title: DL 63 pool b

tag: breed

tag: developmental stage


title: mouse lung tissue at week 30, 17.5 Gy, biological rep2

status: Public on Nov 01 2013

type: RNA

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

country: USA

institute: NIH

description: gene expression data from 17.5 Gy radiation treated mouse lung at 30 weeks, replicate 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  Mouse430_2 microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip array scanner 3000 7 G.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using quantile normalization and reported in log2 scale.

label: biotin

molecule: total RNA

organism: Mus musculus

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

growth_protocol: At 2, 4, 8, 16, and 30 weeks post-ionizing radiation samples of lung were collected in 3 mice at each radiation dose (including 0 Gy).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by cleaning on a Qiagen RNAeasy column.

treatment_protocol: An age-matched cohort of mice received no ionizing radiation while additional cohorts received 5 Gy in a single dose or 17.5 Gy in a single dose.

tag: tissue

value: lung

tag: strain

tag: treatment

value: 17.5 Gy radiation treated

tag: time

value: week 30

tag: gender

value: female

tag: age

value: 10 wk


title: MPI-751_tonsils

city: Leipzig

first: Maciej

last: Rosolowski

address: Härtelstr. 16-18

country: Germany

institute: Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

hyb_protocol: Affymetrix hybridization was carried on U133A GeneChips according to the manufacturer's recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter

scan_protocol: After hybridization of night (16 hours, 45° C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500)

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260)

organism: Homo sapiens

source_name: tonsils

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation

extract_protocol: Tonsillar tissue samples were used as whole tissue RNA extracts of healthy individuals. RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)

tag: type

value: tonsils

tag: tumor


title: mouse lung tissue at week 30, 17.5 Gy, biological rep3

description: gene expression data from 17.5 Gy radiation treated mouse lung at 30 weeks, replicate 3


title: primary breast cancer, sample 79

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol on Affymetrix scanner 3000.

data_processing: Cel files were processed using the affy and frma R packages, available at www.bioconductor.org, using median polish as summarizing method in the fRMA.

source_name: Snap frozen primary breast tumor

label_protocol: Standard Affymetrix protocol.

extract_protocol: Total RNA was extracted with RNABee (Campro, Veenendaal, the Netherlands) according to the manufacturer's procedure.

value: primary breast tumor

tag: tn status

value: triple-negative


title: DL 63 pool a

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from skeletal muscle of peripubertal pigs breed (DL).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Sus scrofa

source_name: Musculus longissimus dorsi tissue from embryo taken at slaughter, pregnancy day 63

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

value: German landrace

value: 63 dpc

value: skeletal muscle


title: primary breast cancer, sample 69


title: primary breast cancer, sample 58


title: MPI-750_tonsils


title: MPI-743_tonsils


title: Normal 20

type: genomic

first: Atsushi

last: Terunuma

address: 37 Convent Drive, 37/3050

department: Dermatology Branch

institute: National Cancer Institute

hyb_protocol: Standard Infinium HD Methylation Assay protocol

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting.

data_processing: GenomeStudio software v2010.3, Methylation module v1.8.5

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Human Breast

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from fresh frozen primary breast tumours following the Qiagen DNeasy Blood and Tissue Kit protocol.  Briefly, tissues were pre-treated with Proteinase K  at 55C over-night, then lysed, bound to the column, washed, and eluted.  DNA was quantified using the nanodrop spectrophotomer.

tag: race

value: African-American

tag: tissue type

value: Non-tumor


title: Tumor 54

source_name: Human Breast Tumor

value: European-American

value: Tumor

tag: estrogen receptor status

value: Negative

tag: triple negative or basal-like subtype

value: Yes

tag: Stage

value: IIA

tag: tumor grade

tag: node status

tag: survival (months)

tag: survival event

value: Alive

tag: death due to cancer

value: No

tag: neoadjuvant therapy

tag: hormone-therapy

tag: chemotherapy


title: Tumor 20

tag: age

value: IIB

value: Dead


title: Tumor 21


title: Normal 11


title: Normal 21


title: Tumor 72

value: Positive

value: I


title: mouse lung tissue at week 30, 17.5 Gy, biological rep1

description: gene expression data from 17.5 Gy radiation treated mouse lung at 30 weeks, replicate 1

