title: LZ IgG1 GFP- #3

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

description:
IgG_LZ_3
Sorted LN IgG1+GFP-CXCR4lowCD86high LZ GC cells.

hyb_protocol: Fragmented samples were hybridised according to NuGEN guidelines for 18hr at 45C on GeneChip Mouse Gene 1.0 ST Array. The arrays were then washed and stained using the standard fluidics protocol (FS450_0007) for gene arrays on the GeneChip Fluidics Station 450.

scan_protocol: The mouse GeneChips were scanned using GeneChip Scanner 3000. The images were analyzed using Expression Console and standard array quality controls analyses were carried out according to the instructions provided by Affymetrix.

data_processing: Data was processed with the three-step method of the AffyPLM package of Bioconductor v2.12 using RMA.2 and quantile normalization in R v 2.15.2.

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgG1 GC LZ B cells, GFP-

label_protocol: SPIA cDNA were prepared according to NuGEN Ovation Pico WTA System v2 Kit's protocol from 2ng of total RNA. 5ug of SPIA cDNA were fragmented and labelled according to NuGEN Encore Biotin Kit's protocol.

extract_protocol: RNA extraction was performed according to the Arcturus Picopure RNA Purification Kit's protocol.

treatment_protocol: Mice were infected with the parasite Nippostrongylus brasiliensis. Mesenteric lymph node (LN) cells were harvested and single cell suspensions were prepared. The cells were stained with fluorescent-labeled antibodies and sorted in an BD FACS Aria II (4/5 lasers).

tag: strain/background

value: CeGFP BALB/c

tag: ki

value: IRES-GFP in Cepsilon 3'UTR

value: Nippostrongylus brasiliensis infection

value: mesenteric lymph nodes

value: IgG1 germinal center Light Zone B cells

tag: gfp


title: 206381 treated -1

status: Public on Oct 31 2013

type: RNA

city: Ann Arbor

first: David

last: Miller

state: MI

address: 3560B MSRB II, 1150 W. Medical Center Dr.

department: Internal Medicine

country: USA

institute: University of Michigan

hyb_protocol: Hybridization with Affymetrix Human Genome U133 Plus 2.0 Genechips conducted by commecial vendor (SeqWright DNA Technology Services, Houston TX).

scan_protocol: Image capture done by commecial vendor with Affymetrix 7G scanner (SeqWright DNA Technology Services, Houston TX).

data_processing: Primary data analysis done by commecial vendor using Mas5.0 algorithm (SeqWright DNA Technology Services, Houston TX).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: BE(2)-C neuronal cells

label_protocol: RNA labelled by commecial vendor (SeqWright DNA Technology Services, Houston TX).

growth_protocol: BE(2)-C neuronal cells grown in DMEM (high glucose formulation) with 0.1 mM non-essential amino acids, 10 U/ml penicillin, 10 ug/ml streptomycin, and 5% bovine growth serum at 37C in 5% CO2.

extract_protocol: Total RNA harvested using Trizol with subsequent purification using RNAsy (both according to the manufacturer's instructions).  Quantity/purity examined by A260/280 and non-denaturing gel electrophorises with EtBr staining.

treatment_protocol: Cells incubated with either DMSO or 25 uM 205432/206381 for 24 h.

tag: treatment


title: LE:HL_60

type: genomic

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

description:
S1975150536
Pro myelocytic leukemia

data_processing:
Probe intensities were normalized using the crlmmCopynumber method from Bioconductor's crlmm package (http://www.bioconductor.org/packages/release/bioc/html/crlmm.html). Log probe intensities were mean centered to have a mean of zero for each sample.
Normalized data consists of mean centered probe intensities (mean of each sample subtracted from the log probe intensities for the sample, to give a mean of zero for the sample). Non-normalized data is the copy number data from crlmmCopynumber method from Bioconductor's crlmm package (http://www.bioconductor.org/packages/release/bioc/html/crlmm.html).

label: biotin, dinitrophenyl

molecule: genomic DNA

source_name: Pro myelocytic leukemia

label_protocol: Done according to array manufacturer's specifications. The labels are C-Bio and A-DNP. C and G nucleotides are biotin labeled and A and T nucleotides were dinitrophenyl labeled

growth_protocol: Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0.5 x 10^6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 37C. Spin down suspended cells, and resuspend in ~3ml growth media. Count cells. Pass 1x10^6 cells into new T162's w 30 ml media. Repeat growth cycle until desired amount of cells are available. Cells are not grown past passage 20.

extract_protocol: Genomic DNA was purified from cells using either the QIAamp DNA Blood Maxi Kit, or the Blood & Cell Culture DNA Maxi Kit (Qiagen Inc., Valencia, CA) according to manufacturer's instructions.  Quality was assessed by optical density 260/280 ratio using a spectrophotometer (Beckman-Coulter, Fullerton, CA) and by 0.8% agarose (SeaKem GTG, FMC BioProducts, Rockland, ME) gel electrophoresis in 1x TAE (Roche, Indianapolis, IN).

treatment_protocol: Untreated

tag: tissue of origin

value: Leukemia

tag: age

tag: gender

value: male

tag: prior treatment

tag: epithelial

value: no

tag: source

value: PBL

tag: ploidy

tag: p53 mutation

value: MT

tag: doubling time (hrs)

tag: contributing institute

value: National Cancer Institute, NIH

tag: contributing person

value: R.C. Gallo

tag: reference


title: DZ IgG1 GFP- #3

description:
IgG_DZ_3
Sorted LN IgG1+GFP-CXCR4highCD86low DZ GC cells.

organism: Mus musculus

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgG1 GC DZ B cells, GFP-

tag: tissue

tag: cell type

value: IgG1 germinal center Dark Zone B cells


title: LE:RPMI_8226

description:
S1975150481
Myeloma

hyb_protocol: Done according to array manufacturer's specifications

source_name: Myeloma

value: PB

value: 3n-, Hypotriploid (58-68)

value: WT

value: G.E. Moore


title: LC:NCI_H23

description:
S1975150437
Adenocarcinoma-undifferentiated

scan_protocol: Done according to array manufacturer's specifications

source_name: Adenocarcinoma

value: Non-Small Cell Lung

value: yes

value: 2n+, Hyperdiploid (47-57)

value: J.D. Minna; A.F. Gazdar


title: LC:NCI_H322M

description:
S1975150666
Small cell Bronchioalveolar Carcinoma

source_name: Small cell Bronchioalveolar Carcinoma


title: LE:K_562

description:
S1975150425
CML

source_name: CML

value: female

value: Bisulfan/PiBr

value: Pleural effusion

value: University of Tennesse

value: H.T. Holden


title: LC:NCI_H460

description:
S1975150439
Large Cell Carcinoma-undifferentiated

source_name: Large Cell Carcinoma

value: male


title: 205432 treated -1


title: DMSO treated -D2

value: DMSO


title: LC:HOP_92_rep2

description:
S1975150457
Large cell-undifferentiated

source_name: Large cell

value: MT

value: Johns Hopkins University


title: LZ IgG1 GFP+ #3

description:
IgG_LZg_3
Sorted LN IgG1+GFP+CXCR4lowCD86high LZ GC cells.

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgG1 GC LZ B cells, GFP+

tag: strain/background

value: CeGFP BALB/c

tag: ki

value: IRES-GFP in Cepsilon 3'UTR

value: Nippostrongylus brasiliensis infection

value: mesenteric lymph nodes

value: IgG1 germinal center Light Zone B cells


title: 110 d57

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: study participant 10

hyb_protocol: After precipitation, purification and quantification the labeled samples were hybridized according to the supplier’s protocol (Agilent Technologies)

scan_protocol: Scanning of microarrays was performed with 5µm resolution, 16 bit and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies)

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA ( Agilent Technologies). The extracted MAGE-ML files were further analyzed with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA). The values are the 'gProcessedSignal' from the Agilent Technologies Feature Extraction and represent signal intensities left after multiplicatively detrended background subtraction. Arrays were normalized to the mean of trimmed positive non-flagged/non-control Reporters.

source_name: d57 post immunization

label_protocol: Total RNA labeling was performed with the one color Quick Amp Labeling Kit (Agilent Technologies)

extract_protocol: Total RNA from PBMCs was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier

treatment_protocol: Cell preparation tubes (CPT) were used for PBMC isolation.

value: PBMC

value: PPD negative


title: LC:NCI_H522

description:
S1975150424
Adenocarcinoma-very poorly differentiated

value: Non-Small Cell Lung

value: yes

value: National Cancer Institute, NIH


title: LE:CCRF_CEM

description:
S1975150330
ALL

source_name: ALL

value: Leukemia

value: female

value: Rad/Mtx/Cyx

value: no

value: Children's Cancer research Foudation

value: G.E. Foley


title: DZ IgG1 GFP+ #3

description:
IgG_DZg_3
Sorted LN IgG1+GFP+CXCR4highCD86low DZ GC cells.

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgG1 GC DZ B cells, GFP+

tag: treatment

value: IgG1 germinal center Dark Zone B cells

tag: gfp


title: 109 d57

description: study participant 9


title: DMSO treated -D1

value: DMSO


title: SUDHL-1, Treated by ALK inhibitor repl 3

city: Philadelphia

first: Wasik

middle: A

last: Mariusz

state: Pennsylvania

address: 422 Curie Blvd

institute: University of Pennsylvania

description: Gene expression profiling of SUDHL-1 cell line

hyb_protocol: according to the manufacturer’s instructions as found in GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 2

data_processing: Microarray data were normalized using the MAS5 algorithm and analyzed using Partek GS (Partek). Differentially expressed genes were identified using ANOVA

label: Biotin

source_name: SUDHL-1 cell line teated by ALK inhibitor

label_protocol: 3ug of input total RNA were amplified and labeled using the Affymetrix 1-cycle kit

growth_protocol: Cells were cultured at 37 °C and 5% CO2 in RPMI medium 1640, supplemented with 2-mM L-glutamine, 10% heat-inactivated FBS (FBS), 1% penicillin/streptomycin mixture and, where applicable, 200 units of IL-2 (Bender MedSystems)

extract_protocol: total RNA was isolated using a TRIZOL and Qiagen Rneasy protocols

treatment_protocol: The ALK+TCL Sudhl-1 cell line was treated in triplicates with the ALK inhibitor, CEP-14083, or the compound's solvent for 6 h

tag: cell line

value: SUDHL-1 Cells derived from the a patient with Anaplastic Large Cell Lymphoma

tag: agent

value: ALK inhibitor CEP-14083


title: 101 d180

description: study participant 1

source_name: d180 post immunization


title: LZ IgG1 GFP- #2

description:
IgG_LZ_2
Sorted LN IgG1+GFP-CXCR4lowCD86high LZ GC cells.

value: CeGFP BALB/c

value: IRES-GFP in Cepsilon 3'UTR

value: Nippostrongylus brasiliensis infection

value: mesenteric lymph nodes


title: 107 d57

description: study participant 7

value: PBMC

value: PPD negative


title: SUDHL-1, Treated by ALK inhibitor repl 2

scan_protocol: according to the manufacturer’s instructions as found in GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 2


title: DZ IgG1 GFP- #2

description:
IgG_DZ_2
Sorted LN IgG1+GFP-CXCR4highCD86low DZ GC cells.


