title: P47T00

status: Public on Nov 01 2015

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

institute: JUH

description:
in vivo
SAMPLE 83

hyb_protocol: Hybridization is performed according to the Illumina “WGGEX Direct Hybridization Assay Guide. Biotinylated probes were prepared from 750 ng of total RNA, using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®. Amplification of RNA was in agreement to the protocol of the Illumina® for the BeadArray Reader 500 X.

scan_protocol: Arrays were readout with the detection system iScan from Illumina.

data_processing: Raw data was pre-processed using GenomeStudio (v 1.9.0). Robust spline normalization (rsn) and detection filtering were performed via the lumi package within Bioconductor and R statistics software (version 3.13). Detection (p<0.01) was required in at least ten samples (out of 90). Candidates were validated by RT-PCR. Annotation was mapped using HumanHT-12_V4_0_R2_15002873_B from Illumina. Analyses were perfomed with respect to individual resolved fold changes (T0-adjusted) as well as global.

label_protocol: Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®. Alexa Fluor 555 Streptavidin (Invitrogen, Karlsruhe). 0,75 µg cRNA of each sample was hybridized on  Human-HT-12-V4 bead chips.

growth_protocol: All samples were taken after official registration and written consent.

extract_protocol:
Blood was drawn before ICU admission and prepared with  PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany). 0,75 µg cRNA of each sample was hybridized on a Human-HT-12-V4  Expression BeadChips from Illumina®. Amplification of RNA was in agreement to the protocol of the Illumina® for the BeadArray Reader 500 X.
Blood was drawn on (D0) and after admission (D1-D21) and prepared with PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany). 200ng of total RNA of each sample were reversely transcribed and amplified using the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChips (Epicentre, Biozym, Hessisch Oldendorf) a Biorad MJ Thermal Cycler (Biorad, München). All cRNA samples were quantified with a NanoDrop spectrophotometer (Nanodrop-Technologies) before proceeding to sample hybridization. Samples were prepared for hybridization according to the Illumina WGGEX Direct Hybridization Assay Guide (Illumina).

treatment_protocol: High standard protocol.

tag: subject id

tag: subject status

value: patients with multi-system trauma (ISS ≥ 17 points)

tag: subject subgroup

value: patients with secondary sepsis after trauma

value: within the first 6 h after trauma (day 0)

value: circulating leukocytes


title: P47T07

type: RNA

country: Germany

description:
in vivo
SAMPLE 87

label: biotin

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Blood was drawn after ICU admission and prepared with  PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany). 0,75 µg cRNA of each sample was hybridized on a Human-HT-12-V4  Expression BeadChips from Illumina®. Amplification of RNA was in agreement to the protocol of the Illumina® for the BeadArray Reader 500 X.
Blood was drawn on (D0) and after admission (D1-D21) and prepared with PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany). 200ng of total RNA of each sample were reversely transcribed and amplified using the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChips (Epicentre, Biozym, Hessisch Oldendorf) a Biorad MJ Thermal Cycler (Biorad, München). All cRNA samples were quantified with a NanoDrop spectrophotometer (Nanodrop-Technologies) before proceeding to sample hybridization. Samples were prepared for hybridization according to the Illumina WGGEX Direct Hybridization Assay Guide (Illumina).

tag: gender

value: male

tag: time point

value: day 7 after trauma

tag: cell type


title: E445-2: parental GSC, untreated

status: Public on Oct 01 2015

city: Los Angeles

first: Cho-Lea

last: Tso

state: CA

address: 10833 Le Conte Avenue

department: Surgery

country: USA

institute: University of California, Los Angeles

description:
Human/patient (brain tumor)
untreated, parental GSC

hyb_protocol: hybridized on Affymetrix GeneChip U133 Plus 2.0 Array

scan_protocol: GeneArray scanner (Affymetrix).

data_processing: The CEL files generated by the Affymetrix Microarray Suite version 5.0 were converted into DCP files using the DNA-Chip Analyzer (dChip 1.3; http://biosun1.harvard.edu/complab/dchip/).

source_name: E445-2: parental GSC, untreated

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

growth_protocol: GSC cultures in stem cell growth media

extract_protocol: Total RNA was extracted from untreated, parental GSC  or treatment resistant GSC clones survived 500uM TMZ treatment, using an RNeasy kit (QIAGEN)

treatment_protocol: untreated or treated with 500uM TMZ

tag: cell line

value: glioblastoma stem cells

tag: treatment

value: untreated, parental GSC


title: patient_6_normal_oviduct

status: Public on Sep 29 2015

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description: LCM from cryosection (normal oviduct).

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

data_processing: Expression console, Partek Genome Suite 6.6

label: Biotin

label_protocol: 3' IVT PLUS Kit (affymetrix)

extract_protocol: PicoPure® RNA Isolation Kit (Life Technologies)

treatment_protocol: FTSC were transformed with retroviral infection of hTERT, SV40 and c-myc and then subcutaneously transplanted into highly immunocompromised NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice.

tag: sample type

value: tissue

tag: tissue

value: LCM from cryosection (normal oviduct)


title: patient_5_normal_oviduct

description: LCM from cryosection (normal oviduct).

scan_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)


title: patient_10_normal_oviduct

description: LCM from cryosection (normal oviduct).


title: P47T03

description:
in vivo
SAMPLE 85

value: day 3 after trauma


title: PCLS_subject 2_DMSO

status: Public on Nov 23 2015

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).

source_name: precision-cut liver slices, after 24h incubation with vehicle (0.1% DMSO)

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Liver biopsies were collected from obese patients undergoing bariatric surgery. After collection, biopsies were immediately placed in ice-cold oxygenated Belzer UW Cold Storage Solution and quickly transferred to the laboratory for further processing. 5 mm cylindrical liver cores were prepared with a surgical biopsy punch and sectioned to 200 μm slices using a Krumdieck tissue slicer.

extract_protocol: Total RNA was prepared from the liver slices using TRIzol reagent and purified using Qiagen RNeasy columns. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Liver slices were incubated in William's E Medium in 6-well plates at 37°C/5% CO2/80% O2 under continuous shaking (70 rpm). Duplicate wells were used per donor with 3 liver slices per well. After 1 hour the media was replaced with fresh William's E Medium in the presence or absence of Wy14643 (100 μM) dissolved in dimethyl sulfoxide (DMSO, final concentration 0.1%). After 24 h incubation, liver slices were snap-frozen in liquid nitrogen and stored in -80°C for RNA isolation.

value: liver

value: vehicle (0.1% DMSO)

value: female

tag: age (yr)

tag: bmi


title: P47T14

description:
in vivo
SAMPLE 89

value: day 14 after trauma


title: P47T21

description:
in vivo
SAMPLE 90

value: day 21 after trauma


title: P47T01

description:
in vivo
SAMPLE 84

value: day 1 after trauma


title: oviduct-pregnant-rep2

status: Public on Nov 04 2015

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

description: Gene expression data from oviduct of pregnant heifers

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the Bovine Gene 1.0 ST Array [CDF: Brainarray bovgene10st_Bt_ENTREZG, version 19.0.0] (Affymetrix)

scan_protocol: GeneChip 3000 7G Scanner with Affymetrix GeneChip Command Console Software (AGCC).

data_processing: alternative CDF (brainarray; bovgene10stbtentrezgenecdf, version 19.0.0) and  signal intensities called using rma preprocessed data

organism: Bos taurus

source_name: oviduct, pregnant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip® 3’ IVT Express Kit User Manual, Affymetrix).

