title: liver cancer HC44

description: miRNA profiling


title: MI-AML040N

status: Public on Mar 01 2015

type: genomic

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

country: USA

institute: University of Michigan

hyb_protocol: Affymetrix Hybridization Oven 640 for 16 hrs at 50 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing:
The DNA was prepared for hybridization to SNP 6.0 arrays according to the manufacturer’s recommendations. Affymetrix CEL files for each blast and buccal sample were analyzed using Genotyping Console software for initial quality control, followed by use of the Affymetrix “Birdseed” algorithm to generate tab-delimited SNP call files in text format. Call rates for the entire group of samples included in this report were between 93.64% and 99.45%, with a mean call rate of 98.17%; none of the tumor DNA samples gave out-of-bounds results.
Sample copy number heatmap displays were obtained from CEL files through use of the freely available software dChip, adapted to run on a 64-bit computer environment. To generate functional and practical displays of LOH, a two-step, internally developed, Java-based software analysis system was employed.  The Pre-LOH Unification Tool (PLUT) served to align all individual patient SNP calls to their respective dbSNP rs ID numbers and genomic physical positions prior to incorporation into the LOH tool version 2, an updated version of the LOH tool able to accommodate Affy SNP 6.0 array data
[primary data description] dChip SNP software (www.dchip.org), build date Feb 25, 2009, compatible with 64-bit OS, analyzed the CEL files.  CEL files were normalized using the invariant set method, followed by model-based expression index calculations, and finally inferred copy number data were generated using a median-smoothing algorithm.  See supplementary file linked to Series record.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: primary human: buccal

label_protocol: The DNA was prepared for hybridization to Affymetrix SNP 6.0 arrays according to the manufacturer's recommendations.

extract_protocol:
[purification protocol] AML blast DNA used for SNP 6.0 profiling was extracted from negatively column enriched AML cell samples as described that were further purified as follows:  post-Miltenyi column samples were washed and stained with FITC-conjugated anti-CD33, PE-conjugated anti-CD13, and APC-conjugated anti-CD45 (all antibodies: eBioscience, San Diego, CA).  After final washing, propidium iodide (PI) was added to a concentration of 1 μg/ml to discriminate dead cells.  Sorting of cells was done on a FACS-ARIA high-speed flow cytometer (Becton Dickinson, Mountain View, CA).  Live cells (PI-negative) were gated for blasts by identifying those cells with intermediate-intensity staining for CD45 and low- to moderate-intensity side scatter. CD33 and CD13 were then used in order to further discriminate myeloid blasts versus contaminating erythroid lineage or other non-myeloid cells.  Cells forming a dense population cloud on the CD33 versus CD13 plots that were either single marker positive or double positive were sorted.  Aliquots of final cell preparations were made for the majority of sorted samples and manually analyzed for cell composition using cytospins and blast counts.
Highly pure blast cells or buccal swabs were digested overnight in 100 mM Tris pH 8.0, 50 mM EDTA, 50 mM NaCl, 0.5% SDS and 100 μg/ml of Proteinase K (Invitrogen) at 560C. DNA was extracted using phenol-chloroform and precipitated using ammonium acetate, ethanol and glycogen.

tag: disease state

value: non-FAB-M3 AML

tag: individual

tag: paired sample

value: normal

tag: cell type

value: buccal cells


title: liver cancer HC37

type: RNA

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

country: Japan

institute: Toray Industries, Inc.

description: miRNA profiling

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: Mean and standard deviation (SD) of the 5% trimmed signals of the negative controls were calculated. Signals of miRNAs over mean+2SD of the negative controls were subtracted with the mean of the negative controls. The undetected signal was replaced with the value that was the least signal intensity on each DNA chip minus 0.1 in log2 scale followed by quantile normalization.

molecule: total RNA

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.). Total RNA was also obtained from the FFPE sections using the Arcturus® Paradise® Extraction and Isolation kit (Life Technologies) in accordance with the manufacturer's instructions.

value: liver cancer

tag: tissue

value: serum

tag: gender

value: Female

tag: tumor stage

value: uncertain

tag: age

tag: operability


title: liver cancer HC36

description: miRNA profiling

value: Male


title: liver cancer HC35

description: miRNA profiling


title: MI-AML036T

source_name: primary human: blood or bone marrow, FACS sort-purified AML blasts

value: tumor

value: FACS sort-purified AML blasts


title: liver cancer HC38

description: miRNA profiling


title: MI-AML035N


title: MI-AML035T


title: MI-AML041N


title: liver cancer HC34

description: miRNA profiling


title: liver cancer HC33

description: miRNA profiling


title: MI-AML033T


title: liver cancer HC32

description: miRNA profiling


title: liver cancer HC31

description: miRNA profiling


title: liver cancer HC27

description: miRNA profiling


title: MI-AML033N


title: liver cancer HC30

description: miRNA profiling


title: liver cancer HC29

description: miRNA profiling


title: liver cancer HC26

description: miRNA profiling


title: liver cancer HC28

description: miRNA profiling


title: liver cancer HC24

description: miRNA profiling


title: liver cancer HC23

description: miRNA profiling


title: MI-AML036N


title: liver cancer HC22

description: miRNA profiling


title: MI-AML032T


title: MI-AML032N


title: liver cancer HC20

description: miRNA profiling


title: MI-AML030T_AML_from_MDS


title: liver cancer HC19

description: miRNA profiling


title: liver cancer HC18

description: miRNA profiling


title: liver cancer HC17

description: miRNA profiling


title: liver cancer HC15

description: miRNA profiling


title: liver cancer HC25

description: miRNA profiling


title: liver cancer HC14

description: miRNA profiling


title: liver cancer HC13

description: miRNA profiling


title: liver cancer HC21

description: miRNA profiling


title: liver cancer HC12

description: miRNA profiling


title: MI-AML026N_BU


title: liver cancer HC11

description: miRNA profiling


title: MI-AML025T_AML_from_MDS


title: liver cancer HC16

description: miRNA profiling


title: MI-AML016T_AML_from_MDS


title: MI-AML030N


title: MI-AML014T


title: MI-AML016N_BU


title: liver cancer HC10

description: miRNA profiling


title: liver cancer HC09

description: miRNA profiling


title: liver cancer HC08

description: miRNA profiling


title: MI-AML014N


title: liver cancer HC06

description: miRNA profiling


title: liver cancer HC07

description: miRNA profiling


title: MI-AML026T_AML_from_MDS


title: liver cancer HC02

description: miRNA profiling


title: liver cancer HC03

description: miRNA profiling


title: liver cancer HC05

description: miRNA profiling


title: liver cancer HC04

description: miRNA profiling


title: liver cancer HC01

description: miRNA profiling


title: esophagus cancer EC50

description: miRNA profiling

value: esophagus cancer


title: benign pancreatic or biliary tract diseases I08

description: miRNA profiling


title: MI-AML013T


title: esophagus cancer EC48

description: miRNA profiling


title: MI-AML025N_BU


title: MI-AML013N_BU


title: esophagus cancer EC49

description: miRNA profiling


title: esophagus cancer EC47

description: miRNA profiling


title: MI-AML012T


title: esophagus cancer EC43

description: miRNA profiling


title: esophagus cancer EC45

description: miRNA profiling


title: esophagus cancer EC44

description: miRNA profiling


title: esophagus cancer EC46

description: miRNA profiling


title: MI-AML012N


title: esophagus cancer EC42

description: miRNA profiling


title: esophagus cancer EC41

description: miRNA profiling


title: MI-AML009N


title: MI-AML009T


title: MI-AML006T


title: esophagus cancer EC34

description: miRNA profiling


title: MI-AML006N


title: esophagus cancer EC40

description: miRNA profiling


title: esophagus cancer EC33

description: miRNA profiling


title: esophagus cancer EC35

description: miRNA profiling


title: esophagus cancer EC38

description: miRNA profiling


title: esophagus cancer EC36

description: miRNA profiling


title: esophagus cancer EC39

description: miRNA profiling


title: esophagus cancer EC32

description: miRNA profiling


title: esophagus cancer EC31

description: miRNA profiling


title: esophagus cancer EC26

description: miRNA profiling


title: esophagus cancer EC37

description: miRNA profiling


title: esophagus cancer EC25

description: miRNA profiling


title: esophagus cancer EC24

description: miRNA profiling


title: esophagus cancer EC28

description: miRNA profiling


title: esophagus cancer EC29

description: miRNA profiling


title: esophagus cancer EC30

description: miRNA profiling


title: esophagus cancer EC22

description: miRNA profiling


title: esophagus cancer EC27

description: miRNA profiling


title: esophagus cancer EC23

description: miRNA profiling


title: esophagus cancer EC21

description: miRNA profiling


title: esophagus cancer EC19

description: miRNA profiling


title: esophagus cancer EC16

description: miRNA profiling


title: esophagus cancer EC20

description: miRNA profiling


title: esophagus cancer EC18

description: miRNA profiling


title: esophagus cancer EC17

description: miRNA profiling


title: esophagus cancer EC15

description: miRNA profiling


title: esophagus cancer EC14

description: miRNA profiling


title: benign pancreatic or biliary tract diseases I06

description: miRNA profiling


title: esophagus cancer EC13

description: miRNA profiling


title: esophagus cancer EC12

description: miRNA profiling


title: esophagus cancer EC11

description: miRNA profiling


title: 4 day differentiated R1 ESCs KD1- biological replicate 4

city: Jerusalem

first: Eran

last: Meshorer

address: Edmond J. Safra Campus

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: Gene expression data from 4 day RA differentiated Smarcd1 knockdown R1 ESCs

hyb_protocol: According to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3000 7G with Autoloader according to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

data_processing: Data processing was performed in GeneExpressionConsole using Robust Multichip Analysis (RMA) probe summarization algorithm. Data was further processed and statistics were generated using R program. Non-expressing genes were filtered out on a pre-determined set point. Differential expression analysis was performed by carrying out a t-test for differences between the average signal values for each gene.

organism: Mus musculus

source_name: 4 day differentiated R1 ESCs with Smarcd1 knockdown

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (based on Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were grown in regular ESC medium with 15% FBS on MEFs treated with mitomycin.

extract_protocol: R1 ESCs were grown on MEFs treated with mitomycin in regular DMEM medium containing 10% ES-grade fetal bovine serum (FBS), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1x Penicillin/ Streptomycin antibiotics, and 1000 U/ml leukemia inhibitory factor (LIF). Differentiation was induced by growing cells in ESC medium with 10% FBS, without LIF and in the presence of RA (1 µM).

treatment_protocol: Smarcd1 knockdown and control clones were grown in regular ESC medium. For differentiaiton 1 µM retenoic acid was used.

value: 4 day RA differentiated R1 ESC


title: 4 day differentiated R1 ESCs KD1- biological replicate 2


title: esophagus cancer EC09

description: miRNA profiling


title: esophagus cancer EC10

description: miRNA profiling


title: 4 day differentiated R1 ESCs KD1- biological replicate 3


title: esophagus cancer EC08

description: miRNA profiling


title: esophagus cancer EC07

description: miRNA profiling


title: 4 day differentiated R1 ESCs Scrambled biological replicate 2

description: Gene expression data from 4 day RA differentiated Scrambled-control R1 ESCs

source_name: 4 day differentiated R1 ESCs (with Scrambled control infection)


title: esophagus cancer EC06

description: miRNA profiling


title: esophagus cancer EC05

description: miRNA profiling


title: 4 day differentiated R1 ESCs KD1- biological replicate 1


title: esophagus cancer EC04

description: miRNA profiling


title: KD2- biological replicate 2

description: Gene expression data from R1 ESCs after Smarcd1 knockdown.