title: 205432 treated -2


title: 106 d57

description: study participant 6


title: CO:HT29

description:
S1975150273
Adenocarcinoma-moderate differentiation

tag: tissue of origin

value: Colon

tag: age

tag: gender

tag: prior treatment

value: yes

value: Primary

value: MT

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor Cells in vitro:115-159, 1975


title: LZ IgG1 GFP+ #2

description:
IgG_LZg_2
Sorted LN IgG1+GFP+CXCR4lowCD86high LZ GC cells.

value: IgG1 germinal center Light Zone B cells


title: 105 d57

description: study participant 5


title: SUDHL-1, control repl 3

source_name: SUDHL-1 cell line

value: control


title: LC:HOP_62

description:
S1975150328
adenocarcinoma-undifferentiated

source_name: adenocarcinoma

value: Non-Small Cell Lung

value: female

tag: epithelial

tag: ploidy

value: 4n+, Hypertetraploid (93-103)

tag: p53 mutation

value: Johns Hopkins University


title: 104 d57

description: study participant 4


title: CO:KM12

description:
S1975150524
Adenocarcinome-poor differentiation

source_name: Adenocarcinome

tag: doubling time (hrs)

tag: contributing institute

value: MD Anderson Hospital and Tumor Institute

tag: contributing person

value: I.J. Fidler, Univ of Texas M.D. Anderson Hospital and Tumor Institute


title: LC:HOP_92_rep1

description:
S1975150317
Large cell-undifferentiated

value: male


title: LC:EKVX

description:
S1975150426
Adenocarcinoma-moderate differentiation

value: Norsk Hydro's Institut, Norway


title: SUDHL-1, control repl 2

value: SUDHL-1 Cells derived from the a patient with Anaplastic Large Cell Lymphoma


title: LC:NCI_H226

description:
S1975150337
Squamous cell carcinoma-very poorly differentiated

source_name: Squamous cell carcinoma

value: None (non smoker)

value: yes

value: 3n, Triploid (69)

value: National Cancer Institute, NIH

value: J.D. Minna; A.F. Gazdar

tag: reference


title: SUDHL-1, Treated by ALK inhibitor repl 1

value: ALK inhibitor CEP-14083


title: CO:SW_620

description:
S1975150336
Carcinoma-undifferentiated

source_name: Carcinoma

value: Colon

value: MT

value: Scott White Clinic

value: A. Leibovitz


title: CO:HCT_15

description:
S1975150513
Adenocarcinoma-poor to moderate differentiation

value: ATCC

value: ATCC (D.L. Dexter, Roger Williams General Hospital)


title: ME:SK_MEL_5

description:
S1975150335
Malignant melanotic melanoma

source_name: Malignant melanotic melanoma

value: Melanoma

value: female

value: no

tag: source

value: Metastasis

value: 4n+, Hypertetraploid (93-103)

value: WT

value: Memorial Sloan Kettering Cancer Center

value: T. Takahashi


title: CO:HCC_2998

description:
S1975150446
carcinoma

source_name: carcinoma

value: yes

value: MD Anderson Hospital and Tumor Institute


title: 103 d57

description: study participant 3

tag: tissue

value: PBMC

tag: cell type

value: PPD negative


title: 101 d57

description: study participant 1


title: Monocytes from ACHF patient post- vs. pre-treatment biological replicate 6 - technical replicate 2

city: Chieti

first: Mirko

last: Pesce

address: Via Vestini

country: Italy

institute: University G. D'Annunzio

description: Biological replicate 6 of 6; technical replicate 2

hyb_protocol: Microarrays were dehydrated in ethanol for 2 minutes at room temperature, and dried using compressed air. Microarrays were rehydrated by soaking in prehybridization solution (5x SSPE pH 7, 0.1% SDS, 1% BSA) for 2 hours at 42°C, then were washed in deionized water twice for 1 minute each, and dried by briefly spinning in a centrifuge. Labeled aRNA was denatured at 95°C for 5 minutes, and applied to microarray slide. Microarrays and labeled aRNA were then covered with cover slips (Knittel Glass), placed in Hyb chamber (Gene Machine) and hybridized for 14-16 hours at 42°C. Microarray slides were washed in 2x SSPE, 0.1% SDS at 42°C for 5 minutes, then in 0.1x SSPE, 0.1% SDS once for 2 minutes at room temperature. Slides were then washed three times for 1 minute each at room temperature in 0.1x SSPE, immediately dried by briefly spinning in a centrifuge, and stored in a dark box.

scan_protocol: After hybridization, Cy5-Cy3 fluorescent signals were captured by a Confocal Laser Scanner ScanArray Express (Packard BioScience) and analysed using the software ScanArray Express - MicroArray Analysis System version 3.0 (Perkin Elmer).

data_processing: The values of the median signal intensity from each spot were subtracted by the local median background intensity. For each slide after local background subtraction, a LOWESS algorithm was used for raw data normalization to evaluate the signal-to-noise ratio of test sample vs. reference signal with the software ScanArray Express - MicroArray Analysis System version 3.0 (Perkin Elmer).

source_name: peripheral blood monocytes from ACHF patients post-ordinary treatment

label_protocol: Five to twenty microgram of amplified aRNA was fluorescently labelled with Cy5 (Amersham, Pharmacia Biotech, Buckinghamshire, UK).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: primary culture

value: ex vivo monocytes

tag: phenotype

value: ACHF patients treated with ordinary drugs

source_name: peripheral blood monocytes from ACHF patients pre-ordinary treatment

value: ACHF patients pre-treatment


title: CO:COLO205

description:
S1975150419
Adenocarcinoma

source_name: Adenocarcinoma

value: Colon

value: male

value: Ascites

value: 3n, Triploid (69)

value: MT

value: Denver Medical Hospital

value: G.E. Moore


title: Monocytes from ACHF patient post- vs. pre-treatment biological replicate 6 - technical replicate 1

description: Biological replicate 6 of 6; technical replicate 1


title: DZ IgG1 GFP- #1

description:
IgG_DZ_1
Sorted LN IgG1+GFP-CXCR4highCD86low DZ GC cells.

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgG1 GC DZ B cells, GFP-

tag: strain/background

value: CeGFP BALB/c

tag: ki

value: IRES-GFP in Cepsilon 3'UTR

tag: treatment

value: Nippostrongylus brasiliensis infection

value: mesenteric lymph nodes

value: IgG1 germinal center Dark Zone B cells

tag: gfp


title: DZ IgG1 GFP+ #1

description:
IgG_DZg_1
Sorted LN IgG1+GFP+CXCR4highCD86low DZ GC cells.


title: SUDHL-1, control repl 1

tag: cell line

value: SUDHL-1 Cells derived from the a patient with Anaplastic Large Cell Lymphoma

tag: agent

value: control


title: Naïve #3

description:
VI3
Sorted LN B220+CD95-CD138-IgG1-IgE- naïve B cells.

source_name: Mesenteric LN, d10 N. brasiliensis infection, Naïve B cells, GFP

value: Naïve B cells


title: DZ IgG1 GFP+ #2

description:
IgG_DZg_2
Sorted LN IgG1+GFP+CXCR4highCD86low DZ GC cells.


title: Monocytes from ACHF patient post- vs. pre-treatment biological replicate 5

description: Biological replicate 5 of 6

value: ex vivo monocytes

value: ACHF patients treated with ordinary drugs


title: CNS:U251

description:
S1975150415
Glioblastoma-undifferentiated

source_name: Glioblastoma

tag: tissue of origin

value: CNS

tag: age

tag: gender

tag: epithelial

value: no

tag: ploidy

value: 2n+, Hyperdiploid (47-57)

value: University of Uppsala, Sweden

value: J Neuropathol Exp Neurol 40:410-427, 1981


title: 109 d29

description: study participant 9

source_name: d29 post immunization

value: PBMC

value: PPD negative


title: Naïve #2

description:
VI2
Sorted LN B220+CD95-CD138-IgG1-IgE- naïve B cells.

value: CeGFP BALB/c


title: LC:A549

description:
S1975150386
Adenocarcinoma-poor to moderate differentiation

value: Non-Small Cell Lung

value: male

value: yes

tag: p53 mutation

value: WT

tag: doubling time (hrs)

tag: contributing institute

value: National Cancer Institute, NIH

tag: contributing person

value: Giard DJ

tag: reference


title: 102 d57

description: study participant 2

source_name: d57 post immunization

tag: tissue

tag: cell type


title: LZ IgG1 GFP- #1

description:
IgG_LZ_1
Sorted LN IgG1+GFP-CXCR4lowCD86high LZ GC cells.

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgG1 GC LZ B cells, GFP-

tag: strain/background

tag: ki

value: IRES-GFP in Cepsilon 3'UTR

value: Nippostrongylus brasiliensis infection

value: mesenteric lymph nodes

value: IgG1 germinal center Light Zone B cells


title: 110 d29

description: study participant 10


title: UV-B regulation of microRNAs in maize

type: other

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

description:
For total description of the protocol used, see
http://www.lcsciences.com/products/genomics/mirna/mirna_microarray/mirna_detail.html

hyb_protocol: Hybridisation was performed overnight on a Paraflo microfluidic chip using a micro-circulation pump (Atactic Technologies, Houston, TX, USA) (Gao et al. 2004; Zhu et al. 2007). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to the target miRNA or other RNA (control or customer-defined sequences) and a spacer segment of polyethylene glycol extending the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photo-generated reagent). The hybridisation melting temperatures were balanced by chemical modifications of the detection probes. Hybridisation was performed with 100 ?L 6× SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C. Subsequent hybridisation detection used fluorescence labelling with tag-specific Cy3 and Cy5 dyes.

scan_protocol: Hybridisation images were collected using GenePix 4000B (Molecular Device, Sunnyvale, CA, USA) and digitised using Array-Pro image analysis software (Media Cybernetics, Bethesda, MD, USA).

data_processing: An in house software for routine array data processing that follows the common practices of DNA array data treatment developed by LC Sciences was used. In their process, data was corrected by subtracting background and normalized to the statistical mean of all detectable transcripts.  The data were processed in a MS Excel spreadsheet using a program routine that performs raw signal background subtraction using a local regression method (Xiaochuan Zhou, unpublished results)   Data normalization, using a cyclic LOWESS (Locally-weighted Regression) method was used to remove system related variations, such as sample amount variations, dye labeling bias, and signal gain differences between scanners, so that biological relevant variations can be faithfully revealed.

molecule: other

organism: Zea mays

source_name: microRNAs from control maize leaves

label_protocol: An oligonucleotide tag was then ligated to the poly(A) tail for subsequent fluorescent dye staining; two different tags (Cy3 and Cy5) were used for our dual-sample experiments.

growth_protocol: control plants grown in the absence of UV-B.

extract_protocol: The total RNA was extracted using Trizol.  2-5 ug total RNA sample was size fractionated using a YM-100 Microcon centrifugal filter (Millipore, Bejing, China). The small RNAs (<300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase.

value: leaf

source_name: microRNAs from UV-B treated maize leaves

growth_protocol: Plants were grown in the absence of UV-B for 4 weeks before treatment.

treatment_protocol: treated with UV-B radiation during 8 hs.


title: Naïve #1

description:
VI1
Sorted LN B220+CD95-CD138-IgG1-IgE- naïve B cells.

tag: treatment

value: Naïve B cells


title: LZ IgG1 GFP+ #1

description:
IgG_LZg_1
Sorted LN IgG1+GFP+CXCR4lowCD86high LZ GC cells.