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocols

value: oviduct

tag: group

value: pregnant


title: E445-1: parental GSC, untreated

source_name: E445-1: parental GSC, untreated


title: oviduct-pregnant-rep3


title: S496-1: parental GSC, untreated

source_name: S496-1: parental GSC, untreated


title: oviduct-cyclic-rep5

description: Gene expression data from oviduct of cyclic heifers

source_name: oviduct, cyclic

value: cyclic


title: patient_8_normal_oviduct

description: LCM from cryosection (normal oviduct).


title: patient_7_normal_oviduct

description: LCM from cryosection (normal oviduct).


title: S496-2: parental GSC, untreated

source_name: S496-2: parental GSC, untreated


title: oviduct-cyclic-rep4


title: oviduct-pregnant-rep4


title: oviduct-pregnant-rep5


title: oviduct-pregnant-rep1


title: oviduct-cyclic-rep3


title: oviduct-cyclic-rep2


title: P47T10

description:
in vivo
SAMPLE 88

value: patients with multi-system trauma (ISS ≥ 17 points)

value: patients with secondary sepsis after trauma

value: day 10 after trauma

value: circulating leukocytes


title: oviduct-cyclic-rep1


title: TB11.0637_tumour

status: Public on Sep 15 2015

type: genomic

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

description:
tumour robotic radical prostatectomy tissue from patient TB11.0637
A2146_processed_data.txt, column TB11.0637_8_T

hyb_protocol: Standard Illumina hyb protocol; samples run by AROS (Denmark)

scan_protocol: Standard Illumina scan protocol; samples run by AROS (Denmark)

data_processing: Data were pre-processed and quality checked using ‘Call Rate QC’ (AROS), gender calls from PennCNV (Wang et al., 2007); sample pairings were confirmed using BADGER (Lynch et al., 2012).

label: Cy3 and Cy5

molecule: genomic DNA

source_name: tissue core

label_protocol: Standard Illumina label protocol; samples run by AROS (Denmark)

growth_protocol: N/A - surgical tissue or whole blood samples

extract_protocol: Qiagen AllPrep, according to manufacturer's instructions.

treatment_protocol: When available (i.e not CRPC samples), matched tumour and benign tissues were identified and prepared from RP surgical tissue as described in Warren et al. (2013).  The Prostate.  73:  194-202.  Matched whole blood samples were obtained from selected samples at treatment clinics.

value: tumour

tag: tumour gleason

tag: tumour %

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)

value: N

tag: positive surgical margins (psm)

value: Y

tag: biochemical relapse (bcr)

tag: time to bcr (months)

value: ERG gene fusion status:N

tag: age at diag

tag: psa at diag

tag: clinical stage

value: T1c NxMx

tag: pathology stage

value: pT2c N0Mx

tag: total follow up (months)


title: TB08.0689_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0689
A2146_processed_data.txt, column TB08.0689_15_T

tag: sample type

value: ERG gene fusion status:2EDEL

value: pT2 N0M0


title: TB11.0081_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.0081
A2146_processed_data.txt, column TB11.0081_8_T

value: pT3a N0Mx


title: TB10.1146_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.1146
A2146_processed_data.txt, column TB10.1146_1_T

value: ERG gene fusion status:UNKNOWN

value: T2b NxMx


title: TB10.1104_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.1104
A2146_processed_data.txt, column TB10.1104_7_T

value: T2a NxMX

value: pT2c NxMx


title: TB09.1424_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.1424
A2146_processed_data.txt, column TB09.1424_1_T

value: ERG gene fusion status:EPSLIT

value: pT3a N0M0


title: TB09.1408_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.1408
A2146_processed_data.txt, column TB09.1408_10_T


title: TB09.1365_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.1365
A2146_processed_data.txt, column TB09.1365_16_T

value: ERG gene fusion status:ESPLIT

value: T3b NxMx

value: pT3a N1Mx


title: TB09.1083_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.1083
A2146_processed_data.txt, column TB09.1083_12_T

value: tumour

value: N

value: T3 N0M0


title: TB09.1008_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.1008
A2146_processed_data.txt, column TB09.1008_12_T

value: Y

value: ERG gene fusion status:EDEL

value: T1c NxMx


title: TB09.0817_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0817
A2146_processed_data.txt, column TB09.0817_7_T

value: ERG gene fusion status:N


title: TB09.1124_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.1124
A2146_processed_data.txt, column TB09.1124_3_T

value: pT3a N0Mx


title: patient_9_normal_oviduct

description: LCM from cryosection (normal oviduct).

value: tissue

tag: tissue

value: LCM from cryosection (normal oviduct)


title: TB09.1402_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.1402
A2146_processed_data.txt, column TB09.1402_21_T

value: ERG gene fusion status:UNKNOWN

value: pT2c N0Mx


title: TB09.1124_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.1124
A2146_processed_data.txt, column TB09.1124_7_B

value: benign

value: see matched tumour sample

value: ERG gene fusion status:see matched tumour sample

value: T2a NxMX


title: patient_2_normal_oviduct

description: LCM from cryosection (normal oviduct).


title: patient_3_normal_oviduct

description: LCM from cryosection (normal oviduct).


title: patient_7_HGSOC

description: LCM from cryosection (HGSOC).

value: LCM from cryosection (HGSOC)


title: patient_6_HGSOC

description: LCM from cryosection (HGSOC).


title: patient_1_normal_oviduct

description: LCM from cryosection (normal oviduct).


title: TB12.2315_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.2315
A2146_processed_data.txt, column TB12.2315_4_T

value: tumour


title: patient_5_HGSOC

description: LCM from cryosection (HGSOC).


title: patient_10_HGSOC

description: LCM from cryosection (HGSOC).


title: TB12.1852_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.1852
A2146_processed_data.txt, column TB12.1852_13_T

value: N

value: ERG gene fusion status:2ESPLIT


title: TB12.2336_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.2336
A2146_processed_data.txt, column TB12.2336_12_T

value: ERG gene fusion status:ESPLIT

value: pT2a NxMx


title: patient_2_HGSOC

description: LCM from cryosection (HGSOC).


title: patient_9_HGSOC

description: LCM from cryosection (HGSOC).


title: patient_1_HGSOC

description: LCM from cryosection (HGSOC).


title: patient_4_normal_oviduct

description: LCM from cryosection (normal oviduct).