tag: tissue

value: lung

tag: strain

tag: treatment

value: 17.5 Gy radiation treated

tag: time

value: week 30

tag: gender

value: female

value: 10 wk


title: MPI-742_tonsils

tag: type

value: tonsils

tag: tumor


title: Tumor 11

tag: race

value: African-American

tag: tissue type

tag: estrogen receptor status

tag: triple negative or basal-like subtype

tag: Stage


title: Tumor 49

value: European-American

value: Tumor

tag: tumor grade

tag: node status

tag: survival (months)

tag: survival event

tag: death due to cancer


title: mouse lung tissue at week 30, 0 Gy, biological rep3

description: gene expression data from control mouse lung at 30 weeks, replicate 3

tag: tissue

value: control

tag: age


title: MPI-740_tonsils


title: primary breast cancer, sample 17

value: primary breast tumor

tag: tn status

value: triple-negative


title: primary breast cancer, sample 49


title: MPI-739_tonsils


title: MPI-741_tonsils


title: mouse lung tissue at week 30, 0 Gy, biological rep1

description: gene expression data from control mouse lung at 30 weeks, replicate 1

tag: strain

tag: treatment

tag: time


title: mouse lung tissue at week 30, 0 Gy, biological rep2

description: gene expression data from control mouse lung at 30 weeks, replicate 2

tag: gender


title: mouse lung tissue at week 30, 5Gy, biological rep2

description: gene expression data from 5 Gy radiation treated mouse lung at 30 weeks, replicate 2

value: 5 Gy radiation treated


title: mouse lung tissue at week 30, 5Gy, biological rep3

description: gene expression data from 5 Gy radiation treated mouse lung at 30 weeks, replicate 3


title: primary breast cancer, sample 119


title: primary breast cancer, sample 37


title: mouse lung tissue at week 30, 5Gy, biological rep1

description: gene expression data from 5 Gy radiation treated mouse lung at 30 weeks, replicate 1


title: primary breast cancer, sample 81


title: primary breast cancer, sample 97


title: primary breast cancer, sample 71


title: MPI-616_tumor_cell_line

extract_protocol: RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)

tag: type

tag: tumor

value: Diffuse large B-cell lymphoma


title: Tumor 55

tag: race

tag: tissue type

tag: estrogen receptor status

value: No

value: IIIA

value: Dead

value: Yes

tag: neoadjuvant therapy

tag: hormone-therapy

tag: chemotherapy


title: MPI-615_tumor_cell_line


title: Tumor 69

value: Negative

tag: Stage

value: I

tag: tumor grade

tag: node status

tag: survival (months)

tag: survival event

value: Alive


title: MPI-614_tumor_cell_line

value: Ramos

value: endemic Burkitt lymphoma


title: Tumor 51

tag: age

value: II

tag: death due to cancer


title: primary breast cancer, sample 18

tag: tissue

tag: tn status


title: Tumor 17

value: African-American

value: Positive

tag: triple negative or basal-like subtype


title: mouse lung tissue at week 16, 17.5 Gy, biological rep3

description: gene expression data from 17.5 Gy radiation treated mouse lung at 16 weeks, replicate 3

value: lung

tag: strain

tag: treatment

value: 17.5 Gy radiation treated

tag: time

value: week 16

tag: gender

value: female

value: 10 wk


title: mouse lung tissue at week 16, 17.5 Gy, biological rep2

description: gene expression data from 17.5 Gy radiation treated mouse lung at 16 weeks, replicate 2


title: MPI-613_tumor_cell_line

tag: type

value: Raji

tag: tumor


title: primary breast cancer, sample 41

value: primary breast tumor

value: triple-negative


title: MPI-610_tumor_cell_line

value: Diffuse large B-cell lymphoma


title: mouse lung tissue at week 16, 5Gy, biological rep2

description: gene expression data from 5 Gy radiation treated mouse lung at 16 weeks, replicate 2

value: 5 Gy radiation treated


title: MPI-612_tumor_cell_line

value: Namalwa


title: mouse lung tissue at week 16, 5Gy, biological rep3

description: gene expression data from 5 Gy radiation treated mouse lung at 16 weeks, replicate 3


title: primary breast cancer, sample 39


title: primary breast cancer, sample 82


title: MPI-609_tumor_cell_line

value: HT


title: mouse lung tissue at week 16, 17.5 Gy, biological rep1

description: gene expression data from 17.5 Gy radiation treated mouse lung at 16 weeks, replicate 1


title: mouse lung tissue at week 16, 5Gy, biological rep1

description: gene expression data from 5 Gy radiation treated mouse lung at 16 weeks, replicate 1