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgG1 GC LZ B cells, GFP+

tag: gfp


title: 108 d29

description: study participant 8


title: Monocytes from ACHF patient post- vs. pre-treatment biological replicate 4

description: Biological replicate 4 of 6

tag: primary culture

value: ex vivo monocytes

tag: phenotype

value: ACHF patients treated with ordinary drugs

value: ACHF patients pre-treatment


title: UV-B regulation of microRNAs in maize-2

treatment_protocol: treated with UV-B radiation during 8 hs

growth_protocol:
Plants were grown in the absence of UV-B for 4 weeks before the treatment.
control plants grown in the absence of UV-B.


title: CNS:SNB_75

description:
S1975150447
Astrocytoma

source_name: Astrocytoma

tag: tissue of origin

value: CNS

value: female

tag: prior treatment

value: no

value: 2n+, Hyperdiploid (47-57)

value: MT

value: NINCDS

value: P.L. Kornblith


title: Monocytes from ACHF patient post- vs. pre-treatment biological replicate 3

description: Biological replicate 3 of 6


title: CNS:SNB_19

description:
S1975150302
Glioblastoma-undifferentiated

tag: age

tag: gender

value: male

tag: epithelial


title: PC IgE GFP+ #4

description:
V4
Sorted LN IgE+GFP+CD95+CD138+ PC.

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgE PC, GFP+

value: CeGFP BALB/c

value: IRES-GFP in Cepsilon 3'UTR

value: IgE plasma cells


title: 106 d29

description: study participant 6

value: PBMC

value: PPD negative


title: Monocytes from ACHF patient post- vs. pre-treatment biological replicate 2 - technical replicate 3

description: Biological replicate 2 of 6; technical replicate 3


title: 107 d29

description: study participant 7


title: CNS:SF_539

description:
S1975150299
Glial cell neoplasm

source_name: Glial cell neoplasm

tag: ploidy

tag: p53 mutation

value: WT

tag: doubling time (hrs)

value: University of California

value: M.L. Rosenblum

value: J Neuropathol Exp Neurol 40:201-229, 1981


title: Monocytes from ACHF patient post- vs. pre-treatment biological replicate 6 - technical replicate 3

description: Biological replicate 6 of 6; technical replicate 3

value: ex vivo monocytes

value: ACHF patients treated with ordinary drugs

value: ACHF patients pre-treatment


title: Monocytes from ACHF patient post- vs. pre-treatment biological replicate 2 - technical replicate 1

description: Biological replicate 2 of 6; technical replicate 1


title: 103 d29

description: study participant 3


title: 104 d29

description: study participant 4


title: PC IgE GFP+ #2

description:
V2
Sorted LN IgE+GFP+CD95+CD138+ PC.

value: Nippostrongylus brasiliensis infection

value: mesenteric lymph nodes


title: Monocytes from ACHF patient post- vs. pre-treatment biological replicate 1 - technical replicate 2

description: Biological replicate 1 of 6; technical replicate 2


title: PC IgG1 GFP+ #2

description:
IV2
Sorted LN IgG1+GFP+CD95+CD138+ PC.

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgG1 PC, GFP+

value: IgG1 plasma cells


title: PC IgE GFP+ #3

description:
V3
Sorted LN IgE+GFP+CD95+CD138+ PC.


title: Monocytes from ACHF patient post- vs. pre-treatment biological replicate 2 - technical replicate 2

description: Biological replicate 2 of 6; technical replicate 2


title: TGF-beta local skin mouse 1

city: Boston

first: Romy

middle: B

last: Christmann

state: MASSACHUSETTS

address: 715 Albany Street E5

institute: Boston University School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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: TGF-beta local

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 7-days subcutaneous pumps were implanted in mice and cytokines were continouslly released in the skin: PBS as a control, IL-13, TSLP or TGF-beta

tag: strain

value: skin from the pump outlet

tag: stimulating agent

value: TGF-beta


title: CO:HCT_116

description:
S1975150764
carcinoma-very poorly differentiated

source_name: carcinoma

value: Colon

value: male

value: yes

value: 2n-, Hypodiploid (35-45)

tag: contributing institute

value: Baylor College

tag: reference


title: PC IgG1 GFP+ #1

description:
IV1
Sorted LN IgG1+GFP+CD95+CD138+ PC.

tag: strain/background

value: CeGFP BALB/c

tag: ki

value: IRES-GFP in Cepsilon 3'UTR

tag: tissue

tag: cell type


title: 102 d29

description: study participant 2

value: PBMC

value: PPD negative


title: GC IgE GFP+ #3

description:
III3
Sorted LN IgE+GFP+B220+CD95+CD138- GC cells.

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgE GC B cells, GFP+

tag: treatment

value: IgE germinal center B cells

tag: gfp


title: BR:T47D

description:
S1975150417
infiltrating ductal carcinoma

source_name: infiltrating ductal carcinoma

tag: tissue of origin

value: Breast

value: female

value: 2n+, Hyperdiploid (47-57)

value: MT

tag: contributing person

value: I. Keydar


title: PC IgE GFP+ #1

description:
V1
Sorted LN IgE+GFP+CD95+CD138+ PC.

value: Nippostrongylus brasiliensis infection

value: mesenteric lymph nodes

value: IgE plasma cells


title: CNS:SF_295_rep1

description:
S1975150314
Glioblastoma-undifferentiated

value: CNS

tag: age

tag: gender

tag: prior treatment

value: Rad

value: no

value: University of California

value: M.L. Rosenblum

value: Acta Neuropathol 75:92-103, 1988


title: 105 d29

description: study participant 5

value: PBMC


title: CNS:SF_268

description:
S1975150300
Glioblastoma-undifferentiated

tag: epithelial

tag: ploidy

tag: p53 mutation

value: Acta Neuropathol 75:92-103, 1987


title: TSLP local skin

source_name: TSLP local skin

tag: strain

value: skin from the pump outlet

tag: stimulating agent

value: TSLP


title: CNS:SF_295_rep2

description:
S1975150346
Glioblastoma-undifferentiated

value: female

tag: doubling time (hrs)

tag: contributing institute

tag: reference


title: Monocytes from ACHF patient post- vs. pre-treatment biological replicate 1 - technical replicate 1

description: Biological replicate 1 of 6; technical replicate 1

source_name: peripheral blood monocytes from ACHF patients post-ordinary treatment

tag: primary culture

value: ex vivo monocytes

tag: phenotype

value: ACHF patients treated with ordinary drugs

source_name: peripheral blood monocytes from ACHF patients pre-ordinary treatment

value: ACHF patients pre-treatment


title: IL-13 local skin

source_name: IL-13 local skin

tag: tissue


title: PBS distal skin

source_name: PBS distal skin

value: skin from the abdomen, far from the pump outlet

value: PBS (control)


title: GC IgE GFP+ #1

description:
III1
Sorted LN IgE+GFP+B220+CD95+CD138- GC cells.

tag: strain/background

value: CeGFP BALB/c

tag: ki

value: IRES-GFP in Cepsilon 3'UTR

tag: treatment

value: Nippostrongylus brasiliensis infection

value: mesenteric lymph nodes

tag: cell type

value: IgE germinal center B cells

tag: gfp


title: 106 d0

description: study participant 6

source_name: naive, pre-immunization

value: PPD negative


title: 109 d0

description: study participant 9


title: 107 d0

description: study participant 7


title: 108 d0

description: study participant 8


title: GC IgG1 GFP+ #3

description:
II3
Sorted LN IgG1+GFP+B220+CD95+CD138- GC cells.

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgG1 GC B cells, GFP+

value: IgG1 germinal center B cells


title: PBS local skin

source_name: PBS local skin


title: 105 d0

description: study participant 5

value: PBMC


title: TGF-beta local skin mouse 2

value: TGF-beta


title: GC IgG1 GFP+ #2

description:
II2
Sorted LN IgG1+GFP+B220+CD95+CD138- GC cells.


title: 104 d0

description: study participant 4


title: GC IgG1 GFP- #3

description:
I3
Sorted LN IgG1+GFP-B220+CD95+CD138- GC cells.

source_name: Mesenteric LN, d10 N. brasiliensis infection, IgG1 GC B cells, GFP-


title: GC IgG1 GFP+ #1

description:
II1
Sorted LN IgG1+GFP+B220+CD95+CD138- GC cells.


title: 103 d0

description: study participant 3


title: 101 d0

description: study participant 1


title: BR:BT_549

description:
S1975150282
Papillary infiltrating ductal carcinoma-mammary gland; breast

tag: tissue of origin

value: Breast

tag: age

tag: gender

value: yes

tag: source

value: Metastasis

tag: contributing person

value: W. Coutinho; E.Y. Lasfargues


title: GC IgG1 GFP- #1

description:
I1
Sorted LN IgG1+GFP-B220+CD95+CD138- GC cells.


title: BR:MCF7

description:
S1975150283
Adenocarcinoma-mammary gland; breast; metastatic site: pleural effusion;

value: female

tag: epithelial

value: Pleural effusion

tag: ploidy

value: 3n-, Hypotriploid (58-68)

tag: p53 mutation

value: WT

value: Michigan Cancer Foundtion

value: C.M. McGrath


title: BR:MDA_MB_231

description:
S1975150427
Adenocarcinoma-mammary gland; breast; epithelial; metastatic site: pleural effusion;

value: 2n+, Hyperdiploid (47-57)

value: MT

tag: doubling time (hrs)

tag: contributing institute

value: MD Anderson Hospital and Tumor Institute

value: R. Cailleau

tag: reference


title: E14 cells_Zfp322a RNAi-rep2

first: Qiang

last: Wu

address: 8 Medical Drive

department: Biochemistry

institute: National University of Singapore

description: Gene expression data from Zfp322a RNAi ( selected by puromycin for 3 days).

data_processing: The data were analyzed using RMA in the bioconducter and normalized using cross correlation.

source_name: E14 cells_Zfp322a RNAi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Murine ES cells (E14) were cultured in ES cell medium consisting of Glasgow Minimum Essential Medium (GMEM; Invitrogen), 15% ES cell qualified fetal bovine serum (FBS; Invitrogen), 0.055 mM β-mercaptoethanol (Sigma), 100 mM sodium pyruvate (Invitrogen), 0.1 mM MEM nonessential amino acid (NEAA, Invitrogen) and 1,000 units/ml of LIF (Millipore).

treatment_protocol: Transfection was conducted using Lipofectamine 2000 (Invitrogen) according to the manual provided.  For shRNA, cells were selected in 6-well culture plate for 3 d using puromycin.  The cells were then harvested for either extraction of protein or RNA.

value: E14 murine embryonic stem cells

tag: genotype

value: Zfp322a Knock-down cells


title: BR:HS578T

description:
S1975150664
Carcinosarcoma-mammary gland; breast

source_name: Carcinosarcoma-mammary gland; breast

value: Primary

value: Naval Bioscience Laboratory

value: A.J. Hackett


title: 102 d0

description: study participant 2

tag: tissue

value: PBMC

value: PPD negative


title: Blnk in Ph+ ALL (Blnk-S3)

city: Los Angeles

first: Markus

last: Müschen

state: CA

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

hyb_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

data_processing: RMA

source_name: Total RNA from Ph+ ALL (Balb/c)

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site.

tag: strain

value: Balb/c

value: 4 weeks

value: BCR-ABL1 transformed pre-B cells

tag: disease state

value: BCR-ABL1-driven ALL

tag: genotype/variation

value: Blnk KO

tag: transduction

value: Blnk (Slp65)


title: E14 cells_control RNAi-rep2

description: Gene expression data from mock RNAi (pSuper.puro transfected cells selected by puromycin for 3 days).

