title: PBX3+MEIS1_3

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

hyb_protocol: RNA was labeled using the Affymetrix IVT Express kit

scan_protocol: Arrays were scanned following manufacturers instructions

data_processing: Microarray CEL files were imported and normalized using RMA function from Partek Genomics Suite 6.0.

source_name: mouse bone marrow samples

label_protocol: biotin

extract_protocol: The total RNA was isolated by use of miRNeasy extraction kit (Qiagen, Valencia, CA).

tag: bmt type


title: PBX3+MEIS1_2

status: Public on Mar 03 2016

type: RNA

state: CA

country: USA

label: biotin

molecule: total RNA

organism: Mus musculus


title: PBX3+MEIS1_1


title: MA9_3


title: S116

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

country: France

institute: Cancer Research Center of Toulouse

description: Reanalysis of GSM525825

hyb_protocol: Samples were then analyzed on Human Genome U133 Plus 2.0 array (Affymetrix®), according to the manufacturer’s procedures.

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

data_processing: All microarray data were simultaneously normalized using the GCRMA algorithm

label: Biotin

organism: Homo sapiens

source_name: Undifferentiated sarcoma

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol  (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA were extracted from frozen tumor samples with TRIzol reagent (Life Technologies, Inc.) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: RNA extracted from frozen tissue of the untreated primary tumor

tag: metastasis

value: No

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support

value: Frozen tumor


title: breast_invasive ductal carcinoma_4502

city: ROTTERDAM

first: Maurice

last: Jansen

address: Wytemaweg 80

department: MEDICAL ONCOLOGY

country: Netherlands

institute: ERASMUS MC - CANCER INSTITUTE

description: mRNA profile_GSM1029705

data_processing:
SDS 2.3 Software
Results of the real-time PCR data are presented as Ct values (raw data), with Ct defined as the threshold cycle number of PCRs at first detection of amplified product. Next, ΔCt normalization was performed using a reference Ct. To establish the reproducibility of the 768 miRNA-assays and to define a reference, a pool of total RNAs from a set of 55 tumor specimens (45-series) was run in triplicate. In total, 314 assays were selected as reference since these assays were negative for no template controls, had results in all three runs with a coefficient of variation less than 2.5% between them, and had for each run correct amplification curves (ΔCt=0.75-1.50 between 0.1/0.2 or 0.05/0.1 threshold). Next, for each individual cancer specimen the median Ct was calculated for these 314 microRNA reference assays. Subsequently, the ΔCt-value was calculated by subtraction of this reference median Ct-value from the Ct-value measured for each target miRNA. Those  ΔCt-values that failed quality controls were flagged. Only data with an undetermined or not amplified well flag were replaced by the minimum ΔCt-value of the dataset (i.e. 0.000507083). All other flagged data were removed. Finally, ΔCt-values were log2 transformed for further analyses (processed data).

label: FAM

source_name: fresh frozen primary breast cancer specimen

label_protocol:
500ng of total RNA was reverse transcribed with MegaPlex RT-Pools (A&B) (40 cycles).  The qPCR reaction on the TaqMan microaRNA array was performed with 6 ul megaplex RT product, 450 ul TaqMan Universal PCR Master MIX, No AmpERase UNG (2x) and 444ul nuclease-free water.
Individual Taqman Probes & Primers, Tiled-Low Density Array
7900 Real Time PCR System

extract_protocol: RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.

tag: gender

value: female

tag: age at diagnosis

tag: treatment type

value: letrozole

tag: age at start therapy

tag: menopausal status at start therapy

value: post

tag: tissue

value: breast

tag: tumor type

value: invasive ductal carcinoma

tag: location

tag: grade

tag: estrogen receptor status

value: positive

tag: progesterone receptor status

tag: her2 status

value: negative

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

value: EMC

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: MA9_2

tag: bmt type


title: S121

description: Reanalysis of GSM525831

source_name: Myxofibrosarcoma

tag: metastasis

value: Yes

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: HOXA9+PBX3_2


title: S252

description: Reanalysis of GSM526057


title: HOXA9+PBX3_3


title: MA9_1


title: S115

description: Reanalysis of GSM525824


title: S249

description: Reanalysis of GSM526054


title: S251

description: Reanalysis of GSM526056


title: S114

description: Reanalysis of GSM525823

source_name: Dedifferentiated liposarcoma


title: S117

description: Reanalysis of GSM525826


title: S119

description: Reanalysis of GSM525828


title: S112

description: Reanalysis of GSM525821

source_name: Other


title: S113

description: Reanalysis of GSM525822


title: HOXA9+MEIS1_2


title: HOXA9+PBX3_1


title: HOXA9+MEIS1_3


title: S111

description: Reanalysis of GSM525820


title: HOXA9_2


title: PL16 NC_3

value: Normal Control


title: PL01 NC_1


title: HOXA9+MEIS1_1


title: PL18 NC_5


title: S110

description: Reanalysis of GSM525819


title: S109

description: Reanalysis of GSM525817

source_name: Leiomyosarcoma


title: S107

description: Reanalysis of GSM525815


title: S103

description: Reanalysis of GSM525811


title: S105

description: Reanalysis of GSM525813


title: HOXA9_3


title: S97

description: Reanalysis of GSM525986


title: S108

description: Reanalysis of GSM525816


title: HOXA9_1


title: S104

description: Reanalysis of GSM525812


title: PL17 NC_4


title: S93

description: Reanalysis of GSM525982


title: S95

description: Reanalysis of GSM525984


title: PL08 NC_2


title: S99

description: Reanalysis of GSM525988


title: S106

description: Reanalysis of GSM525814


title: S94

description: Reanalysis of GSM525983


title: S89

description: Reanalysis of GSM525977


title: S91

description: Reanalysis of GSM525980


title: S88

description: Reanalysis of GSM525976


title: S102

description: Reanalysis of GSM525810


title: S96

description: Reanalysis of GSM525985


title: S98

description: Reanalysis of GSM525987


title: S100

description: Reanalysis of GSM525808


title: S92

description: Reanalysis of GSM525981


title: S90

description: Reanalysis of GSM525979


title: S83

description: Reanalysis of GSM525971


title: S246

description: Reanalysis of GSM526051


title: S84

description: Reanalysis of GSM525972


title: S248

description: Reanalysis of GSM526053


title: S85

description: Reanalysis of GSM525973


title: S82

description: Reanalysis of GSM525970


title: S247

description: Reanalysis of GSM526052


title: S81

description: Reanalysis of GSM525969


title: S78

description: Reanalysis of GSM525965


title: S87

description: Reanalysis of GSM525975


title: S86

description: Reanalysis of GSM525974


title: S76

description: Reanalysis of GSM525963


title: S79

description: Reanalysis of GSM525966


title: S245

description: Reanalysis of GSM526050


title: S101

description: Reanalysis of GSM525809


title: S80

description: Reanalysis of GSM525968


title: S72

description: Reanalysis of GSM525959


title: S68

description: Reanalysis of GSM525954


title: S70

description: Reanalysis of GSM525957


title: S75

description: Reanalysis of GSM525962


title: S77

description: Reanalysis of GSM525964


title: S73

description: Reanalysis of GSM525960


title: S66

description: Reanalysis of GSM525952


title: S74

description: Reanalysis of GSM525961


title: S67

description: Reanalysis of GSM525953


title: S62

description: Reanalysis of GSM525948


title: S69

description: Reanalysis of GSM525955


title: S71

description: Reanalysis of GSM525958


title: S58

description: Reanalysis of GSM525943


title: S65

description: Reanalysis of GSM525951


title: S61

description: Reanalysis of GSM525947


title: S63

description: Reanalysis of GSM525949


title: S242

description: Reanalysis of GSM526047


title: S64

description: Reanalysis of GSM525950


title: S244

description: Reanalysis of GSM526049


title: S60

description: Reanalysis of GSM525946


title: S243

description: Reanalysis of GSM526048


title: S59

description: Reanalysis of GSM525944


title: S57

description: Reanalysis of GSM525942


title: S241

description: Reanalysis of GSM526046


title: S53

description: Reanalysis of GSM525938


title: S240

description: Reanalysis of GSM526045


title: S239

description: Reanalysis of GSM526044


title: S159

description: Reanalysis of GSM525872


title: S49

description: Reanalysis of GSM525933


title: S56

description: Reanalysis of GSM525941


title: S54

description: Reanalysis of GSM525939


title: S48

description: Reanalysis of GSM525932


title: S304

description: Reanalysis of GSM526109


title: S52

description: Reanalysis of GSM525937


title: S236

description: Reanalysis of GSM526041


title: S51

description: Reanalysis of GSM525936


title: S50

description: Reanalysis of GSM525935


title: S238

description: Reanalysis of GSM526043


title: S47

description: Reanalysis of GSM525931


title: S43

description: Reanalysis of GSM525927


title: S2

description: Reanalysis of GSM525901


title: S314


title: S38

description: Reanalysis of GSM525921


title: S237

description: Reanalysis of GSM526042


title: S40

description: Reanalysis of GSM525924


title: S183

description: Reanalysis of GSM525899


title: S44

description: Reanalysis of GSM525928


title: S46

description: Reanalysis of GSM525930


title: S42

description: Reanalysis of GSM525926


title: S35

description: Reanalysis of GSM525918


title: S33

description: Reanalysis of GSM525916


title: S41

description: Reanalysis of GSM525925


title: S235

description: Reanalysis of GSM526040


title: S39

description: Reanalysis of GSM525922


title: S45

description: Reanalysis of GSM525929


title: DZ12-sectored-Red26 (S50R)

type: genomic

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

description: DZ12-derived Red sectored colonies

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The ratio of the medians (635 nm/532 nm) for each probe was used for analysis, and replicate probe medians were averaged. The data was centered around one by dividing each probe median by the average of all of the probe medians in order to normalize for differences in the hybridization levels for the reference and experimental strain samples. The data were plotted separately for each haploid parental strain and, in plots showing whole chromosomes, the medians were “smoothed” by averaging over nine consecutive probes. In the labels of the oligonucleotides “SF”, “SR”, “YF” and “YR” refer to the orientation and origin of the sequences used for the oligonucleotides on the microarrays. “S” and “Y” indicate whether the oligonucleotide contains sequences identical to the reference S288c genome (closely related to W303-1A) or the YJM789 genome, respectively. “F” and “R” indicate whether the orientation (5’ to 3’) is identical to the orientation in SGD (“F” standing for forward) or opposite to that shown in SGD (“R” for reverse). Thus, “F” and “R” have the sequences of the complementary Watson and Crick strands at each position. For all oligonucleotides for a particular SNP, the number used to label the coordinate is the coordinate of the first base of the oligonucleotide in the “F” orientation. In addition, the oligonucleotides for the YJM789-derived sequences were labeled with the same coordinate as the S288c-derived sequences. The sequence information for the YJM789 sequences was from SGD based on the paper by (Wei et al., 2007. PNAS 104:12825-12830). The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: DZ12-derived sectored colonies

label_protocol: The description of the labeling and hybridization protocol are copied with minor modifications from the Supplementary Information of our previous publication: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were cultured in low-gal (2% yeast extract, 2% peptone and 3% raffinose, 0.005% galactose) or high-gal medium (2% yeast extract, 2% peptone and 3% raffinose, 0.05% galactose) to extract DNA

extract_protocol: Genomic DNA were prepared DNA by standard procedures (St. Charles et al., 2012).