title: Normal 18

tag: race

tag: tissue type

value: Non-tumor


title: MPI-611_tumor_cell_line


title: primary breast cancer, sample 40


title: MPI-608_tumor_cell_line

value: endemic Burkitt lymphoma


title: Tumor 16

value: Tumor

tag: estrogen receptor status

value: No

tag: Stage

value: IIB

tag: tumor grade

value: Alive

tag: neoadjuvant therapy

tag: hormone-therapy

value: Yes

tag: chemotherapy


title: primary breast cancer, sample 128

tag: tissue


title: mouse lung tissue at week 16, 0 Gy, biological rep3

description: gene expression data from control mouse lung at 16 weeks, replicate 3

value: lung

value: control

value: week 16

tag: age


title: Tumor 19

value: African-American

value: Negative

tag: triple negative or basal-like subtype

tag: node status

tag: survival (months)

tag: survival event

value: Dead

tag: death due to cancer


title: MPI-607_tumor_cell_line

tag: type


title: Normal 15


title: Tumor 18

value: IIIa


title: mouse lung tissue at week 16, 0 Gy, biological rep2

description: gene expression data from control mouse lung at 16 weeks, replicate 2

tag: strain

tag: treatment

tag: time

tag: gender

value: female

value: 10 wk


title: MPI-606_tumor_cell_line

tag: tumor

value: sproadic Burkitt lymphoma


title: primary breast cancer, sample 118

value: primary breast tumor

tag: tn status

value: triple-negative


title: mouse lung tissue at week 16, 0 Gy, biological rep1

description: gene expression data from control mouse lung at 16 weeks, replicate 1


title: mouse lung tissue at week 8, 17.5 Gy, biological rep3

description: gene expression data from 17.5 Gy radiation treated mouse lung at 8 weeks, replicate 3

value: 17.5 Gy radiation treated

value: week 8


title: primary breast cancer, sample 129


title: MPI-545_naive_B_cells

extract_protocol: Naive B cells were isolated from peripheral blood samples of healthy individuals. For the isolation, FACS sorting employing antibodies against CD19 and IgD was used. RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)


title: MPI-544_post_GC_B_cells

extract_protocol: Post GC memory B cells were isolated from peripheral blood samples of healthy individuals. For the isolation, FACS sorting employing antibodies against CD19 and CD27 was used. RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)


title: Tumor 52

tag: race

value: European-American

tag: tissue type

value: Tumor

tag: estrogen receptor status

value: No

tag: Stage

value: IIIA

tag: tumor grade

tag: neoadjuvant therapy


title: primary breast cancer, sample 24

tag: tissue


title: primary breast cancer, sample 77


title: mouse lung tissue at week 8, 17.5 Gy, biological rep2

description: gene expression data from 17.5 Gy radiation treated mouse lung at 8 weeks, replicate 2

value: lung

tag: age


title: MPI-605_tumor_cell_line


title: Tumor 12

value: Positive

tag: triple negative or basal-like subtype

value: IIA

tag: node status

tag: survival (months)

tag: survival event

value: Alive

tag: hormone-therapy

value: Yes

tag: chemotherapy


title: Tumor 50

tag: death due to cancer


title: primary breast cancer, sample 92


title: MPI-502_tumor_cell_line

tag: type

tag: tumor

value: Multiple myeloma


title: Tumor 47

tag: race

value: Dead


title: primary breast cancer, sample 132

tag: tn status


title: mouse lung tissue at week 8, 5Gy, biological rep3

description: gene expression data from 5 Gy radiation treated mouse lung at 8 weeks, replicate 3

tag: strain

tag: treatment

value: 5 Gy radiation treated

tag: time

tag: gender

value: female

value: 10 wk


title: mouse lung tissue at week 8, 17.5 Gy, biological rep1

description: gene expression data from 17.5 Gy radiation treated mouse lung at 8 weeks, replicate 1

tag: tissue


title: Tumor 48

tag: age

tag: tissue type

tag: estrogen receptor status

tag: Stage

value: IIIB

tag: tumor grade

tag: neoadjuvant therapy


title: MPI-501_tumor_cell_line

value: Diffuse large B-cell lymphoma


title: mouse lung tissue at week 8, 5Gy, biological rep2

description: gene expression data from 5 Gy radiation treated mouse lung at 8 weeks, replicate 2

value: week 8


title: Tumor 09

value: African-American

tag: triple negative or basal-like subtype

value: IIB

tag: node status

tag: survival (months)

