGF1 (D07_12)

description: Neonatal rat coardiomyocytes

tag: strain

tag: cell type

tag: agent


title: Control (B07_10)

description: Neonatal rat coardiomyocytes


title: Patient016-time1

description:
Sample name: LARC-RRP-016-1
Raw data file: 14340548_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: inclusion date

tag: date of local relapse

tag: slide block

tag: hybridization order


title: oral mucosa fibroblasts rep2

description: oral mucosa fibroblasts (OF3B)

source_name: oral mucosa fibroblasts

tag: age

tag: gender

value: oral mucosa fibroblasts


title: Patient016-time4

description:
Sample name: LARC-RRP-016-4
Raw data file: 14340548_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling date

tag: t stage

tag: date of metastatic disease

tag: trg score

tag: ypt stage

tag: hybridization date

tag: barcode


title: Patient016-time2

description:
Sample name: LARC-RRP-016-2
Raw data file: 14340550_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: n stage

tag: censoring date

tag: ypn stage

tag: ctcae grade diarrhea at crt completion

tag: pmt

tag: slide print batch


title: PE (B05_02)

description: Neonatal rat coardiomyocytes

tag: strain

tag: cell type

tag: agent


title: Patient015-time5

description:
Sample name: LARC-RRP-015-5
Raw data file: 14340543_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: inclusion date

tag: date of local relapse

tag: slide block

tag: hybridization order


title: Patient014-time5

description:
Sample name: LARC-RRP-014-5
Raw data file: 14340580_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling date

tag: t stage

tag: date of metastatic disease

tag: trg score

tag: ypt stage


title: Patient015-time4

description:
Sample name: LARC-RRP-015-4
Raw data file: 14340542_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: n stage

tag: censoring date

tag: ypn stage

tag: hybridization date

tag: barcode


title: Patient015-time1

description:
Sample name: LARC-RRP-015-1
Raw data file: 14340542_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ctcae grade diarrhea at crt completion

tag: pmt

tag: slide print batch


title: dermal fibroblasts rep1

description: dermal fibroblasts

tag: age

tag: gender

tag: cell type


title: oral mucosa fibroblasts  rep1

description: oral mucosa fibroblasts (OF2)


title: Patient015-time2

description:
Sample name: LARC-RRP-015-2
Raw data file: 14340543_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: inclusion date

tag: date of local relapse

tag: slide block

tag: hybridization order


title: Patient014-time4

description:
Sample name: LARC-RRP-014-4
Raw data file: 14340579_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling date

tag: t stage

tag: date of metastatic disease

tag: trg score

tag: ypt stage


title: Patient014-time2

description:
Sample name: LARC-RRP-014-2
Raw data file: 14340580_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: n stage

tag: censoring date

tag: ypn stage

tag: hybridization date

tag: barcode


title: oral mucosa fibroblasts rep3

description: oral mucosa fibroblasts (OF4B)

tag: age

tag: gender


title: oral mucosa fibroblasts-derived iPSCs rep3

description: oral mucosa fibroblasts (OF4B)-derived iPSCs, clone 4-5

tag: cell type


title: mRNA-iPS2

city: Bundanggu

first: Kangin

last: lee

state: Seongnam

address: 335 Pankyoro

department: Biomedical Science

country: South Korea

institute: CHA University

description: SAMPLE 3

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

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

value: iPS cells

tag: generated using

value: ECM-based xeno-free culture system with a microRNA-enhanced mRNA reprogramming method


title: Fibroblast

description: SAMPLE 2

source_name: Fibroblast

value: Fibroblast


title: Patient014-time1

description:
Sample name: LARC-RRP-014-1
Raw data file: 14340579_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: inclusion date

tag: date of local relapse

tag: ctcae grade diarrhea at crt completion

tag: pmt

tag: slide print batch


title: Patient013-time5

description:
Sample name: LARC-RRP-013-5
Raw data file: 14340457_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling date

tag: t stage

tag: date of metastatic disease

tag: trg score

tag: slide block

tag: hybridization order


title: Patient017-time1

description:
Sample name: LARC-RRP-017-1
Raw data file: 14341363_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: n stage