source_name: R1 ESCs with Smarcd1 knockdown

value: R1 ESC


title: KD2- biological replicate 1


title: 4 day differentiated R1 ESCs Scrambled biological replicate 1


title: KD1- biological replicate 2


title: esophagus cancer EC02

description: miRNA profiling


title: esophagus cancer EC03

description: miRNA profiling


title: esophagus cancer EC01

description: miRNA profiling


title: stomach cancer SC50

description: miRNA profiling

value: stomach cancer


title: KD1- biological replicate 1


title: stomach cancer SC48

description: miRNA profiling


title: Scrambled biological replicate 2

description: Gene expression data from scrambled-control R1 ESCs

source_name: R1 ESCs (with Scrambled control infection)


title: stomach cancer SC47

description: miRNA profiling


title: Scrambled biological replicate 1


title: stomach cancer SC46

description: miRNA profiling


title: stomach cancer SC45

description: miRNA profiling


title: stomach cancer SC44

description: miRNA profiling


title: stomach cancer SC43

description: miRNA profiling


title: Control # 3

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

hyb_protocol: The labelled samples were hybridized to the Mouse Gene 1.0 ST GeneChip array (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained with phycoerytrin-conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450

scan_protocol: The arrays were scanned in the Affymetrix GeneArray® 3000 scanner

data_processing: Arrays were normalized using standard RMA background correction and quantile normalization using the 'affy' package from bioconductor in R version 2.15. Significance of singular genes was assessed using an ANOVA approach across the different groups, and adjusted for multiple testing by estimating false discovery rates (FDR).

label: Biotin

source_name: Non-induced control

label_protocol: Labelled using the Pico amplification kit (Nugen, San Carlos, USA), according to the manufacturers´ instructions

extract_protocol: mirVanaTM miRNA isolation kit (Ambion, Denmark) according to the manufacturers´ instructions

treatment_protocol: Arthritis was induced in male DBA/1JBom mice by intradermal injection of 100 µl chicken collagen type II (CII) (2mg/ml) (Sigma) in Complete Freunds Adjuvans (CFA) (0,5mg/ml) (Sigma) on day 1 and boosted on day 21 with CII in Incomplete Freunds Adjuvans (IFA)(Sigma). The control group was not induced.

tag: strain

value: Whole tarsal joint


title: stomach cancer SC42

description: miRNA profiling


title: Control # 1


title: stomach cancer SC49

description: miRNA profiling


title: stomach cancer SC41

description: miRNA profiling


title: stomach cancer SC39

description: miRNA profiling


title: stomach cancer SC38

description: miRNA profiling


title: Animal # 21

source_name: Tarsal joint with clinical declining arthritis score (clinical arthritis score 3 persisting for >2 weeks)


title: Control # 2


title: stomach cancer SC36

description: miRNA profiling


title: stomach cancer SC40

description: miRNA profiling


title: stomach cancer SC34

description: miRNA profiling


title: Animal # 10


title: stomach cancer SC37

description: miRNA profiling


title: stomach cancer SC35

description: miRNA profiling


title: stomach cancer SC32

description: miRNA profiling


title: Animal # 60

source_name: Tarsal joint with clinical score 3 arthritis in 3-4 weeks


title: IC131N

city: Melbourne

first: Sally

last: Hunter

state: VIC

address: 7 St Andrew's Pl

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

description: HYBRIDISED TO SNP181

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: CHP files were generated using the Affymetrix Genotyping Console algorithm Birdseed v2. Total and allele-specific copy number analysis was performed using Partek Genomics Suite 6.5, using both paired copy number generation.

label: BIOTIN

source_name: Serous ovarian tumor

label_protocol: As per manufacturer's recommendations (Affymetrix)

extract_protocol: Genomic DNA was extracted from tissues (epithelium and stroma) microdissected mucinous ovarian tumours stained with haematoxylin and eosin, and from lymphcoytes obtained from peripheral blood (for matched normal DNA)  using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Qubit.

value: Peripheral Blood Lymphocytes

tag: tumour histology

value: SEROUS

tag: diagnosis

value: HIGH GRADE CARCINOMA

tag: somatic ras/raf mutations

value: WT

tag: age at diagnosis

value: Unknown


title: stomach cancer SC31

description: miRNA profiling


title: P1805N

description: HYBRIDISED TO SNP181


title: IC131T

description: HYBRIDISED TO SNP181

value: Tumor epithelium


title: stomach cancer SC33

description: miRNA profiling

value: serum


title: VOA818T

description: HYBRIDISED TO SNP6


title: Animal # 15


title: Animal # 29


title: Animal # 54


title: P1805T

description: HYBRIDISED TO SNP181


title: stomach cancer SC27

description: miRNA profiling


title: VOA617T

description: HYBRIDISED TO SNP6

value: LOW GRADE CARCINOMA

value: BRAF p.V600E


title: VOA324T

description: HYBRIDISED TO SNP6


title: stomach cancer SC26

description: miRNA profiling

value: Male

value: uncertain


title: Animal # 52

source_name: Tarsal joint with clinical score 3 arthritis in 1-2 weeks


title: stomach cancer SC29

description: miRNA profiling

value: Female


title: VOA1841T

description: HYBRIDISED TO SNP6

value: KRAS p.G12V


title: VOA1133T

description: HYBRIDISED TO SNP6


title: VOA221T

description: HYBRIDISED TO SNP6


title: PHI679_07T

description: HYBRIDISED TO SNP6

value: NRAS p.Q61R


title: VOA875T

description: HYBRIDISED TO SNP6


title: VOA814T

description: HYBRIDISED TO SNP6

value: KRAS p.G12R


title: stomach cancer SC25

description: miRNA profiling

value: stomach cancer


title: stomach cancer SC30

description: miRNA profiling


title: stomach cancer SC24

description: miRNA profiling


title: stomach cancer SC28

description: miRNA profiling


title: VOA1177T

description: HYBRIDISED TO SNP6


title: Animal # 43

value: Whole tarsal joint


title: PHI33_07T

description: HYBRIDISED TO SNP6


title: stomach cancer SC23

description: miRNA profiling


title: VOA1802T

description: HYBRIDISED TO SNP6


title: Animal # 33


title: stomach cancer SC22

description: miRNA profiling


title: Animal # 57

description: excluded in analysis due to QC fail

source_name: Tarsal joint with clinical score 3 arthritis in 0-3 days


title: PHI629_07T

description: HYBRIDISED TO SNP6


title: VOA1056T

description: HYBRIDISED TO SNP6


title: VOA378T

description: HYBRIDISED TO SNP6


title: stomach cancer SC21

description: miRNA profiling


title: stomach cancer SC20

description: miRNA profiling


title: stomach cancer SC19

description: miRNA profiling


title: stomach cancer SC15

description: miRNA profiling


title: stomach cancer SC14

description: miRNA profiling


title: Animal # 16


title: stomach cancer SC17

description: miRNA profiling


title: stomach cancer SC16

description: miRNA profiling


title: stomach cancer SC13

description: miRNA profiling


title: liver_NEMOΔhepa_p21_KO, replicate2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 Fluidics Station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.28.2).

source_name: liver, hepatocyte-specific NEMO and global p21 double-knockout mouse

label_protocol: The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA; P/N 900671) was used for the preparation of labeled cDNA from 100ng of total RNA without rRNA reduction.

growth_protocol:
Hepatocyte-specific NEMO null (NEMOΔhepa) mice were generated as described before (Beraza et al., 2009, J Exp Med [PMID: 19635861]). From these NEMOΔhepa mice, by crossing them with constitutive p21-/- mice, NEMO/p21 double-knockout animals were generated.
Mice were kept on standard laboratory chow diet and had free access to water. Hepatic expression profiles of the three genotypes (wild type, and the two knockouts) was performed on male mice, that were all aged between 8-9 weeks.

extract_protocol: Total RNA was purified from liver tissue using Trizol reagent (Invitrogen, Karlsruhe, Germany) and purified using RNeasy microkit (Qiagen, Venlo, The Netherlands). RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

tag: strain/background

tag: genotype/variation

value: hepatocyte-specific NEMO -- global p21 double-knockout

tag: Sex

value: male

value: 8-9 wks

value: liver


title: stomach cancer SC11

description: miRNA profiling

tag: disease state


title: liver_NEMOΔhepa_p21_KO, replicate3


title: IC515T

description: HYBRIDISED TO SNP6

value: SEROUS

value: HIGH GRADE CARCINOMA

value: WT


title: stomach cancer SC12

description: miRNA profiling

value: serum


title: stomach cancer SC10

description: miRNA profiling


title: PHI155_07T

description: HYBRIDISED TO SNP6

value: Tumor epithelium


title: stomach cancer SC09

description: miRNA profiling

value: Male


title: IC586T

description: HYBRIDISED TO SNP6

value: LOW GRADE CARCINOMA

value: BRAF p.V600E


title: stomach cancer SC07

description: miRNA profiling

value: Female

value: uncertain


title: stomach cancer SC08

description: miRNA profiling


title: stomach cancer SC04

description: miRNA profiling


title: stomach cancer SC03

description: miRNA profiling


title: IC515G

description: HYBRIDISED TO SNP6

source_name: Lymphocyte DNA

value: Peripheral Blood Lymphocytes


title: stomach cancer SC05

description: miRNA profiling

value: stomach cancer


title: stomach cancer SC02

description: miRNA profiling


title: PHI629_07S

description: HYBRIDISED TO SNP6

value: Tumor stroma

value: Wild-type


title: liver_NEMOΔhepa, replicate2

source_name: liver, hepatocyte-specific NEMO knockout mouse

value: hepatocyte-specific NEMO knockout (NEMOΔhepa)

value: male


title: stomach cancer SC01

description: miRNA profiling


title: stomach cancer SC18

description: miRNA profiling


title: liver_NEMOΔhepa, replicate1

value: 8-9 wks

value: liver


title: Animal # 18

value: Whole tarsal joint


title: colon cancer CC50

description: miRNA profiling

value: colon cancer


title: liver_NEMOΔhepa, replicate3


title: colon cancer CC49

description: miRNA profiling

value: serum


title: stomach cancer SC06

description: miRNA profiling


title: liver_WT, replicate2

source_name: liver, wild type mouse (C57/BL6)

value: wild type


title: IC482T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: SEROUS


title: liver_WT, replicate1


title: liver_NEMOΔhepa_p21_KO, replicate1

value: hepatocyte-specific NEMO -- global p21 double-knockout


title: colon cancer CC47

description: miRNA profiling

value: Male


title: colon cancer CC48

description: miRNA profiling

value: Female

value: uncertain


title: liver_WT, replicate3


title: colon cancer CC45

description: miRNA profiling


title: colon cancer CC46

description: miRNA profiling


title: IC482G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes

value: LOW GRADE CARCINOMA


title: colon cancer CC44

description: miRNA profiling


title: TMem mix 18 hr - repeat 3 - mAdbID:126148

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 126148

hyb_protocol: Terminally labeled cDNA were hybridized to the Mouse Gene 1.0 ST array (Affymetrix) according to the manufacturers' instructions.

scan_protocol: Arrays were then scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Affymetrix RMA Data Processing
Calculation Method: Using Robust Multichip Average (RMA) normalization after background subtraction, the statistically significant gene expression changes were functionally analyzed using Partek Genomic Suite 6.6 (St. Louis, MO).