title: P47T05

description:
in vivo
SAMPLE 86

tag: subject id

tag: subject status

value: patients with multi-system trauma (ISS ≥ 17 points)

tag: gender

value: male

tag: subject subgroup

value: patients with secondary sepsis after trauma

tag: time point

value: day 5 after trauma

tag: cell type

value: circulating leukocytes


title: TB12.1843_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.1843
A2146_processed_data.txt, column TB12.1843_8_T

tag: tumour gleason

tag: tumour %

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)

value: ERG gene fusion status:N

value: T2 N0Mx


title: patient_8_HGSOC

description: LCM from cryosection (HGSOC).

value: tissue


title: patient_3_HGSOC

description: LCM from cryosection (HGSOC).


title: patient_4_HGSOC

description: LCM from cryosection (HGSOC).


title: TB10.0709_germline

description:
whole blood sample from patient TB10.0709
A2146_processed_data.txt, column TB10.0709_G

source_name: blood

value: blood

value: see matched tumour sample

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)

tag: time to bcr (months)

tag: age at diag

value: T2b N0M0

value: pT3a N0MX


title: TB10.1217_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.1217
A2146_processed_data.txt, column TB10.1217_10_T

value: tumour

tag: psa at diag

tag: clinical stage

value: T1c NxMx

tag: pathology stage

value: pT2c NxMx

tag: total follow up (months)


title: TB08.0618_germline

description:
whole blood sample from patient TB08.0618
A2146_processed_data.txt, column TB08.0618_G

tag: sample type

value: N

value: ERG gene fusion status:see matched tumour sample


title: TB11.0695_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.0695
A2146_processed_data.txt, column TB11.0695_9_T

value: Y

value: pT3a N0Mx


title: TB11.0135_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.0135
A2146_processed_data.txt, column TB11.0135_8_T


title: TB11.2182_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.2182
A2146_processed_data.txt, column TB11.2182_1_T

value: pT2c N0Mx


title: TB08.0519_germline

description:
whole blood sample from patient TB08.0519
A2146_processed_data.txt, column TB08.0519_G

value: T3 NxMx

value: pT4 N0Mx


title: ALCaP01_germline

description:
whole blood sample from patient ALCaP01
A1942_rerun_processed_data.txt, column ALCaP01_G

value: ERG gene fusion status:N/A

value: UNKNOWN


title: TB08.1044_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.1044_7_T
A1942_rerun_processed_data.txt, column TB08.1044_7_T

value: ERG gene fusion status:N

value: T1c N0Mx

value: pT3a NxMx


title: ALCaP04_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient ALCaP04_T
A1942_rerun_processed_data.txt, column ALCaP04_T

value: unknown

value: ERG gene fusion status:unknown


title: NS021_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient NS021_T
A1942_rerun_processed_data.txt, column NS021_T

value: tumour


title: SHchTURP03_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient SHchTURP03_T
A1942_rerun_processed_data.txt, column SHchTURP03_T

value: unkown


title: TB09.0850_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0850_9_B
A1942_rerun_processed_data.txt, column TB09.0850_9_B

value: benign


title: TB09.0592_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0592_B
A1942_rerun_processed_data.txt, column TB09.0592_B

value: N

value: ERG gene fusion status:2ESPLIT (see matched tumour sample0

value: T2b N1Mx

value: pT3a N1Mx


title: TB12.0144_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.0144
A2146_processed_data.txt, column TB12.0144_1_T

value: Y

value: ERG gene fusion status:2ESPLIT

value: pT3b N1Mx


title: TB10.0830_germline

description:
whole blood sample from patient TB10.0830
A2146_processed_data.txt, column TB10.0830_G

value: blood

value: see matched tumour sample

value: ERG gene fusion status:see matched tumour sample

value: T1c NxMx

value: pT3b NxMx


title: TB11.2279_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.2279
A2146_processed_data.txt, column TB11.2279_13_T

value: ERG gene fusion status:EDEL

value: pT3a NxMx


title: H1 ESC BMP4+A83-01

status: Public on Aug 31 2015

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

description:
ESC derived from human male blastocysts (H1, NIH code WA01)
Gene expression of H1 ESC after 6 days in MEF-CM+BMP4 (10 ng/ml) +A83-01 (1 μM)

hyb_protocol: Purified cRNA (1 µg) was fragmented to uniform size and applied to Agilent 4x44K v2 microarrays (Design ID 026655, Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 h on a rotating incubator and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner at 5 µm resolution.

data_processing: Data was analyzed with Agilent Feature Extraction and GeneSpring GX v7.3.1 software packages.

source_name: H1 ESC of 6 days culture with MEF-CM+BMP4 (10 ng/ml)+A83-01 (1 μM)

label_protocol: First and second strand cDNA was prepared from the total RNA samples. cRNA target was prepared from the DNA template and verified on the Bioanalyzer.

growth_protocol: V-iPSC were cultured in (1) MEF-CM+FGF2 (10 ng/ml), (2) MEF-CM+BMP4 (10 ng/ml), (3) MEF-CM+BMP4+A83-01 (1 μM) and H1 hESC were cultured in (4) MEF-CM+BMP4 (10 ng/ml), (5) MEF-CM+BMP4+A83-01 (1 μM) for 6 days.

extract_protocol: RNAs were extracted with STAT60 (Tel-Test, Friendswood, TX) and 1-bromo-3-chloro-propane (Sigma) and were purified using Ribopure (Ambion) RNA isolation kit.

treatment_protocol: H1 ESC and V-iPSC were propagated in a monolayer of γ-irradiated MEF conditioned doxycycline (DOX)-free standard hESC medium (MEF-CM) containing FGF2 (10 ng/ml) with daily refreshment. To study the effects of BMP4 (10 ng/ml) with or without supplementation of ALK4/5/7 inhibitor (A83-01; 1 μM) to the PSC, respective reagents were added to FGF2-free MEF-CM from the second day culture of following passage for up to six additional days.

value: embryonic stem cells

tag: cell line


title: tumour tissue_robotic radical prostatetctomy_STKHLM8341

status: Public on Jul 30 2015

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Bead level data were pre-processed to remove spatial artifacts, log2 transformed and quantile normalized using the beadarray package in Bioconductor prior to analysis (Dunning et al, 2007). The ComBAT method (Johnson et al., 2007), as implemented in the sva Bioconductor package, was used address batch effects in the expression data.  Downstream analyses were restricted to 'perfect' probes only (Barbosa-Morais et al., 2010), and whenever a gene-centric analysis was required we chose the probe with the highest Inter-quartile range (IQR) to represent each gene. Probes (genes) were ranked by IQR values, and the 100 most variable probes across expression data were selected for clustering, based on k-means method (see Chalise et al. (2014) for a review on clustering methods), where each observation belongs to the cluster with the nearest mean that best describes that cluster. A linear modelling approach was used to estimate the expression of each probe in the five subtypes, and the set of matched benign samples. Differential expression statistics for the comparison of each subtype to benign were then generated following Bayes' shrinkage of variance (Smyth 2004).

source_name: primary tumour tissue from robotic radical prostatectomy (RRP) surgery

label_protocol: cRNA was generated and biotin-labelled using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: N/A - surgical tissue samples

treatment_protocol: Matched tumour and benign tissues were identified and prepared from RP surgical tissue as described in Warren et al. (2013).  The Prostate.  73:  194-202.  Prepared H&E slides of the tumour regions were macrodissected to yield samples of at least 70% tumour content.