source_name: E14 cells_control RNAi

tag: cell type

value: Mock knock-down cells


title: GC IgE GFP+ #2

description:
III2
Sorted LN IgE+GFP+B220+CD95+CD138- GC cells.

tag: strain/background

value: CeGFP BALB/c

tag: ki

value: IRES-GFP in Cepsilon 3'UTR

tag: treatment

value: Nippostrongylus brasiliensis infection

value: mesenteric lymph nodes

value: IgE germinal center B cells

tag: gfp


title: E14 cells_Zfp322a RNAi-rep1

value: E14 murine embryonic stem cells

value: Zfp322a Knock-down cells


title: E14 cells_control RNAi-rep1


title: 110 d0

description: study participant 10


title: Blnk in Ph+ ALL (pMIG-S3)

scan_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

tag: age

value: pMIG


title: Blnk in Ph+ ALL (Blnk-S1)


title: Blnk in Ph+ ALL (Blnk-S2)


title: siAKR1B10

city: Sapporo

first: Masashi

last: Idogawa

country: Japan

institute: Sapporo Medical University

description: Gene expression after the transfection of siAKR1B10 without adriamycin treatment

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing:
Agilent Feature Extraction Software (v 10.7) was used for background subtraction.
Log2 values were calculated by Limma (R package) for the normalization in each cell line.

source_name: HCT116, siAKR1B10

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: H1299 and HCT116 cells were cultured in DMEM and McCoy's 5A medium with 10% FCS, respectively.

extract_protocol: 24h after infection or second transfection, total RNA was extracted by RNeasy mini kit (QIAGEN) according to manufacturer's protocol. RNA was quantified using the NanoDrop spectrophotometer.

treatment_protocol: H1299 cells were infected with adenoviruses expressing p53, p63g or p73b at 25 moi. HCT116 cells were transfected with siRNAs targeting AKR1B10 or negative control. 4h after the transfection, these cells were treated with adriamycin (0.5 ug/ml). 24h after the treatment, siRNAs were transfected into cells again.

tag: cell line

tag: sirna


title: Blnk in Ph+ ALL (pMIG-S2)


title: p73b

description: Gene expression after Ad-p73b infection

tag: infection


title: siAKR1B10+ADR

description: Gene expression after the transfection of siAKR1B10 with adriamycin treatment

source_name: HCT116, siAKR1B10+ADR

value: adriamycin


title: Liver of salmon fed with a  plant diet, fish 4

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with GenePix 4100A DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1 and GenePix Pro 6.0. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Liver of salmon fed with a fish meal based diet, pool of 10 fish

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol using Agilent Quick Amp Labelling Kit

growth_protocol: Salmon (initial average weight 362 ± 95g) was kep in tanks with sea water

extract_protocol: RNA was isolated using TRIzol® (Invitrogen), and purified with PureLink RNA mini kits

treatment_protocol: The fish were fed continuously and approximately 20% in excess of expected feed intake a plant based diet with and without 1.5% cholesterol

value: liver


title: Liver of salmon fed with a  plant diet, fish 3


title: Liver of salmon fed with a  plant diet, fish 5

source_name: Liver of salmon fed with a  plant diet, fish 4


title: siCont+ADR

description: Gene expression after the transfection of siControl with adriamycin treatment

source_name: HCT116, siCont+ADR

value: siControl


title: p63g

description: Gene expression after Ad-p63g infection


title: Liver of salmon fed with a  plant diet, fish 1


title: siCont

description: Gene expression after the transfection of siControl without adriamycin treatment

source_name: HCT116, siCont


title: p53

description: Gene expression after Ad-p53 infection


title: LacZ

description: Gene expression after Ad-LacZ infection

source_name: H1299, LacZ

value: Ad-LacZ


title: Liver of salmon fed with a cholesterol supplemented plant diet, fish 5

source_name: Liver of salmon fed with a cholesterol supplemented plant diet, fish 4


title: Liver of salmon fed with a cholesterol supplemented plant diet, fish 4


title: Liver of salmon fed with a cholesterol supplemented plant diet, fish 2


title: Liver of salmon fed with a cholesterol supplemented plant diet, fish 3


title: WHI3_rep2

city: Stony Brook

first: Ying

last: Cai

state: New York

address: Life Sciences Building Rm 363

department: Molecular Genetics and Microbiology

institute: Stony Brook University

description: Biological replicate 2 of 2. RNA immunoprecipitated by WHI3

hyb_protocol: Labeled samples were boiled in hybridization buffer ( 25% formamide, 5xSSC, %0.1 SDS, 100ug/mL ssDNA) following resuspension, Boiled sample is then hybridized to the homemade Stonybrook_Redgreengene.com-S.cerevisiae-9.2k-A11 array at 50°C for 16-20 hours. After hybridization, array were rinsed 2x in wash buffer (2xSSC, 1% SDS, 50°C), washed 10 minutes x2 in wash buffer and then rinsed 4x with 1xSSC (RT). Arrays were dried by centrifugation for immediate scan.

scan_protocol: Array were scanned on GenePix 4000B (Axon Instrument) controlled by GenePix Pro 5.1 software.  Images were quantified using GenePix Pro.

data_processing: The net intensity of each spot was calculated by subtracting the median of the local background from the foreground, and the red/green ratio was loess normalized.  Flagged spots were removed for analysis.  Spot values were averaged for multiple independent spots with the same probe.

organism: Saccharomyces cerevisiae

label_protocol: 20-25 µg input RNA and all of the immunoprecipitated RNA was used for labeling by an aminoallyl labeling method adapted from The Institute for Genomic Research, Standard Operating Procedure SOP #M004. Briefly, the RNA was reverse transcribed with SuperScript®II (invitrogen) and Oligo-dT, 2mM dNTPs and 0. 3mM amino-allyl-dUTP (Ambion) was added for incorporation into the cDNA. The labeled cDNA was purified and coupled with the appropriate NHS-ester Cy-dye (Amersham). All the labeled cDNAs from immunoprecipitated RNA were hybridized against total RNA containing 50 pmol of incorporated dye.

growth_protocol: Cells were grown in YPD at 30°C to log phase for harvest.

extract_protocol: To immunoprecipitate RNA, 8L of yeast cells carrying Whi3 or Whi3-dRRM tagged with the TAP tag were grown in YP to log phase. Cells were harvested, resuspended in cold lysis buffer (10mM Hepes-Na, pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 0.5 mM DTT and protease inhibitors) and lysed by passing through a French press twice. KCl and Triton were added to the extract to a final concentration of 200 mM KCl and 1% Triton. After centrifugation at 4000 rpm for 5 min and 15000 rpm for 15 min at 4°C, aliquots of the supernatants were saved for assays of input protein and RNA, and the rest was passed through columns filled with 100 µl IgG Sepharose 6 Fast Flow (GE Healthcare) (The protein A moiety of the TAP tag binds to IgG.). After three washes with IPP150 (10mM Tris-Cl, pH 8, 150 mM NaCl, 0.1% Triton), the IgG beads were resuspended in 600 µl TES (10mM Tris-HCl, pH8, 10mM EDTA, pH8, 0.5% SDS). To isolate the RNA associated with beads, equal volume of acid phenol was added, vortexed and incubated at 65°C for 15 min. After two rounds of acid phenol extraction, the isolated RNA was ethanol precipitated from the aqueous phase for labeling. Total RNA used for the microarray referece was extracted by acid phenol method.

tag: strain background

tag: sample type

value: immunoprecipated RNA

value: reference RNA


title: Liver of salmon fed with a cholesterol supplemented plant diet, fish 1


title: ctrl_rep2

description: Biological replicate 2 of 2. RNA immunoprecipitated by whi3-dRRM


title: Liver of salmon fed with a  plant diet, fish 2


title: TSCC 3A cy5/NC 3B cy3

status: Public on Oct 30 2013

city: Beijing

first: Ling-fei

last: Jia

address: 22 Zhongguancun Avenue South, Haidian District

country: China

institute: Peking University School and Hospital of Stomatology

description:
Sample 6
compare miRNA expression profiles in in Tongue squamous cell carcinoma (TSCC) and matched nonmalignant tissues (NC)

hyb_protocol: standard CapitalBio Methods: Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 15ul of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide. The array was hybridized at 42℃ overnight and  washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Luxscan 10K/A (CapitalBio)

data_processing: Intensity data was extracted from the TIFF images using LuxScanTM 3.0 software (CapitalBio Corp, Peking, China). The low-intensity spots were removed for which fewer than 30% of the signal pixels exceeded the median background plus two times its standard deviation.

source_name: Human tongue tissue, TSCC

label_protocol: 4μg of the Low-molecular-weight RNAs were isolated from total RNAs by a PEG solution precipitation method and labelled with 5-phosphate-cytidyl-uridyl-Cy3-3(Dharmacon, Chicago, United States) or Cy5 using T4 RNA ligase (NEB, Beijing, China) at 4°C for 4 hours in the dark. Eight synthetic small RNAs were spiked in for exogenous control.

growth_protocol: All paired primary TSCC samples were divided into two groups, one group is the TSCC from anterior portions of the tongue, and the other group is the TSCC adjacent histological normal tissues. All samples were obtained from 4 patients who were admitted to the Department of Oral and Maxillofacial Surgery of Peking University School of Stomatology.

extract_protocol: Total RNA was isolated from tumor and normal samples by using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA)

treatment_protocol: No treatment

tag: individual

value: TSCC

source_name: Human tongue tissue, NC

value: NC


title: TSCC 3A cy3/NC 3B cy5

description:
Sample 5
compare miRNA expression profiles in in Tongue squamous cell carcinoma (TSCC) and matched nonmalignant tissues (NC)

tag: tissue


title: ctrl_rep1

description: Biological replicate 1 of 2. RNA immunoprecipitated by whi3-dRRM


title: TSCC 4A cy3/NC 4B cy5

description:
Sample 7
compare miRNA expression profiles in in Tongue squamous cell carcinoma (TSCC) and matched nonmalignant tissues (NC)


title: TSCC 4A cy5/NC 4B cy3

description:
Sample 8
compare miRNA expression profiles in in Tongue squamous cell carcinoma (TSCC) and matched nonmalignant tissues (NC)


title: GC IgG1 GFP- #2

description:
I2
Sorted LN IgG1+GFP-B220+CD95+CD138- GC cells.

value: IgG1 germinal center B cells


title: WHI3_rep1

description: Biological replicate 1 of 2. RNA immunoprecipitated by WHI3


title: TSCC 2A cy3/NC 2B cy5

description:
Sample 3
compare miRNA expression profiles in in Tongue squamous cell carcinoma (TSCC) and matched nonmalignant tissues (NC)


title: TSCC 2A cy5/NC 2B cy3

description:
Sample 4
compare miRNA expression profiles in in Tongue squamous cell carcinoma (TSCC) and matched nonmalignant tissues (NC)


title: TSCC 5A cy5/NC 5B cy3

description:
Sample 2
compare miRNA expression profiles in in Tongue squamous cell carcinoma (TSCC) and matched nonmalignant tissues (NC)


title: TSCC 5A cy3/NC 5B cy5

description:
Sample 1
compare miRNA expression profiles in in Tongue squamous cell carcinoma (TSCC) and matched nonmalignant tissues (NC)


title: SNm1

first: Zhao

last: Mengxin

address: Haidian District, Zhongguancun Street

institute: Tsinghua University

description: GeoChip data for vegetational Acrisol sample collected at Hailun, replicate 1