treatment_protocol: The expression of POL3 were downregulated using either low-gal medium or YPD medium.

tag: ploidy

value: Diploid

tag: background

tag: strain

value: diploid strain DZ12

tag: growth protocol

value: YPD medium

source_name: Control strain JSC24

value: control strain JSC24


title: S182

description: Reanalysis of GSM525898


title: S32

description: Reanalysis of GSM525915


title: S158

description: Reanalysis of GSM525871


title: S34

description: Reanalysis of GSM525917


title: S155

description: Reanalysis of GSM525868


title: S31

description: Reanalysis of GSM525914


title: S312


title: DZ12-sectored-Red23 (S40R)

description: DZ12-derived Red sectored colonies


title: S30

description: Reanalysis of GSM525913


title: S37

description: Reanalysis of GSM525920


title: S176

description: Reanalysis of GSM525891


title: S234

description: Reanalysis of GSM526039


title: S36

description: Reanalysis of GSM525919


title: S28

description: Reanalysis of GSM525910


title: S233

description: Reanalysis of GSM526038


title: S24

description: Reanalysis of GSM525906


title: DZ12-sectored-Red22 (S34R)

description: DZ12-derived Red sectored colonies


title: S23

description: Reanalysis of GSM525905


title: S29

description: Reanalysis of GSM525911


title: S22

description: Reanalysis of GSM525904


title: DZ12-sectored-Red24 (S47R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red25 (S49R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red20 (S30R)

description: DZ12-derived Red sectored colonies


title: S25

description: Reanalysis of GSM525907


title: DZ12-sectored-Red14 (S22R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red18 (S28R)

description: DZ12-derived Red sectored colonies


title: S27

description: Reanalysis of GSM525909


title: DZ12-sectored-Red21 (S33R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red13 (S20R)

description: DZ12-derived Red sectored colonies


title: S26

description: Reanalysis of GSM525908


title: S153

description: Reanalysis of GSM525866


title: DZ12-sectored-Red17 (S25R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red19 (S29R)

description: DZ12-derived Red sectored colonies


title: S17

description: Reanalysis of GSM525884


title: S313


title: S167

description: Reanalysis of GSM525881


title: S20

description: Reanalysis of GSM525902


title: S21

description: Reanalysis of GSM525903


title: S19

description: Reanalysis of GSM525900


title: DZ12-sectored-Red16 (S24R)

description: DZ12-derived Red sectored colonies


title: S16

description: Reanalysis of GSM525873


title: S18

description: Reanalysis of GSM525895


title: DZ12-sectored-Red12 (S16R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red11 (S15R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red15 (S23R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red9 (S13R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red10 (S14R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red8 (S12R)

description: DZ12-derived Red sectored colonies


title: S178

description: Reanalysis of GSM525893


title: DZ12-sectored-Red7 (S10R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red4 (S4R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-White24 (S47W)

description: DZ12-derived white sectored colonies


title: S296

description: Reanalysis of GSM526101


title: S157

description: Reanalysis of GSM525870


title: DZ12-sectored-Red6 (S6R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-White20 (S30W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White21 (S33W)

description: DZ12-derived white sectored colonies


title: S15

description: Reanalysis of GSM525862


title: DZ12-sectored-Red2 (S2R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red1 (S1R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-White26 (S50W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White23 (S40W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White19 (S29W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White25 (S49W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White22 (S34W)

description: DZ12-derived white sectored colonies


title: S232

description: Reanalysis of GSM526037


title: DZ12-sectored-Red5 (S5R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-White18 (S28W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White15 (S23W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White16 (S24W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White17 (S25W)

description: DZ12-derived white sectored colonies


title: S14

description: Reanalysis of GSM525851


title: S11

description: Reanalysis of GSM525818


title: S231

description: Reanalysis of GSM526036


title: S12

description: Reanalysis of GSM525829


title: S10

description: Reanalysis of GSM525807


title: S13

description: Reanalysis of GSM525840


title: DZ12-sectored-White14 (S22W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White13 (S20W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White12 (S16W)

description: DZ12-derived white sectored colonies


title: S9

description: Reanalysis of GSM525978


title: DZ12-sectored-White7 (S10W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White6 (S6W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White11 (S15W)

description: DZ12-derived white sectored colonies


title: S230

description: Reanalysis of GSM526035


title: DZ12-sectored-White10 (S14W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White9 (S13W)

description: DZ12-derived white sectored colonies


title: S168

description: Reanalysis of GSM525882


title: S179

description: Reanalysis of GSM525894


title: S7

description: Reanalysis of GSM525956


title: DZ12-sectored-White4 (S4W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White1 (S1W)

description: DZ12-derived white sectored colonies


title: 0215F-02_14-WT-5xfAD2

city: Irvine

first: Mathew

last: Blurton-Jones

address: 3014 Gross Hall

department: Department of Neurobiology & Behavior

institute: University of California, Irvine

description: Gene expression data from Mouse Whole Brain

hyb_protocol: Following fragmentation, 5.1μg of ss-ccDNA were hybridized for 17hr at 45C GeneChip transcriptome assays 1.0. Genechips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip Scanner 3000 7G.

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package oligo

source_name: mouse whole brain

label_protocol: Biotinglated ss-ccDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Genechip WT PLUS reagent manual 2013)

growth_protocol: All animals were group housed on a 12h/12h light/dark cycle with access to food and water ad libitum.

extract_protocol: Total RNA was extracted by TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers’ protocols

treatment_protocol: The cerebellum was removed and the forebrain hemisected along the midsagittal plane.  Half forebrains were then flash frozen and stored at -80c.

tag: tissue

value: brain

tag: genotype

tag: age

value: 6-7 months

tag: Sex


title: DZ12-sectored-White5 (S5W)

description: DZ12-derived white sectored colonies


title: 0215F-02_15-WT-5xfAD3


title: S229

description: Reanalysis of GSM526034

value: Frozen tumor


title: DZ12-sectored-White8 (S12W)

description: DZ12-derived white sectored colonies


title: S8

description: Reanalysis of GSM525967

value: No


title: 0215F-02_13-WT-WT4

value: female


title: 0215F-02_11-Rag-WT4


title: 0215F-02_12-Rag-5xfAD4


title: S311


title: S156

description: Reanalysis of GSM525869


title: 0215F-02_16-WT-5xfAD4


title: 0215F-02_08-WT-WT3


title: S6

description: Reanalysis of GSM525945


title: 0215F-02_10-Rag-WT3


title: S5

description: Reanalysis of GSM525934


title: 0215F-02_05-WT-5xfAD1


title: 0215F-02_06-WT-WT1


title: DZ12-sectored-White2 (S2W)

description: DZ12-derived white sectored colonies


title: 0215F-02_09-Rag-WT2


title: 0215F-02_07-WT-WT2


title: 0215F-02_03-Rag-5xfAD2


title: S225

description: Reanalysis of GSM526030


title: S227

description: Reanalysis of GSM526032


title: 0215F-02_04-Rag-5xfAD3


title: 0215F-02_01-Rag-5xfAD1


title: UC-182 Endometrial Biopsy-Normal Control

city: San Francisco

first: Linda

middle: C.

last: Giudice

address: 499 Illinois St., Sixth Floor

department: Center for Reproductive Health at Mission Bay

institute: UC San Francisco

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing: GeneSpringGX 12.0, Microarray Technology: Affymetrix.ExonExprChip.HuGene-1_0-st-v1, Summarization Algorithm: ExonRMA16, Normalization: Quantile, Baseline Transformation: median of all samples

source_name: Endometrium

label_protocol: RNA was reverse transcribed/amplified into cDNA using the NuGEN FFPE kit, and sense-strand cDNA targets were created using the NuGEN WT-Ovation Exon Module, followed by fragmentation and labeling using NuGEN Encore Biotin Module for hybridization to Affymetrix Human Gene 1.0 ST arrays.

extract_protocol: Cells were subject to RNA isolation and purification, with DNAse treatment, RNeasy Plus minikit.