source_name: in vitro differentiated TMem, mix, 18h

label_protocol: cDNA were reverse trancribed, fragmented and labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was extracted using the QiaShredders and RNeasy Mini kits (QIAGEN) followed by whole transcriptome amplification using WT Expression kit (Life Technologies, Carlsbad, CA).

value: female

value: 6-12 weeks

value: Spleen

tag: developmental stage

value: adult

value: in vitro differentiated Pmel-1 CD8+ T(Mem)

tag: sample type

value: FACS-sorted in vitro differentiated TMem 18h after stimulation in the presence of TN using CD3-specific and CD28-specific antibodies and IL-2.

value: Ly5.2 Pmel-1 Tg


title: colon cancer CC42

description: miRNA profiling

source_name: Serum

value: colon cancer

value: serum


title: TN mix 18 hr - repeat 3 - mAdbID:126147

description: mAdb experiment ID: 126147

source_name: TN, mix, 18h

tag: cell type

value: Naive Pmel-1 CD8+ T(N)

value: FACS-sorted TN-derived Pmel-1 CD8+ T cells 18h in the presence of TMem using CD3-specific and CD28-specific antibodies and IL-2.

value: Ly5.1 Pmel-1 Tg


title: IC471G

description: HYBRIDISED TO SNP6

tag: tissue

value: SEROUS


title: IC471T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: WT


title: colon cancer CC41

description: miRNA profiling

tag: gender

value: Male

value: uncertain


title: colon cancer CC40

description: miRNA profiling

tag: tumor stage


title: colon cancer CC39

description: miRNA profiling

tag: age


title: TN mix 18 hr - repeat 1 - mAdbID:126145

description: mAdb experiment ID: 126145

value: female


title: TMem alone 18 hr - repeat 3 - mAdbID:126144

description: mAdb experiment ID: 126144

source_name: in vitro differentiated TMem, alone, 18h

value: 6-12 weeks

value: FACS-sorted in vitro differentiated TMem 18h after stimulation using CD3-specific and CD28-specific antibodies and IL-2.


title: TN mix 18 hr - repeat 2 - mAdbID:126146

description: mAdb experiment ID: 126146

value: Spleen

value: adult


title: colon cancer CC43

description: miRNA profiling

tag: operability


title: colon cancer CC38

description: miRNA profiling

value: Female


title: colon cancer CC37

description: miRNA profiling


title: TMem alone 18 hr - repeat 2 - mAdbID:126143

description: mAdb experiment ID: 126143

tag: strain

value: in vitro differentiated Pmel-1 CD8+ T(Mem)

value: Ly5.2 Pmel-1 Tg


title: colon cancer CC36

description: miRNA profiling

value: colon cancer

value: serum


title: colon cancer CC34

description: miRNA profiling


title: colon cancer CC35

description: miRNA profiling


title: colon cancer CC33

description: miRNA profiling


title: IC462G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes

tag: tumour histology

value: LOW GRADE CARCINOMA


title: colon cancer CC32

description: miRNA profiling


title: TMem alone 18 hr - repeat 1 - mAdbID:126142

description: mAdb experiment ID: 126142


title: IC462T

description: HYBRIDISED TO SNP6

value: SEROUS

tag: diagnosis

value: KRAS p.G12D


title: TN alone 18 hr - repeat 3 - mAdbID:126141

description: mAdb experiment ID: 126141

source_name: TN, alone, 18h

value: Naive Pmel-1 CD8+ T(N)

value: FACS-sorted TN-derived Pmel-1 CD8+ T cells 18h using CD3-specific and CD28-specific antibodies and IL-2.

value: Ly5.1 Pmel-1 Tg


title: IC558T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: BORDERLINE

tag: somatic ras/raf mutations

value: BRAF p.V600E


title: TMem alone 0 hr - repeat 3 - mAdbID:126138

description: mAdb experiment ID: 126138

source_name: in vitro differentiated TMem, alone, 0h

value: female

value: 6-12 weeks

value: Spleen

value: FACS-sorted in vitro differentiated TMem without stimulation.


title: IC558S

description: HYBRIDISED TO SNP6

value: Tumor stroma

value: Wild-type

tag: age at diagnosis


title: colon cancer CC30

description: miRNA profiling

value: colon cancer

value: serum

value: Male

value: uncertain


title: colon cancer CC29

description: miRNA profiling


title: TN alone 18 hr - repeat 2 - mAdbID:126140

description: mAdb experiment ID: 126140

value: adult


title: colon cancer CC27

description: miRNA profiling


title: TN alone 18 hr - repeat 1 - mAdbID:126139

description: mAdb experiment ID: 126139

value: Naive Pmel-1 CD8+ T(N)


title: colon cancer CC28

description: miRNA profiling


title: colon cancer CC26

description: miRNA profiling


title: colon cancer CC31

description: miRNA profiling


title: TMem alone 0 hr - repeat 2 - mAdbID:126137

description: mAdb experiment ID: 126137

value: in vitro differentiated Pmel-1 CD8+ T(Mem)

value: Ly5.2 Pmel-1 Tg


title: colon cancer CC25

description: miRNA profiling


title: IC558G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes

value: SEROUS


title: colon cancer CC23

description: miRNA profiling

value: Female


title: IC510T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: BORDERLINE

value: KRAS p.G12D


title: TMem alone 0 hr - repeat 1 - mAdbID:126136

description: mAdb experiment ID: 126136

value: female

value: 6-12 weeks

value: Spleen

value: FACS-sorted in vitro differentiated TMem without stimulation.


title: colon cancer CC24

description: miRNA profiling

value: colon cancer

value: serum


title: colon cancer CC22

description: miRNA profiling

value: Male

value: uncertain


title: TN alone 0 hr - repeat 3 - mAdbID:126135

description: mAdb experiment ID: 126135

source_name: TN, alone, 0h

value: adult

value: Naive Pmel-1 CD8+ T(N)

value: FACS-sorted naive Pmel-1 CD8+ T cells without stimulation.

value: Ly5.1 Pmel-1 Tg


title: IC510S

description: HYBRIDISED TO SNP6

value: Tumor stroma

value: SEROUS

value: Wild-type


title: colon cancer CC20

description: miRNA profiling


title: IC486T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: BORDERLINE

value: BRAF p.V600E


title: colon cancer CC21

description: miRNA profiling

value: Female


title: TN alone 0 hr - repeat 1 - mAdbID:126133

description: mAdb experiment ID: 126133

value: female

value: 6-12 weeks

value: Spleen


title: TN alone 0 hr - repeat 2 - mAdbID:126134

description: mAdb experiment ID: 126134


title: IC486S

description: HYBRIDISED TO SNP6


title: IC486G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes


title: colon cancer CC16

description: miRNA profiling

value: colon cancer

value: serum

value: Male


title: IC362T

description: HYBRIDISED TO SNP6

value: KRAS p.G12V


title: colon cancer CC15

description: miRNA profiling

value: uncertain


title: IC508G

description: HYBRIDISED TO SNP6


title: colon cancer CC18

description: miRNA profiling


title: TMem mix 96 hr - repeat 3 - mAdbID:126132

description: mAdb experiment ID: 126132

source_name: in vitro differentiated TMem, mix, 96h

value: adult

value: in vitro differentiated Pmel-1 CD8+ T(Mem)

value: FACS-sorted in vitro differentiated TMem 96h after stimulation in the presence of TN using CD3-specific and CD28-specific antibodies and IL-2.

value: Ly5.2 Pmel-1 Tg


title: colon cancer CC14

description: miRNA profiling


title: colon cancer CC13

description: miRNA profiling


title: TMem mix 96 hr - repeat 2 - mAdbID:126131

description: mAdb experiment ID: 126131


title: IC229S

description: HYBRIDISED TO SNP6

value: Tumor stroma

value: SEROUS

value: Wild-type


title: colon cancer CC17

description: miRNA profiling


title: IC508T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: BORDERLINE

value: KRAS p.G12D


title: IC508S

description: HYBRIDISED TO SNP6


title: colon cancer CC19

description: miRNA profiling


title: colon cancer CC11

description: miRNA profiling

value: Female


title: IC362G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes


title: colon cancer CC10

description: miRNA profiling

value: colon cancer


title: colon cancer CC09

description: miRNA profiling

value: serum


title: TMem mix 96 hr - repeat 1 - mAdbID:126130

description: mAdb experiment ID: 126130

value: female

value: 6-12 weeks

value: Spleen


title: TN mix 96 hr - repeat 3 - mAdbID:126129

description: mAdb experiment ID: 126129

source_name: TN, mix, 96h

value: adult

value: Naive Pmel-1 CD8+ T(N)

value: FACS-sorted TN-derived Pmel-1 CD8+ T cells 96h in the presence of TMem using CD3-specific and CD28-specific antibodies and IL-2.

value: Ly5.1 Pmel-1 Tg


title: colon cancer CC08

description: miRNA profiling

value: Male

value: uncertain


title: colon cancer CC07

description: miRNA profiling


title: colon cancer CC06

description: miRNA profiling


title: IC20T

description: HYBRIDISED TO SNP6

value: SEROUS

value: BRAF p.V600E


title: IC20G

description: HYBRIDISED TO SNP6

value: BORDERLINE


title: 9795T

description: HYBRIDISED TO SNP6

value: Tumor epithelium


title: colon cancer CC04

description: miRNA profiling


title: TN mix 96 hr - repeat 1 - mAdbID:126127

description: mAdb experiment ID: 126127


title: colon cancer CC05

description: miRNA profiling


title: colon cancer CC03

description: miRNA profiling

value: Female


title: TN mix 96 hr - repeat 2 - mAdbID:126128

description: mAdb experiment ID: 126128


title: colon cancer CC02

description: miRNA profiling


title: colon cancer CC12

description: miRNA profiling


title: TMem alone 96 hr - repeat 3 - mAdbID:126126

description: mAdb experiment ID: 126126

source_name: in vitro differentiated TMem, alone, 96h

value: in vitro differentiated Pmel-1 CD8+ T(Mem)

value: FACS-sorted in vitro differentiated TMem 96h after stimulation using CD3-specific and CD28-specific antibodies and IL-2.

value: Ly5.2 Pmel-1 Tg


title: TMem alone 96 hr - repeat 2 - mAdbID:126125

description: mAdb experiment ID: 126125

value: female


title: colon cancer CC01

description: miRNA profiling

value: colon cancer

value: serum


title: 9795G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes


title: healthy control S093

description: miRNA profiling

value: healthy control


title: IC229T

description: HYBRIDISED TO SNP6

source_name: Serous ovarian tumor

value: WT


title: healthy control S091

description: miRNA profiling


title: healthy control S092

description: miRNA profiling


title: healthy control S090

description: miRNA profiling


title: healthy control S089

description: miRNA profiling


title: TMem alone 96 hr - repeat 1 - mAdbID:126124

description: mAdb experiment ID: 126124

value: 6-12 weeks

value: Spleen

value: adult


title: TN alone 96 hr - repeat 2 - mAdbID:126122

description: mAdb experiment ID: 126122

source_name: TN, alone, 96h

value: Naive Pmel-1 CD8+ T(N)

value: FACS-sorted TN-derived Pmel-1 CD8+ T cells 96h using CD3-specific and CD28-specific antibodies and IL-2.