tag: censoring date

tag: ypt stage

tag: ypn stage

tag: hybridization date

tag: barcode


title: Patient013-time4

description:
Sample name: LARC-RRP-013-4
Raw data file: 14340456_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: inclusion date


title: Patient013-time2

description:
Sample name: LARC-RRP-013-2
Raw data file: 14340457_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of local relapse

tag: ctcae grade diarrhea at crt completion


title: Patient011-time5

description:
Sample name: LARC-RRP-011-5
Raw data file: 14340589_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: pmt

tag: slide print batch


title: Patient013-time1

description:
Sample name: LARC-RRP-013-1
Raw data file: 14340456_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling date

tag: t stage


title: H9-hESC

description: SAMPLE 1

tag: cell type

value: hESC


title: Patient011-time2

description:
Sample name: LARC-RRP-011-2
Raw data file: 14340589_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: trg score

tag: slide block


title: Patient011-time4

description:
Sample name: LARC-RRP-011-4
Raw data file: 14340588_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: n stage

tag: censoring date

tag: hybridization order


title: Patient011-time1

description:
Sample name: LARC-RRP-011-1
Raw data file: 14340588_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypt stage

tag: ypn stage

tag: hybridization date


title: Patient008-time5

description:
Sample name: LARC-RRP-008-5
Raw data file: 14340624_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: inclusion date

tag: barcode


title: Patient009-time1

description:
Sample name: LARC-RRP-009-1
Raw data file: 14340665_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of local relapse

tag: ctcae grade diarrhea at crt completion

tag: pmt


title: Patient008-time2

description:
Sample name: LARC-RRP-008-2
Raw data file: 14340623_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling date

tag: t stage

tag: slide print batch


title: Patient009-time2

description:
Sample name: LARC-RRP-009-2
Raw data file: 14340664_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: trg score


title: Patient009-time5

description:
Sample name: LARC-RRP-009-5
Raw data file: 14340665_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: n stage

tag: slide block


title: Patient008-time1

description:
Sample name: LARC-RRP-008-1
Raw data file: 14340624_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: censoring date

tag: hybridization order


title: Patient007-time5

description:
Sample name: LARC-RRP-007-5
Raw data file: 14340662_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypt stage

tag: ypn stage


title: Patient006-time1

description:
Sample name: LARC-RRP-006-1
Raw data file: 14341351_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: hybridization date


title: Patient006-time4

description:
Sample name: LARC-RRP-006-4
Raw data file: 14341351_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: barcode


title: Patient005-time5

description:
Sample name: LARC-RRP-005-5
Raw data file: 14340466_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of local relapse

tag: ctcae grade diarrhea at crt completion


title: Patient007-time2

description:
Sample name: LARC-RRP-007-2
Raw data file: 14340662_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling date

tag: pmt


title: Patient007-time4

description:
Sample name: LARC-RRP-007-4
Raw data file: 14340661_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: slide print batch


title: Patient007-time1

description:
Sample name: LARC-RRP-007-1
Raw data file: 14340661_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: trg score


title: Patient005-time4

description:
Sample name: LARC-RRP-005-4
Raw data file: 14340465_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: n stage

tag: slide block


title: Patient005-time2

description:
Sample name: LARC-RRP-005-2
Raw data file: 14340466_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: censoring date

tag: hybridization order


title: Patient004-time2

description:
Sample name: LARC-RRP-004-2
Raw data file: 14340667_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: ypt stage

tag: ypn stage


title: Patient005-time1

description:
Sample name: LARC-RRP-005-1
Raw data file: 14340465_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: hybridization date


title: Patient004-time1

description:
Sample name: LARC-RRP-004-1
Raw data file: 14340666_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: inclusion date

tag: barcode


title: Patient004-time4

description:
Sample name: LARC-RRP-004-4
Raw data file: 14340666_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of local relapse

tag: ctcae grade diarrhea at crt completion


title: Patient004-time5

description:
Sample name: LARC-RRP-004-5
Raw data file: 14340667_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling date

tag: pmt


title: Patient003-time2

description:
Sample name: LARC-RRP-003-2
Raw data file: 14340587_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: t stage

tag: slide print batch


title: Patient003-time1

description:
Sample name: LARC-RRP-003-1
Raw data file: 14340586_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of metastatic disease