tag: disease

value: No Adenomyosis

tag: fresh tissue sample/time in culture

value: Fresh Tissue Sample

tag: cell type

value: Whole Endometrial Tissue


title: S228

description: Reanalysis of GSM526033


title: S223

description: Reanalysis of GSM526028


title: UC-251 Endometrial Biopsy-Normal Control


title: UC-207 Endometrial Biopsy-Normal Control


title: UC-034 Endometrial Biopsy-Adenomyosis

value: Adenomyosis


title: S224

description: Reanalysis of GSM526029


title: UC-065 Endometrial Biopsy-Adenomyosis


title: S220

description: Reanalysis of GSM526025


title: S213

description: Reanalysis of GSM526018


title: UC-230 Endometrial Biopsy-Normal Control


title: S218

description: Reanalysis of GSM526023


title: 421 Endometrial Biopsy-Adenomyosis


title: 0215F-02_02-Rag-WT1


title: S216

description: Reanalysis of GSM526021


title: UC-137 Endometrial Biopsy-Normal Control


title: S226

description: Reanalysis of GSM526031


title: S214

description: Reanalysis of GSM526019


title: S219

description: Reanalysis of GSM526024


title: S221

description: Reanalysis of GSM526026


title: S222

description: Reanalysis of GSM526027


title: control vs JAK inhibitor

city: Urayasu-shi

first: Keigo

last: Ikeda

state: Chiba

address: 2-1-1 Tomioka

department: Institutes for Environmental and Gender Specific Medicine

country: Japan

institute: Juntendo University

hyb_protocol: Labeled targets were competitively hybridized to 3D-Gene mouse Oligo chip 24k (TORAY Industries Inc.).

scan_protocol: The signal intensity data from scanned hybridization images using GenePix4400A (Molecular devices) were quantified to identify the gene expression.

data_processing: The obtained numerical data were normalized using housekeeping gene Atp5f1 per slide and per channel. Genes with mean fluorescence intensities less than or equal to 100 comparing with background, based on the results of dye-swapping experiments, were considered negatively expressed.

source_name: cont spl CD4

label_protocol: Fluorescence labeled complementary antisense RNA (aRNA) targets were synthesized using AminoAllyl MessageAmpTM II aRNA amplification Kit (Ambion).  The amplified aRNA targets synthesized from treated mouse CD4+ T cells were coupled with Cy5.  The aRNA targets synthesized from non-treated mouse CD4+ T cells were coupled with Cy3 for the two-color microarray method.

extract_protocol: Splenic CD4+ T cells RNA were isolated by RNeasy mini kit (QIAGEN).

treatment_protocol: 24 weeks Age-matched female NZBWF1 was randomized, ear tagged for identification, and initial baseline measurements including body mass and serum were collected before dosing.  Both mice were oral administration of tofacitinib (TOFA, CP-690550, Pfizer) in saline at 30 mg/kg six times in a week.  Dexamethasone (DEXA, Decadron, MSD K.K.) was provided as standard of care at 0.5 mg/kg, s.c. injection, three times a week.  Control was provided orally, six times a week and s.c injection. three times a week, as saline only.  These treatments were continued for 11 weeks in NZBWF1

value: Splenic CD4+ T cells

tag: treatment

value: control

source_name: JAKi spl CD4

value: JAK inhibitor


title: S215

description: Reanalysis of GSM526020

tag: metastasis


title: control vs JAK inhibitor + dexamethasone

source_name: JAKi+Dex spl CD4

value: JAK inhibitor + dexamethasone


title: S205

description: Reanalysis of GSM526010

value: Yes

tag: time


title: RC-ZT14

city: Houston

first: Zheng

state: Texas

address: 6431 Fannin street, MSB3.135

department: Department of Biochemistry and Molecular Biology

institute: UT health science center at houston

description: ZT14, Pooled

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The samples were scanned with BeadArray Reader (Illumina, CA).

data_processing: Data were normalized by using quantile normalisation with GenomeStudio software

source_name: Regulatroy chow ZT14

growth_protocol: Animals housed under a 12hr:12hr light:dark cycle. Animals were fed ad libitum.

extract_protocol: Total RNA was extracted by using QIAGEN RNeasy mini kit in accordance with the protocol provided with the kit

treatment_protocol: C57BL/6J mice with HFD treatment were orally administered to vehicle or 200mg/kg of nobiletin every other day. After 10 weeks of treatment, livers were rapidly collected and frozen in liquid nitrogen.   All samples stored at -80 until RNA preparation.

value: 18 wks

tag: diet

value: regulatory chow

value: vehicle

tag: harvest timepoint

value: liver


title: S211

description: Reanalysis of GSM526016

tag: paired rna-seq

tag: cinsarc

tag: material support


title: NOB-ZT14

description: ZT14, Pooled

source_name: HFD with Nobiletin ZT214

label_protocol: Standard Illumina hybridization protocol

tag: strain

value: high fat diet

value: nobiletin


title: S212

description: Reanalysis of GSM526017

value: Frozen tumor


title: 230-238 GFP+, biological replicate 3

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing: Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v2.15) 'affy' package using the rma() function

source_name: 230-238 GFP+, biological replicate 3

label_protocol: 100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: The 230-238 cell line was either infected with a plasmid encoding the GFP protein or a plasmid encoding both the GFP and FOG1 proteins. After infection, cells were put in culture in RPMI1640 medium for 3 days before to be sorted for being GFP+. They were put back again in culture for 4 days more after the sort. Then, RNA isolation was performed using the following QIAGEN kit: RNeasy micro without DNase treatment.

extract_protocol: The mRNA extraction was performed without DNase I treatment using the RNeasy Mini Kit from QIAGEN.

tag: cell line


title: HFD-ZT14

description: ZT14, Pooled

source_name: High fat diet ZT14

tag: tissue


title: control vs dexamethasone

source_name: Dex spl CD4

value: dexamethasone


title: rice calli at 1g-ground control, biological rep2

city: Shanghai

first: Jin

last: Jing

address: No. 300 Fenglin Road

institute: Shanghai Insitute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Gene expression data from rice calli grow about 324h under 1g-ground controls

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

source_name: rice calli exposured to 1g-ground control

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Calli grown on N6 medium (containing 2 mg/L2,4-D, 1% agar), at 23 ± 2°C in the dark.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Calli exposured to microgravity about 324h

value: 1g-ground control

value: 17 days old


title: 230-238 GFP+, biological replicate 1

source_name: 230-238 GFP+, biological replicate 1


title: RC-ZT2

description: ZT2, Pooled

source_name: Regulatory chow ZT2


title: NOB-ZT2

description: ZT2, Pooled

source_name: HFD with Nobiletin ZT2


title: S210

description: Reanalysis of GSM526015

source_name: Myxofibrosarcoma

value: No


title: S208

description: Reanalysis of GSM526013

source_name: Leiomyosarcoma


title: S209

description: Reanalysis of GSM526014


title: 230-238 GFP+FOG1, biological replicate 2


title: rice calli at 1g-ground control, biological rep3


title: 230-238 GFP+, biological replicate 2

source_name: 230-238 GFP+, biological replicate 2


title: S206

description: Reanalysis of GSM526011


title: 230-238 GFP+FOG1, biological replicate 3


title: S199

description: Reanalysis of GSM526004

source_name: Other


title: S207

description: Reanalysis of GSM526012


title: HFD-ZT2

description: ZT2, Pooled

source_name: High fat diet ZT2


title: 230-238 GFP+FOG1, biological replicate 1


title: rice calli at 1g-inflight control, biological rep2

description: Gene expression data from rice calli grow about 324h under 1g-flight controls

source_name: rice calli exposured to 1g-flight control

value: 1g-inflight control


title: S204

description: Reanalysis of GSM526009


title: rice calli at 1g-ground control, biological rep1


title: rice calli at 1g-inflight control, biological rep1


title: rice calli at 1g-inflight control, biological rep3


title: rice calli at spaceflight control, biological rep3

description: Gene expression data from rice calli grow about 324h under spaceflight

source_name: rice calli exposured to spaceflight control

value: 324h spaceflight control


title: rice calli at spaceflight control, biological rep4


title: rice calli at spaceflight control, biological rep1


title: S200

description: Reanalysis of GSM526005

source_name: Undifferentiated sarcoma


title: EC9706 cells_harvested 72h_transfection with pSilencer3.1-H1-neo-Bit1-shRNA_rep1

city: Zhengzhou

first: chen

last: jing

state: Henan

address: 100 KeXue Avenue

institute: Zhengzhou University

description: Gene expression after 72h after transfection with pSilencer3.1-H1 -neo-Bit1-shRNA,EC9706 cells.

hyb_protocol: Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: EC9706 cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: EC9706 cells were harvested 72 h after transfection with pSilencer3.1-H1 -neo-Bit1-shRNA or pSilencer3.1-H1-neo-negative-shRNA. Approximate 1 × 106 cells from each sample were subjected to gene microarray assay. Total RNA was extracted using TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions and analyzed with Agilent SurePrint G3 Human GE 8 × 60 K Microarray (Agilent technologies) by the Shanghai Biochip Company (Shanghai, China).


title: HOC313-LM-metastatic site-3-2

city: Tokyo

first: Tomoki

last: Muramatsu

address: 1-5-45 Yushima Bunkyo-ku

department: Medical research institute

institute: Tokyo Medical and Dental University

description: Transplantation tumor in metastatic site

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 SurePrint G3 Human GE 8x60K (G4851A) 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: high-metastatic subline

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.

growth_protocol: HOC313-P and -LM were maintained in appropriate media, D-MEM medium supplemented with 10%fetal bovine serum.

extract_protocol: RNA fractions were prepared using TRIsure (BIOLINE,London, UK) following the manufacturer's recommendations. The protocol includes clean up step after TURBO DNA-free™ Kit (Ambion, Austin, TX) digestion. RNAs were quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: HOC313-P and -LM were injected to subcutaneous in mice.

value: Oral squamous cell carcinoma


title: S201

description: Reanalysis of GSM526006


title: EC9706 cells_harvested 72h_transfection with pSilencer3.1-H1-neo-Bit1-shRNA_rep2


title: S196

description: Reanalysis of GSM526001


title: HOC313-LM-primary site-6-1

description: Transplantation tumor in primary site


title: HOC313-LM-primary site-7-2

description: Transplantation tumor in primary site


title: HOC313-LM-primary site-7-1

description: Transplantation tumor in primary site


title: EC9706 cells_harvested 72h_transfection with pSilencer3.1-H1-neo-negative-shRNA_rep1

description: Gene expression after 72h after transfection with pSilencer3.1-H1-neo-negative-shRNA,EC9706 cells.