tag: extra capsular extension (ece)

tag: derived data (iclusterplus group)


title: tumour tissue_robotic radical prostatetctomy_STKHLM7472


title: V3 iPSC FGF2

description:
iPSC derived with lentiviral transduction (V) from human umbilical cords from male infants whose gestational age 39 weeks
Gene expression of V-iPSC after 6 days in MEF-CM+FGF2 (10 ng/ml)

source_name: V3-iPSC of 6 days culture with MEF-CM+FGF2 (10 ng/ml)

tag: cell type

value: induced pluripotent stem cells


title: tumour tissue_robotic radical prostatetctomy_STKHLM9157

tag: tumour gleason


title: tumour tissue_robotic radical prostatetctomy_STKHLM9246

tag: tumour %


title: tumour tissue_robotic radical prostatetctomy_STKHLM8462


title: tumour tissue_robotic radical prostatetctomy_STKHLM8453


title: tumour tissue_robotic radical prostatetctomy_STKHLM9161


title: tumour tissue_robotic radical prostatetctomy_STKHLM8393


title: tumour tissue_robotic radical prostatetctomy_STKHLM7072


title: V3 iPSC BMP4+A83-01

description:
iPSC derived with lentiviral transduction (V) from human umbilical cords from male infants whose gestational age 39 weeks
Gene expression of V-iPSC after 6 days in MEF-CM+BMP4 (10 ng/ml)+A83-01 (1 μM)

source_name: V3-iPSC of 6 days culture with MEF-CM+BMP4 (10 ng/ml)+A83-01 (1 μM)


title: tumour tissue_robotic radical prostatetctomy_STKHLM8105


title: tumour tissue_robotic radical prostatetctomy_STKHLM8319


title: V3 iPSC BMP4

description:
iPSC derived with lentiviral transduction (V) from human umbilical cords from male infants whose gestational age 39 weeks
Gene expression of V-iPSC after 6 days in MEF-CM+BMP4 (10 ng/ml)

source_name: V3-iPSC of 6 days culture with MEF-CM+BMP4 (10 ng/ml)


title: tumour tissue_robotic radical prostatetctomy_STKHLM7179


title: tumour tissue_robotic radical prostatetctomy_STKHLM8659


title: tumour tissue_robotic radical prostatetctomy_STKHLM7493


title: tumour tissue_robotic radical prostatetctomy_STKHLM7312


title: tumour tissue_robotic radical prostatetctomy_STKHLM7106


title: tumour tissue_robotic radical prostatetctomy_STKHLM7421


title: H1 ESC BMP4

description:
ESC derived from human male blastocysts (H1, NIH code WA01)
Gene expression of H1 ESC after 6 days in MEF-CM+BMP4 (10 ng/ml)

source_name: H1 ESC of 6 days culture with MEF-CM+BMP4 (10 ng/ml)


title: tumour tissue_robotic radical prostatetctomy_STKHLM8035


title: tumour tissue_robotic radical prostatetctomy_STKHLM7213


title: tumour tissue_robotic radical prostatetctomy_STKHLM6929


title: tumour tissue_robotic radical prostatetctomy_STKHLM6836


title: tumour tissue_robotic radical prostatetctomy_STKHLM7067


title: tumour tissue_robotic radical prostatetctomy_STKHLM6094


title: tumour tissue_robotic radical prostatetctomy_STKHLM6159


title: tumour tissue_robotic radical prostatetctomy_STKHLM6370


title: tumour tissue_robotic radical prostatetctomy_STKHLM6439


title: tumour tissue_robotic radical prostatetctomy_STKHLM6631


title: tumour tissue_robotic radical prostatetctomy_STKHLM5867


title: tumour tissue_robotic radical prostatetctomy_STKHLM5964


title: tumour tissue_robotic radical prostatetctomy_STKHLM5950


title: tumour tissue_robotic radical prostatetctomy_STKHLM5574

value: unknown

value: UNKNOWN


title: tumour tissue_robotic radical prostatetctomy_STKHLM5650

value: N


title: tumour tissue_robotic radical prostatetctomy_STKHLM5690


title: tumour tissue_robotic radical prostatetctomy_STKHLM6032


title: tumour tissue_robotic radical prostatetctomy_STKHLM5967


title: tumour tissue_robotic radical prostatetctomy_STKHLM5571


title: tumour tissue_robotic radical prostatetctomy_STKHLM5441


title: tumour tissue_robotic radical prostatetctomy_STKHLM5445

tag: clinical stage:


title: tumour tissue_robotic radical prostatetctomy_STKHLM5465


title: tumour tissue_robotic radical prostatetctomy_STKHLM5627


title: tumour tissue_robotic radical prostatetctomy_STKHLM5469


title: tumour tissue_robotic radical prostatetctomy_STKHLM5388


title: tumour tissue_robotic radical prostatetctomy_STKHLM5428


title: tumour tissue_robotic radical prostatetctomy_STKHLM5279


title: tumour tissue_robotic radical prostatetctomy_STKHLM5316


title: tumour tissue_robotic radical prostatetctomy_STKHLM5176


title: tumour tissue_robotic radical prostatetctomy_STKHLM7100


title: tumour tissue_robotic radical prostatetctomy_STKHLM4972


title: tumour tissue_robotic radical prostatetctomy_STKHLM4966


title: tumour tissue_robotic radical prostatetctomy_STKHLM4988


title: tumour tissue_robotic radical prostatetctomy_STKHLM4940


title: tumour tissue_robotic radical prostatetctomy_STKHLM4956


title: tumour tissue_robotic radical prostatetctomy_STKHLM5872


title: tumour tissue_robotic radical prostatetctomy_STKHLM4920


title: tumour tissue_robotic radical prostatetctomy_STKHLM5433


title: tumour tissue_robotic radical prostatetctomy_STKHLM4917


title: tumour tissue_robotic radical prostatetctomy_STKHLM5612


title: tumour tissue_robotic radical prostatetctomy_STKHLM5248


title: tumour tissue_robotic radical prostatetctomy_STKHLM4856


title: tumour tissue_robotic radical prostatetctomy_STKHLM4875


title: tumour tissue_robotic radical prostatetctomy_STKHLM4891


title: tumour tissue_robotic radical prostatetctomy_STKHLM4890


title: tumour tissue_robotic radical prostatetctomy_STKHLM4929


title: tumour tissue_robotic radical prostatetctomy_STKHLM4757


title: tumour tissue_robotic radical prostatetctomy_STKHLM4925


title: tumour tissue_robotic radical prostatetctomy_STKHLM4847


title: tumour tissue_robotic radical prostatetctomy_STKHLM4870


title: tumour tissue_robotic radical prostatetctomy_STKHLM4755


title: tumour tissue_robotic radical prostatetctomy_STKHLM4841


title: tumour tissue_robotic radical prostatetctomy_STKHLM4666


title: tumour tissue_robotic radical prostatetctomy_STKHLM4750


title: tumour tissue_robotic radical prostatetctomy_STKHLM4659


title: tumour tissue_robotic radical prostatetctomy_STKHLM4605


title: tumour tissue_robotic radical prostatetctomy_STKHLM4487


title: tumour tissue_robotic radical prostatetctomy_STKHLM4608


title: tumour tissue_robotic radical prostatetctomy_STKHLM4787


title: tumour tissue_robotic radical prostatetctomy_STKHLM4421


title: tumour tissue_robotic radical prostatetctomy_STKHLM4596


title: tumour tissue_robotic radical prostatetctomy_STKHLM4433


title: tumour tissue_robotic radical prostatetctomy_STKHLM4441


title: tumour tissue_robotic radical prostatetctomy_STKHLM4753


title: tumour tissue_robotic radical prostatetctomy_STKHLM4650


title: tumour tissue_robotic radical prostatetctomy_STKHLM4165


title: tumour tissue_robotic radical prostatetctomy_STKHLM3821


title: tumour tissue_robotic radical prostatetctomy_STKHLM3953

value: Tx


title: tumour tissue_robotic radical prostatetctomy_STKHLM3805


title: tumour tissue_robotic radical prostatetctomy_STKHLM3759


title: tumour tissue_robotic radical prostatetctomy_STKHLM11405


title: matched benign tissue_robotic radical prostatectomy_TB12.1505

source_name: tissue from robotic radical prostatectomy (RRP) surgery

treatment_protocol: When available (i.e not CRPC samples), matched tumour and benign tissues were identified and prepared from RP surgical tissue as described in Warren et al. (2013).  The Prostate.  73:  194-202.

value: Benign


title: tumour tissue_robotic radical prostatetctomy_STKHLM12012

value: Y


title: matched benign tissue_robotic radical prostatectomy_TB12.1852


title: matched benign tissue_robotic radical prostatectomy_TB12.2315


title: matched benign tissue_robotic radical prostatectomy_TB12.1843


title: matched benign tissue_robotic radical prostatectomy_TB12.1498


title: matched benign tissue_robotic radical prostatectomy_TB12.0677


title: matched benign tissue_robotic radical prostatectomy_TB12.1231


title: matched benign tissue_robotic radical prostatectomy_TB12.1447


title: matched benign tissue_robotic radical prostatectomy_TB12.2336


title: matched benign tissue_robotic radical prostatectomy_TB12.0322


title: tumour tissue_robotic radical prostatetctomy_STKHLM4661


title: matched benign tissue_robotic radical prostatectomy_TB12.0654


title: matched benign tissue_robotic radical prostatectomy_TB12.0942


title: matched benign tissue_robotic radical prostatectomy_TB12.1408


title: tumour tissue_robotic radical prostatetctomy_STKHLM3878


title: matched benign tissue_robotic radical prostatectomy_TB12.0135


title: matched benign tissue_robotic radical prostatectomy_TB12.0170


title: matched benign tissue_robotic radical prostatectomy_TB12.0518


title: matched benign tissue_robotic radical prostatectomy_TB11.2442


title: matched benign tissue_robotic radical prostatectomy_TB12.0144


title: matched benign tissue_robotic radical prostatectomy_TB11.2230


title: tumour tissue_robotic radical prostatetctomy_STKHLM11198


title: matched benign tissue_robotic radical prostatectomy_TB11.2279


title: matched benign tissue_robotic radical prostatectomy_TB11.1943


title: tumour tissue_robotic radical prostatetctomy_STKHLM5605


title: matched benign tissue_robotic radical prostatectomy_TB11.1861


title: matched benign tissue_robotic radical prostatectomy_TB11.1083


title: matched benign tissue_robotic radical prostatectomy_TB11.0598


title: matched benign tissue_robotic radical prostatectomy_TB11.0695


title: matched benign tissue_robotic radical prostatectomy_TB11.0135


title: matched benign tissue_robotic radical prostatectomy_TB11.1766


title: matched benign tissue_robotic radical prostatectomy_TB11.1447


title: matched benign tissue_robotic radical prostatectomy_TB11.0205


title: matched benign tissue_robotic radical prostatectomy_TB11.0637


title: matched benign tissue_robotic radical prostatectomy_TB11.1912


title: matched benign tissue_robotic radical prostatectomy_TB11.1833


title: matched benign tissue_robotic radical prostatectomy_TB11.0387


title: matched benign tissue_robotic radical prostatectomy_TB11.0340


title: matched benign tissue_robotic radical prostatectomy_TB10.1416


title: matched benign tissue_robotic radical prostatectomy_TB11.1437


title: matched benign tissue_robotic radical prostatectomy_TB11.0308


title: matched benign tissue_robotic radical prostatectomy_TB11.0081


title: matched benign tissue_robotic radical prostatectomy_TB11.0675


title: matched benign tissue_robotic radical prostatectomy_TB10.1104


title: matched benign tissue_robotic radical prostatectomy_TB11.0461


title: matched benign tissue_robotic radical prostatectomy_TB11.1693


title: matched benign tissue_robotic radical prostatectomy_TB11.1889


title: matched benign tissue_robotic radical prostatectomy_TB10.1217


title: matched benign tissue_robotic radical prostatectomy_TB11.0753


title: matched benign tissue_robotic radical prostatectomy_TB10.1146


title: matched benign tissue_robotic radical prostatectomy_TB10.0709


title: tumour tissue_robotic radical prostatetctomy_STKHLM4322


title: matched benign tissue_robotic radical prostatectomy_TB10.0529


title: matched benign tissue_robotic radical prostatectomy_TB10.1062


title: matched benign tissue_robotic radical prostatectomy_TB10.0830


title: matched benign tissue_robotic radical prostatectomy_TB10.0244


title: matched benign tissue_robotic radical prostatectomy_TB09.1365


title: matched benign tissue_robotic radical prostatectomy_TB09.1254


title: matched benign tissue_robotic radical prostatectomy_TB09.1424


title: matched benign tissue_robotic radical prostatectomy_TB09.1402


title: matched benign tissue_robotic radical prostatectomy_TB09.0817


title: matched benign tissue_robotic radical prostatectomy_TB10.0747


title: matched benign tissue_robotic radical prostatectomy_TB09.0238


title: matched benign tissue_robotic radical prostatectomy_TB08.0997


title: matched benign tissue_robotic radical prostatectomy_TB08.1115


title: matched benign tissue_robotic radical prostatectomy_TB08.1063


title: matched benign tissue_robotic radical prostatectomy_TB09.1124


title: matched benign tissue_robotic radical prostatectomy_TB09.1008


title: matched benign tissue_robotic radical prostatectomy_TB08.0978


title: matched benign tissue_robotic radical prostatectomy_TB08.0872


title: matched benign tissue_robotic radical prostatectomy_TB08.0598


title: matched benign tissue_robotic radical prostatectomy_TB08.0618


title: matched benign tissue_robotic radical prostatectomy_TB08.0341


title: matched benign tissue_robotic radical prostatectomy_TB09.1083


title: matched benign tissue_robotic radical prostatectomy_TB08.1083


title: matched benign tissue_robotic radical prostatectomy_TB08.0667


title: tumour tissue_robotic radical prostatectomy_TB12.2315

value: Tumour

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)