tag: trg score


title: Patient003-time5

description:
Sample name: LARC-RRP-003-5
Raw data file: 14340587_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: n stage

tag: slide block


title: Patient003-time4

description:
Sample name: LARC-RRP-003-4
Raw data file: 14340586_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: censoring date

tag: hybridization order


title: Patient006-time5

description:
Sample name: LARC-RRP-006-5
Raw data file: 14341352_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: ypt stage

tag: ypn stage


title: Patient006-time2

description:
Sample name: LARC-RRP-006-2
Raw data file: 14341352_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling point

tag: hybridization date


title: Patient002-time5

description:
Sample name: LARC-RRP-002-5
Raw data file: 14340449_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: inclusion date

tag: barcode


title: Patient002-time2

description:
Sample name: LARC-RRP-002-2
Raw data file: 14340449_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: date of local relapse

tag: ctcae grade diarrhea at crt completion


title: Patient002-time1

description:
Sample name: LARC-RRP-002-1
Raw data file: 14340448_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling date

tag: pmt


title: Patient001-time4

description:
Sample name: LARC-RRP-001-4
Raw data file: 14340572_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: t stage

tag: slide print batch


title: Patient001-time5

description:
Sample name: LARC-RRP-001-5
Raw data file: 14340574_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: date of metastatic disease

tag: trg score


title: Patient001-time1

description:
Sample name: LARC-RRP-001-1
Raw data file: 14340572_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: n stage

tag: slide block


title: M61_IPB

description:
Cells were grown in the presence of 20mM IPTG and synchronised by alpha factor arrest and release into nocodazole-containing medium for 2 hours at 25C
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MR_v04

tag: strain

tag: genotype/variation

value: MATa T7 promoter-GAL2, SCC1-PK3::HIS3, ADH1 promoter-NLS-T7 polymerase::TRP1, ADH1 promoter-NLS-LacI::LEU2

tag: antibody

value: anti-Pk Clone V5 vendor:Serotec

tag: sample type

value: IP


title: 3546_input

description:
Cells were grown in YP-Raffinose and synchronised by alpha-factor block and release at 30C into nocodazole-containing medium for 2 hours
total DNA
Sc03b_MR_v04

value: MATa, cyc1-5000 cyc7-67 cyh2 sua7-1 Scc1-3PK::LEU2

value: input


title: 3546_IP

description:
Cells were grown in YP-Raffinose and synchronised by alpha-factor block and release at 30C into nocodazole-containing medium for 2 hours
Immunoprecipitated DNA
Sc03b_MR_v04


title: 3545_input

value: MATa, cyc1-5000 cyc7-67 cyh2 Scc1-3PK::LEU2


title: M59_IPH

description:
Cells were synchronised by alpha factor block and release into nocodazole containing medium at 25C. After 1 hour, cells were shifted to 16C. After another 1 hour an aliquot of the same culture was taken following galactose addition at 21 minutes
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MR_v04

value: MATa GAL2 promoter-UTP20, SCC1-Pk9::TRP1


title: 3545_IP


title: M50_IPA

description:
Cells were grown in YP-Raffinose and synchronised by alpha-factor block and release at 25C into medium containing 0.2 M hydroxyurea for 1.5 hours
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04

value: MATa, SCC1-Pk9::TRP1


title: M50_IPB

description:
Cells were grown in YP-Raffinose and synchronised by alpha-factor block and release at 25C into medium containing 0.2 M hydroxyurea for 1.5 hours and galactose was added for an extra hour
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MF_v04


title: M59_IPF

description:
Cells were synchronised by alpha factor block and release into nocodazole containing medium at 25C. After 1 hour, cells were shifted to 16C. After another 1 hour an aliquot of the same culture was taken following galactose addition at 15 minutes
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MR_v04


title: Patient002-time4

description:
Sample name: LARC-RRP-002-4
Raw data file: 14340448_60%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 2)

tag: sampling point

tag: censoring date

tag: ypt stage

tag: ypn stage

tag: hybridization order

tag: hybridization date


title: M59_IPD

description:
Cells were synchronised by alpha factor block and release into nocodazole containing medium at 25C. After 1 hour, cells were shifted to 16C. After another 1 hour an aliquot of the same culture was taken following galactose addition at 9 minutes
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MR_v04