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

organism: uncultured bacterium

source_name: Soil microbes in three latitudinal gradient sites

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

growth_protocol: In August 2009, soil samples were collected from all of the plots. Five soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

tag: soil site

value: Hailun

tag: soil type

value: Acrisol

tag: vegatation

value: vegetational soil


title: GENOMIC

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

hyb_protocol: Slides were hybridized using Nimblegen's standard protocol.

scan_protocol: Nimblegen slides were scanned on an Axon Gene Pix 4200A scanner with 100% gain

data_processing: Slides were analyzed with Nimblescan, with no local alignment and a border value of -1. Data from potentially cross-hybridizing probes (matching at 50 or more of 60 nucleotides to a second location in the genome) was removed. Probes with low intensity in the genomic control (5th percentile or lower) were also removed.

label: Alexa 555

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

source_name: GENOMIC

label_protocol: First-strand cDNA was synthesized with random hexamer primers using SuperScript indirect cDNA labeling system (Invitrogen); the reaction buffer was supplemented with actinomycin D to inhibit second-strand synthesis.  First-strand cDNA was labeled with Alexa 555.  About 2 ug of labeled first-strand cDNA was hybridized to the array. For the genomic control, we used DNA from cells in stationary phase to minimize copy number variation across the chromosome.  Genomic DNA was extracted using the DNeasy blood tissue kit (Qiagen) and labeled with Nimblegen's comparative genomic hybridization protocol. Briefly, genomic DNA was sonicated to 200-1000 bp and amplified using Klenow fragment and Cy3-labeled random nonamer primers.

extract_protocol: Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyzer; only samples with an RNA integrity number of around 9 or better were used.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA.

value: gDNA control


title: Cm1

description: GeoChip data for vegetational Cambisol sample collected at Fengqiu, replicate 1

treatment_protocol: In August 2009, soil samples were collected from all of the plots. Five soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.

value: Fengqiu

value: Cambisol


title: SNm3

description: GeoChip data for vegetational Acrisol sample collected at Hailun, replicate 3


title: SCm3

description: GeoChip data for vegetational Acrisol sample collected at Fengqiu, replicate 3


title: CNm1

description: GeoChip data for vegetational Cambisol sample collected at Hailun, replicate 1


title: Cm3

description: GeoChip data for vegetational Cambisol sample collected at Fengqiu, replicate 3


title: CSm3

description: GeoChip data for vegetational Cambisol sample collected at Yingtan, replicate 3

value: Yingtan


title: Cm2

description: GeoChip data for vegetational Cambisol sample collected at Fengqiu, replicate 2


title: ETOH

description: Mid-log phase in ZRMG + 7% ethanol (OD=0.694), 1 biological replicate

source_name: ZM4 with ethanol

tag: media

value: ZRMG + 7% ethanol

tag: temperature


title: CSm1

description: GeoChip data for vegetational Cambisol sample collected at Yingtan, replicate 1


title: CSm2

description: GeoChip data for vegetational Cambisol sample collected at Yingtan, replicate 2


title: CNm3

description: GeoChip data for vegetational Cambisol sample collected at Hailun, replicate 3


title: SNm2

description: GeoChip data for vegetational Acrisol sample collected at Hailun, replicate 2


title: CNm2

description: GeoChip data for vegetational Cambisol sample collected at Hailun, replicate 2


title: WT in xylose (14044065)

city: Montreal

first: Daniel

last: Dignard

state: QC

address: 6100, Royalmount

department: HHT

country: Canada

institute: NRC

description: Sample name: 14044065.txt Ca

hyb_protocol: The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done in a "SlideBooster" chamber (Advalytik)

scan_protocol: ScanArray Gx scanner (Perkin Elmer) at 10-µm resolution

data_processing: Expression array data were normalized as following : Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans SC5314

source_name: [test] SC5314

label_protocol: Indirect labeling with Cy3 and Cy5 was performed. For expression profiling experiment, 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of amino-allyl-dUTP (Sigma A-410) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB cat.70054Z) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The cDNAs were purified with QIAquick PCR Purification Kit (Qiagen) with 5mM potassium phosphate pH8.5 replacing the tris in the wash and elution buffers. The cDNAs were labeled with mono-reactive dyes (GE-Healthcare/ Amersham: cy3 cat. PA23001, cy5 cat. PA25001). The labeled DNA was purified with QIAquick PCR Purification Kit (Qiagen).

growth_protocol: For S.cerevisiae microarrays, starter cultures of S288c strain were in raffinose medium (SR) as carbon source, and grown at 30C to an OD600 of 0.7 - 0.8. The cells were then washed with sterile water. The cell pellet was resuspended in S-based medium (no sugar) and an equal amount of cells transferred in no sugar (S) or xylose (SX) medium for experiments samples or in glucose (SD) medium for the reference samples. The cultures was incubated for ~2h until an increase in the OD600 was observed for the reference culture in glucose. For C.albicans microarrays, starter culture of SC5314 was in SD (glucose) medium. The overnight culture was washed with water and used to inoculate xylose (SX) or glucose (SD) medium at an OD600 of 0.1 and grown at 30C for ~5-6 h to an OD600 of ~0.8 .

extract_protocol: Total RNA was extracted by mechanical disruption of the cells with glass beads using the FastPrep-24 (MP Biomedical). Thereafter, total RNA was isolated and purified with the Rneasy kit (Qiagen cat.74104).

tag: genotype/variation

value: WT

tag: carbon source

value: xylose (SX)

source_name: [reference] SC5314

value: glucose (SD)


title: SCm1

description: GeoChip data for vegetational Acrisol sample collected at Fengqiu, replicate 1


title: SCm2

description: GeoChip data for vegetational Acrisol sample collected at Fengqiu, replicate 2


title: Sm3

description: GeoChip data for vegetational Acrisol sample collected at Yingtan, replicate 3


title: Dormant_15h-1 with array type SUNFLOWER from Affymetrix

city: evry

first: caius

last: jose

state: essonne

address: 2 rue gaston cremieux

department: URGV

country: France

institute: transcriptomic platform

description: Identification of transcripts that are addressed to traduction in imbibed seeds in relation with dormancy: comparison of the translatome in Dormant versus Non-Dormant seeds

hyb_protocol: labelled extract quantity: 5ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Helianthus annuus

label_protocol: labelling Biotin indirect, amplification=yes, total RNA  .

growth_protocol: seed - Field conditions

treatment_protocol: oracz et al 2009, plant physiol.150, 494-505

tag: treatment

value: imbibed at 10 C for 15h

tag: dormancy

value: dormant

tag: dev.stage (boyes et al. plant cell 2001)

value: mature seed


title: MIN

description: Mid-log phase in ZMMG, 1 biological replicate

source_name: ZM4 grown in a defined glucose medium (ZMMG)

value: minimal ZMMG


title: WT in xylose (14044066)

description: Sample name: 14044066.txt Ca


title: Dormant_15h-2 with array type SUNFLOWER from Affymetrix


title: HEAT

description: Grow to log phase in rich media (OD = 0.5) and then heat shock at 40C for one hour, 1 biological replicate

source_name: ZM4 heat shock

value: ZRMG

value: 40C for one hour


title: Sm2

description: GeoChip data for vegetational Acrisol sample collected at Yingtan, replicate 2


title: RICH

description: Mid-log phase in ZRMG, 1 biological replicate

source_name: ZM4 grown in a rich glucose medium (ZMRG)

value: rich ZRMG


title: NonDormant_3h-3 with array type SUNFLOWER from Affymetrix

value: imbibed at 10 C for 3h

value: non-dormant


title: NonDormant_3h-2 with array type SUNFLOWER from Affymetrix


title: NSm1

description: GeoChip data for vegetational Phaeozem sample collected at Yingtan, replicate 1

value: Phaeozem

value: vegetational soil


title: Dormant_3h-3 with array type SUNFLOWER from Affymetrix


title: NSm2

description: GeoChip data for vegetational Phaeozem sample collected at Yingtan, replicate 2


title: Sm1

description: GeoChip data for vegetational Acrisol sample collected at Yingtan, replicate 1

value: Acrisol


title: NCm2

description: GeoChip data for vegetational Phaeozem sample collected at Fengqiu, replicate 2

value: Fengqiu


title: Dormant_3h-1 with array type SUNFLOWER from Affymetrix


title: NCm1

description: GeoChip data for vegetational Phaeozem sample collected at Fengqiu, replicate 1


title: Blnk in Ph+ ALL (pMIG-S1)

source_name: Total RNA from Ph+ ALL (Balb/c)

tag: strain

value: Balb/c

tag: age

value: 4 weeks

tag: cell type

value: BCR-ABL1 transformed pre-B cells

tag: disease state

value: BCR-ABL1-driven ALL

value: Blnk KO

tag: transduction

value: pMIG


title: Nm3

description: GeoChip data for vegetational Phaeozem sample collected at Hailun, replicate 3

value: Hailun


title: Dormant_15h-3 with array type SUNFLOWER from Affymetrix

value: imbibed at 10 C for 15h

value: dormant

value: mature seed


title: NCm3

description: GeoChip data for vegetational Phaeozem sample collected at Fengqiu, replicate 3


title: NSm3

description: GeoChip data for vegetational Phaeozem sample collected at Yingtan, replicate 3

value: Yingtan


title: NonDormant_15h-1 with array type SUNFLOWER from Affymetrix


title: Dormant_24h-2 with array type SUNFLOWER from Affymetrix

value: imbibed at 10 C for 24h


title: W20 LIVER

city: Bethesda

first: Amit

last: Kumar

state: MD

address: 14A Service Rd West., Room 176

department: NIDDK

institute: National Institutes of Health

description: Gene expression data from male wild type mice's liver - Biological replicate 3

hyb_protocol: Following labeling, samples were mixed with hybridization reagents (Affymetrix Inc. CA) and injected into affymetrix Mouse Gene 1.0 ST arrays and incubated for 18 +  2hours in hybridization oven rotating at 60 rpm at 45oC (Affymetrix Inc, CA) .