title: S198

description: Reanalysis of GSM526003


title: HOC313-LM-metastatic site-7-1


title: S194

description: Reanalysis of GSM525999


title: rice calli at spaceflight control, biological rep2


title: HOC313-LM-metastatic site-6-2


title: HOC313-LM-metastatic site-3-1


title: HOC313-LM-primary site-6-2

description: Transplantation tumor in primary site


title: HOC313-P-metastatic site-8-1

source_name: low-metastatic subline


title: S195

description: Reanalysis of GSM526000


title: EC9706 cells_harvested 72h_transfection with pSilencer3.1-H1-neo-negative-shRNA_rep2


title: S203

description: Reanalysis of GSM526008


title: HOC313-LM-metastatic site-6-1


title: S192

description: Reanalysis of GSM525997


title: S197

description: Reanalysis of GSM526002


title: HOC313-P-metastatic site-8-2


title: S217

description: Reanalysis of GSM526022


title: HOC313-LM-primary site-3-2

description: Transplantation tumor in primary site


title: HOC313-LM-metastatic site-7-2


title: S202

description: Reanalysis of GSM526007


title: HOC313-LM-primary site-3-1

description: Transplantation tumor in primary site


title: S193

description: Reanalysis of GSM525998


title: HOC313-P-primary site-7-2

description: Transplantation tumor in primary site


title: HOC313-P-primary site-1-2

description: Transplantation tumor in primary site


title: HOC313-P-primary site-8-1

description: Transplantation tumor in primary site


title: HOC313-P-primary site-1-1

description: Transplantation tumor in primary site


title: S191

description: Reanalysis of GSM525996


title: HOC313-P-primary site-8-2

description: Transplantation tumor in primary site


title: S187

description: Reanalysis of GSM525992


title: S189

description: Reanalysis of GSM525994


title: HOC313-P-primary site-7-1

description: Transplantation tumor in primary site


title: S185

description: Reanalysis of GSM525990


title: HOC313-P-Dish-2

description: Dish culture


title: HOC313-LM-Dish-1

description: Dish culture


title: S190

description: Reanalysis of GSM525995


title: S186

description: Reanalysis of GSM525991


title: S3

description: Reanalysis of GSM525912

source_name: Dedifferentiated liposarcoma


title: S188

description: Reanalysis of GSM525993


title: HOC313-LM-Dish-2

description: Dish culture


title: EB technical rep 2

city: Taipa

first: Jung

middle: Woo

last: Park

state: Macau

department: Faculty of Health Sciences

institute: University of Macau

description: Spontaneous differentation

scan_protocol: Standard Illumina scanning protocol

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

source_name: Human EB

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

extract_protocol: Total RNA was isolated from sample cells by PureLink kit RNA mini kit (Ambion)

value: Embryoid bodies


title: S4

description: Reanalysis of GSM525923


title: MFS iPSC technical rep 2

description: Undifferenitated

source_name: Human iPSC

value: induced pluripotent stem cells

tag: genotype/disease state

value: Marfan Syndrome


title: HOC313-P-Dish-1

description: Dish culture


title: RNA in fft2D

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

scan_protocol: Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing:
CEL files were normalized using quantile normalization in TAS (Affymetrix) and visualized using Podbat (www.podbat.org).
Text files contain log2 scores for enrichment over anti-myc control (for ChIP samples) and log2 scores for enrichment over wildtype RNA levels (for RNA). Tab-delimited files contain, in order: chromosome, start, end, strand, score.

organism: Schizosaccharomyces pombe

source_name: Fft2D RNA

label_protocol: Biotin-labeled according to standard Affymetrix protocols.

growth_protocol: Cultures were grown at 30°C to a density of 7e6 cells/ml.

extract_protocol: DNA was immunoprecipitated as described earlier (Durand-Dubief, 2009) using 2µg mouse anti-myc 9E10 Sigma M4439 antibody per 100µl chromatin extracts.

tag: genotype

value: h- fft2D::kanMX ura4D18 leu1-32 ade6-216

source_name: wildtype RNA


title: EB technical rep 1

description: Spontaneous differentation


title: RNA in fft3D

source_name: Fft3D RNA

value: h+ fft3D::hphMX ura4D18 leu1-32 ade6-216


title: MCF7_MIND_sample1

city: Lausanne

first: George

middle: A

last: Sflomos

address: SV 2815, Batiment SV, Station 19

department: ISREC

institute: EPFL

hyb_protocol: Affymetrix Human Genome U133Plus 2.0 arrays were hybridized with 11 micrograms of biotinylated amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0001)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each experiment separately (Expression Console version 1.3.1).

source_name: xenograft MCF7-MIND

label_protocol: For all samples, 100 ng of total RNA was used to perform target preparation using the MessageAmp™ II-Biotin Enhanced kit (Life technologies).

extract_protocol: Xenografted MCF7 were FACS sorting based on DsRED expression; total RNA was extracted using Trizol Reagent (Invitrogen), purified with the miRNeasy Mini Kit (Qiagen), and quantity and quality were assessed by NanoDrop®ND-1000 spectrophotometer and RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, USA). Only samples with RIN score >7.0 were included.

tag: source cell type

value: MCF7-DsRED/luc2 cells

tag: host strain info

value: 8-12 wk-old female SCID Beige mice

tag: sample group

value: intraductal xenograft

value: xenografted, FACS-sorted MCF7


title: MFS iPSC technical rep 1

description: Undifferenitated


title: mcMFS SMC technical rep 2

description: Differentiated from iPSC

source_name: Human SMC

value: Smooth muscle cells

value: mutation corrected


title: mcMFS SMC biological rep 1

description: Differentiated from iPSC


title: MCF7_fatpad_sample2

source_name: xenograft MCF7-FP

value: fat pad xenograft

tag: cell type


title: MCF7_MIND_sample2


title: SaOS2_anti-sense APC_REC_rep2

city: Delhi

first: Gurudutta

middle: U

last: Gangenahalli

state: Delhi

address: Brig. S. K. Mazumdar Marg, Timarpur

department: Stem Cell Research Division

country: India

institute: Institute of Nuclear Medicine & Allied Sciences

description: Transfected cells treated with doxycycline for 3 days and cultured for additional 3 days without doxycycline

hyb_protocol: standard Illumina hybridisation protocol

data_processing: The data were normalised using quantile normalisation.

source_name: SaOS2 cells, anti-sense APC, recovery, 3day, replicate2

label_protocol: Cy3 label

growth_protocol: SaOS2 cells were cultured in HG-DMEM supplemmented with 10% FBS, 100μg/ml G418 and 50μg/ml Hygromycin. The medium was changed twice per week and the cells were passaged upon attaining confluency.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: SaOS2 cells were treated with doxycycline (1μg/ml) for 3 days with medium containing doxycycline changed every alternate day. After 3 days, first set of cells was harvested by trypsination and stored in RNAlater. Second set of cells was shifted to growth medium (without doxycycline) after 3 days of treatment and cultured for additional 3 days to allow for the cells to recover from the treatment. After 3 days of doxycycline removal, these cells were harvested by trypsination and stored in RNAlater.

value: bone

tag: treatment stage

value: Recovery, 3 days post doxycycline


title: MCF7_MIND_sample3


title: RNA in fft2D fft3D

description:
Text files contain log2 scores for enrichment over wildtype RNA levels (for RNA).
Tab-delimited files contain, in order: chromosome, start, end, strand, score.

data_processing:
CEL files were normalized using quantile normalization in TAS (Affymetrix) and visualized using Podbat (www.podbat.org).
Text files contain log2 scores for enrichment over anti-myc control for ChIP samples or  log2 scores for enrichment over wildtype RNA levels (for RNA). Tab-delimited files contain, in order: chromosome, start, end, strand, score.

source_name: Fft2D fft3D RNA

extract_protocol: not provided

value: h+ fft2D::kanMX fft3D::hphMX ura4D18 leu1-32 ade6-216


title: MFS SMC technical rep 2

description: Directed differentiation from iPSC


title: mcMFS SMC biological rep 2

description: Differentiated from iPSC


title: MFS SMC biological rep 2

description: Differentiated from iPSC


title: MCF7_fatpad_sample3


title: mcMFS SMC technical rep 1

description: Differentiated from iPSC


title: MFS SMC technical rep 1

description: Directed differentiation from iPSC


title: SaOS2_anti-sense APC_REC_rep3

source_name: SaOS2 cells, anti-sense APC, recovery, 3day, replicate3


title: MCF7_fatpad_sample1


title: Fft2-ChIP in fft3D

description:
Text files contain log2 scores for enrichment over anti-myc control for ChIP samples
Tab-delimited files contain, in order: chromosome, start, end, strand, score.
All ChIP comparisions were made to the same wildtype anti-myc samples:  WT_anti_myc_1.CEL and WT_anti_myc_2.CEL

source_name: Fft2 ChIP DNA

value: fft3D::hph fft2-myc::KanMX ade6-M210or216 leu1-32 ura4-D18

source_name: anti-myc ChIP DNA


title: SaOS2_anti-sense APC_REC_rep1

source_name: SaOS2 cells, anti-sense APC, recovery, 3day, replicate1


title: MFS SMC biological rep 1

description: Directed differentiation from iPSC


title: SaOS2_anti-sense APC_rep3

description: Transfected cells treated with doxycycline for 3 days

source_name: SaOS2 cells, anti-sense APC, 3day, replicate3

value: Doxycycline, 3 days


title: Fft3-ChIP in fft2D

source_name: Fft3 ChIP DNA

value: Fft3-myc::hph fft2D::Kan


title: SaOS2_anti-sense APC_rep1

source_name: SaOS2 cells, anti-sense APC, 3day, replicate1


title: Fft3-ChIP in wt

value: fft3-myc:kanMX ura4D18 leu1-32 ade6-216


title: SaOS2_control_rep2

description: control cells

source_name: SaOS2 cells, control, replicate2

value: Control


title: SaOS2_control_rep1

description: control cells

source_name: SaOS2 cells, control, replicate1


title: Fft2-ChIP in wt

value: fft2-myc:kanMX ura4D18 leu1-32 ade6-216


title: BP3+PDPN+ LNMC, biological rep3

city: Fredriksberg C

first: William

middle: Winston

last: Agace

address: Bülowsvej 27

department: National Veterinary Institute, Section for Immunology and Vaccinology

country: Denmark

institute: Technical University of Denmark

description: Gene expression data from the PDGFRβ+podoplanin(PDPN)+BP3+ subset of lymph node mesenchymal cells

hyb_protocol: Affymetrix microarray hybridization was carried out at a genomics core facility: Center of Excellence for Fluorescent Bioanalytics (KFB, University of Regensburg, Germany)

scan_protocol: Microarray scanns were taken with GeneChip Scanner 3000 at a genomics core facility: Center of Excellence for Fluorescent Bioanalytics (KFB, University of Regensburg, Germany)

data_processing: Raw data was background corrected, normalized and summarized into probe sets using the RMA algorithm in the Affymetrix Expression Console software. Probe sets without annotation were removed from the dataset and only one copy was retained of multiple probe sets that represented the same gene and exhibited identical expression values on all arrays.