title: M61_IPA

description:
Cells were synchronised by alpha factor arrest and release into nocodazole-containing medium for 2 hours at 25C
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MR_v04


title: Patient001-time2

description:
Sample name: LARC-RRP-001-2
Raw data file: 14340574_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)

tag: sampling date

tag: inclusion date

tag: date of local relapse

tag: ctcae grade diarrhea at crt completion

tag: barcode

tag: pmt


title: M59_IPE

description:
Cells were synchronised by alpha factor block and release into nocodazole containing medium at 25C. After 1 hour, cells were shifted to 16C. After another 1 hour an aliquot of the same culture was taken following galactose addition at 12 minutes
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MR_v04


title: M59_IPA

description:
Cells were synchronised by alpha factor block and release into nocodazole containing medium at 25C. After 1 hour, cells were shifted to 16C. After another 1 hour, time point 0 was taken
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MR_v04


title: HCS_6 (BCC control) [circRNA]

city: Bochum

first: Michael

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

country: Germany

institute: Ruhr-University Bochum

description: We identified 23 up- and 48 down-regulated circRNAs differentially expressed in BCC compared to non-lesional skin.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, next heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the hybridization gasket slide and assembled to the circRNA 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 using the Agilent Scanner G2505C (Agilent Technologies, Santa Clara, USA).

data_processing: Scanned array images were imported into Agilent Feature Extraction software (version 11.0.1.1; Agilent Technologies, Santa Clara, USA) for raw data extraction and analysis. Quantile normalization of raw data and subsequent data processing were performed using the R software package (version 2.15, http://www.r-project.org/). After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least in 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analysis. The normalized and log2 transformed data were averaged across the samples, and a group-wise comparison was performed between BCC and non-lesional epithelial skin as a control.

source_name: skin

label_protocol: Sample labeling and array hybridization was performed according to the manufacturer’s protocol (Arraystar, Rockville, USA). In order to remove linear RNAs and enrich circRNA, total RNA was digested with RNase R (Epicentre, Madison, USA). Random priming method (Arraystar Super RNA Labeling Kit; Arraystar, Rockville, USA) was used to amplify and transcribe the enriched circRNA into fluorescent cRNA. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen, Hilden, Germany). Concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: During micrographic controlled excision of nodular BCCs with cold steel under local anaesthesia, 4-mm punch biopsies were taken from the centre of the tumor and from non-lesional epithelial skin of healthy individuals serving as control (NLES, control). The samples were subsequently placed in RNAlater (Qiagen, Hilden, Germany) and stored at - 80 °C. After extraction of total RNA with TRIzol (Life Technologies, Carlsbad, USA) according to the manufacturer's protocol, NanoDrop ND-1000 (NanoDrop, Wilmington, USA) was used for measuring RNA quantity and quality.

tag: gender

value: Male

tag: tissue

value: non-lesional skin (control)


title: HCS_11 (BCC control) [circRNA]

value: Female


title: HCS_8 (BCC control) [circRNA]


title: BCC_59T [circRNA]

source_name: basal cell carcinoma

value: basal cell carcinoma


title: BCC_47T [circRNA]


title: Fah_100%

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

source_name: healthy liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Qiagen RNAeasy Kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were kept under standard conditions with 12h day-night cycle and access to food and water ad libitum.Drinking water was supplemented with 2-(2-nitro-4-trifluoromethylbenzyol)-1,3-cyclohexandione (NTBC) at a concentration of 7.5μg/ml to simulate 100% NTBC treatment. Experimental setup was designed with repeated cycles of NTBC withdrawal and NTBC treatment. 2xoff/on= Fah-/- and FCR mice were cycled twice and livers were collected after the off (0% NTBC) and on phases (100% NTBC), respectively. Fah-/- mice and  FCR mice were either exposed to two courses of NTBC withdrawal (0% NTBC) and resupplementation (off) or continuously kept on 100% NTBC (100%).