value: Ly5.1 Pmel-1 Tg


title: TN alone 96 hr - repeat 3 - mAdbID:126123

description: mAdb experiment ID: 126123


title: healthy control S088

description: miRNA profiling

value: Male

value: uncertain


title: healthy control S087

description: miRNA profiling


title: healthy control S085

description: miRNA profiling

value: Female


title: healthy control S086

description: miRNA profiling


title: healthy control S084

description: miRNA profiling


title: 9795S

description: HYBRIDISED TO SNP6

value: Tumor stroma

value: SEROUS

value: BORDERLINE

value: Wild-type


title: healthy control S083

description: miRNA profiling

value: serum


title: TMem mix 18 hr - repeat 1 - mAdbID:126119

description: mAdb experiment ID: 126119

value: female

value: in vitro differentiated Pmel-1 CD8+ T(Mem)

value: FACS-sorted in vitro differentiated TMem 18h after stimulation in the presence of TN using CD3-specific and CD28-specific antibodies and IL-2.

value: Ly5.2 Pmel-1 Tg


title: healthy control S082

description: miRNA profiling

value: healthy control


title: TMem mix 18 hr - repeat 2 - mAdbID:126120

description: mAdb experiment ID: 126120

value: 6-12 weeks

value: Spleen

value: adult


title: TN alone 96 hr - repeat 1 - mAdbID:126121

description: mAdb experiment ID: 126121

value: Naive Pmel-1 CD8+ T(N)

value: FACS-sorted TN-derived Pmel-1 CD8+ T cells 96h using CD3-specific and CD28-specific antibodies and IL-2.

value: Ly5.1 Pmel-1 Tg


title: 9663G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes


title: healthy control S081

description: miRNA profiling

value: Male

value: uncertain


title: healthy control S080

description: miRNA profiling


title: 9663T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: SEROUS

value: BORDERLINE

value: BRAF p.V600E


title: 9663S

description: HYBRIDISED TO SNP6

value: Tumor stroma

value: Wild-type


title: healthy control S077

description: miRNA profiling

value: serum


title: healthy control S079

description: miRNA profiling

value: healthy control

value: Female


title: healthy control S074

description: miRNA profiling


title: healthy control S075

description: miRNA profiling


title: healthy control S071

description: miRNA profiling


title: healthy control S072

description: miRNA profiling


title: 9341S

description: HYBRIDISED TO SNP6


title: 893S

description: HYBRIDISED TO SNP6


title: 9341T

description: HYBRIDISED TO SNP6


title: healthy control S069

description: miRNA profiling


title: healthy control S068

description: miRNA profiling


title: 9341G

description: HYBRIDISED TO SNP6


title: healthy control S070

description: miRNA profiling


title: healthy control S067

description: miRNA profiling


title: SKBR3_control_1

city: Linköping

first: Agneta

last: Jansson

address: Cell biology floor 9

department: IKE

country: Sweden

institute: Linköping university

description: Gene expression data from mock-transfected SKBR3 cells, harvested after 48h.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a Human Genome Focus Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

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

source_name: SKBR3, mock transfected, harvested after 48h

label_protocol: Biotinylated cRNA were prepared  from 5 ug total RNA according to the standard Affymetrix protocol.

growth_protocol: Breast cancer cell lines SKBR3 and ZR75-1 were cultured in phenol-red free Optimem-I supplemented with 4% foetal bovine serum and incubated at 37°C in 5% CO2.

extract_protocol: RNA was prepared using Trizol following the manufacturer's instructions. RNA was cleaned using the RNeasy MinElute Cleanup Kit according to the manufacturer’s protocol. RNA preparations were thereafter quantified and qualitatively evaluated using the Agilent 2100 Bioanalyzer.

treatment_protocol: Twenty-four hours after seeding, the cells were transfected with a HSD17B14-plasmid, using FuGene-6 transfection reagent . Control cells were incubated with the same amount of a vector missing the HSD17B14 insert. 48 hours after transfection, cells were harvested and immediately prepared for RNA isolation.

tag: cell line

value: breast cancer

tag: er status

value: ER -

tag: transfection

value: mock


title: 893G

description: HYBRIDISED TO SNP6


title: SKBR3_control_2


title: 8897S

description: HYBRIDISED TO SNP6


title: healthy control S076

description: miRNA profiling

tag: disease state


title: healthy control S066

description: miRNA profiling


title: healthy control S065

description: miRNA profiling


title: SKBR3_transfected_2

description: Gene expression data from HSD17B14-transfected SKBR3 cells, harvested after 48h.

source_name: SKBR3, HSD17B14 transfected, harvested after 48h


title: IC229G

description: HYBRIDISED TO SNP6

source_name: Lymphocyte DNA


title: 8897G

description: HYBRIDISED TO SNP6


title: healthy control S063

description: miRNA profiling


title: 8632T

description: HYBRIDISED TO SNP6


title: healthy control S073

description: miRNA profiling


title: healthy control S060

description: miRNA profiling


title: SKBR3_transfected_1


title: healthy control S062

description: miRNA profiling


title: healthy control S061

description: miRNA profiling


title: ZR75-1_control_2

description: Gene expression data from mock-transfected ZR75-1 cells, harvested after 48h.

source_name: ZR75-1, mock transfected, harvested after 48h

value: ER +


title: healthy control S059

description: miRNA profiling


title: healthy control S058

description: miRNA profiling


title: ZR75-1_control_1


title: ZR75-1_transfected_2

description: Gene expression data from HSD17B14-transfected ZR75-1 cells, harvested after 48h.

source_name: ZR75-1, HSD17B14 transfected, harvested after 48h


title: 8591T

description: HYBRIDISED TO SNP6

value: KRAS p.G12V


title: healthy control S057

description: miRNA profiling


title: 8897T

description: HYBRIDISED TO SNP6


title: healthy control S056

description: miRNA profiling


title: 8591S

description: HYBRIDISED TO SNP6


title: healthy control S054

description: miRNA profiling


title: healthy control S064

description: miRNA profiling


title: 8517G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes


title: ZR75-1_transfected_1


title: healthy control S053

description: miRNA profiling

value: Male


title: 893T

description: HYBRIDISED TO SNP6

value: KRAS p.G12D


title: healthy control S052

description: miRNA profiling

value: uncertain


title: healthy control S051

description: miRNA profiling


title: healthy control S050

description: miRNA profiling


title: healthy control S048

description: miRNA profiling


title: 8632G

description: HYBRIDISED TO SNP6

value: SEROUS


title: healthy control S047

description: miRNA profiling


title: healthy control S046

description: miRNA profiling


title: 8430T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: BORDERLINE


title: AML-19P CD34+CD38- cells

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Gene expression data from Lin-CD34+CD38- leukaemia stem cells

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Arrays were scanned with a GeneChip3000 7G scanner

data_processing: Probe level quantile normalisation and robust multi-array analysis on the raw CEL files were performed using the affy package of the Bioconductor project. Differentially expressed probe sets were identified using limma with fold change >1.5 and p<0.01.

source_name: childhood AML diagnostic BM

label_protocol: Fragmented and Labelled with NuGEN Encore Biotin Module

growth_protocol: washed in RPMI with 10%FCS and Pen/strep

extract_protocol: Trizol/chloroform/RNAeasy (Qiagen) integrated method - amplified using NuGEN WTA Pico Ovation V2 kit

treatment_protocol: none (the samples had been frozen in 10%DMSO/90%FCS)