value: ERG gene fusion status:N

value: pT2a NxMx


title: tumour tissue_robotic radical prostatectomy_TB12.1498

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)

value: T3a N0Mx

value: pT3b N0Mx


title: matched benign tissue_robotic radical prostatectomy_TB08.0489


title: tumour tissue_robotic radical prostatectomy_TB12.1447

tag: time to bcr (months)

value: ERG gene fusion status:ESPLIT

tag: age at diag

value: T1c NxMx


title: tumour tissue_robotic radical prostatectomy_TB12.0560

tag: psa at diag

tag: clinical stage

value: T2b N0Mx

value: pT3b N1Mx


title: tumour tissue_robotic radical prostatectomy_TB12.1408

value: T2 N0M0

tag: pathology stage

tag: total follow up (months)


title: tumour tissue_robotic radical prostatectomy_TB12.2336

tag: sample type


title: tumour tissue_robotic radical prostatectomy_TB12.0942

value: ERG gene fusion status:2EDEL

value: pT3a NxMx


title: tumour tissue_robotic radical prostatectomy_TB12.0322

value: ERG gene fusion status:EDEL

value: pT3a N0Mx


title: tumour tissue_robotic radical prostatectomy_TB12.0677

value: N

value: ERG gene fusion status:2ESPLIT


title: tumour tissue_robotic radical prostatectomy_TB12.1852

value: Y

value: pT2c N0Mx


title: tumour tissue_robotic radical prostatectomy_TB12.0392

value: Tumour

value: ERG gene fusion status:N

value: T2 N0Mx

value: pT3a N0MX


title: tumour tissue_robotic radical prostatectomy_TB12.1231

value: ERG gene fusion status:ESPLIT

value: T2 NxMX


title: tumour tissue_robotic radical prostatectomy_TB12.1843

value: T1c NxMx


title: tumour tissue_robotic radical prostatectomy_TB11.2230


title: tumour tissue_robotic radical prostatectomy_TB11.2279


title: tumour tissue_robotic radical prostatectomy_TB12.0518


title: tumour tissue_robotic radical prostatectomy_TB11.1912


title: tumour tissue_robotic radical prostatectomy_TB11.1943


title: tumour tissue_robotic radical prostatectomy_TB12.0144


title: tumour tissue_robotic radical prostatectomy_TB11.1693


title: tumour tissue_robotic radical prostatectomy_TB12.0135

value: pT3b N1Mx


title: tumour tissue_robotic radical prostatectomy_TB11.1083

value: T2a N1M0


title: matched benign tissue_robotic radical prostatectomy_TB11.1035

value: Benign


title: tumour tissue_robotic radical prostatectomy_TB11.2442

value: T3a N0M0

value: pT3b N1M1


title: tumour tissue_robotic radical prostatectomy_TB12.0654

value: ERG gene fusion status:EDEL

value: pT3a NxMx


title: tumour tissue_robotic radical prostatectomy_TB11.1437

value: N


title: tumour tissue_robotic radical prostatectomy_TB12.1505

value: Y


title: tumour tissue_robotic radical prostatectomy_TB11.1833

value: T1c NXMX


title: tumour tissue_robotic radical prostatectomy_TB11.0753

value: Tumour

value: ERG gene fusion status:UNKNOWN

value: pT2c NxMx


title: tumour tissue_robotic radical prostatectomy_TB11.0675

value: pT3a N0Mx


title: tumour tissue_robotic radical prostatectomy_TB11.1861

value: ERG gene fusion status:2EDEL

value: T2 N0M0

value: pT2c N0Mx


title: tumour tissue_robotic radical prostatectomy_TB11.1889

value: T1c NxMx


title: tumour tissue_robotic radical prostatectomy_TB11.0695

value: ERG gene fusion status:N


title: tumour tissue_robotic radical prostatectomy_TB11.2182

value: pT3a N0MX


title: tumour tissue_robotic radical prostatectomy_TB11.1035


title: tumour tissue_robotic radical prostatectomy_TB11.0637


title: tumour tissue_robotic radical prostatectomy_TB11.1766


title: tumour tissue_robotic radical prostatectomy_TB11.1447

value: T2b N0M0


title: tumour tissue_robotic radical prostatectomy_TB12.0170

value: T2 N0Mx


title: tumour tissue_robotic radical prostatectomy_TB11.0461

value: ERG gene fusion status:2ESPLIT


title: tumour tissue_robotic radical prostatectomy_TB11.0598


title: tumour tissue_robotic radical prostatectomy_TB11.0387

value: T3a N0Mx


title: tumour tissue_robotic radical prostatectomy_TB11.0135

value: N

value: T2c NxMx


title: tumour tissue_robotic radical prostatectomy_TB11.0340

value: Y

value: ERG gene fusion status:EDEL

value: pT3a NxMx


title: tumour tissue_robotic radical prostatectomy_TB11.0308

value: Tumour

value: T2b N0Mx


title: tumour tissue_robotic radical prostatectomy_TB10.1104

value: T2b NxMx

value: pT3a N0Mx


title: tumour tissue_robotic radical prostatectomy_TB10.0747

value: pT3b NxMx


title: tumour tissue_robotic radical prostatectomy_TB09.1424

value: ERG gene fusion status:ESPLIT

value: T1c NxMx


title: tumour tissue_robotic radical prostatectomy_TB10.0709

value: ERG gene fusion status:N

value: pT3a N0MX


title: tumour tissue_robotic radical prostatectomy_TB11.0081

value: pT2c NxMx


title: tumour tissue_robotic radical prostatectomy_TB10.1217

value: T2 N0Mx


title: tumour tissue_robotic radical prostatectomy_TB09.1254

value: T3b NxMx

value: pT3a N1Mx


title: tumour tissue_robotic radical prostatectomy_TB11.0205

value: ERG gene fusion status:2ESPLIT

value: T1c N0Mx


title: tumour tissue_robotic radical prostatectomy_TB10.0230

value: Y

value: N


title: tumour tissue_robotic radical prostatectomy_TB09.1402

value: Tumour

value: ERG gene fusion status:UNKNOWN


title: tumour tissue_robotic radical prostatectomy_TB10.1062

value: T2a NxMX


title: tumour tissue_robotic radical prostatectomy_TB09.0817

value: pT2 N0Mx


title: tumour tissue_robotic radical prostatectomy_TB09.1365

value: pT2c N0Mx


title: tumour tissue_robotic radical prostatectomy_TB10.0323

value: T3a N0Mx


title: tumour tissue_robotic radical prostatectomy_TB09.1408

value: T2b NxMx

value: pT3a N0M0


title: tumour tissue_robotic radical prostatectomy_TB09.1083

value: ERG gene fusion status:N

value: pT3a N0Mx


title: tumour tissue_robotic radical prostatectomy_TB10.0529

value: T2b N0M0

value: pT3a N0MX


title: tumour tissue_robotic radical prostatectomy_TB10.0244

value: T3a NxMx


title: tumour tissue_robotic radical prostatectomy_TB09.0962

value: ERG gene fusion status:ESPLIT

value: T1c NxMx


title: tumour tissue_robotic radical prostatectomy_TB10.1416

value: Y