source_name: BP3+PDPN+ mesenchymal cells lymph node

label_protocol: Isolated total RNA was reverse transcribed, amplified, fragmented and biotin-labelled using Ovation Pico WTA System V2 and Encore Biotin Module (NuGEN) according to manufacturer's protocol and hybridized to the Affymetrix Mouse Gene 1.1 ST Array at a genomics core facility: Center of Excellence for Fluorescent Bioanalytics (KFB, University of Regensburg, Germany).

extract_protocol: Total RNA was isolated using RNeasy Micro Kit (QIAGEN, Germantown, MD) according to manufacturer's instructions

treatment_protocol: Cell suspensions of thymus and lymph nodes were prepared with liberase TM (0.32 Wunsch U mL-1, Roche Diagnostics) and DNase I (50 Kunitz U mL-1, Sigma-Aldrich).

tag: age

value: 2 weeks

value: pooled inguinal, axillary, brachial lymph nodes


title: BP3-PDPN+ LNMC, biological rep2

description: Gene expression data from the PDGFRβ+podoplanin(PDPN)+BP3- subset of lymph node mesenchymal cells

source_name: BP3-PDPN+ mesenchymal cells lymph node


title: BP3-PDPN+ LNMC, biological rep1


title: SaOS2_control_rep3

description: control cells

source_name: SaOS2 cells, control, replicate3


title: BP3+PDPN+ LNMC, biological rep1


title: SaOS2_anti-sense APC_rep2

source_name: SaOS2 cells, anti-sense APC, 3day, replicate2


title: PDPN- LNMC, biological rep3

description: Gene expression data from the PDGFRb+podoplanin(PDPN)-Ly51+ subset of lymph node mesenchymal cells

source_name: PDPN- mesenchymal cells lymph node


title: BP3+PDPN+ LNMC, biological rep2


title: A549_CDDP_48h_rep3

city: Vancouver

first: Ada

last: Leung

state: British Columbia

address: 675 West 10th Avenue

department: Experimental Therapeutics

country: Canada

institute: BC Cancer Research Centre

hyb_protocol: service provided by The Centre for Applied Genomics at the Hospital for Sick Children, Toronto, Canada

data_processing: The data were analyzed using the Affymetrix Expression Console software and Affymetrix Power Tools. For quality control, the data were normalized using RMA normalization. MDS was also applied to the dataset. Differential and alternate gene expression analyses were carried out using the Limma package in R.

source_name: lung cancer, cisplatin-treated, 48h

growth_protocol: Cells were seeded at 5000 cells/well in 96-well plates in RPMI1640 supplemented with 10% FBS and 2mM L-glutamine

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit as per manufacturer's instructions

treatment_protocol: Cisplatin was added at an 10% inhibitory concentration (IC10) for the indicated time points 24 hours following cell seeding

tag: treatment

value: cisplatin

tag: time


title: BP3-PDPN+ LNMC, biological rep3


title: PDPN- LNMC, biological rep1


title: PDPN- TMC, biological rep3

description: Gene expression data from the PDGFRb+podoplanin(PDPN)-Ly51+ subset of thymic mesenchymal cells

source_name: PDPN- mesenchymal cells thymus

value: thymus


title: A549_CDDP_48h_rep2

scan_protocol: service provided by The Centre for Applied Genomics at the Hospital for Sick Children, Toronto, Canada


title: A549_CDDP_48h_rep1

label_protocol: service provided by The Centre for Applied Genomics at the Hospital for Sick Children, Toronto, Canada


title: PDPN- TMC, biological rep2


title: A549_UT_48h_rep2

source_name: lung cancer, untreated, 48h

value: untreated


title: PDPN- LNMC, biological rep2


title: BP3-PDPN+ TMC, biological rep2

description: Gene expression data from the PDGFRβ+podoplanin(PDPN)+BP3- subset of thymic mesenchymal cells

source_name: BP3-PDPN+ mesenchymal cells thymus


title: BP3-PDPN+ TMC, biological rep1


title: A549_UT_48h_rep3


title: BP3-PDPN+ TMC, biological rep3


title: A549_CDDP_24h_rep2

source_name: lung cancer, cisplatin-treated, 24h


title: A549_UT_48h_rep1


title: A549_CDDP_24h_rep3


title: A549_CDDP_24h_rep1


title: A549_UT_24h_rep2

source_name: lung cancer, untreated, 24h


title: PDPN- TMC, biological rep1


title: DZ12-sectored-Red34 (S60R)

description: DZ12-derived Red sectored colonies

source_name: DZ12-derived sectored colonies

tag: ploidy

value: Diploid

tag: background

value: diploid strain DZ12

tag: growth protocol

value: YPD medium

source_name: Control strain JSC24

value: control strain JSC24


title: A549_UT_24h_rep1


title: SF Rapamycin, bio rep 3

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

description:
Solt_Farber_Rapamycin_3a
Array on rapamycin animal 3

hyb_protocol: 60 ul total hyb volume with 3.5 ug labeled dsDNA, 60 rpm 47 C for 17 h

scan_protocol: Wash/Stain protocol FS450_0007 was used for washing and staining of the rat Gene ST 1.0 arrays.  Arrays were scanned using an Affymetrix GeneScanner 3000 7G

data_processing: Partek Genomics Suite v6.6 was used.  Differential gene expression was determined using RMA for normalization and ANOVA with contrast.  Differentially regulated genes had an FDR corrected p-value <0.05

organism: Rattus norvegicus

label_protocol: SensationPlus™ FFPE Amplification and WT Labeling Kit from Affymetrix was used according to the manufacturer's directions.  150 ng total RNA input, 25 ug  in vitro transcribed RNA and 3.5 ug labeled dsDNA per sample was used for hybridization.

growth_protocol: All animals were housed under standard conditions with access to food and water ad libitum.  Rodents were euthanized by exsanguination under isoflurane anesthesia.

extract_protocol: RNA was isolated from FFPE sections using Qiagen’s FFPE RNeasy Kit according to the manufacturer's directions.

treatment_protocol: Liver was harvested and tissue fixed in 10% neutral buffered formalin.  Fixed tissue was subsequently embedded in paraffin. Sections were stained with Arcturus Paradise Plus staining solution according to manufacturer's directions.Laser capture microdissection was performed to isolate regions of interest.

value: Liver

tag: gender

value: Male

tag: animal model

value: Rats were given an i.p. injection of diethylnitrosamine (200mg/kg) on day 1.  On day 14 rats were implanted i.p. with a 2.5mg 14-day time release 2-acetylaminofluorene pellet.  On day 21 rats were given a 2/3 partial hepatectomy and a subcutaneous 21-day time release rapamycin (2.5mg/kg/day) pellet.  Animals were euthanized on day 70 of the protocol.

tag: tissue features

value: GSTP + Persistent Focal Lesions

value: mTOR inhibitor rapamycin


title: DZ12-sectored-Red32 (S57R)

description: DZ12-derived Red sectored colonies

data_processing: The ratio of the medians (635 nm/532 nm) for each probe was used for analysis, and replicate probe medians were averaged. The data was centered around one by dividing each probe median by the average of all of the probe medians in order to normalize for differences in the hybridization levels for the reference and experimental strain samples. The data were plotted separately for each haploid parental strain and, in plots showing whole chromosomes, the medians were “smoothed” by averaging over nine consecutive probes. In the labels of the oligonucleotides “SF”, “SR”, “YF” and “YR” refer to the orientation and origin of the sequences used for the oligonucleotides on the microarrays. “S” and “Y” indicate whether the oligonucleotide contains sequences identical to the reference S288c genome (closely related to W303-1A) or the YJM789 genome, respectively. “F” and “R” indicate whether the orientation (5’ to 3’) is identical to the orientation in SGD (“F” standing for forward) or opposite to that shown in SGD (“R” for reverse). Thus, “F” and “R” have the sequences of the complementary Watson and Crick strands at each position. For all oligonucleotides for a particular SNP, the number used to label the coordinate is the coordinate of the first base of the oligonucleotide in the “F” orientation. In addition, the oligonucleotides for the YJM789-derived sequences were labeled with the same coordinate as the S288c-derived sequences. The sequence information for the YJM789 sequences was from SGD based on the paper by (Wei et al., 2007. PNAS 104:12825-12830). The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

extract_protocol: Genomic DNA were prepared DNA by standard procedures (St. Charles et al., 2012).