value: leukemia stem cell CD34+CD38-

tag: chemo-resistance cell type

value: CD34-CD38- > other

tag: chemo-resistance lc50 type

value: childhood AML

tag: subject


title: healthy control S045

description: miRNA profiling

source_name: Serum

value: healthy control

tag: tissue

value: serum


title: 8517T

description: HYBRIDISED TO SNP6

value: WT


title: AML-17P CD34-CD38- cells

description: Gene expression data from Lin-CD34-CD38- leukaemia stem cells

tag: cell type

value: leukemia stem cell CD34-CD38-


title: AML-19P CD34-CD38- cells


title: AML-17P CD34+CD38+ cells

description: Gene expression data from Lin-CD34+CD38+ leukaemia stem cells

value: leukemia stem cell CD34+CD38+


title: 7315S

description: HYBRIDISED TO SNP6

value: Tumor stroma

value: Wild-type


title: healthy control S044

description: miRNA profiling

tag: gender

tag: tumor stage


title: healthy control S040

description: miRNA profiling

tag: age

tag: operability


title: healthy control S042

description: miRNA profiling


title: healthy control S039

description: miRNA profiling


title: healthy control S041

description: miRNA profiling


title: healthy control S038

description: miRNA profiling


title: AML-17P CD34+CD38- cells


title: 7315G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes

tag: tumour histology


title: 8430G

description: HYBRIDISED TO SNP6

tag: diagnosis


title: AML-19P CD34+CD38+ cells


title: AML-15P CD34-CD38- cells


title: 7198G

description: HYBRIDISED TO SNP6

tag: somatic ras/raf mutations


title: 8430S

description: HYBRIDISED TO SNP6

tag: age at diagnosis


title: healthy control S036

description: miRNA profiling

value: Male


title: healthy control S037

description: miRNA profiling


title: 7315T

description: HYBRIDISED TO SNP6

value: BRAF p.V600E


title: AML-15P CD34+CD38+ cells


title: healthy control S035

description: miRNA profiling

value: uncertain


title: healthy control S033

description: miRNA profiling


title: healthy control S031

description: miRNA profiling


title: AML-11P CD34-CD38- cells


title: healthy control S030

description: miRNA profiling


title: AML-15P CD34+CD38- cells


title: 7198S

description: HYBRIDISED TO SNP6

value: SEROUS


title: 7198T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: KRAS p.G12V


title: healthy control S027

description: miRNA profiling


title: healthy control S026

description: miRNA profiling


title: healthy control S028

description: miRNA profiling


title: AML-11P CD34+CD38+ cells


title: healthy control S023

description: miRNA profiling


title: AML-10P CD34-CD38- cells


title: healthy control S025

description: miRNA profiling


title: healthy control S029

description: miRNA profiling

value: Female


title: 5594T

description: HYBRIDISED TO SNP6

value: BORDERLINE


title: healthy control S022

description: miRNA profiling


title: 5594S

description: HYBRIDISED TO SNP6


title: 6176G

description: HYBRIDISED TO SNP6


title: healthy control S021

description: miRNA profiling


title: healthy control S020

description: miRNA profiling


title: healthy control S018

description: miRNA profiling


title: 6176T

description: HYBRIDISED TO SNP6


title: AML-10P CD34+CD38+ cells

value: childhood AML


title: AML-11P CD34+CD38- cells

value: leukemia stem cell CD34+CD38-

value: CD34-CD38- > other


title: AML-10P CD34+CD38- cells


title: AML-6P CD34-CD38- cells


title: healthy control S032

description: miRNA profiling

value: healthy control

value: serum


title: 5402G

description: HYBRIDISED TO SNP6


title: AML-6P CD34+CD38+ cells

value: leukemia stem cell CD34+CD38+


title: 5402T

description: HYBRIDISED TO SNP6

value: WT


title: 5036S

description: HYBRIDISED TO SNP6

value: Tumor stroma

value: Wild-type


title: healthy control S013

description: miRNA profiling

value: Male


title: AML-6P CD34+CD38- cells


title: healthy control S012

description: miRNA profiling


title: AML-5P CD34-CD38- cells

value: leukemia stem cell CD34-CD38-


title: healthy control S014

description: miRNA profiling

value: uncertain


title: healthy control S011

description: miRNA profiling


title: healthy control S010

description: miRNA profiling


title: 5036T

description: HYBRIDISED TO SNP6

value: SEROUS


title: healthy control S007

description: miRNA profiling


title: 5036G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes


title: healthy control S017

description: miRNA profiling


title: healthy control S006

description: miRNA profiling


title: healthy control S009

description: miRNA profiling


title: 5594G

description: HYBRIDISED TO SNP6


title: healthy control S015

description: miRNA profiling


title: 4836T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: BRAF p.V600E


title: healthy control S005

description: miRNA profiling


title: AML-5P CD34+CD38+ cells


title: healthy control S008

description: miRNA profiling


title: AML-2P CD34-CD38- cells


title: AML-5P CD34+CD38- cells


title: healthy control S003

description: miRNA profiling


title: healthy control S002

description: miRNA profiling

value: Female


title: AML-2P CD34+CD38- cells

value: childhood AML


title: 4836S

description: HYBRIDISED TO SNP6

value: BORDERLINE


title: AML-2P CD34+CD38+ cells

value: CD34-CD38- > other


title: healthy control E069

description: miRNA profiling

value: healthy control


title: healthy control S001

description: miRNA profiling

value: serum


title: AML-1P CD34-CD38- cells


title: 5002G

description: HYBRIDISED TO SNP6


title: healthy control E068

description: miRNA profiling


title: healthy control E067

description: miRNA profiling


title: 5002T

description: HYBRIDISED TO SNP6

value: HRAS p.G13R


title: healthy control E066

description: miRNA profiling


title: healthy control S016

description: miRNA profiling


title: healthy control E065

description: miRNA profiling


title: 4808G

description: HYBRIDISED TO SNP6


title: healthy control E063

description: miRNA profiling


title: healthy control E064

description: miRNA profiling


title: AML-1P CD34+CD38+ cells

value: leukemia stem cell CD34+CD38+


title: healthy control E062

description: miRNA profiling


title: 4808T

description: HYBRIDISED TO SNP6

value: ERBB2 p.M774_A775insAYVM


title: healthy control S004

description: miRNA profiling


title: healthy control E059

description: miRNA profiling


title: healthy control E061

description: miRNA profiling


title: 4836G

description: HYBRIDISED TO SNP6


title: AML-1P CD34+CD38- cells

value: leukemia stem cell CD34+CD38-


title: healthy control E058

description: miRNA profiling

value: Male


title: 4466T

description: HYBRIDISED TO SNP6


title: 4466S

description: HYBRIDISED TO SNP6

value: Tumor stroma

value: Wild-type


title: healthy control E057

description: miRNA profiling

value: uncertain


title: healthy control E055

description: miRNA profiling


title: healthy control E056

description: miRNA profiling


title: healthy control E054

description: miRNA profiling


title: healthy control E053

description: miRNA profiling


title: healthy control E052

description: miRNA profiling


title: 4452S

description: HYBRIDISED TO SNP6

value: SEROUS


title: 4466G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes


title: healthy control E049

description: miRNA profiling


title: healthy control E048

description: miRNA profiling


title: healthy control E046

description: miRNA profiling


title: healthy control E045

description: miRNA profiling


title: healthy control E044

description: miRNA profiling


title: healthy control E042

description: miRNA profiling


title: healthy control E051

description: miRNA profiling


title: healthy control E050

description: miRNA profiling


title: healthy control E040

description: miRNA profiling


title: healthy control E041

description: miRNA profiling


title: 4452T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: KRAS p.G12D


title: 4242T

description: HYBRIDISED TO SNP6

value: WT


title: healthy control E038

description: miRNA profiling


title: 4242S

description: HYBRIDISED TO SNP6

value: BORDERLINE


title: healthy control E037

description: miRNA profiling


title: 4452G

description: HYBRIDISED TO SNP6


title: healthy control E036

description: miRNA profiling


title: healthy control E034

description: miRNA profiling


title: 3964S

description: HYBRIDISED TO SNP6


title: healthy control E033

description: miRNA profiling

value: Female


title: 4242G

description: HYBRIDISED TO SNP6


title: healthy control E035

description: miRNA profiling

value: healthy control


title: healthy control E032

description: miRNA profiling

value: serum


title: healthy control E029

description: miRNA profiling


title: healthy control E030

description: miRNA profiling


title: 3964G

description: HYBRIDISED TO SNP6


title: healthy control E027

description: miRNA profiling


title: healthy control E031

description: miRNA profiling


title: 3905T

description: HYBRIDISED TO SNP6

value: KRAS p.G12D; p.G469A


title: 3964T

description: HYBRIDISED TO SNP6

value: BRAF p.V600E


title: healthy control E024

description: miRNA profiling


title: healthy control E039

description: miRNA profiling


title: healthy control E025

description: miRNA profiling


title: healthy control E023

description: miRNA profiling


title: healthy control E028

description: miRNA profiling


title: 3485G

description: HYBRIDISED TO SNP6


title: healthy control E026

description: miRNA profiling


title: healthy control E022

description: miRNA profiling


title: 3485S

description: HYBRIDISED TO SNP6


title: healthy control E020

description: miRNA profiling


title: healthy control E021

description: miRNA profiling


title: 3485T

description: HYBRIDISED TO SNP6

value: KRAS p.G12V


title: 3905G

description: HYBRIDISED TO SNP6


title: healthy control E016

description: miRNA profiling


title: healthy control E018

description: miRNA profiling


title: healthy control E014

description: miRNA profiling


title: healthy control E011

description: miRNA profiling


title: healthy control E012

description: miRNA profiling


title: 2952T

description: HYBRIDISED TO SNP6

value: KRAS p.Q61H


title: 2813T

description: HYBRIDISED TO SNP6


title: healthy control E019

description: miRNA profiling

value: Male


title: healthy control E010

description: miRNA profiling


title: 3905S

description: HYBRIDISED TO SNP6

value: Tumor stroma


title: 2813G

description: HYBRIDISED TO SNP6


title: 2989T

description: HYBRIDISED TO SNP6


title: healthy control E008

description: miRNA profiling


title: 2989G

description: HYBRIDISED TO SNP6


title: healthy control E009

description: miRNA profiling


title: healthy control E007

description: miRNA profiling


title: 2952G

description: HYBRIDISED TO SNP6


title: healthy control E004

description: miRNA profiling


title: 2713T

description: HYBRIDISED TO SNP6


title: healthy control E001

description: miRNA profiling


title: biliary tract cancer B103

description: miRNA profiling

value: biliary tract cancer

value: inoperable


title: healthy control E002

description: miRNA profiling

value: uncertain


title: healthy control E006

description: miRNA profiling


title: biliary tract cancer B102

description: miRNA profiling


title: healthy control E015

description: miRNA profiling


title: biliary tract cancer B101

description: miRNA profiling


title: 2952S

description: HYBRIDISED TO SNP6

value: SEROUS

value: Wild-type


title: biliary tract cancer P91

description: miRNA profiling


title: 2713S

description: HYBRIDISED TO SNP6


title: biliary tract cancer B100

description: miRNA profiling


title: healthy control E003

description: miRNA profiling


title: 2744T

description: HYBRIDISED TO SNP6

value: Tumor epithelium


title: biliary tract cancer B99

description: miRNA profiling


title: biliary tract cancer B97

description: miRNA profiling


title: 2713G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes


title: biliary tract cancer B96

description: miRNA profiling


title: biliary tract cancer B98

description: miRNA profiling


title: biliary tract cancer B95

description: miRNA profiling


title: biliary tract cancer B93

description: miRNA profiling


title: 2615S

description: HYBRIDISED TO SNP6

value: BORDERLINE


title: biliary tract cancer B94

description: miRNA profiling

value: Female


title: 2744G

description: HYBRIDISED TO SNP6


title: 2813S

description: HYBRIDISED TO SNP6


title: biliary tract cancer B90

description: miRNA profiling


title: biliary tract cancer B92

description: miRNA profiling

value: operable


title: 2615G

description: HYBRIDISED TO SNP6


title: biliary tract cancer B88

description: miRNA profiling

value: serum


title: biliary tract cancer B89

description: miRNA profiling


title: biliary tract cancer B86

description: miRNA profiling


title: biliary tract cancer B85

description: miRNA profiling


title: 2615T

description: HYBRIDISED TO SNP6


title: biliary tract cancer B84

description: miRNA profiling


title: biliary tract cancer B91

description: miRNA profiling


title: healthy control E005

description: miRNA profiling

value: healthy control


title: biliary tract cancer B81

description: miRNA profiling


title: biliary tract cancer B79

description: miRNA profiling


title: biliary tract cancer B80

description: miRNA profiling


title: biliary tract cancer B83

description: miRNA profiling


title: 2602G

description: HYBRIDISED TO SNP6


title: biliary tract cancer B77

description: miRNA profiling


title: 2602T

description: HYBRIDISED TO SNP6


title: 2469T

description: HYBRIDISED TO SNP6

value: KRAS p.G12D


title: 2359T

description: HYBRIDISED TO SNP6

value: BRAF p.V600E


title: biliary tract cancer B76

description: miRNA profiling


title: biliary tract cancer B75

description: miRNA profiling


title: biliary tract cancer B78

description: miRNA profiling


title: biliary tract cancer B74

description: miRNA profiling


title: 2359G

description: HYBRIDISED TO SNP6


title: biliary tract cancer B73

description: miRNA profiling


title: biliary tract cancer B71

description: miRNA profiling


title: 2244G

description: HYBRIDISED TO SNP6


title: 2469G

description: HYBRIDISED TO SNP6


title: biliary tract cancer B69

description: miRNA profiling


title: biliary tract cancer B68

description: miRNA profiling


title: biliary tract cancer B82

description: miRNA profiling


title: 2244T

description: HYBRIDISED TO SNP6

value: KRAS p.G12V


title: 2088T

description: HYBRIDISED TO SNP6

value: WT


title: biliary tract cancer B66

description: miRNA profiling


title: biliary tract cancer B67

description: miRNA profiling

value: Male


title: 2244S

description: HYBRIDISED TO SNP6

value: Tumor stroma


title: biliary tract cancer B65

description: miRNA profiling

value: biliary tract cancer


title: biliary tract cancer B63

description: miRNA profiling

value: uncertain


title: 2602S

description: HYBRIDISED TO SNP6

value: SEROUS


title: biliary tract cancer B60

description: miRNA profiling


title: biliary tract cancer B64

description: miRNA profiling


title: biliary tract cancer B61

description: miRNA profiling


title: 2072G

description: HYBRIDISED TO SNP6


title: biliary tract cancer B58

description: miRNA profiling


title: biliary tract cancer B62

description: miRNA profiling


title: biliary tract cancer B59

description: miRNA profiling


title: biliary tract cancer B57

description: miRNA profiling


title: biliary tract cancer B56

description: miRNA profiling


title: 2072T

description: HYBRIDISED TO SNP6

value: KRAS p.G12V; BRAF p.G464V


title: Placenta 5 Hypoxic 72h rep1

city: Pittsburgh

first: Jean-Francois

last: Mouillet

state: PA

address: 204 Craft Ave

department: MWRI - OBGYN and Reproductive Sciences

institute: University of Pittsburgh

description:
mRNA expression in primary trophoblasts
mR.510.H72.5

hyb_protocol: The hybridization was performed using  Gene Expression Hybridization Kit and Gene Expression Wash Buffer Kit from Agilent following the manufacturer's instructions

scan_protocol: Slides were scanned on Agilent Technologies Scanner G2505C using the protocol GE1_107_Sep09

data_processing: The raw data were log2 transformed and normalized using the cyclic loess normalization algorithm. The values from duplicated probes were averaged. The data then were transformed back to signal intensity values

source_name: Primary human trophoblast third trimester

label_protocol: The labeling was performed using  Low Input Quick Amp Labeling Kit, One-Color  from Agilent following the manufacturer's instructions

growth_protocol: Primary trophoblasts were isolated from third trimester placentas after Trypsin/Dispase/DNaseI digestion followed by purification on a Percoll gradient. Primary trophoblasts were cultured for 48h  to 72h in DMEM supplemented with 10% FBS (Fetal Bovine Serum), 20 mM Hepes ph 7.4, and a mixture of penicilin-streptomycin-fungizone. Cells were maintained at 37ºC/5% CO2

extract_protocol: Total RNA were prepared using miRNeasy Mini Kit following the manufacturer's instructions

treatment_protocol: 3.3 million cells were seeded in 35 mm tissue culture plates. After 4 h, nonadherent cells were removed by three washes in PBS. The culture were replenished with 2 ml of culture medium, and were divided to standard or hypoxic growth conditions (20% O2, 8% O2, or 1% O2).