tag: survival event

tag: hormone-therapy

tag: chemotherapy


title: mouse lung tissue at week 8, 5Gy, biological rep1

description: gene expression data from 5 Gy radiation treated mouse lung at 8 weeks, replicate 1

tag: strain


title: MPI-500_tumor_cell_line

tag: type

tag: tumor


title: primary breast cancer, sample 16

value: primary breast tumor

tag: tn status

value: triple-negative


title: Tumor 45

tag: race

value: European-American

value: Tumor

value: No

tag: death due to cancer


title: primary breast cancer, sample 26

tag: tissue


title: Tumor 14

tag: age

tag: tissue type

tag: estrogen receptor status

value: Negative

value: IIA

value: Alive


title: MPI-498_tumor_cell_line

value: Raji

value: endemic Burkitt lymphoma


title: MPI-499_tumor_cell_line

value: Multiple myeloma


title: primary breast cancer, sample 121


title: MPI-497_tumor_cell_line


title: MPI-496_tumor_cell_line

value: Namalwa


title: mouse lung tissue at week 8, 0 Gy, biological rep2

description: gene expression data from control mouse lung at 8 weeks, replicate 2

value: lung

tag: treatment

value: control

tag: time

tag: gender

value: female

value: 10 wk


title: Tumor 46

value: Positive

tag: triple negative or basal-like subtype

tag: Stage

tag: tumor grade

tag: node status

tag: survival (months)

tag: neoadjuvant therapy


title: mouse lung tissue at week 8, 0 Gy, biological rep3

description: gene expression data from control mouse lung at 8 weeks, replicate 3

tag: strain

value: week 8


title: primary breast cancer, sample 123

value: primary breast tumor

tag: tn status

value: triple-negative


title: Tumor 08

tag: race

value: African-American

value: Tumor

value: Yes

tag: survival event

tag: hormone-therapy

tag: chemotherapy


title: Tumor 10

tag: age

tag: tissue type

value: No

value: IIA

tag: death due to cancer


title: MPI-495_tumor_cell_line

tag: type

tag: tumor

value: Primary mediastinal B-cell lymphoma


title: Tumor 44

value: European-American

tag: estrogen receptor status

value: Negative

tag: triple negative or basal-like subtype

value: IIIB

value: Dead


title: primary breast cancer, sample 53

tag: tissue


title: mouse lung tissue at week 4, 17.5 Gy, biological rep2

description: gene expression data from 17.5 Gy radiation treated mouse lung at 4 weeks, replicate 2

value: lung

tag: treatment

value: 17.5 Gy radiation treated

tag: time

value: week 4

tag: gender


title: primary breast cancer, sample 45


title: mouse lung tissue at week 4, 17.5 Gy, biological rep3

description: gene expression data from 17.5 Gy radiation treated mouse lung at 4 weeks, replicate 3

tag: strain

value: female

value: 10 wk


title: mouse lung tissue at week 4, 17.5 Gy, biological rep1

description: gene expression data from 17.5 Gy radiation treated mouse lung at 4 weeks, replicate 1


title: MPI-494_tumor_cell_line

value: Diffuse large B-cell lymphoma


title: primary breast cancer, sample 105

value: primary breast tumor

tag: tn status

value: triple-negative


title: primary breast cancer, sample 43


title: MPI-493_tumor_cell_line


title: MPI-492_tumor_cell_line

value: Multiple myeloma


title: mouse lung tissue at week 4, 5Gy, biological rep3

description: gene expression data from 5 Gy radiation treated mouse lung at 4 weeks, replicate 3

value: 5 Gy radiation treated


title: primary breast cancer, sample 46


title: primary breast cancer, sample 9


title: Tumor 42

tag: race

value: Tumor

value: No

tag: Stage

tag: tumor grade

tag: node status

tag: survival (months)

tag: neoadjuvant therapy


title: mouse lung tissue at week 4, 5Gy, biological rep2

description: gene expression data from 5 Gy radiation treated mouse lung at 4 weeks, replicate 2

tag: age


title: mouse lung tissue at week 8, 0 Gy, biological rep1

description: gene expression data from control mouse lung at 8 weeks, replicate 1