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner 3000 operated by Gene Chip Operating Software, version 1. 4 (GCOS 1.4)

data_processing: The microarray raw data was analyzed using Partek software, version 6.3 Copyright 2008 Partek Inc., St. Louis, MO, USA. Raw data were subjected to Robust Multichip Average (RMA) quantile normalization to remove biases introduced by technical and experimental effects. All expression data were log base 2 -transformed to get near normal distribution for accurate statistical inference.

source_name: Male wild type (WT) mice, Biological replicate 3

label_protocol: 100 ng of RNA from each sample was amplified to generate cDNA using NUGEN Applause WT – Amp ST system (NuGEN Technologies, CA), according to the manufacturer’s instructions. 2.5 µg of cDNA was fragmented and biotinylated using Encore Biotin module (NUGEN Technologies, CA).

growth_protocol: Mice were kept on a 12-h light/dark cycle, they were allowed free access to diet (Picolab rodent diet #5053) and fresh water.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's (Qiagen) instructions.

treatment_protocol: Death of the mice was caused by subjecting them to CO2. Liver, Skeletal muscle, and adipose tissues were flash frozen in liquid nitrogen, stored at -80 oC, shipped on dry ice overnight, and kept at -80 oC prior to processing

value: Liver

tag: genotype

value: Wild Type

value: 10 weeks

tag: genetic background

value: FVB/N


title: Nm2

description: GeoChip data for vegetational Phaeozem sample collected at Hailun, replicate 2

tag: soil site

value: Phaeozem

value: vegetational soil


title: Dormant_3h-2 with array type SUNFLOWER from Affymetrix

value: imbibed at 10 C for 3h


title: NonDormant_15h-2 with array type SUNFLOWER from Affymetrix

value: non-dormant


title: NonDormant_3h-1 with array type SUNFLOWER from Affymetrix


title: NonDormant_24h-1 with array type SUNFLOWER from Affymetrix


title: W20 FAT

description: Gene expression data from male wild type mice's adipose - Biological replicate 3

tag: tissue

value: Adipose


title: NonDormant_24h-2 with array type SUNFLOWER from Affymetrix


title: W19 FAT

description: Gene expression data from male wild type mice's adipose - Biological replicate 2

source_name: Male wild type (WT) mice, Biological replicate 2


title: W19 LIVER

description: Gene expression data from male wild type mice's liver - Biological replicate 2


title: M18 LIVER

description: Gene expression data from male MKR mice's liver - Biological replicate 3

source_name: Male MKR mice, Biological replicate 3

value: MKR Mice - Mutation in skeletal muscle IGF1 Receptor


title: W20 MUSCLE

description: Gene expression data from male wild type mice's skeletal muscle - Biological replicate 3

value: Skeletal Muscle


title: Nm1

description: GeoChip data for vegetational Phaeozem sample collected at Hailun, replicate 1

value: Hailun

tag: soil type

tag: vegatation


title: CN3

description: GeoChip data for bare Cambisol sample collected at Hailun, replicate 3

value: Cambisol

value: bare soil


title: W19 MUSCLE

description: Gene expression data from male wild type mice's skeletal muscle - Biological replicate 2


title: M18 MUSCLE

description: Gene expression data from male MKR mice's skeletal muscle - Biological replicate 3


title: W16 FAT

description: Gene expression data from male wild type mice's adipose - Biological replicate 1

source_name: Male wild type (WT) mice, Biological replicate 1


title: Dormant_24h-1 with array type SUNFLOWER from Affymetrix

description: Identification of transcripts that are addressed to traduction in imbibed seeds in relation with dormancy: comparison of the translatome in Dormant versus Non-Dormant seeds

value: dormant

value: mature seed


title: W16 MUSCLE

description: Gene expression data from male wild type mice's skeletal muscle - Biological replicate 1


title: CN2

description: GeoChip data for bare Cambisol sample collected at Hailun, replicate 2


title: M12 MUSCLE

description: Gene expression data from male MKR mice's skeletal muscle - Biological replicate 2

source_name: Male MKR mice, Biological replicate 2


title: W16 LIVER

description: Gene expression data from male wild type mice's liver - Biological replicate 1


title: M18 FAT

description: Gene expression data from male MKR mice's adipose - Biological replicate 3


title: CN1

description: GeoChip data for bare Cambisol sample collected at Hailun, replicate 1


title: CS3

description: GeoChip data for bare Cambisol sample collected at Yingtan, replicate 3

value: Yingtan


title: NonDormant_15h-3 with array type SUNFLOWER from Affymetrix

value: imbibed at 10 C for 15h


title: CS2

description: GeoChip data for bare Cambisol sample collected at Yingtan, replicate 2


title: M12 FAT

description: Gene expression data from male MKR mice's adipose - Biological replicate 2


title: M12 LIVER

description: Gene expression data from male MKR mice's liver - Biological replicate 2

value: Liver


title: NonDormant_24h-3 with array type SUNFLOWER from Affymetrix

value: imbibed at 10 C for 24h


title: Dormant_24h-3 with array type SUNFLOWER from Affymetrix


title: M11 MUSCLE

description: Gene expression data from male MKR mice's skeletal muscle - Biological replicate 1

source_name: Male MKR mice, Biological replicate 1

value: 10 weeks

value: FVB/N


title: M11 FAT

description: Gene expression data from male MKR mice's adipose - Biological replicate 1


title: C3

description: GeoChip data for bare Cambisol sample collected at Fengqiu, replicate 3

value: Fengqiu


title: C2

description: GeoChip data for bare Cambisol sample collected at Fengqiu, replicate 2


title: CS1

description: GeoChip data for bare Cambisol sample collected at Yingtan, replicate 1


title: C1

description: GeoChip data for bare Cambisol sample collected at Fengqiu, replicate 1


title: SEOC_57093_2

city: Frederick

first: Ludmila

last: Szabova

address: 1050 Boyles Street

department: CAPR

institute: Frederick National Laboratory for Cancer Research

hyb_protocol: Labeled cDNA (4.4 ug) of each sample was hybridized to Affymetrix mouse 430 2.0 GeneChip array.at 45°C for 16 hrs. GeneChip arrays were washed on Affymetrix Fluidics Station 450 using manufacturer’s recommended scripts and scanned on Affymetrix GeneChip scanner 3000. Data were collected using Affymetrix AGCC software.

data_processing: The obtained .cel files were processed and normalized by RMA (robust multi-chip average). Data were merged and analyzed together with previously published mouse (GSE46469) and human datasets (doi:  10.1038/nature10166) as described previously (doi:  10.1158/0008-5472.CAN-11-3834).

source_name: ovarian tumor

label_protocol: RNA (10 ng) was amplified and labeled with Ovation Whole Blood Solution kit (Nugen) following manufacturer’s protocol.

extract_protocol: Total RNA was isolated from flash frozen tumor pieces using TRIZOL reagent (Invitrogen) according the manufacturer’s protocol with the modification of binding the precipitated RNA on RNAeasy column (Qiagen) for consequent washing and elution.

value: FVB/NJ

value: K18 D/D, cp D/D

value: ovarian tumor

tag: tumor stage

value: IIIA

tag: passage

value: p1 passage


title: DNA prime-VACV boost_B5

city: Shanghai

first: Hu

last: Zhidong

address: 2901 Caolang Road, Jinshan district

institute: Shanghai public health clinical center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: DNA prime-VACV boost

label_protocol: Amplified and biotin labeled by Illumina Total Prep RNA Amplification Kit (Ambion, USA)

growth_protocol: Spleens were mechanically disrupted and splenocytes were filtrated through mesh gauze. Red blood cells were lysed with RBC lysis buffer.

extract_protocol: Total RNA was extracted by the RNeasy Mini Kit (QIAGEN, Germany).

treatment_protocol: CD45.1-PE antibody (clone A20, Biolegend, USA) and anti-PE MicroBeads (Miltenyi, Germany) were used for enrichment of antigen-specific CD8+ T  cells.

value: Balb/c

tag: immunization method

value: primed with DNA and boosted by VACV

value: spleen

value: splenocytes

tag: cell subtype

value: antigen-specific CD8+ T cells

tag: time point

value: 4 weeks after vaccination


title: DNA prime-VACV boost_B4


title: DNA prime-VACV boost_B6


title: DNA prime-DNA boost_A6

source_name: DNA prime-DNA boost

value: primed with DNA and boosted by DNA


title: Cancer Associate Fibroblast, Extra-High migratory group sample

city: Madrid

first: Cristina

last: Pena

address: Joaquín Rodrigo, 2. Peine 7, Planta 3 28222 Majadahonda. Madrid, SPAIN

department: Oncology Department

country: Spain

institute: Hospital Universitario Puerta de Hierro

hyb_protocol: biotinylated cDNA was hybridized to Affymetrix GeneChip® Human Gene 1.0 ST arrays [HuGene-1_0-st].

scan_protocol: GenChips were scanned using the GCS3000 Affymetrix Platform

data_processing: Affymatrix CEL files were background corrected and normalized using Bioconductor package “affy” by RMA normalization.

source_name: Human colon tumor samples

label_protocol: Labeling was developed with the Affymetrix protocol (Affymetrix expression manual). Affymetrix Terminal Labeling Kit (P/N 702808 Rev. 3)

extract_protocol: Total RNA was extracted from CAF samples with TRIzol reagent (TRIzol, Invitrogen-Gibco), in line with the manufacturer’s protocol.

tag: phenotype

value: Extra-High migratory group sample

value: Cancer Associated Fibroblast

value: Colon mucosa


title: DNA prime-DNA boost_A5

tag: strain


title: Cancer Associate Fibroblast, Low migratory group sample

value: Low migratory group sample


title: Cancer Associate Fibroblast, High migratory group sample

value: High migratory group sample


title: Normal Fibroblast, biological rep1

source_name: Human colon normal samples

value: normal

value: Normal Fibroblast


title: Normal Fibroblast, biological rep2


title: SN3

description: GeoChip data for bare Acrisol sample collected at Hailun, replicate 3

source_name: Soil microbes in three latitudinal gradient sites

value: Hailun

value: Acrisol

value: bare soil


title: SEOC_32233_2

scan_protocol: scanned on Affymetrix GeneChip scanner 3000

value: FVB/NJ

tag: genotype/variation

value: K18 D/D, cp D/D

value: ovarian tumor

value: IV

value: primary tumor


title: SEOC_63846_2

value: p2 passage


title: MCF7_xeno,1

city: Turku

first: Vesa

last: Hongisto

address: Itainen Pitkakatu 4c

department: Medical Biotechnology

country: Finland

institute: VTT Technical Research Centre of Finland

hyb_protocol: Standard Illumina hybridization protocol. 750 ng of each cRNA-sample was hybridized to Illumina Sentrix® HumanHT-12 v4 Expression Bead Chip at 58 C over night according to Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide –protocol (part #11322355, rev.A)

scan_protocol: Standard Illumina scanning protocol. Chips were scanned with Illumina Bead Array Reader (Factor=1.5, PMT=552, Filter=100%) and the raw numerical values were obtained from GenomeStudio v. 2011.1; Gene Expression Module v.  1.9.0

data_processing: The Illumina data was preprocessed by Bioconductor beadarray and lumi packages (Du et al., 2008). The lumiExpresso function was used with default settings, including the variance stabilizing transformation and quantile normalization across samples. (Du P, Kibbe WA, Lin SM. (2008). Lumi: A pipeline for processing illumina microarray. Bioinformatics 24: 1547-1548.)

source_name: MCF7 breast cancer cell line

label_protocol: Hybridization were detected with 1 μg/ml Cyanine3-streptavidin

growth_protocol: MCF7 cells were cultivated in Dulbecco’s modified Eagles medium (DMEM, glucose 1 g/l; Sigma Aldrich) supplemented with 10 % FBS, 2 mM L-glutamine and 1 % penicillin/streptomycin.

extract_protocol: RNA isolation was done using mirVana™ (Life technologies) kit according to manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser. Gene expression was analyzed using illumina HumanHT-12 v 4.0 Expression BeadChip (>47 000 probes). Two biological replicates were used for each sample. 300 ng total-RNA was amplified with Illumina® TotalPrep™ RNA Amplification Kit (Applied Biosystems cat # AMIL1791)

treatment_protocol: For gene expression studies MCF7 cell were grown in 6 well plates in 2D (7d), PH (4 and 7 days) or MG (4 and 7 days) models. Matrigel was dissolved prior to RNA isolation using Dispase (BD Biosciences). To obtain xenograft tumors of MCF7 cells, the fat pads of BALB/C-nude mice were injected with 1*10-6 MCF7 cells in 25 ml of medium and 25 ml of Matrigel. The tumors were collected 43 days after injection at 99 - 158 mm2. Tumor size was calculated from palpation results using (lenght/2 * width/2) * π. PolyHEMA plates were coated prior to use with 2.3 ml / well of PolyHEMA (poly (2-hydroxyethyl methacrylate), Polysciences Inc.), ethanol (>99 %) and sterile water in a 4:90:6 ratios. The plates were left to dry for 7 days at 37oC (or until the wells were dry).The Matrigel membrane was created by pipetting of ice-cold Matrigel dilution (1/2 Matrigel (Basement Membrane Matrix Growth Factor Reduced, BD Biosciences) and 1/2 Opti-MEM® (Life technologies)) to 6-well plates. The membrane was left to polymerize to cell culture inbubator for 20 minutes, after which the cells in cell culture medium were added on top.