value: Primary trophoblast cells

value: Placenta

tag: culture conditions

value: hypoxic

tag: time


title: 2088S

description: HYBRIDISED TO SNP6

value: BORDERLINE

value: Wild-type


title: biliary tract cancer B55

description: miRNA profiling

value: serum

value: operable


title: 2006T

description: HYBRIDISED TO SNP6

value: Tumor epithelium


title: Placenta 5 Standard 72h rep1

description:
mRNA expression in primary trophoblasts
mR.509.N72.5

value: standard


title: 2006S

description: HYBRIDISED TO SNP6


title: 2007G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes


title: biliary tract cancer B54

description: miRNA profiling

value: Female


title: biliary tract cancer B52

description: miRNA profiling

value: Male


title: 2006G

description: HYBRIDISED TO SNP6


title: biliary tract cancer B53

description: miRNA profiling


title: biliary tract cancer B51

description: miRNA profiling


title: Placenta 5 Hypoxic 48h rep1

description:
mRNA expression in primary trophoblasts
mR.508.H48.5


title: 2088G

description: HYBRIDISED TO SNP6


title: biliary tract cancer B50

description: miRNA profiling


title: 1832T

description: HYBRIDISED TO SNP6

value: KRAS p.[G12G, G13R]


title: biliary tract cancer B49

description: miRNA profiling

value: biliary tract cancer


title: Placenta 5 Standard 48h rep1

description:
mRNA expression in primary trophoblasts
mR.507.N48.5


title: biliary tract cancer B48

description: miRNA profiling

value: uncertain


title: 2007T

description: HYBRIDISED TO SNP6

value: SEROUS

value: BRAF p.V600E


title: biliary tract cancer B46

description: miRNA profiling


title: biliary tract cancer B45

description: miRNA profiling


title: Placenta 5 Hypoxic 24h rep1

description:
mRNA expression in primary trophoblasts
mR.506.H24.5

value: Primary trophoblast cells


title: biliary tract cancer B44

description: miRNA profiling


title: 1832S

description: HYBRIDISED TO SNP6

value: Tumor stroma


title: Placenta 5 Standard 24h rep1

description:
mRNA expression in primary trophoblasts
mR.505.N24.5

value: Placenta


title: biliary tract cancer B43

description: miRNA profiling


title: biliary tract cancer B41

description: miRNA profiling


title: biliary tract cancer B42

description: miRNA profiling


title: Placenta 5 Hypoxic 12h rep1

description:
mRNA expression in primary trophoblasts
mR.504.H12.5

value: hypoxic


title: 1457T

description: HYBRIDISED TO SNP6

value: BORDERLINE


title: biliary tract cancer B40

description: miRNA profiling

value: serum


title: 1832G

description: HYBRIDISED TO SNP6


title: Placenta 5 Standard 12h rep1

description:
mRNA expression in primary trophoblasts
mR.503.N12.5


title: biliary tract cancer B39

description: miRNA profiling

value: operable


title: Placenta 5 Standard 0h rep1

description:
mRNA expression in primary trophoblasts
mR.500.T0.5


title: biliary tract cancer B37

description: miRNA profiling

value: inoperable


title: biliary tract cancer B36

description: miRNA profiling


title: 1457S

description: HYBRIDISED TO SNP6

value: Wild-type


title: biliary tract cancer B35

description: miRNA profiling


title: Placenta 4 Hypoxic 72h rep1

description:
mRNA expression in primary trophoblasts
mR.410.H72.4


title: biliary tract cancer B32

description: miRNA profiling


title: biliary tract cancer B33

description: miRNA profiling


title: Placenta 4 Standard 72h rep1

description:
mRNA expression in primary trophoblasts
mR.409.N72.4

value: standard


title: biliary tract cancer B31

description: miRNA profiling


title: biliary tract cancer B30

description: miRNA profiling

value: Female


title: Placenta 4 Hypoxic 48h rep1

description:
mRNA expression in primary trophoblasts
mR.408.H48.4


title: Placenta 4 Standard 48h rep1

description:
mRNA expression in primary trophoblasts
mR.407.N48.4


title: biliary tract cancer B29

description: miRNA profiling

value: Male


title: 1408S

description: HYBRIDISED TO SNP6


title: Placenta 4 Hypoxic 24h rep1

description:
mRNA expression in primary trophoblasts
mR.406.H24.4


title: biliary tract cancer B28

description: miRNA profiling


title: biliary tract cancer B27

description: miRNA profiling


title: 1408T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: WT


title: biliary tract cancer B26

description: miRNA profiling

value: biliary tract cancer

value: uncertain


title: biliary tract cancer B25

description: miRNA profiling


title: biliary tract cancer B24

description: miRNA profiling


title: 1457G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes

value: SEROUS


title: Placenta 4 Hypoxic 12h rep1

description:
mRNA expression in primary trophoblasts
mR.404.H12.4

value: Primary trophoblast cells


title: 1277G

description: HYBRIDISED TO SNP6


title: biliary tract cancer B22

description: miRNA profiling


title: Placenta 4 Standard 24h rep1

description:
mRNA expression in primary trophoblasts
mR.405.N24.4

value: Placenta


title: 12168S

description: HYBRIDISED TO SNP6

value: Tumor stroma


title: Placenta 4 Standard 12h rep1

description:
mRNA expression in primary trophoblasts
mR.403.N12.4


title: biliary tract cancer B21

description: miRNA profiling


title: 12168T

description: HYBRIDISED TO SNP6

value: BORDERLINE


title: biliary tract cancer B20

description: miRNA profiling

value: serum


title: 1268G

description: HYBRIDISED TO SNP6


title: Placenta 4 Hypoxic 6h rep1

description:
mRNA expression in primary trophoblasts
mR.402.H6.4

value: hypoxic


title: 1277T

description: HYBRIDISED TO SNP6

value: ERBB2 p.M774_A775insAYVM


title: Placenta 4 Standard 6h rep1

description:
mRNA expression in primary trophoblasts
mR.401.N6.4


title: 12168G

description: HYBRIDISED TO SNP6


title: 1268T

description: HYBRIDISED TO SNP6

value: BRAF p.V600E


title: biliary tract cancer B19

description: miRNA profiling

value: operable


title: biliary tract cancer B18

description: miRNA profiling

value: Female


title: biliary tract cancer B23

description: miRNA profiling

value: Male

value: inoperable


title: biliary tract cancer B17

description: miRNA profiling


title: biliary tract cancer B16

description: miRNA profiling


title: Tie2-Chd1_Mut_rep4

city: San Francisco

first: Fong Ming

last: Koh

state: CA

address: 35 Medical Center Way RMB-912D

department: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research

institute: University of California, San Francisco

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Gene expression data were quantile normalized and sample heterogeneity was assessed in R with the SampleNetwork function (Oldham et al, BMC Systems Biology 2012). Batch normalization was conducted using ComBat (Johnson et al, Biostatistics 2007) with embryo genotype as a covariate.

source_name: E10.5 CD31+ tdTomato+ cells_Mutant embryo

label_protocol: Total RNA was amplified with Ovation PicoSL WTA System V2 (NuGEN), and labeled with Encore BiotinIL Module (NuGEN).

extract_protocol: Total RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). Quality control was performed using Agilent Bioanalyzer.

treatment_protocol: Embryos were dissected at E10.5 and treated with Collagenase Type IV (Gibco) and Dnase I (Worthington). Cells were stained with fluorescently labeled antibodies and CD31+ tdTomato+ cells were sorted by FACS into RNAlater solution (Ambion).

tag: strain background

tag: developmental stage

tag: genotype/variation

value: Mutant; endothelial-specific deletion of Chd1

value: CD31+ tdTomato+ cells


title: Tie2-Chd1_Mut_rep3


title: Placenta 2 Hypoxic 72h rep1

description:
mRNA expression in primary trophoblasts
mR.210.H72.2


title: Placenta 4 Standard 0h rep1

description:
mRNA expression in primary trophoblasts
mR.400.T0.4

value: standard


title: biliary tract cancer B14

description: miRNA profiling

tag: disease state

value: biliary tract cancer

value: uncertain


title: Tie2-Chd1_Mut_rep2


title: biliary tract cancer B15

description: miRNA profiling


title: biliary tract cancer B13

description: miRNA profiling


title: Placenta 2 Standard 72h rep1

description:
mRNA expression in primary trophoblasts
mR.209.N72.2

value: Primary trophoblast cells


title: biliary tract cancer B11

description: miRNA profiling


title: biliary tract cancer B12

description: miRNA profiling


title: Placenta 2 Hypoxic 48h rep1

description:
mRNA expression in primary trophoblasts
mR.208.H48.2

value: Placenta


title: 1162T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

value: SEROUS


title: 1162G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes

value: BORDERLINE


title: biliary tract cancer B07

description: miRNA profiling

value: serum


title: biliary tract cancer B08

description: miRNA profiling


title: 11241G

description: HYBRIDISED TO SNP6


title: Tie2-Chd1_CreHet_rep3

source_name: E10.5 CD31+ tdTomato+ cells_CreHet control embryo

value: CreHet; control


title: Tie2-Chd1_CreHet_rep4


title: 11241T

description: HYBRIDISED TO SNP6

value: KRAS p.Q61L


title: biliary tract cancer B09

description: miRNA profiling

value: Female


title: biliary tract cancer B06

description: miRNA profiling

value: Male

value: operable


title: Placenta 2 Hypoxic 24h rep1

description:
mRNA expression in primary trophoblasts
mR.206.H24.2

value: hypoxic


title: biliary tract cancer B05

description: miRNA profiling


title: biliary tract cancer B03

description: miRNA profiling


title: 11122S

description: HYBRIDISED TO SNP6

value: Tumor stroma

value: Wild-type


title: 11122G

description: HYBRIDISED TO SNP6


title: Placenta 2 Standard 24h rep1

description:
mRNA expression in primary trophoblasts
mR.205.N24.2

value: standard


title: 11122T

description: HYBRIDISED TO SNP6

value: WT


title: biliary tract cancer B02

description: miRNA profiling

value: biliary tract cancer

value: uncertain


title: 11241S

description: HYBRIDISED TO SNP6


title: Tie2-Chd1_CreHet_rep1

value: CD31+ tdTomato+ cells


title: Placenta 2 Standard 48h rep1

description:
mRNA expression in primary trophoblasts
mR.207.N48.2

value: Primary trophoblast cells

value: Placenta


title: Placenta 2 Hypoxic 12h rep1

description:
mRNA expression in primary trophoblasts
mR.204.H12.2


title: pancreatic cancer P101

description: miRNA profiling

value: pancreatic cancer

value: cStage IV

value: inoperable


title: pancreatic cancer B38

description: miRNA profiling

value: serum

value: pStage IIB


title: biliary tract cancer B01

description: miRNA profiling

value: Female


title: iPGC-1β/APCmin 12

city: London

first: Elena

last: Bellafante

address: Guy's Campus

department: Women's Health

institute: KCL

description: replicate 1

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <200 were excluded. Data were analyzed with Genome Studio Software (Differential Expression Analysis with Mann-Whitney error model plus False Discovery Rate, FDR).