tag: strain background

tag: genotype/variation

value: liver

tag: tissue type

value: healthy liver


title: FCR_off

source_name: inflamed liver

value: Fah_del_tm1Mgo Rag2_del_tm1Fwa common gamma chain del tm1Wjl

value: inflamed liver


title: Fah_off

source_name: tumor

value: tumor


title: Fah_2xoff/on


title: FCR_2xoff/on


title: FCR_100%

source_name: normal liver

value: normal liver


title: M59_IPC

description:
Cells were synchronised by alpha factor block and release into nocodazole containing medium at 25C. After 1 hour, cells were shifted to 16C. After another 1 hour, an aliquot of the same culture was taken following galactose addition at 6 minutes
Immunoprecipitated DNA
Processed data files were only temporarily created, but not saved, by the software that used the CEL files to generate the graphical result output files. Therefore there are no quantitative processed data available for this sample.
Sc03b_MR_v04

tag: strain

tag: antibody

value: anti-Pk Clone V5 vendor:Serotec

tag: sample type


title: BCC_55T [circRNA]


title: Cardiomyocytes_4

status: Public on Apr 20 2016

city: Hamburg

first: Ingra

last: Mannhardt

address: Martinistr. 26

institute: University Medical Center Hamburg-Eppendorf

description:
9477874022_c
Replicate 4
SAMPLE 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The array data have been quantile normalized on probe level without background correction. Data have been log2 transformed after an offset addition (+16).

source_name: Cardiomyocytes

label_protocol: Illumina TotalPrep-96 RNA Amplification Kit von Ambion; Biotinylation.

growth_protocol: After differentiation, cardiomyocytes were dissociated with collagenase (200 U/ml) and cultivated in a fibrin matrix as engineered heart tissue for 21 days or as age-matched cultures in standard 2D monolayer. The culture medium consisted of DMEM, 1% penicillin/streptomycin, 10% horse serum, 10 µg/ml insulin, 33 µg/ml aprotinin. Culture medium was changed Mondays, Wednesdays and Fridays.

extract_protocol: Total RNA was extracted with the RNeasy® mini kit , Qiagen 74104

treatment_protocol: Please see Mannhardt et al. 2016, Stem Cell Reports

tag: cell type

value: hiPSC-CM

tag: age

value: 14 days after start of differentiation


title: Cardiomyocytes_2

description:
9422487059_a
Replicate 2
SAMPLE 2


title: Cardiomyocytes EHT_2

description:
9477874022_b
Replicate 2
SAMPLE 11

source_name: Cardiomyocytes EHT

tag: culture conditions

value: 35 days after start of differentiation


title: Cardiomyocytes 2D_2

description:
9422487054_d
Replicate 2
SAMPLE 6

source_name: Cardiomyocytes 2D


title: Cardiomyocytes 2D_3

description:
9422487059_c
Replicate 3
SAMPLE 7


title: Cardiomyocytes EHT_5

description:
9477874022_j
Replicate 5
SAMPLE 14


title: Cardiomyocytes 2D_5

description:
9477874022_e
Replicate 5
SAMPLE 9


title: BAN_1nM DHT_48h_repA

city: Cologne

first: Axel

last: HILLMER

address: Kerpener Str. 62

department: Institute of Pathology

institute: University of Cologne

data_processing: The data was log2 transformation and quantile normalized using the LUMI in R

source_name: BAN

label_protocol: Biotinylated cRNA were prepared with Epicentre TargetAmp Nano-g Biotin-aRNA labelling kit

extract_protocol: Total RNA was isolated with Qiagen RNeasy kit and on-column DNase treatment according to manufacturer’s recommendation. Quality control was performed with Agilent Bioanalyzer.

tag: cell line

value: BAN

tag: agent

value: DHT

tag: dose

tag: time (treatment duration)