tag: cell line

tag: culture method

value: as xenografts in the fat pads of BALB/C-nude mice


title: SEOC_61333_2


title: M11 LIVER

description: Gene expression data from male MKR mice's liver - Biological replicate 1

value: Liver

value: MKR Mice - Mutation in skeletal muscle IGF1 Receptor

tag: age

value: 10 weeks

value: FVB/N


title: DNA prime-DNA boost_A4

value: Balb/c

value: primed with DNA and boosted by DNA

value: spleen

tag: cell type

value: splenocytes

value: antigen-specific CD8+ T cells

value: 4 weeks after vaccination


title: SEOC_63935_2

value: FVB/NJ


title: MCF7_PH_4d,1

value: polyHEMA anchorage independent 3D culture for four days


title: SN2

description: GeoChip data for bare Acrisol sample collected at Hailun, replicate 2

value: Hailun

value: Acrisol

value: bare soil


title: SEOC_64644_2

value: B1 D/D, K18 tg, cp D/D

value: ovarian tumor

value: IIIA

value: p3 passage


title: SN1

description: GeoChip data for bare Acrisol sample collected at Hailun, replicate 1


title: MCF7_PH_7d,1

value: polyHEMA anchorage independent 3D culture for seven days


title: MCF7_MG_7d,1

value: Matrigel on-top 3D culture for seven days


title: SEOC_59232_2

value: K18 D/D, cp D/D

value: IIIB

value: p1 passage


title: SC3

description: GeoChip data for bare Acrisol sample collected at Fengqiu, replicate 3

value: Fengqiu


title: SEOC_34429_2

value: IV

value: primary tumor


title: SC1

description: GeoChip data for bare Acrisol sample collected at Fengqiu, replicate 1


title: MCF7_MG_4d,1

value: Matrigel on-top 3D culture for four days


title: Cancer Associate Fibroblast, Medium migratory group sample

value: Medium migratory group sample

value: Cancer Associated Fibroblast

value: Colon mucosa


title: S3

description: GeoChip data for bare Acrisol sample collected at Yingtan, replicate 3

value: Yingtan

value: Acrisol

value: bare soil


title: S2

description: GeoChip data for bare Acrisol sample collected at Yingtan, replicate 2


title: MCF7_PH_7d


title: MCF7_MG_7d


title: SC2

description: GeoChip data for bare Acrisol sample collected at Fengqiu, replicate 2


title: SEOC_65021_2

value: FVB/NJ

value: B1 D/D, K18 tg, cp D/D

value: ovarian tumor

value: IIA


title: SEOC_61362_2

value: p2 passage


title: SEOC_61345_2


title: MCF7_xeno

value: as xenografts in the fat pads of BALB/C-nude mice


title: MCF7_2D,1

value: 2D monolayer cell culture


title: MCF7_MG_4d


title: MCF7_2D


title: MCF7_PH_4d

value: polyHEMA anchorage independent 3D culture for four days


title: SEOC_57454_2

value: IIB

value: p1 passage


title: SEOC_57452_2

value: IIIA


title: NS2

description: GeoChip data for bare Phaeozem sample collected at Yingtan, replicate 2

value: Phaeozem


title: S1

description: GeoChip data for bare Acrisol sample collected at Yingtan, replicate 1


title: NS3

description: GeoChip data for bare Phaeozem sample collected at Yingtan, replicate 3


title: JIMT_MG_7d,1

label_protocol: standard

growth_protocol: JIMT1 cells were cultivated in a 1:1 mixture of Ham’s F-12 + glutamax medium (Gibco Invitrogen, USA) and Dulbecco’s modified Eagles medium (DMEM, glucose 4.5 g/l; Sigma Aldrich), with 10 % FBS, 2 mM L-glutamine, 0.01 mg/ml insulin, and 1 % penicillin/streptomycin. JIMT1 (DSMZ GmbH, Germany) is a HER2+, ER-, PR-, epithelial-like cell line established from a pleural effusion of a 62-year-old female with trastuzumab-resistant ductal breast cancer (Tanner et al. 2004).

extract_protocol: RNA isolation was done using mirVana™ (Life technologies) kit according to manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser. Gene expression was analyzed using illumina HumanHT-12 v 4.0 Expression BeadChip (>47 000 probes). Two biological replicates were used for each sample.

treatment_protocol: For gene expression studies JIMT1 cell were grown in 6 well plates in 2D (7d), PH (4 and 7 days) or MG (4 and 7 days) models. Matrigel was dissolved prior to RNA isolation using Dispase (BD Biosciences). To obtain xenograft tumors of JIMT1 cells, the fat pads of BALB/C-nude mice were injected with 1*10-6 JIMT1 cells in 25 ml of medium and 25 ml of Matrigel. The tumors were collected 43 days after injection at 99 - 158 mm2. Tumor size was calculated from palpation results using (lenght/2 * width/2) * π. PolyHEMA plates were coated prior to use with 2.3 ml/well of PolyHEMA (poly (2-hydroxyethyl methacrylate), Polysciences Inc.), ethanol (>99 %) and sterile water in a 4:90:6 ratios. The plates were left to dry for 7 days at 37oC (or until the wells were dry).The Matrigel membrane was created by pipetting of ice-cold Matrigel dilution (1/2 Matrigel (Basement Membrane Matrix Growth Factor Reduced, BD Biosciences) and 1/2 Opti-MEM® (Life technologies)) to 6-well plates. The membrane was left to polymerize to cell culture inbubator for 20 minutes, after which the cells in cell culture medium were added on top.

value: breast cancer cells

value: Matrigel on-top 3D culture for seven days


title: JIMT_MG_4d,1

value: Matrigel on-top 3D culture for four days


title: SEOC_39877_2

value: IB

value: primary tumor


title: JIMT_xeno


title: SEOC_60514_2

value: FVB/NJ

value: K18 D/D, cp D/D


title: JIMT_PH_4d,1


title: SEOC_62803_2

value: ovarian tumor


title: JIMT_2D,1


title: JIMT_PH_7d,1

value: polyHEMA anchorage independent 3D culture for seven days


title: JIMT_xeno,1


title: JIMT_PH_7d


title: NS1

description: GeoChip data for bare Phaeozem sample collected at Yingtan, replicate 1

value: Yingtan

value: bare soil


title: SEOC_56230_2


title: NC3

description: GeoChip data for bare Phaeozem sample collected at Fengqiu, replicate 3

value: Fengqiu


title: NC2

description: GeoChip data for bare Phaeozem sample collected at Fengqiu, replicate 2


title: NC1

description: GeoChip data for bare Phaeozem sample collected at Fengqiu, replicate 1


title: SEOC_56234_2

value: IIA


title: N2

description: GeoChip data for bare Phaeozem sample collected at Hailun, replicate 2

value: Hailun


title: N1

description: GeoChip data for bare Phaeozem sample collected at Hailun, replicate 1


title: JIMT_2D

value: 2D monolayer cell culture


title: patient 107 HN2327ms

city: Thessaloniki

first: elena

last: fountzilas

address: School of Medicine, Pathology Department

department: Medical Oncology

country: Greece

institute: Aristotle University of Thessaloniki, Greece

description: validation set

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Raw data were processed using Robust Multi-Array (RMA) analysis, BRB arraytools sofware

source_name: fresh frozen laryngeal tumor

label_protocol: RNA was labelled using the Roche Microarray cDNA Synthesis

growth_protocol: Tumor specimens, collected from patients at the time of surgery, were immediately frozen in liquid nitrogen and then stored in -80˚C until RNA isolation

extract_protocol: RNeasy Mini Protocol, (Qiagen, CA, USA)

tag: dfs (months)

tag: dfs status (1 = recurred)

tag: grade

value: fresh frozen laryngeal tumor

tag: group

value: validation set


title: N3

description: GeoChip data for bare Phaeozem sample collected at Hailun, replicate 3

tag: soil site

tag: soil type

value: Phaeozem

tag: vegatation


title: patient 100 HN2313ms

description: validation set

tag: tissue


title: SEOC_62338_2

value: B1 D/D, K18 tg, cp D/D

tag: tumor stage

value: IIIA

tag: passage

value: p4 passage


title: patient 106 HN2326ms

description: validation set


title: SEOC_29255_2

value: IV

value: primary tumor


title: SEOC_65026_2

value: FVB/NJ

value: p5 passage


title: patient 103 HN2322ms

description: validation set


title: JIMT_MG_7d

value: breast cancer cells

value: Matrigel on-top 3D culture for seven days


title: patient 109 HN2329ms

description: validation set


title: patient 108 HN2328ms

description: validation set


title: patient 105 HN2325ms

description: validation set


title: patient 99 HN2312ms

description: validation set


title: JIMT_PH_4d

value: polyHEMA anchorage independent 3D culture for four days


title: patient 102 HN2321ms

description: validation set


title: patient 104 HN2324ms

description: validation set


title: JIMT_MG_4d

value: Matrigel on-top 3D culture for four days


title: SEOC_65076_2

value: ovarian tumor


title: patient 97 HN2308ms

description: validation set


title: SEOC_60530_2

value: IIA

value: p3 passage


title: SEOC_62337_2


title: patient 98 HN2310ms

description: validation set

value: fresh frozen laryngeal tumor


title: patient 101 HN2319ms

description: validation set

value: validation set


title: patient 95 HN2306ms

description: validation set


title: SEOC_61742_2


title: patient 96 HN2307ms

description: validation set


title: SEOC_57078_2

value: p2 passage


title: patient 94 HN2305ms

description: validation set


title: SEOC_47362_2

value: B1 D/D, K18 tg, cp D/D

value: p1 passage


title: patient 91 HN2301ms

description: validation set


title: SEOC_47343_2

value: IIIA


title: patient 89 HN2299ms

description: validation set


title: patient 83 HN2291ms

description: validation set


title: patient 92 HN2302ms

description: validation set


title: patient 86 HN2296ms

description: validation set


title: SEOC_57080_2

value: no data


title: MLL-AF9_GMP_NTC_2

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

hyb_protocol: A WT-Ovation Exon Module kit (NuGEN) was used to generate sense transcript cDNA which was then fragmented, biotin labeled and hybridized to GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix, CA) using an Encore Biotin Module kit (NuGEN), according to manufacturer’s instructions.

scan_protocol: Hybridized arrays were washed using the GeneChip Fluidics Station 450 (Affymetrix) using protocol 001 and scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Exon array data were processed using an R/Bioconductor package, as previously described (Okoniewski and Miller, 2008). Background adjustment, quantile normalization and summarization of probe-level intensity were performed using the robust multi-array average algorithm (Irizarry et al., 2003). 267,824 probesets annotated in Ensembl mouse genome build 56 as 'exonic' and not 'multitarget', with their expression values, were extracted in CSV file format. The csv file was used to calculate 'gene level summaries', which represent the mean expression of all exonic probesets mapping to each of 23,770 Ensembl annotated genes ['gene_level_summary.txt' available as Series supplementary file].
probe group file: MoEx-1_0-st-v1.r2.pgf
Sample data table contains exon-level RMA normalized and summarized signal intensities from probe sets. The 'gene_level_summary.txt' file contains gene level summaries of RMA normalized and summarized signal intensities from probe sets.