tag: strain


title: SF Rapamycin, bio rep 3c

description:
Solt_Farber_Rapamycin_3c
Array on rapamycin animal 3 with RNA extracted from a second round of laser capture

tag: tissue


title: DZ12-sectored-Red33 (S59R)

description: DZ12-derived Red sectored colonies


title: A549_UT_24h_rep3

tag: cell line


title: DZ12-sectored-Red31 (S56R)

description: DZ12-derived Red sectored colonies


title: SF Rapamycin, bio rep 3b

description:
Solt_Farber_Rapamycin_3b
Duplicate array on same RNA as 3a


title: SF Rapamycin, bio rep 1


title: SF Placebo, bio rep 3

value: Rats were given an i.p. injection of diethylnitrosamine (200mg/kg) on day 1.  On day 14 rats were implanted i.p. with a 2.5mg 14-day time release 2-acetylaminofluorene pellet.  On day 21 rats were given a 2/3 partial hepatectomy and a subcutaneous 21-day time release placebo pellet.  Animals were euthanized on day 70 of the protocol.

value: placebo


title: SF Rapamycin, bio rep 2


title: DZ12-sectored-Red30 (S55R)

description: DZ12-derived Red sectored colonies


title: SF Placebo, bio rep 2


title: DZ12-sectored-Red27 (S51R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red28 (S52R)

description: DZ12-derived Red sectored colonies


title: DZ12-sectored-Red3 (S3R)

description: DZ12-derived Red sectored colonies


title: SF Placebo, bio rep 1


title: AAF/PH, bio rep 1

value: On day 1 rats were implanted i.p. with a 2.5mg 14-day time release 2-acetylaminofluorene pellet.  On day 7 rats were given a 2/3 partial hepatectomy.   Animals were euthanized on day 14 of the protocol.

value: Oval Cells


title: DZ12-sectored-Red29 (S54R)

description: DZ12-derived Red sectored colonies


title: Adult Liver, bio rep 3

value: Normal, Unmanipulated

value: Normal


title: AAF/PH, bio rep 2


title: DZ12-sectored-White34 (S60W)

description: DZ12-derived white sectored colonies


title: AAF/PH, bio rep 3


title: DZ12-sectored-White31 (S56W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White32 (S57W)

description: DZ12-derived white sectored colonies


title: JX-9

city: Boston

first: XIAOJUN

last: LIU

state: Massachusetts

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

description: Gene expression data from NRVMs transfected with miR-222 precursor

hyb_protocol: The cRNA was hybridized to a microarray chip and the bound cRNA was stained with fluorescent streptavidin.

scan_protocol: The microarray chip was then scanned using a laser. The positions and intensities of the fluorescent emissions were captured.

data_processing: Array normalization and expression value calculation were performed by using DNA-Chip Analyzer (dChip).

source_name: primary neonatal rat ventricular cardiomyocytes (NRVMs)

label_protocol: Using oligonucleotide microarrays, the RNA of interest was converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA.

growth_protocol: Isolated primary neonatal rat ventricular cardiomyocytes were plated in 6 cm BD Primaria tissue culture dishes.

extract_protocol: Forty-eight hours after transfection, RNAs from cultured cells and tissues were isolated with Tryzol (Invitrogen) following the manufactures’ manuals.

treatment_protocol: Transfection of microRNA precursors or scramble control (0.4 μM) was carried out using Lipofectamine RNAiMAX (Invitrogen) as recommended by the manufacturer.

value: NRVMs

tag: transfection

value: miR-222 precursor


title: Adult Liver, bio rep 2


title: JX-11


title: Adult Liver, bio rep 1


title: DZ12-sectored-White33 (S59W)

city: Hangzhou

first: Daoqiong

institute: College of Life Sciences, Zhejiang University

description: DZ12-derived white sectored colonies

label_protocol: The description of the labeling and hybridization protocol are copied with minor modifications from the Supplementary Information of our previous publication: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

value: Diploid


title: JX-7


title: Not stimulation

city: Kumamoto

first: Wakana

last: Nakayama

address: 1-1-1 Honjo

department: Department of Dermatology & Plastic Surgery

institute: Faculty of Life Sciences, Kumamoto University

description: The cDNA was mixed with RT2 SYBR Green/Rox qPCR Master Mix (SABioscience), and the mixture was added to 96-well Extracellular Matrix and Adhesion Molecules PCR Array (Qiagen).

hyb_protocol: The first-strand cDNA was synthesized using RT2 First Strand Kit (SABiosciences, Frederick, MD). cDNA was mixed with RT2 SYBR Green/ROX qPCR Master Mix (SABioscience), and the mixture was added into 96-well Extracellular Matrix and Adhesion Molecules PCR Array (Qiagen)

scan_protocol: PCR was performed on Takara Thermal Cycler Dice (TP800)® following the manufacture’s protocol.

data_processing:
Threshold cycle (Ct) for each RNA was extracted using Thermal Cycler Dice Real Time System ver2.10B (Takara Bio Inc., Shiga, Japan). The raw Ct was normalized using the values of housekeeping gene.
Series supplementary file contains relative expression level was calculated as 1/2(the raw Ct of each mRNA – Ct of housekeeping genes).

source_name: dermal fibroblast

growth_protocol: Human dermal fibroblasts were obtained by skin biopsy from skin biopsy specimens of 3 healthy donors. Monolayer cultures were maintained at 37ºC in 5% CO2 in air.

extract_protocol: Total RNA was extracted from cultured cells with ISOGEN (Nippon Gene, Tokyo, Japan).

treatment_protocol: Fibroblasts were serum-starved for 24 hours, then were treated with IL-12, IL-23 or IL-27 (100ng/ml) for 12 hours.

value: dermal fibroblasts

value: skin

value: the absence of cytokine


title: DZ12-sectored-White3 (S3W)

last: Zheng

address: 866 Yuhangtang Road

description: DZ12-derived white sectored colonies

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

value: diploid strain DZ12

value: YPD medium

value: control strain JSC24


title: JX-6

description: Gene expression data from NRVMs transfected with control microRNA precursor

value: control microRNA precursor


title: DZ12-sectored-White30 (S55W)

description: DZ12-derived white sectored colonies


title: IL-27

value: the presence of IL-27


title: IL-12

value: the presence of IL-12


title: DZ12-sectored-White28 (S52W)

description: DZ12-derived white sectored colonies


title: DZ12-sectored-White27 (S51W)

description: DZ12-derived white sectored colonies


title: Pool 2 (No. 1-4) Mouse Blood N=4 [7449 1-2]

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description:
7449 1-2
Blood Pool 2-Control (Cy5) x Treatment FR (Cy3)
Dye-swap (Cy5/Cy3) of Control vs 50% FR Treatment Blood Pool 2

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1; Normalization is performed by LOWESS (locally weighted linear regression) which calculates the log ratio of dye-normalized Cy3- and Cy5-signals, as well as the final error of log ratio. The statistical significance of the log ratio values obtained for individual microarray probes is calculated using the “most conservative error model” default function of the Feature Extraction software, by which both a propagated and a universal error model are evaluated, and the higher (more conservative estimate of error) p-value of two error models is reported (Agilent Technologies).

source_name: Blood Pool2 50% FR Treatment Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Male C57BL/6J mice at 9 weeks (Japan SLC, Hamamatsu, Japan ; n=8 / group) were exposed to 50% FR (chow ; CE-2, CLEA, Tokyo Japan) for 2 weeks

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: Control (normal diet), Treatment (food restriction diet)

value: 9 weeks

value: male

tag: exposed to

value: 50% food restricition (FR)

value: blood

source_name: Blood Pool2 Control Cy5

value: normal (control) diet


title: Pool 3 (No. 5-8) Mouse Blood N=4 [7449 1-3]

description:
7449 1-3
Blood Pool 3-Control (Cy3) x Treatment FR (Cy5)
Dye-swap (Cy3/Cy5) of Control vs 50% FR Treatment Blood Pool 3

source_name: Blood Pool3 Control Cy3

source_name: Blood Pool3 50% FR Treatment Cy5


title: JX-8

value: NRVMs


title: IL-23

value: the presence of IL-23


title: JX-4


title: DZ12-sectored-White29 (S54W)

description: DZ12-derived white sectored colonies

value: Diploid


title: Pool 1 (No. 1-8) Mouse Blood N=8 [7215 1-2]

description:
7215 1-2
Blood Pool 1-Control (Cy5) x Treatment FR (Cy3)
Dye-swap (Cy5/Cy3) of Control vs 50% FR Treatment Blood Pool 1

source_name: Blood Pool1 50% FR Treatment Cy3

source_name: Blood Pool1 Control Cy5


title: NCvsNN-Infantile Hemangioma-3

city: Jinan

first: Xiaowen

last: Liu

state: Shandong

address: Jingwu Road 324

institute: Shandong Provincial Hospital affiliated to Shandong University

description: Biological replicate 3 of 3.Infantile hemangioma

hyb_protocol: According to the Agilent lncRNA Microarray Protocol (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction(v10.7).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Total RNA from pooled infantile hemangioma

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent lncRNA microarray, according to manufacturer's protocol.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Paired tissues of infantile hemangioma and peri-tumor tissues from every patient were quick-frozen by liquid nitrogen as soon as possible and then were moved to -80℃ condition for long-term storage

value: female

source_name: Total RNA from pooled adjacent nontumor skin


title: 6Cvs6N-Infantile Hemangioma-2

description: Biological replicate 2 of 3.Infantile hemangioma


title: Pool 2 (No. 1-4) Mouse Blood N=4 [7449 1-1]

description:
7449 1-1
Blood Pool 2-Control (Cy3) x Treatment FR (Cy5)
Dye-swap (Cy3/Cy5) of Control vs 50% FR Treatment Blood Pool 2

source_name: Blood Pool2 Control Cy3

source_name: Blood Pool2 50% FR Treatment Cy5


title: Pool 3 (No. 5-8) Mouse Blood N=4 [7449 1-4]

description:
7449 1-4
Blood Pool 3-Control (Cy5) x Treatment FR (Cy3)
Dye-swap (Cy5/Cy3) of Control vs 50% FR Treatment Blood Pool 3

source_name: Blood Pool3 50% FR Treatment Cy3

source_name: Blood Pool3 Control Cy5


title: CRC Patient 51

status: Public on Mar 02 2016

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: RMA-sketch normalization on the core probeset using Affymetrix Power Tools (APT) followed by batch correction using the ComBat algorithm.