title: tumour tissue_robotic radical prostatectomy_TB10.0830

value: N


title: tumour tissue_robotic radical prostatectomy_TB09.0725

value: Tumour


title: tumour tissue_robotic radical prostatectomy_TB09.0720

value: ERG gene fusion status:EDEL


title: tumour tissue_robotic radical prostatectomy_TB10.1146

value: ERG gene fusion status:UNKNOWN

value: pT2c NxMx


title: tumour tissue_robotic radical prostatectomy_TB09.1124

value: T2b Nxmx

value: pT3a NxMx


title: tumour tissue_robotic radical prostatectomy_TB09.1008

value: T3 N0M0

value: pT2c N0Mx


title: tumour tissue_robotic radical prostatectomy_TB09.0592

value: ERG gene fusion status:2ESPLIT

value: pT2 N0Mx


title: tumour tissue_robotic radical prostatectomy_TB09.0504

value: ERG gene fusion status:N

value: pT3a N0Mx


title: tumour tissue_robotic radical prostatectomy_TB09.0448

value: pT2a NxMx


title: tumour tissue_robotic radical prostatectomy_TB09.0238

value: T2 N0M0

value: pT3b N0Mx


title: tumour tissue_robotic radical prostatectomy_TB08.1026

value: Y

value: T1c N0Mx


title: tumour tissue_robotic radical prostatectomy_TB09.0295

value: Tumour

value: N

value: T1c N0M0


title: tumour tissue_robotic radical prostatectomy_TB09.0219

value: T1c NxMx


title: tumour tissue_robotic radical prostatectomy_TB08.1115


title: tumour tissue_robotic radical prostatectomy_TB08.1063


title: tumour tissue_robotic radical prostatectomy_TB08.0958

value: ERG gene fusion status:ESPLIT

value: T3b N0M0

value: pT3a N0M0


title: tumour tissue_robotic radical prostatectomy_TB08.1044

value: T3a N0M0

value: pT3a N1Mx


title: tumour tissue_robotic radical prostatectomy_TB09.0550

value: ERG gene fusion status:2ESPLIT

value: T2b N1Mx


title: tumour tissue_robotic radical prostatectomy_TB08.0689

value: ERG gene fusion status:EDEL

value: pT2 N0Mx


title: tumour tissue_robotic radical prostatectomy_TB08.1015

value: ERG gene fusion status:2EDEL

value: pT3a N0Mx


title: tumour tissue_robotic radical prostatectomy_TB08.0987

value: Y

value: ERG gene fusion status:N

value: T2 NxMX


title: tumour tissue_robotic radical prostatectomy_TB08.1019

value: Tumour

value: N

value: T1c N0Mx


title: tumour tissue_robotic radical prostatectomy_TB09.0413

value: T1c NxMx


title: tumour tissue_robotic radical prostatectomy_TB08.0978

value: ERG gene fusion status:UNKNOWN

value: T2a N0M0


title: tumour tissue_robotic radical prostatectomy_TB08.1116

value: pT1c NxMx


title: tumour tissue_robotic radical prostatectomy_TB08.0927

value: T1c N0M0

value: pT3a N0MX


title: tumour tissue_robotic radical prostatectomy_TB08.0997

value: T2 N0M0

value: pT3a N0M0


title: tumour tissue_robotic radical prostatectomy_TB08.0848

value: ERG gene fusion status:ESPLIT

value: pT2c N0M0


title: tumour tissue_robotic radical prostatectomy_TB09.0421

value: ERG gene fusion status:2EDEL

value: pT3a N0Mx


title: tumour tissue_robotic radical prostatectomy_TB09.0443

value: Y

value: ERG gene fusion status:EDEL

value: pT2c N0Mx


title: tumour tissue_robotic radical prostatectomy_TB08.0816

value: Tumour

value: N

value: T3a N0M0


title: tumour tissue_robotic radical prostatectomy_TB08.1083

value: ERG gene fusion status:2ESPLIT

value: UNKNOWN


title: tumour tissue_robotic radical prostatectomy_TB08.0872

value: T1c NxMx

value: pT2 N0Mx


title: tumour tissue_robotic radical prostatectomy_TB08.0949

value: ERG gene fusion status:N

value: pT2 N0M0


title: tumour tissue_robotic radical prostatectomy_TB08.0877


title: tumour tissue_robotic radical prostatectomy_TB08.0719


title: tumour tissue_robotic radical prostatectomy_TB08.0763

value: T3 N0Mx


title: tumour tissue_robotic radical prostatectomy_TB08.0667


title: benign tissue_robotic radical prostatectomy_TB08.0589

value: Benign


title: tumour tissue_robotic radical prostatectomy_TB08.0262

value: T2 NxMx

value: pT3a NxMx


title: tumour tissue_robotic radical prostatectomy_TB08.0341


title: tumour tissue_robotic radical prostatectomy_TB08.0598

value: pT3a N0MX


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_ARM001

source_name: tissue from channel trans-urethral resection of the prostate (chTURP)

value: unknown

value: ERG gene fusion status:unknown


title: tumour tissue_robotic radical prostatectomy_TB08.0311

value: Y

value: ERG gene fusion status:2EDEL

value: pT3a N0Mx


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_NS022

value: Tumour

value: N


title: tumour tissue_robotic radical prostatectomy_TB08.0618


title: tumour tissue_robotic radical prostatectomy_TB08.0588

value: ERG gene fusion status:2ESPLIT


title: tumour tissue_robotic radical prostatectomy_TB08.0489

value: ERG gene fusion status:ESPLIT

value: T2 N0Mx


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_ARM003

value: UNKNOWN


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_NS021


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_NS028


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_NS015


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_NS026


title: tumour tissue_robotic radical prostatectomy_TB08.0519

value: ERG gene fusion status:EDEL

value: T3 NxMx

value: pT4 N0Mx


title: tumour tissue_robotic radical prostatectomy_TB08.0327

value: T3a N0M0

value: pT2 N0Mx


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_ALCaP04


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_NS014


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_NS031


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_ALCaP01


title: tumour tissue_robotic radical prostatectomy_TB08.0533

value: ERG gene fusion status:N

value: T1c NxMx


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_ALCaP09

value: unknown

value: ERG gene fusion status:unknown


title: TUMOR, Chronic lymphocytic leukemia sample [1284]

status: Public on Dec 04 2014

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: Tumor  vs normal

hyb_protocol: The protocol Oligonucleotide Array-Based CGH for Genomic DNA Analysis (ULS labeling for Blood, Cells, Tissues or FFPE) was used.

scan_protocol: Scanned on an Agilent G2565B scanner.