value: control

value: week 8


title: Tumor 68

value: European-American

tag: tissue type

value: Negative

value: IIB

tag: survival event

tag: death due to cancer

value: Yes

tag: hormone-therapy

tag: chemotherapy


title: Tumor 43

tag: estrogen receptor status

tag: triple negative or basal-like subtype

value: Dead


title: Tumor 41

value: Positive


title: MPI-491_tumor_cell_line

tag: type

tag: tumor


title: mouse lung tissue at week 4, 5Gy, biological rep1

description: gene expression data from 5 Gy radiation treated mouse lung at 4 weeks, replicate 1

tag: tissue

value: lung

tag: strain

tag: treatment

tag: time

value: week 4

tag: gender

value: female


title: S496RZC1:TRGC

city: Los Angeles

first: Cho-Lea

last: Tso

state: CA

address: 10833 Le Conte Avenue

department: Surgery

institute: University of California, Los Angeles

description: clone selected by RT+TMZ

hyb_protocol: hybridized on Affymetrix GeneChip U133 Plus 2.0 Array

scan_protocol: GeneArray scanner (Affymetrix).

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

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

growth_protocol: GSC cultures in stem cell growth media

extract_protocol: Total RNA was extracted from cells using an RNeasy kit (QIAGEN)

treatment_protocol: untreated, treated with RT, or treated with RT+TMZ

tag: cell type

value: glioblastoma stem cells


title: Tumor 07

tag: race

value: African-American

tag: Stage

value: IIA

tag: node status

tag: survival (months)

tag: neoadjuvant therapy


title: Tumor 39

tag: age

tag: tissue type

tag: tumor grade

tag: survival event

value: Alive

tag: death due to cancer

tag: hormone-therapy


title: S496RC1:TRGC

description: clone selected by RT


title: E496-2:TSGC

description: untreated clone


title: MPI-489_tumor_cell_line

tag: type

tag: tumor

value: Primary mediastinal B-cell lymphoma


title: MPI-490_tumor_cell_line

value: Diffuse large B-cell lymphoma


title: MPI-488_tumor_cell_line


title: mouse lung tissue at week 4, 0 Gy, biological rep3

description: gene expression data from control mouse lung at 4 weeks, replicate 3

tag: tissue

tag: strain

tag: treatment

value: control

value: 10 wk


title: MPI-487_tumor_cell_line

value: Gumbus

value: sproadic Burkitt lymphoma


title: Tumor 38

value: European-American

value: Tumor

tag: estrogen receptor status

value: Negative

tag: triple negative or basal-like subtype

value: IIB

value: No

tag: chemotherapy


title: Tumor 06

tag: race

tag: Stage

tag: node status

value: Dead

value: Yes


title: E445RZC2:TRGC

description: clone selected by RT+TMZ

tag: cell type

value: glioblastoma stem cells


title: mouse lung tissue at week 4, 0 Gy, biological rep1

description: gene expression data from control mouse lung at 4 weeks, replicate 1

value: lung

tag: time

value: week 4

tag: gender

value: female

tag: age


title: MPI-486_tumor_cell_line


title: mouse lung tissue at week 2, 17.5 Gy, biological rep3

description: gene expression data from 17.5 Gy radiation treated mouse lung at 2 weeks, replicate 3

value: 17.5 Gy radiation treated

value: week 2


title: mouse lung tissue at week 2, 17.5 Gy, biological rep2

description: gene expression data from 17.5 Gy radiation treated mouse lung at 2 weeks, replicate 2


title: Tumor 05

value: African-American

tag: tissue type

tag: tumor grade

tag: survival (months)

tag: survival event

tag: death due to cancer

tag: neoadjuvant therapy


title: E496-1:TSGC

description: untreated clone


title: E445RC2:TRGC

description: clone selected by RT


title: MPI-485_tumor_cell_line

tag: type

value: DoGum

tag: tumor


title: mouse lung tissue at week 4, 0 Gy, biological rep2

description: gene expression data from control mouse lung at 4 weeks, replicate 2

tag: tissue

tag: strain

tag: treatment

value: control

value: 10 wk


title: mouse lung tissue at week 2, 17.5 Gy, biological rep1

description: gene expression data from 17.5 Gy radiation treated mouse lung at 2 weeks, replicate 1


title: E445-2:TSGC

description: untreated clone


title: E445-1:TSGC

description: untreated clone


title: mouse lung tissue at week 2, 5Gy, biological rep3

description: gene expression data from 5 Gy radiation treated mouse lung at 2 weeks, replicate 3