source_name: primary colon adenocarcinoma

label_protocol: Approximately 3 ug of total RNA was processed to produce biotinylated sense DNA.

extract_protocol: Surgically isolated proximal colon cancer specimens were immediately frozen in liquid nitrogen. Total RNA was extracted from cancer tissue using the AllPrep DNA/RNA Micro Kit (Qiagen).

value: primary colon adenocarcinoma

tag: apc status

value: mut

tag: tumor stage

value: Tumor stage III

tag: rfs time in days

tag: rfs event

tag: analysis batch


title: CRC Patient 50

value: wt


title: CRC Patient 44


title: Pool 1 (No. 1-8) Mouse Blood N=8 [7215 1-1]

description:
7215 1-1
Blood Pool 1-Control (Cy3) x Treatment FR (Cy5)
Dye-swap (Cy3/Cy5) of Control vs 50% FR Treatment Blood Pool 1

source_name: Blood Pool1 Control Cy3

tag: age

source_name: Blood Pool1 50% FR Treatment Cy5


title: 2Cvs2N-Infantile Hemangioma-1

description: Biological replicate 1 of 3.Infantile hemangioma


title: CRC Patient 49


title: CRC Patient 48


title: CRC Patient 46

value: Tumor stage IV


title: CRC Patient 52


title: CRC Patient 42


title: CRC Patient 39


title: CRC Patient 43


title: CRC Patient 41


title: CRC Patient 40


title: CRC Patient 37


title: CRC Patient 36


title: JX-3

source_name: primary neonatal rat ventricular cardiomyocytes (NRVMs)

tag: cell type

value: control microRNA precursor


title: N065

city: Singapore

first: Sanjanaa

last: Nagarajan

state: Singapore

address: 11 Hospital Drive

department: Department of Medical Sciences

country: Singapore

institute: National Cancer Centre Singapore

description:
Hybridized to SNP6 array
raw B-allele frequency value; 'LRR' = normalized logR value; 'normalized_BAF' = normalized B-allele frequency (after TumorBoost); 'nA' = copy number of allele A; 'nB' = copy number of allele B (for the matche normal tissue only the raw BAF value is provided, as this is the only information necessary for processing the tumor using TumorBoost and ASCAT)

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The data in each tumor raw CEL file was normalized using CRMA-v2 and TumorBoost, and then analyzed with version 2 of the ASCAT algorithm which simultaneously models the aberrant cell fraction, regions of copy number changes and allele counts. The matched normal CEL file is used as a reference in this processing. For each heterozygous position found in the normal tissue, the minor allele frequency (BAF) and the log of the ratio of the total signal intensity in the tumor and matched non-tumor sample (Log R) were calculated for the tumor tissue. ASCAT determined the aberrant cell fraction and mean genomic ploidy that best fits these points.

source_name: Type II Enteropathy-associated T-cell lymphoma Sample N065

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA from snap frozen patient specimens and whole blood was extracted using Blood & Cell Culture DNA Kit (Qiagen)

tag: tissue type

value: Matched whole blood

tag: disease state


title: T066

source_name: Type II Enteropathy-associated T-cell lymphoma Sample T066

value: Tumor tissue


title: CRC Patient 38


title: CRC Patient 47


title: T065

source_name: Type II Enteropathy-associated T-cell lymphoma Sample T065


title: N063

source_name: Type II Enteropathy-associated T-cell lymphoma Sample N063


title: JX-5


title: CRC Patient 32


title: T063

source_name: Type II Enteropathy-associated T-cell lymphoma Sample T063


title: CRC Patient 26


title: CRC Patient 25


title: CRC Patient 33


title: N013

source_name: Type II Enteropathy-associated T-cell lymphoma Sample N013


title: CRC Patient 34


title: CRC Patient 27


title: CRC Patient 35


title: CRC Patient 28


title: N066

source_name: Type II Enteropathy-associated T-cell lymphoma Sample N066


title: CRC Patient 16


title: CRC Patient 20


title: CRC Patient 19


title: CRC Patient 21


title: CRC Patient 18


title: CRC Patient 30


title: CRC Patient 14


title: CRC Patient 23


title: CRC Patient 31


title: CRC Patient 22


title: CRC Patient 17


title: CRC Patient 15


title: CRC Patient 12


title: CRC Patient 11


title: T013

source_name: Type II Enteropathy-associated T-cell lymphoma Sample T013


title: CRC Patient 13


title: CRC Patient 6


title: CRC Patient 8


title: CRC Patient 10


title: CRC Patient 3


title: CRC Patient 9


title: CRC Patient 5


title: CRC Patient 2


title: CRC Patient 7


title: CRC Patient 4


title: 2458-HX-P0M1-P1M1-P2M5-P3M1

city: Cambridge

first: Joshua

middle: M

last: Korn

state: MA

address: 250 Mass Ave

institute: Novartis

description: PDX tumor at ~400mm3

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: GCRMA

source_name: PDX

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: All tumors were grown in nude mice

extract_protocol: RNA was extracted with RNeasy extraction kits (Qiagen) with on-column DNA digestion

treatment_protocol: No treatment

tag: model number

tag: passage

tag: primary site

value: ovary


title: CRC Patient 1


title: 3029-HX-P0M1-P1M1

description: PDX tumor at ~400mm3

value: lung


title: 3783-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 2219-HX-P0M2-P1M2-P2M1

description: PDX tumor at ~400mm3

value: pancreas


title: 2459-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3671-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 1298-HX-P0M1-P1M1-P2M1-P3M2-P4M2-P5M1

description: PDX tumor at ~400mm3

value: breast


title: 2458-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2208-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2511-HX-P0M1-P1M1-P2M8-P3M4-P4M1-P5M1

description: PDX tumor at ~400mm3


title: 3629-HX-P0M1-P1M1

description: PDX tumor at ~400mm3

value: kidney


title: 2283-HX-P0M1-P1M2-P2M1-P3M2-P4M3-P5M1

description: PDX tumor at ~400mm3


title: 2042-HX-P0M1-P1M3-P2M1-P3M4

description: PDX tumor at ~400mm3


title: 2459-HX-P0M1-P1M1-P2M5

description: PDX tumor at ~400mm3


title: 2655-HX-P0M2-P1M2-P2M5

description: PDX tumor at ~400mm3


title: 3286-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 2219-HX-P0M1-P1M2-P2M1-P3M1

description: PDX tumor at ~400mm3


title: CRC Patient 45


title: 3450-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1172-HX-P0M1-P1M3

description: PDX tumor at ~400mm3


title: CRC Patient 29


title: 931-HX-P0M1-P1M1-P2M1-P3M2-P4M2

description: PDX tumor at ~400mm3


title: 2514-HX-P0M2-P1M1-P2M7-P3M2-P4M1-P5M1

description: PDX tumor at ~400mm3


title: 3216-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2793-HX-P0M1-P1M2-P2M1-P2M1-P3M1

description: PDX tumor at ~400mm3

value: endometrium


title: 2461-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3

value: stomach


title: 2026-HX-P0M2-P1M3-P2M3-P3M4

description: PDX tumor at ~400mm3


title: 3615-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3570-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1492-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 3661-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 988-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 2793-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 3202-HX-P0M1-P1M1-P2M5

description: PDX tumor at ~400mm3


title: 3816-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3298-HX-P0M1-P1M3

description: PDX tumor at ~400mm3


title: 2461-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3729-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1317-HX-P0M3

description: PDX tumor at ~400mm3


title: 1443-HX-P0M2-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3202-HX-P0M1-P1M1-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 1027-HX-P0M2-P1M1-P2M4

description: PDX tumor at ~400mm3


title: 931-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 2483-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 2145-HX-P0M1-P1M3

description: PDX tumor at ~400mm3


title: 1362-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2487-HX-P0M1

description: PDX tumor at ~400mm3


title: 2524-HX-P0M1

description: PDX tumor at ~400mm3


title: 2306-HX-P0M1-P1M2

description: PDX tumor at ~400mm3

value: skin


title: 1963-HX-P0M1-P1M4-P2M1

description: PDX tumor at ~400mm3


title: 1318-HX-P0M1-P1M1-P2M4

description: PDX tumor at ~400mm3


title: 931-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2430-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3

value: oesophagus


title: 1867-HX-P0M1

description: PDX tumor at ~400mm3


title: 2633-HX-P0M1

description: PDX tumor at ~400mm3


title: 1027-HX-P0M4-P1M2

description: PDX tumor at ~400mm3


title: 1867-HX-P0M1-P1M2-P2M1

description: PDX tumor at ~400mm3


title: 2306-HX-P0M1-P1M2-P2M1

description: PDX tumor at ~400mm3


title: 2220-HX-P0M1-P1M4-P2M4

description: PDX tumor at ~400mm3


title: 1329-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1228-HX-P0M1

description: PDX tumor at ~400mm3


title: 3736-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 3439-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1228-HX-P0M2

description: PDX tumor at ~400mm3


title: 3041-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 2403-HX-P0M2-P1M1-P2M5

description: PDX tumor at ~400mm3


title: 2347-HX-P0M1-P1M2-P2M2

description: PDX tumor at ~400mm3


title: 988-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3486-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3877-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1309-HX-P0M1

description: PDX tumor at ~400mm3


title: 3773-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 3083-HX-P0M1-P1M5-P2M1-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 3949-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3766-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 3687-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3843-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3425-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3200-HX-P0M1-P1M4-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3408-HX-P0M1-P1M1-P2M1-P3M2

description: PDX tumor at ~400mm3


title: 1948-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3846-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2470-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3684-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 4426-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1538-HX-P0M2-P1M3-P2M1

description: PDX tumor at ~400mm3


title: 4267-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3870-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 3042-HX-P0M1-P1M4-P2M5-P3M1-P4M1-P5M1

description: PDX tumor at ~400mm3


title: 3949-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 4163-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3252-HX-P0M1-P1M1-P2M1-P3M2