data_processing: Raw data were generated from scanned images using Agilent Feature Extraction Software (10.10.1.1). Log2ratios of background corrected values for tumour over normal DNA were calculated. Normalization was carried out on Agilent's CGH Analytics, integrated on the Agilent Genomic Workbench Standard Edition 6.5.0.58, using data from the internal set of control probes included in the microarray. Detection of Copy Number Alterations (CNAs) was performed using the ADM-2 algorithm, also implemented within the Agilent's genomics suite Genomic Workbench v5.0, with a threshold of 6.5 and a minimum of 5 consecutive probes and Nexus 6.0 Discovery Edition (Biodiscovery, El segundo, CA).

extract_protocol: Genomic DNA was extracted from 134 CLL samples using Qiagen extraction kits. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

tag: gender

value: Male

source_name: Normal DNA from male donor

tag: reference

value: Normal DNA from male donor


title: TUMOR, Chronic lymphocytic leukemia sample [1285]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [1287]

description: Tumor  vs normal


title: tumour tissue_castrate-resistant prostate cancer (CRPC)_NS020

value: Tumour


title: TUMOR, Chronic lymphocytic leukemia sample [1286]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [1280]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [1279]

description: Tumor  vs normal

value: Female

source_name: Normal DNA from female donor

value: Normal DNA from female donor


title: TUMOR, Chronic lymphocytic leukemia sample [1283]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [1282]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [1181]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [740]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [827]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [741]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [1281]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [793]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [1096]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [722]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [645]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [724]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [711]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [661]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [669]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [1278]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [896]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [667]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [658]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [656]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [631]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [642]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [587]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [604]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [605]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [531]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [537]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [553]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [527]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [507]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [520]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [467]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [487]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [436]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [431]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [498]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [447]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [446]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [385]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [511]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [390]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [448]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [460]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [410]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [418]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [485]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [306]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [384]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [457]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [303]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [217]

description: Tumor  vs normal

source_name: Pool normal DNA 25M/25F

value: Pool normal DNA 25M/25F


title: TUMOR, Chronic lymphocytic leukemia sample [238]

description: Tumor  vs normal

source_name: Normal DNA from the same CLL patient

value: Normal DNA from the same CLL patient


title: TUMOR, Chronic lymphocytic leukemia sample [290]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [375]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [241]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [289]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [212]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [399]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [158]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [202]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [184]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [167]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [199]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [140]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [96]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [169]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [143]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [111]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [115]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [153]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [163]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [162]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [113]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [129]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [102]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [93]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [89]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [112]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [138]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [114]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [118]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [209]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [116]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [181]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [94]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [92]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [102-2]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [145]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [73]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [87]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [85]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [67]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [58]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [70]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [50]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [82]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [40]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [79]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [68]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [60]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [38]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [83]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [49]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [77]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [42]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [35]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [44]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [74]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [53]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [66]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [27]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [34]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [30]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [23]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [24]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [78]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [69]

description: Tumor  vs normal


title: ChIP-Seq analysis of H3K27ac in human liver cells; DNA_Lib 1056

status: Public on Jul 18 2013

type: SRA

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1056
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14636
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3345
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1112809_BI.Adult_Liver.H3K27ac.4.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1056.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adult Liver H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Adult Liver, Donor 4, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17231
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,017,206
FINDPEAKS_SCORE: 0.5945
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.598
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9982
IROC_PERCENTILE: 75
POISSON_SCORE: 0.6525
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

ANALYSIS FILE NAME: GSM1112809_BI.Adult_Liver.H3K27ac.4.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1056.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Adult Liver, Donor 4, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17414
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: AL H3K27ac 4 56
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K27ac Donor 4 Library DNA_Lib 1056 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,017,206
FINDPEAKS_SCORE: 0.5945
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.598
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9982
IROC_PERCENTILE: 75
POISSON_SCORE: 0.6525
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

source_name: normal adult liver; DNA_Lib 1056

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample common name

value: Adult Liver

tag: sra sample accession

value: surgery

tag: disease

value: Unknown

value: Primary Tissue

value: liver

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K27ac in human liver cells; DNA_Lib 1057

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1057
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14635
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5941
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1112808_BI.Adult_Liver.H3K27ac.3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1057.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adult Liver H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Adult Liver, Donor 3, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17229
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,877,848
FINDPEAKS_SCORE: 0.389
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.4123
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9975
IROC_PERCENTILE: 67
POISSON_SCORE: 0.47
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

ANALYSIS FILE NAME: GSM1112808_BI.Adult_Liver.H3K27ac.3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1057.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Adult Liver, Donor 3, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17412
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: AL H3K27ac 3 57
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K27ac Donor 3 Library DNA_Lib 1057 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,877,848
FINDPEAKS_SCORE: 0.389
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.4123
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9975
IROC_PERCENTILE: 67
POISSON_SCORE: 0.47
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

source_name: normal adult liver; DNA_Lib 1057


title: ChIP-Seq analysis of H3K27me3 in human liver cells; DNA_Lib 1058

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1058
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14641
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3345
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1112814_BI.Adult_Liver.H3K27me3.4.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1058.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adult Liver H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Adult Liver, Donor 4, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17214
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,336,294
FINDPEAKS_SCORE: 0.0083
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.0955
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.5246
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2214
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.81

**********************************************************************

ANALYSIS FILE NAME: GSM1112814_BI.Adult_Liver.H3K27me3.4.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1058.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Adult Liver, Donor 4, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17397
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: AL H3K27me3 4 58
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K27me3 Donor 4 Library DNA_Lib 1058 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,336,294
FINDPEAKS_SCORE: 0.0083
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.0955
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.5246
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2214
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.81

**********************************************************************

source_name: normal adult liver; DNA_Lib 1058

value: Millipore

value: Histone H3K27me3


title: TUMOR, Chronic lymphocytic leukemia sample [8]

description: Tumor  vs normal

value: Male

value: Normal DNA from male donor


title: TUMOR, Chronic lymphocytic leukemia sample [10]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [5]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [6]

description: Tumor  vs normal

value: Female

value: Normal DNA from female donor


title: TUMOR, Chronic lymphocytic leukemia sample [13]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [1]

description: Tumor  vs normal

value: Normal DNA from the same CLL patient


title: TUMOR, Chronic lymphocytic leukemia sample [20]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [7]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [4]

description: Tumor  vs normal


title: TUMOR, Chronic lymphocytic leukemia sample [36]

description: Tumor  vs normal

value: Pool normal DNA 25M/25F


title: TUMOR, Chronic lymphocytic leukemia sample [2]

description: Tumor  vs normal


title: 217_VC

status: Public on Apr 25 2013

city: New York

first: Jun

last: Zhu

state: NY

address: One Gustave L Levy, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn Medical School at Mount Sinai

description: visual cortex

hyb_protocol: Microarrays are incubated at 40C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

label_protocol: Samples were amplified and labeled using a custom automated two-cycle version of the MessageAmp II kit from Ambion. Hybridizations to custom Agilent microarrays were completed as described in by Hughes et al. Nat Biotech (2001), 19(4):342-7. Sample amplification, labeling, and microarray processing were performed by the Rosetta Inpharmatics Gene Expression Laboratory in Seattle, Wash.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment  Qiagen RNeasy spin columns with DNAse treatment

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tag: tissue

value: brain

value: N

value: M

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