label_protocol: RNA quality was confirmed using an Agilent Bioanalyzer (Agilent Technologies, CA) prior to cDNA amplification of 1ng (samples 1, 4, 7, 10, 13, 16) or 40ng (all other samples) RNA using the Ovation Pico WTA System (NuGEN, CA), according to manufacturer’s instructions.

growth_protocol: MLL-AF9 GMP-like cells or normal GMP cells were FACS purified direct from euthanised mice and then infected with the indicated knockdown or control lentiviral vectors by spinoculation for 30 minutes at 1350xg at 32°C. Cells were then cultured for a further 42 hours in lentiviral supernatant medium [consisting of RPMI, 20% FBS, 8 μg/ml polybrene, 5% X63 supernatant (Karasuyama and Melchers, 1988) and recombinant growth factors (SCF 20ng/ml, IL3 10ng/ml, IL6 0ng/ml and GM-CSF 10ng/ml)] prior to extraction of RNA from successfully infected cells.

extract_protocol: RNA was extracted using QIAshredder spin columns and an RNeasy Plus Micro kit (Qiagen, UK).

tag: background strain

value: MLL-AF9 AML GMP-like cells

value: control

tag: infected with

value: non-tageting control lentiviral vectors


title: MLL-AF9_GMP_NTC_3

tag: genotype/variation


title: patient 84 HN2293ms

description: validation set


title: SEOC_30200_2

tag: strain

value: FVB/NJ

value: IV

value: primary tumor


title: patient 88 HN2298ms

description: validation set


title: patient 87 HN2297ms

description: validation set


title: patient 90 HN2300ms

description: validation set


title: patient 85 HN2295ms

description: validation set


title: normal epithelium_sample 3_1

source_name: normal ovarian epithelium

value: wild type

value: normal ovarian epithelium


title: MLL-AF9_GMP_EPC2_3

value: EPC2 knockdown

value: lentiviral vectors targeting EPC2 for knockdown


title: patient 81 HN2289ms

description: validation set

value: fresh frozen laryngeal tumor


title: normal epithelium_sample 2_1


title: MLL-AF9_GMP_EPC2_1


title: MLL-AF9_GMP_EPC2_2


title: MLL-AF9_GMP_EPC1_3

value: EPC1 knockdown

value: lentiviral vectors targeting EPC1 for knockdown


title: MLL-AF9_GMP_NTC_1


title: patient 79 HN2286ms

description: validation set

value: validation set


title: patient 78 HN2285ms

description: validation set


title: patient 80 HN2287ms

description: validation set


title: patient 82 HN2290ms

description: validation set


title: patient 76 HN2283ms

description: validation set


title: patient 73 HN2280ms

description: validation set


title: MLL-AF9_GMP_EPC1_1


title: normal epithelium_sample 1_1


title: patient 75 HN2282ms

description: validation set


title: SEOC_R5848_1

value: B1 fl/fl, K18 tg, p53 fl/fl

value: ovarian tumor


title: SEOC_R5855_1


title: SEOC_R5854_1


title: patient 77 HN2284ms

description: validation set


title: SEOC_R5843_1

value: IB


title: Normal_GMP_NTC_3

value: granulocyte-macrophage progenitor (GMP) cells


title: patient 72 HN2279ms

description: validation set


title: MLL-AF9_GMP_EPC1_2

value: MLL-AF9 AML GMP-like cells


title: patient 74 HN2281ms

description: validation set


title: Normal_GMP_NTC_2

value: control

value: non-tageting control lentiviral vectors


title: Normal_GMP_NTC_1


title: patient 93 HN2303ms

description: validation set


title: patient 69 HN2275ms

description: validation set


title: SEOC_R5838_1

value: FVB/NJ

value: K18 tg, p53 fl/fl


title: patient 57 HN2262ms

description: training set

value: training set


title: Normal_GMP_EPC2_2


title: patient 71 HN2278ms

description: validation set


title: patient 63 HN2268ms

description: validation set


title: patient 67 HN2273ms

description: validation set


title: patient 64 HN2270ms

description: validation set


title: Normal_GMP_EPC2_3


title: SEOC_R5831_1

value: IV


title: SEOC_236477_1


title: patient 56 HN2261ms

description: training set


title: patient 62 HN2267ms

description: validation set


title: patient 68 HN2274ms

description: validation set


title: patient 61 HN2266ms

description: validation set


title: SEOC_238767_1


title: SEOC_R5810_1

value: no data


title: SEOC_238721_1


title: patient 66 HN2272ms

description: validation set


title: patient 58 HN2263ms

description: training set


title: patient 60 HN2265ms

description: validation set


title: Normal_GMP_EPC2_1

value: EPC2 knockdown

value: lentiviral vectors targeting EPC2 for knockdown


title: patient 65 HN2271ms

description: validation set

value: fresh frozen laryngeal tumor


title: patient 70 HN2276ms

description: validation set


title: Normal_GMP_EPC1_1

value: EPC1 knockdown

value: lentiviral vectors targeting EPC1 for knockdown


title: patient 59 HN2264ms

description: training set


title: SEOC_R5817_1

value: B1 fl/fl, K18 tg, p53 fl/fl


title: patient 54 HN2259ms

description: training set


title: Normal_GMP_EPC1_3


title: Normal_GMP_EPC1_2


title: patient 44 HN2247ms

description: training set


title: patient 50 HN2254ms

description: training set


title: SEOC_235746_1

value: ovarian tumor


title: patient 45 HN2248ms

description: training set


title: patient 52 HN2257ms

description: training set


title: patient 51 HN2255ms

description: training set


title: patient 53 HN2258ms

description: training set


title: patient 46 HN2249ms

description: training set


title: patient 55 HN2260ms

description: training set


title: patient 49 HN2253ms

description: training set


title: patient 43 HN2246ms

description: training set


title: patient 42 HN2244ms

description: training set


title: SEOC_235132_1


title: patient 48 HN2252ms

description: training set


title: SEOC_216648_1


title: SEOC_25604_1

value: B2 fl/fl, K18 tg, p53 m/fl

value: IIB


title: SEOC_195571_1


title: SEOC_30200_1


title: patient 40 HN2241ms

description: training set


title: patient 41 HN2242ms

description: training set


title: patient 47 HN2250ms

description: training set


title: SEOC_23185_1


title: SEOC_235744_1

value: IIIB


title: SEOC_23615_1

value: B1 fl/fl, K18 tg, p53 m/fl

value: IIA


title: SEOC_24661_1

value: FVB/NJ


title: patient 36 HN2237ms

description: training set


title: SEOC_21981_1


title: patient 37 HN2238ms

description: training set


title: SEOC_23172_1


title: patient 38 HN2239ms

description: training set


title: patient 35 HN2236ms

description: training set


title: patient 39 HN2240ms

description: training set


title: SEOC_48_1


title: SEOC_15825_1


title: SEOC_22864_1


title: patient 33 HN2234ms

description: training set


title: Telogen + KrasG12D_ventral

first: William

last: Lowry

address: 621 Charles Young

institute: UCLA

hyb_protocol: Labeled cRNA was mixed with hybridization mix according to Affymetrix protocol and hybridized in Affymetrix GeneChip hybridization oven 645 at 45C for 16 hours with rotation at 60 rpm

scan_protocol: Scanning was performed on Affymetrix 7G scanner with target intensity 500

data_processing: Cel files were imported into Genespring and RMA normalized.  Probesets not expressed in at least 10% of samples were eliminated

source_name: HFSCs from telogen + KrasG12D

label_protocol: Labeling was performed with Ambion MESSAGEAMP PREMIER kit (cat#: 4383452)

growth_protocol: mice were housed under standard conditions according to animal safety protocol

extract_protocol: Cells were lysed, and run through Stratagene Total RNA isolation kit

treatment_protocol: Phenotypes shown from treated animals were produced 3-4 weeks after mifepristone administration, without the beginning of the next anagen cycle. For Figure 1B, animals were treated later in telogen (10 weeks postnatal), allowing for anagen to proceed 1 week following.  Skin was harvested 3 weeks post initial mifepristone administration.   Whole dorsal and ventral mouse K15-CrePR; LSLYFP, K15-CrePR; KrasG12D; LSLYFP and K15-CrePR; KrasG12D; Ptenff; LSLYFP was extracted, diced and digested with collagenase (20mg/ml) for 2 hours at 37C, then an equal volume of .25% trypsin was added and digestion continued for an additional hour at 37C.  Digested tissue was mechanically dispersed via pipette and filtered with a 100uM cell strainer, collected at 300g and washed twice with PBS.  The cells were then filtered through a 40uM cell strainer and FACS processed.  YFP+ and YFP- cell populations were collected in lysis buffer (Stratagene) and stored at -80.

tag: strain background

value: mixed between C57/Bl6 and FVB

value: K15-CrePR; KrasG12D; LSLYFP

value: ventral skin

value: hair follicle stem cells (HFSCs)


title: patient 34 HN2235ms

description: training set

tag: age

value: training set


title: Telogen + KrasG12D/-Pten_dorsal

source_name: HFSCs from telogen + KrasG12D/-Pten

value: K15-CrePR; KrasG12D; Ptenff; LSLYFP

value: dorsal skin

tag: cell type


title: Telogen + KrasG12D_dorsal


title: Telogen + KrasG12D/-Pten_ventral


title: LN4D6 CREB3L1 HA ChIP

city: Saskatoon

first: Deborah

last: Anderson

state: Saskatchewan

address: 107 Wiggins Road

institute: University of Saskatchewan

description: Chip-chip LN4D6 CREB3L1 cells HA (CREB3L1)

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction software at Nimblegen.
The ratio_peaks.gff is the ratio of signal for each transcript on the chip between the ChIP sample and the input, which is used to determine if a positive signal is unique to the ChIP sample. The 'ratio_peaks_mapToFeatures_All_Peaks.txt' file contains data with the identity of the feature on it e.g. name and accession number.

organism: Rattus norvegicus

source_name: CREB3L1 (HA) ChIP DNA from LN4D6 CREB3L1 cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 or Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Chromatin Immunoprecipitation (ChIP) assay was performed using an EpiQuick™ Chromatin Immunoprecipitation Kit (Epigentek™) and a HA-X (F-7) antibody (Santa Cruz).  All procedures were carried out according to the manufacturer’s specifications.  The ChIP DNA was then amplified using a GenomePLex Whole Genome Amplification Kit -4 (WGA-4) (Sigma), according to the manufacturer’s specifications.  The amplified DNA was then purified using a QIAquick® PCR purification kit (Qiagen).

tag: cell line

value: rat mammary tumor cells

tag: transfected with

tag: chip antibody

value: HA-X (F-7) antibody

tag: chip antibody vendor

value: Santa Cruz

source_name: Input DNA from LN4D6 CREB3L1


title: patient 29 HN2230ms

description: training set

tag: dfs (months)

tag: dfs status (1 = recurred)

tag: grade

value: fresh frozen laryngeal tumor

tag: group


title: patient 30 HN2231ms

description: training set

tag: tissue


title: patient 28 HN2229ms

description: training set


title: Telogen Control_ventral

source_name: HFSCs from telogen control

value: K15-CrePR; LSLYFP


title: patient 32 HN2233ms

description: training set


title: patient 31 HN2232ms

description: training set


title: patient 27 HN2228ms

description: training set


title: Telogen Control_dorsal

label: YFP