description: PDX tumor at ~400mm3

value: bone


title: 2602-HX-P0M1-P1M1-P2M5

description: PDX tumor at ~400mm3


title: 2992-HX-P0M2-P1M4-P2M1

description: PDX tumor at ~400mm3


title: 2263-HX-P0M1-P1M4-P2M3

description: PDX tumor at ~400mm3


title: 2148-HX-P0M1-P1M4-P2M4-P3M4

description: PDX tumor at ~400mm3


title: 2092-HX-P0M1-P1M4-P2M2

description: PDX tumor at ~400mm3


title: 3926-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 4074-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3801-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3189-HX-P0M1-P1M1-P2M1-P3M3-P4M1-P5M1

description: PDX tumor at ~400mm3


title: 2700-HX-P0M1-P1M1-P2M1-P3M3-P4M1-P5M1

description: PDX tumor at ~400mm3


title: 2921-HX-P0M2-P1M2-P2M8-P3M4-P4M1-P5M1

description: PDX tumor at ~400mm3


title: 2659-HX-P0M1-P1M4-P2M8-P3M3

description: PDX tumor at ~400mm3


title: 3136-HX-P0M1-P1M4-P2M2-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 988-HX-P0M3-P1M1

description: PDX tumor at ~400mm3


title: 2129-HX-P0M1-P1M2-P2M1

description: PDX tumor at ~400mm3


title: 3114-HX-P0M1-P1M4-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2357-HX-P0M1-P1M2-P2M7-P3M1

description: PDX tumor at ~400mm3


title: 3237-HX-P0M1-P1M2-P2M4-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 4157-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2822-HX-P0M1-P1M1-P2M7-P3M1

description: PDX tumor at ~400mm3


title: 2861-HX-P0M1-P1M1-P2M1-P3M4-P4M1

description: PDX tumor at ~400mm3


title: 4304-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 4455-HX-P0M1-P1M4-P2M2

description: PDX tumor at ~400mm3


title: 3093-HX-P0M1-P1M1-P2M1-P3M2-P4M1-P5M1

description: PDX tumor at ~400mm3


title: 4476-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2781-HX-P0M1-P1M3-P2M6-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2483-HX-P0M3-P1M2-P2M3-P3M4-P4M1

description: PDX tumor at ~400mm3


title: 3972-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 4537-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2655-HX-P0M2-P1M2-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 4538-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 4484-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 4226-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2129-HX-P0M1-P1M2-P2M2-P3M1

description: PDX tumor at ~400mm3


title: 4530-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 4538-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 4173-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 4668-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1828-HX-P0M1

description: PDX tumor at ~400mm3


title: 1947-HX-P0M1

description: PDX tumor at ~400mm3


title: 2803-HX-P0M2-P1M1-P2M8-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3990-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 4361-HX-P0M1-P1M4

description: PDX tumor at ~400mm3


title: 2043-HX-P0M1

description: PDX tumor at ~400mm3


title: 2088-HX-P0M1

description: PDX tumor at ~400mm3


title: 4360-HX-P0M1-P1M3

description: PDX tumor at ~400mm3


title: 2043-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3237-HX-P0M1-P1M2-P2M4

description: PDX tumor at ~400mm3


title: 3114-HX-P0M1-P1M4-P2M1

description: PDX tumor at ~400mm3


title: 2163-HX-P0M1

description: PDX tumor at ~400mm3


title: 2030-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 4832-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2145-HX-P0M1

description: PDX tumor at ~400mm3


title: 1784-HX-P0M1

description: PDX tumor at ~400mm3


title: 2088-HX-P0M1-P1M4

description: PDX tumor at ~400mm3


title: 4455-HX-P0M1-P1M4

description: PDX tumor at ~400mm3


title: 2781-HX-P0M1-P1M3-P2M6

description: PDX tumor at ~400mm3


title: 2353-HX-P0M1-P1M2-P2M3-P3M3-P4M1-P5M1, 2

description: PDX tumor at ~400mm3


title: 3093-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 2527-HX-P0M1-P1M2-P2M3

description: PDX tumor at ~400mm3


title: 2129-HX-P0M1

description: PDX tumor at ~400mm3


title: 3020-HX-P0M1-P1M4-P2M1

description: PDX tumor at ~400mm3


title: 3189-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 2199-HX-P0M1

description: PDX tumor at ~400mm3


title: 2336-HX-P0M1-P1M2-P2M1

description: PDX tumor at ~400mm3


title: 2700-HX-P0M1-P1M1-P2M1-P3M3

description: PDX tumor at ~400mm3


title: 3042-HX-P0M1-P1M4-P2M5

description: PDX tumor at ~400mm3


title: 2094-HX-P0M1

description: PDX tumor at ~400mm3


title: 3201-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1835-HX-P0M1-P1M2-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3038-HX-P0M1-P1M1-P2M5

description: PDX tumor at ~400mm3


title: 1323-HX-P0M2-P1M2

description: PDX tumor at ~400mm3


title: 2238-HX-P0M2-P1M2

description: PDX tumor at ~400mm3


title: 3829-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3127-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2081-HX-P0M2-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 2376-HX-P0M2-P1M2-P2M1-P3M2

description: PDX tumor at ~400mm3


title: 1189-HX-P0M1-P1M1-P2M2

description: PDX tumor at ~400mm3


title: 1167-HX-P0M3

description: PDX tumor at ~400mm3


title: 1159-HX-P0M3

description: PDX tumor at ~400mm3


title: 3116-HX-P0M2-P1M4-P2M5

description: PDX tumor at ~400mm3


title: 3102-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 3982-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3543-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3676-HX-P0M1-P1M1-P2M5-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 4032-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1963-HX-P0M1-P1M4-P2M1-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 4015-HX-P0M2-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 1189-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 1309-HX-P0M2

description: PDX tumor at ~400mm3


title: 2300-HX-P0M1

description: PDX tumor at ~400mm3


title: 4018-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1538-HX-P0M1

description: PDX tumor at ~400mm3


title: 1480-HX-P0M1

description: PDX tumor at ~400mm3


title: 4087-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 4138-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 4412-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1402-HX-P0M1

description: PDX tumor at ~400mm3


title: 4316-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1402-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2096-HX-P0M1-P1M1-P2M2

description: PDX tumor at ~400mm3


title: 1403-HX-P0M2

description: PDX tumor at ~400mm3


title: 2081-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2046-HX-P0M1

description: PDX tumor at ~400mm3


title: 2046-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2127-HX-P0M2-P1M2-P2M1-P3M1-P4M2

description: PDX tumor at ~400mm3


title: 1865-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1725-HX-P0M1-P1M1-P2M2-P3M1-P4M3

description: PDX tumor at ~400mm3


title: 4279-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1095-HX-P0M1

description: PDX tumor at ~400mm3


title: 1865-HX-P0M1

description: PDX tumor at ~400mm3


title: 1327-HX-P0M1

description: PDX tumor at ~400mm3


title: 2017-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1683-HX-P0M1

description: PDX tumor at ~400mm3


title: 1993-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1004-HX-P0M2-P1M1-P2M1-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 1586-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 2017-HX-P0M1

description: PDX tumor at ~400mm3


title: 2182-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2127-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 3682-HX-P0M2-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 1318-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3662-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1451-HX-P0M4-P1M1-P2M2-P3M1-P4M2

description: PDX tumor at ~400mm3


title: 2127-HX-P0M1

description: PDX tumor at ~400mm3


title: 3682-HX-P0M2-P1M1-P2M1-P3M2

description: PDX tumor at ~400mm3


title: 3740-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1403-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 1536-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 3904-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3939-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2096-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 4213-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3800-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1963-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1441-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 1536-HX-P0M1

description: PDX tumor at ~400mm3


title: 1493-HX-P0M1

description: PDX tumor at ~400mm3


title: 2081-HX-P0M1

description: PDX tumor at ~400mm3


title: 1500-HX-P0M2

description: PDX tumor at ~400mm3


title: 1479-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 1726-HX-P0M2-P1M2-P2M4-P3M4-P4M1

description: PDX tumor at ~400mm3


title: 1493-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3196-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1500-HX-P0M2-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 3050-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1317-HX-P0M1-P1M3-P2M1-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 2527-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1480-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2991-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 2094-HX-P0M1-P1M1-P2M1-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 3224-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2633-HX-P0M1-P1M3-P2M7-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1658-HX-P0M2

description: PDX tumor at ~400mm3


title: 1004-HX-P0M2

description: PDX tumor at ~400mm3


title: 1746-HX-P0M1

description: PDX tumor at ~400mm3

value: liver


title: 1644-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 1725-HX-P0M1

description: PDX tumor at ~400mm3


title: 1008-HX-P0M1-P1M2-P2M3-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3252-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2082-HX-P0M1-P1M4-P2M3-P3M2

description: PDX tumor at ~400mm3


title: 3217-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1633-HX-P0M1-P1M2-P2M4-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 1433-HX-P0M1-P1M1-P2M3-P3M1

description: PDX tumor at ~400mm3


title: 2613-HX-P0M1-P1M3-P2M4-P3M3

description: PDX tumor at ~400mm3


title: 2838-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 2116-HX-P0M1-P1M2-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 2895-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 2920-HX-P0M2-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 2613-HX-P0M1-P1M3-P2M4

description: PDX tumor at ~400mm3


title: 1644-HX-P0M1

description: PDX tumor at ~400mm3


title: 2915-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 2572-HX-P0M3-P1M4

description: PDX tumor at ~400mm3


title: 1468-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 2715-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2564-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1407-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1655-HX-P0M1

description: PDX tumor at ~400mm3


title: 1349-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1832-HX-P0M1-P1M1-P2M2-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2339-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1370-HX-P0M1-P1M4

description: PDX tumor at ~400mm3


title: 1433-HX-P0M1

description: PDX tumor at ~400mm3


title: 2471-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2484-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 1786-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1832-HX-P0M1

description: PDX tumor at ~400mm3


title: 1451-HX-P0M1

description: PDX tumor at ~400mm3


title: 1367-HX-P0M1-P1M3

description: PDX tumor at ~400mm3


title: 1371-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1356-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 2163-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3