source_name: mouse ileum tumor 12

label_protocol: Standard Illumina Protocol

extract_protocol: Total RNA was extracted using the Qiazol reagent, following manufacturer's instructions. Quality control was performed with Biorad Experion.

tag: strain

value: FVB/N

value: 3-4 months old

value: ileum tumor


title: iPGC-1β/APCmin 11

description: replicate 1

source_name: mouse ileum tumor 11

tag: tissue


title: pancreatic cancer B87

description: miRNA profiling

value: cStage III


title: Tie2-Chd1_Mut_rep1

value: Mutant; endothelial-specific deletion of Chd1

tag: cell type


title: pancreatic cancer P99

description: miRNA profiling

tag: gender

value: Male


title: pancreatic cancer P98

description: miRNA profiling

tag: tumor stage


title: iPGC-1β/APCmin 10

description: replicate 1

source_name: mouse ileum tumor 10

tag: age


title: pancreatic cancer P97

description: miRNA profiling

tag: operability


title: biliary tract cancer B04

description: miRNA profiling

value: biliary tract cancer

value: operable


title: pancreatic cancer P100

description: miRNA profiling


title: Placenta 2 Hypoxic 6h rep1

description:
mRNA expression in primary trophoblasts
mR.202.H6.2

value: hypoxic


title: Tie2-Chd1_CreHet_rep2

value: CreHet; control

value: CD31+ tdTomato+ cells


title: 1066T

description: HYBRIDISED TO SNP6

value: Tumor epithelium

tag: tumour histology

value: SEROUS

value: BORDERLINE

value: KRAS p.G12V


title: Placenta 2 Standard 12h rep1

description:
mRNA expression in primary trophoblasts
mR.203.N12.2

value: Primary trophoblast cells

value: Placenta

value: standard


title: 10744G

description: HYBRIDISED TO SNP6

value: Peripheral Blood Lymphocytes

tag: diagnosis


title: pancreatic cancer P96

description: miRNA profiling

value: pancreatic cancer

value: serum

value: cStage IV

value: inoperable


title: pancreatic cancer P95

description: miRNA profiling

value: Male

value: cStage III


title: pancreatic cancer P94

description: miRNA profiling


title: biliary tract cancer B10

description: miRNA profiling

value: biliary tract cancer

value: Female

value: uncertain


title: iPGC-1β/APCmin 9

description: replicate 1

source_name: mouse ileum tumor 9

value: FVB/N

value: 3-4 months old

value: ileum tumor


title: Placenta 2 Standard 0h rep1

description:
mRNA expression in primary trophoblasts
mR.200.T0.2


title: pancreatic cancer P93

description: miRNA profiling


title: 1066G

description: HYBRIDISED TO SNP6

value: SEROUS

value: BORDERLINE

tag: somatic ras/raf mutations


title: Placenta 1 Hypoxic 72h rep2

description:
mRNA expression in primary trophoblasts
mR.104.H72.1

value: Primary trophoblast cells

value: Placenta

value: hypoxic


title: iPGC-1β/APCmin 8

description: replicate 1

source_name: mouse ileum tumor 8


title: pancreatic cancer P89

description: miRNA profiling

value: pancreatic cancer


title: pancreatic cancer P87

description: miRNA profiling

value: serum


title: pancreatic cancer P88

description: miRNA profiling

value: cStage IV


title: Placenta 1 8% 72h rep1

description:
mRNA expression in primary trophoblasts
mR.103.T72x8.1


title: Placenta 1 Hypoxic 24h rep2

description:
mRNA expression in primary trophoblasts
mR.102.H24.1


title: pancreatic cancer P86

description: miRNA profiling

value: inoperable


title: Placenta 1 8% 24h rep1

description:
mRNA expression in primary trophoblasts
mR.101.T24x8.1


title: FVBN/APCmin 5

description: replicate 1

source_name: mouse ileum tumor 5

value: FVBN/APCmin


title: pancreatic cancer P85

description: miRNA profiling

value: Male


title: pancreatic cancer P90

description: miRNA profiling


title: pancreatic cancer P84

description: miRNA profiling


title: 10115T

description: HYBRIDISED TO SNP6

source_name: Serous ovarian tumor

value: Tumor epithelium

value: BRAF p.V600E

tag: age at diagnosis


title: Placenta 2 Standard 6h rep1

description:
mRNA expression in primary trophoblasts
mR.201.N6.2

tag: culture conditions

value: standard


title: 10744T

description: HYBRIDISED TO SNP6

value: KRAS p.G12A


title: pancreatic cancer P83

description: miRNA profiling


title: pancreatic cancer P82

description: miRNA profiling

value: cStage III


title: pancreatic cancer P81

description: miRNA profiling


title: pancreatic cancer P78

description: miRNA profiling

value: Female


title: pancreatic cancer P80

description: miRNA profiling


title: FVBN/APCmin 4

description: replicate 1

source_name: mouse ileum tumor 4

value: FVB/N

value: 3-4 months old

value: ileum tumor


title: pancreatic cancer P77

description: miRNA profiling


title: pancreatic cancer P79

description: miRNA profiling


title: Placenta 1 Standard 0h rep2

description:
mRNA expression in primary trophoblasts
mR.100.T0.1

value: Primary trophoblast cells

value: Placenta

tag: time


title: FVBN/APCmin 2

description: replicate 1

source_name: mouse ileum tumor 2


title: FVBN/APCmin 1

description: replicate 1

source_name: mouse ileum tumor 1


title: Placenta 1 Hypoxic 48h rep1

description:
mRNA expression in primary trophoblasts
mR.8.H48.1

value: hypoxic


title: FVBN/APCmin 3

description: replicate 1

source_name: mouse ileum tumor 3


title: pancreatic cancer P76

description: miRNA profiling

value: pancreatic cancer

value: serum


title: pancreatic cancer P75

description: miRNA profiling

value: inoperable


title: Placenta 1 Hypoxic 72h rep1

description:
mRNA expression in primary trophoblasts
mR.10.H72.1


title: Placenta 1 Standard 72h rep1

description:
mRNA expression in primary trophoblasts
mR.9.N72.1


title: pancreatic cancer P74

description: miRNA profiling

value: pStage IIA

value: operable


title: iPGC-1β 10

description: replicate 1

source_name: mouse ileum 10

value: ileum


title: 10744S

description: HYBRIDISED TO SNP6

value: Tumor stroma

value: SEROUS

value: BORDERLINE

value: Wild-type


title: pancreatic cancer P73

description: miRNA profiling

value: Male

value: cStage IV


title: pancreatic cancer P71

description: miRNA profiling

value: pStage IIB


title: Placenta 1 Standard 48h rep1

description:
mRNA expression in primary trophoblasts
mR.7.N48.1

value: standard


title: Placenta 1 Standard 24h rep1

description:
mRNA expression in primary trophoblasts
mR.5.N24.1

value: Primary trophoblast cells


title: iPGC-1β 7

description: replicate 1

source_name: mouse ileum 7

value: FVB/N

value: 3-4 months old


title: iPGC-1β 8

description: replicate 1

source_name: mouse ileum 8


title: pancreatic cancer P67

description: miRNA profiling

source_name: Serum

value: pancreatic cancer


title: pancreatic cancer P69

description: miRNA profiling

value: serum


title: pancreatic cancer P68

description: miRNA profiling

value: cStage III


title: pancreatic cancer P72

description: miRNA profiling


title: Placenta 1 Hypoxic 24h rep1

description:
mRNA expression in primary trophoblasts
mR.6.H24.1

source_name: Primary human trophoblast third trimester

value: Placenta

value: hypoxic


title: pancreatic cancer P66

description: miRNA profiling

value: operable


title: iPGC-1β 9

description: replicate 1

source_name: mouse ileum 9

value: ileum


title: Placenta 1 Standard 12h rep1

description:
mRNA expression in primary trophoblasts
mR.3.N12.1


title: pancreatic cancer P62

description: miRNA profiling

value: ypStage IIB


title: pancreatic cancer P63

description: miRNA profiling


title: pancreatic cancer P65

description: miRNA profiling

value: ypStage IB


title: FVBN 5

description: replicate 1

source_name: mouse ileum 5

value: wild-type


title: pancreatic cancer P61

description: miRNA profiling

value: Male


title: pancreatic cancer P60

description: miRNA profiling


title: 10115G

description: HYBRIDISED TO SNP6

source_name: Lymphocyte DNA

value: Peripheral Blood Lymphocytes

value: SEROUS

value: BORDERLINE


title: Placenta 1 Hypoxic 6h rep1

description:
mRNA expression in primary trophoblasts
mR.2.H6.1

value: Primary trophoblast cells


title: pancreatic cancer P59

description: miRNA profiling

value: cStage IV

value: inoperable


title: FVBN 3

description: replicate 1

source_name: mouse ileum 3

value: FVB/N

value: 3-4 months old


title: iPGC-1β 6

description: replicate 1

source_name: mouse ileum 6


title: FVBN 4

description: replicate 1

source_name: mouse ileum 4


title: FVBN 2

description: replicate 1

source_name: mouse ileum 2


title: pancreatic cancer P55

description: miRNA profiling

value: pancreatic cancer

value: serum

value: Female


title: pancreatic cancer P54

description: miRNA profiling

value: cStage III


title: Placenta 1 Standard 6h rep1

description:
mRNA expression in primary trophoblasts
mR.1.N6.1

value: Placenta

value: standard


title: pancreatic cancer P58

description: miRNA profiling


title: pancreatic cancer P57

description: miRNA profiling


title: pancreatic cancer P56

description: miRNA profiling


title: Placenta 1 Standard 0h rep1

description:
mRNA expression in primary trophoblasts
mR.0.T0.1


title: FVBN 1

description: replicate 1

source_name: mouse ileum 1

value: ileum


title: pancreatic cancer P53

description: miRNA profiling


title: Placenta 1 Hypoxic 12h rep1

description:
mRNA expression in primary trophoblasts
mR.4.H12.1

value: hypoxic


title: tail-1892

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

description: Gene expression data from untreated P56 mouse skin

hyb_protocol: 90 microliters of hybridization sample were incubated in the Affymetrix GeneTitan Hybridization Oven instrument for 16 hours at 48C

scan_protocol: Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the MoGene-1_1-st-v1-96 fluidics script and GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates.  Arrays were scanned in the Affymetrix GeneTitan Multi-Channel (MC) instrument with the AGCC GeneTitan Instrument Control.

data_processing: CEL files were background corrected and normalized with RMA using oligo in R and a custom probe database which avoids SNPs in FVB and Spretus genomes. Data were batch-corrected for plate and genotype and then log2 transformed.

source_name: tail skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Mice were housed in standard conditions with standard chow and water ad libitum