title: Cardiomyocytes EHT_4

description:
9477874022_g
Replicate 4
SAMPLE 13


title: Cardiomyocytes_1

description:
9422487054_b
Replicate 1
SAMPLE 1


title: Cardiomyocytes EHT_6

description:
9477874022_k
Replicate 6
SAMPLE 15


title: Cardiomyocytes_3

description:
9422487059_b
Replicate 3
SAMPLE 3


title: Cardiomyocytes EHT_1

description:
9477874022_a
Replicate 1
SAMPLE 10


title: BAN_1nM DHT_36h_repC


title: BAN_1nM DHT_6h_repC


title: Cardiomyocytes EHT_3

description:
9477874022_f
Replicate 3
SAMPLE 12


title: BAN_1nM DHT_30min_repB


title: BAN_1nM DHT_24h_repC


title: Cardiomyocytes 2D_4

description:
9477874022_d
Replicate 4
SAMPLE 8


title: BAN_1nM DHT_6h_repB


title: BAN_1nM DHT_30min_repC


title: BAN_1nM DHT_3h_repB


title: BAN_1nM DHT_36h_repB


title: BAN_1nM DHT_30min_repA


title: Cardiomyocytes 2D_1

description:
9422487054_c
Replicate 1
SAMPLE 5


title: BAN_1nM DHT_48h_repC


title: BAN_1nM DHT_3h_repA


title: BAN_1nM DHT_48h_repB


title: BAN_1nM DHT_6h_repA


title: BAN_1nM DHT_36h_repA


title: BAN_1nM DHT_1h_repB


title: BAN_1nM DHT_16h_repC


title: BAN_1nM DHT_20h_repB


title: BAN_1nM DHT_15min_repC


title: BAN_1nM DHT_1h_repC


title: BAN_1nM DHT_24h_repA


title: BAN_1nM DHT_15min_repB


title: BAN_1nM DHT_1h_repA


title: BAN_1nM DHT_16h_repB


title: BAN_1nM DHT_20h_repC


title: BAN_1nM DHT_20h_repA


title: BAN_1nM DHT_12h_repB


title: BAN_10nM DHT_48h_repC


title: BAN_1nM DHT_16h_repA


title: BAN_10nM DHT_6h_repB


title: BAN_10nM DHT_48h_repA


title: BAN_1nM DHT_24h_repB


title: BAN_10nM DHT_6h_repC


title: BAN_10nM DHT_6h_repA


title: BAN_1nM DHT_0h_repB


title: BAN_10nM DHT_3h_repB


title: BAN_10nM DHT_36h_repB


title: BAN_1nM DHT_15min_repA


title: BAN_1nM DHT_0h_repA


title: BAN_10nM DHT_48h_repB


title: BAN_1nM DHT_12h_repA


title: BAN_10nM DHT_3h_repC


title: BAN_10nM DHT_3h_repA


title: BAN_1nM DHT_12h_repC


title: BAN_10nM DHT_36h_repC


title: BAN_10nM DHT_30min_repC


title: BAN_10nM DHT_36h_repA


title: BAN_10nM DHT_15min_repC


title: BAN_10nM DHT_15min_repA


title: BAN_10nM DHT_30min_repB


title: BAN_10nM DHT_20h_repC


title: BAN_10nM DHT_1h_repA


title: BAN_10nM DHT_1h_repC


title: BAN_10nM DHT_16h_repC


title: BAN_10nM DHT_30min_repA


title: BAN_10nM DHT_16h_repB


title: BAN_10nM DHT_15min_repB


title: BAN_10nM DHT_24h_repC


title: F10-5-G

city: Urbana

first: Junmin

last: Lee

state: IL

address: 1304 W. Green St.

department: Materials Science and Engineering

country: USA

institute: University of Illinois at Urbana-Chanpaign

hyb_protocol: not provided

scan_protocol: Gene expression profiling performed using Illumina iScan Sentrix BeachChip technology at the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign using standard Illumina protocols

data_processing:
Illumina gene array data was preprocessed using GenePattern. The background values were subtracted and hresholded.
The data was then normalized using the quantile method. Heatmaps of fold changes over glass in gene expression were visualized using the Gene-E software package.

source_name: B16F10 cells cultured on patterned gels for 5 days

label_protocol: not provided

growth_protocol: Adherent B16F0 and B16F10 cells were cultured for five days on spiral patterns, non-patterned gels, or glasses.

extract_protocol: Cells were lysed directly in Trizol reagent (Invitrogen) according to the vendor's instructions. Total RNA from each sample (12 duplicates) was extracted and quantified by photospectrometry using a NanoDrop ND-1000 (ThermoFisher). RNA quality was confirmed by an Agilent Bioanalyzer

value: skin melanoma


title: BAB_1nM DHT_48h_repB

source_name: BAB

value: BAB


title: BAN_10nM DHT_24h_repA