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol: Mice were aged to 8 weeks, untreated

value: tail skin

value: 8 weeks

value: KO

tag: plate

value: no

tag: Sex

value: F


title: tail-1897

value: M


title: tail-1896


title: pancreatic cancer P52

description: miRNA profiling

value: cStage IV

value: inoperable


title: tail-1895


title: iKOPGC-1β 7

description: replicate 1

value: 3-4 months old

tag: genotype/variation


title: iKOPGC-1β 6

description: replicate 1


title: pancreatic cancer P51

description: miRNA profiling

tag: disease state

value: pancreatic cancer

value: Male


title: pancreatic cancer P50

description: miRNA profiling

value: serum


title: iPGC-1β/APCmin 7

description: replicate 1

source_name: mouse ileum tumor 7

tag: strain

value: FVB/N

value: ileum tumor


title: pancreatic cancer P49

description: miRNA profiling

tag: tissue

value: pStage IIB

value: operable


title: iKOPGC-1β 8

description: replicate 1

value: ileum


title: FVBN/APCmin 6

description: replicate 1

source_name: mouse ileum tumor 6

value: FVBN/APCmin


title: tail-1891

value: tail skin

value: 8 weeks


title: tail-1890

value: KO

value: no


title: PGC-1β fl/? 3

description: replicate 1

value: PGC-1β fl/?


title: PGC-1β fl/? 4

description: replicate 1


title: pancreatic cancer P47

description: miRNA profiling

value: cStage IV


title: pancreatic cancer P48

description: miRNA profiling

value: Female

value: cStage III

value: inoperable


title: pancreatic cancer P46

description: miRNA profiling

value: pancreatic cancer

value: Male


title: pancreatic cancer P45

description: miRNA profiling

value: serum


title: pancreatic cancer P43

description: miRNA profiling


title: pancreatic cancer P41

description: miRNA profiling


title: pancreatic cancer P42

description: miRNA profiling


title: pancreatic cancer P44

description: miRNA profiling


title: pancreatic cancer P40

description: miRNA profiling


title: pancreatic cancer P37

description: miRNA profiling


title: pancreatic cancer P38

description: miRNA profiling


title: tail-1889

value: M


title: pancreatic cancer P36

description: miRNA profiling


title: pancreatic cancer P39

description: miRNA profiling


title: tail-1888

value: F


title: pancreatic cancer P35

description: miRNA profiling


title: PGC-1β fl/? 1

description: replicate 1

value: 3-4 months old


title: PGC-1β fl/? 2

description: replicate 1

value: ileum


title: tail-1886


title: tail-1887


title: pancreatic cancer P33

description: miRNA profiling


title: aCGH - Cell line 2224

description: No additional information.

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Agilent Scanning Protocol Other: Chips were scanned by Agilent Technologies Scanner G2505B US45103062. Scan_MicronsPerPixelX: 5. Scan_MicronsPerPixelY: 5.

data_processing:
Partek Data Processing Protocol
Calculation Method: Data was extracted using Agilent's Feature Extraction Software, FeatureExtractor_Version: 9.5.1.1, Protocol_Name: CGH-v4_95_Feb07. Copy number variation was measured according to Partek Genomic Suite. After circler binary segmentation normalization, copy number gains and losses were detected using a hidden Markov model algorithm in the Partek copy number workflow for unpaired samples. Amplifications were defined as segments with log2 ratios greater than 0.15. Deletions were defined as segments with log2 ratios less than -0.3. Segments were defined as regions that differed from neighboring regions by at least 2 signal-to-noise ratio in at least 10 markers. Regions identified were annotated using NCBI RefSeq hg19.

source_name: Normal PBMC

label_protocol:
Cy3 Labeling Protocol
Other: A 1.5 ug of total RNA was labeled with Cy3.

extract_protocol:
Extraction Protocol
Other: Extracted and purified using the Qiagen Mini Kit (Qiagen, Valencia,CA).

value: Blood

tag: cell type

value: Peripheral Blood Mononuclear Cell (PBMC)

tag: other

value: PBMCs of a healthy female donor.

source_name: Cell line 2224

label_protocol:
Cy5 Labeling Protocol
Other: A 1.5 ug of total RNA was labeled with Cy5.

tag: cell line

value: metastatic melanoma


title: iKOPGC-1β 5

description: replicate 1

tag: age


title: pancreatic cancer P32

description: miRNA profiling

tag: gender

tag: tumor stage

tag: operability


title: aCGH - Cell line 3107

description: No additional information.

source_name: Cell line 3107


title: pancreatic cancer P31

description: miRNA profiling


title: tail-1883

value: tail skin

value: 8 weeks

value: KO

value: no


title: pancreatic cancer P34

description: miRNA profiling

value: pStage IIA

value: uncertain

value: operable


title: tail-1885


title: aCGH - Cell line 2523

description: No additional information.

source_name: Cell line 2523


title: aCGH - Cell line 1866

description: No additional information.

source_name: Cell line 1866


title: pancreatic cancer P30

description: miRNA profiling

source_name: Serum

value: pancreatic cancer

value: Male

value: cStage IV

value: inoperable


title: pancreatic cancer P29

description: miRNA profiling

value: serum

value: Female

value: cStage III


title: pancreatic cancer P28

description: miRNA profiling


title: tail-1884

value: M


title: tail-1882

value: F


title: pancreatic cancer P27

description: miRNA profiling


title: pancreatic cancer P26

description: miRNA profiling

value: pStage IIB


title: aCGH - Cell line 261IV7p

description: No additional information.

value: Blood

value: Peripheral Blood Mononuclear Cell (PBMC)

value: PBMCs of a healthy female donor.

source_name: Cell line 261IV7p

value: metastatic melanoma


title: pancreatic cancer P24

description: miRNA profiling


title: tail-1881

value: tail skin

value: 8 weeks

value: KO

value: no


title: tail-1880


title: pancreatic cancer P22

description: miRNA profiling

value: pancreatic cancer


title: aCGH - Cell line 1182

description: No additional information.

source_name: Cell line 1182


title: aCGH - Cell line 938

description: No additional information.

source_name: Cell line 938


title: pancreatic cancer P21

description: miRNA profiling


title: pancreatic cancer P25

description: miRNA profiling

value: Male

value: cStage IV


title: tail-1875


title: tail-1876


title: tail-1873


title: aCGH - Cell line 62428

description: No additional information.

source_name: Cell line 62428


title: pancreatic cancer P19

description: miRNA profiling

value: serum

value: operable


title: pancreatic cancer P20

description: miRNA profiling

value: cStage III

value: inoperable


title: pancreatic cancer P23

description: miRNA profiling

value: Female


title: tail-1872

value: M


title: aCGH - Cell line A375

description: No additional information.

value: Blood

source_name: Cell line A375


title: pancreatic cancer P18

description: miRNA profiling


title: pancreatic cancer P70

description: miRNA profiling

value: pStage IIB


title: pancreatic cancer P17

description: miRNA profiling


title: tail-1868


title: tail-1866

value: F


title: aCGH - Cell line 1290p14

description: No additional information.

value: Peripheral Blood Mononuclear Cell (PBMC)

value: PBMCs of a healthy female donor.

source_name: Cell line 1290p14

value: metastatic melanoma


title: CBF1OX high light A

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis Genome ATH1 Array were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 7G

organism: Solanum tuberosum

source_name: CBF1OX high light

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Potato plants (Solanum tuberosum cv. Désirée) were grown under sterile conditions in glass bottles containing Murashige and Skoog (MS, Sigma) medium solidified with 0.8% phytoagar (Sigma). Plants were propagated in vitro and grown under 16 h light (50 µmol m-2 s-1cool-white fluorescent illumination)/8 h dark cycles, at 22C. The analysis of physiological and molecular responses of plants to different stress treatments  was conducted on plants transferred to plastic pots containing a mixture of perlite:vermiculite:peat moss (1:1:1), and acclimated for one month under the same light and temperature conditions in which the treatments were applied.

extract_protocol: Total RNA extraction was performed using RNaeasy Mini kit system according to the manufacturer's instructions.

treatment_protocol:
Low temperature: To analyze the effect of low temperature conditions, plants were first grown under long days (16 h light/8 h darkness) with fluorescent illumination (50 µmol m-2 s-1) at 22 ºC. After one month, half of the plants were exposed to 4 ºC under similar light conditions, while the remaining plants were kept at 22 ºC.
High light: The effect of high light stress was evaluated on plants grown first under long day conditions in a growth chamber illuminated with high pressure sodium lamps at 50 µmol m-2 s-1, at 22 ºC. After one month, half of the plants were exposed to 800 µmol m-2 s-1 at 22 ºC, while the remaining plants were kept under 50 µmol m-2 s-1 at 22 ºC.
Drought: for drought stress, plants were grown under natural radiation in a greenhouse in 3 liter pots supplemented with daily irrigation until water soil capacity was saturated. After one month under this condition, irrigation was interrupted for half of the plants while the remaining plants continued with the previous daily irrigation regime.

tag: cultivar

value: cv. Désirée

value: AtCBF1OX transgenic

tag: stress condition

value: high light

value: young leaves


title: aCGH - Cell line 1858m

description: No additional information.

source_name: Cell line 1858m


title: CBF1OX high light B


title: tail-1862

source_name: tail skin

value: tail skin

value: 8 weeks

value: KO

value: no


title: pancreatic cancer P15

description: miRNA profiling

value: pancreatic cancer

value: serum

value: cStage IV

value: inoperable


title: CBF1OX control B (high light experiment)

source_name: CBF1OX control (high light experiment)

value: none (control condition)


title: FL_Fr.B/C.4

city: Philadelphia

first: Kyoko

last: Hayakawa

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

description: Gene expression of fetal liver Fr.B/C, replicate 4

hyb_protocol: Follow Agilent 60-mer oligo array hybridization protocol.

scan_protocol: Arrays were scanned by following scanning protocol recommended by Agilent, and spot quantifications were done using feature extraction software

data_processing: data were bakcground corrected using normexp method then loess normalized using bioconduction package limma

source_name: Fetal liver, Fr.B/C, replicate 4

label_protocol: Amplified RNAs were labeled with cy3 or cy5 dye

extract_protocol: RNA was extracted using the acid phenol method. 100ng of total RNA was used for RNA amplificaiton followingAmbion RNA amplification protocol.

treatment_protocol:
For each bone marrow sort, 16 female BALB/c mice were sacrificed and a single cell suspension was prepared from bone marrow after flushing femur and tibia using a 1ml syringe and a 25 gauge needle.  This generated 1 Fr. A and 1 Fr. B/C sample. Total of 4 sorts
For each fetal liver sort, a BALB/c mouse with embryos at day 16 of gestation was sacrificed, embryos (average of 8) were sacrificed, and a single cell suspension was prepared from liver by gentle dissociation between 2 frosted glass slides.  This generated 1 Fr. A and 1 Fr. B/C sample. Total of 4 sorts.

value: BALB/c

tag: developmental stage

value: Fetus

value: Fetal Liver

source_name: reference

tag: rna source

value: total RNA from six cell lines (R1, RS2, J558, EL4, DN3, and P388d)


title: pancreatic cancer P14

description: miRNA profiling

value: Male


title: FL_Fr.B/C.3

description: Gene expression of fetal liver Fr.B/C, replicate 3

source_name: Fetal liver, Fr.B/C, replicate 3


title: tail-1861

tag: plate

value: M


title: pancreatic cancer P13

description: miRNA profiling

value: Female


title: WT high light B

description: WTHLB

source_name: WT high light

value: cv. Désirée

value: wild type

value: high light

value: young leaves


title: FL_Fr.B/C.2

description: Gene expression of fetal liver Fr.B/C, replicate 2

source_name: Fetal liver, Fr.B/C, replicate 2


title: aCGH - Cell line 888

description: No additional information.

source_name: Normal PBMC

value: Blood

value: Peripheral Blood Mononuclear Cell (PBMC)

value: PBMCs of a healthy female donor.

source_name: Cell line 888

value: metastatic melanoma


title: WT high light A

description: WTHLA