value: 5 Gy radiation treated


title: Tumor 36

tag: race

value: European-American

value: Tumor

tag: estrogen receptor status

value: Positive

tag: triple negative or basal-like subtype

tag: Stage

value: II

value: Alive

tag: hormone-therapy

tag: chemotherapy


title: MPI-484_tumor_cell_line

value: DoGKit

value: HIV-associated Burkitt lymphoma


title: D431RZ2: TRGC

description: clone selected by RT plus Temozolomide (TMZ)

source_name: D431RZ2: TRGC

tag: cell type

value: glioblastoma stem cells


title: MPI-483_tumor_cell_line

value: Daudi

value: endemic Burkitt lymphoma


title: 03-inf 24h

city: XI'AN

first: Li

last: Dengyun

address: Xinong Raod 22

country: China

institute: NWSUAF

description: 24 h post Porcine Alveolar Macrophages infected by  porcine reproductive and respiratory syndrome virus

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization  images  were  collected  using  a  laser  scanner  (GenePix 4000B,  Molecular  Device)  and  digitized  using  Array-Pro  image  analysis  software (Media Cybernetics).

data_processing: Data  were  analyzed  by  first  subtracting  the  background  and  then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

source_name: Porcine Alveolar Macrophages

label_protocol: The assay started from 2 to 5 µg total RNA sample were 3’-extended with a poly(A)  tail  using  poly(A)  polymerase.  An  oligonucleotide  tag  was  then  ligated  to  the poly(A) tail for later fluorescent dye staining

extract_protocol: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada), following the manufacturer's recommended protocol.

tag: age

value: PAM

tag: infection

value: PRRSV strain HuN4

tag: time


title: Tumor 04

value: African-American

tag: tissue type

value: No

value: IIIB

tag: tumor grade

tag: node status

tag: survival (months)

tag: survival event

value: Dead

tag: death due to cancer

value: Yes


title: 02-inf 12h

description: 12h post Porcine Alveolar Macrophages infected by  porcine reproductive and respiratory syndrome virus


title: Normal 05

value: Non-tumor


title: mouse lung tissue at week 2, 5Gy, biological rep1

description: gene expression data from 5 Gy radiation treated mouse lung at 2 weeks, replicate 1

tag: tissue

value: lung

tag: strain

tag: treatment

value: 5 Gy radiation treated

value: week 2

tag: gender

value: female

value: 10 wk


title: 01-Con

description: uninfected Porcine Alveolar Macrophages

value: control


title: mouse lung tissue at week 2, 5Gy, biological rep2

description: gene expression data from 5 Gy radiation treated mouse lung at 2 weeks, replicate 2


title: D431RC2: Treatment resistant GSC (TRGC)

description: clone selected by radition treatment (RT)

source_name: D431RC2: Treatment resistant GSC (TRGC)

value: glioblastoma stem cells


title: Tumor 03

tag: race

value: Tumor

tag: estrogen receptor status

value: Negative

tag: triple negative or basal-like subtype

tag: Stage

value: IIB

tag: neoadjuvant therapy


title: mouse lung tissue at week 2, 0 Gy, biological rep2

description: gene expression data from control mouse lung at 2 weeks, replicate 2

tag: age


title: D431-2: Treatment sensitive GSC (TSGC)

description: untreated clone

source_name: D431-2: Treatment sensitive GSC (TSGC)

tag: cell type


title: del_hnoC-anaerobic-15hrs-rep3

city: San Diego

first: Lars

last: Plate

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Standard Agilent protocol.

scan_protocol: Standard Agilent protocol.

data_processing: The microarray data were analyzed using the limma package in the R computing environment. Data were background corrected using the normexp method with an offset of 1, and quantile normalized between arrays.

organism: Shewanella oneidensis MR-1

source_name: del_hnoC, rep3

label_protocol: Cy3-labeled cRNA was generated using the Low Input Quick Amp WT Labeling Kit (Agilent) with 100 ng of input RNA.

growth_protocol: Growth in MM mineral medium, 29ºC, anaerobic, stationary, in 12-well microtiter plates, 3mL cultures, 15hrs

extract_protocol: 2.5 mL of the culture were treated with RNAprotect (Qiagen) and total RNA was extracted from the samples using the RNeasy mini kit (Qiagen). Samples were treated twice with DnaseI (Qiagen) purified using the RNAeasy mini kit.

tag: genotype/variation


title: mouse lung tissue at week 2, 0 Gy, biological rep1

description: gene expression data from control mouse lung at 2 weeks, replicate 1

tag: time


title: del_hnoC-anaerobic-15hrs-rep2

source_name: del_hnoC, rep2


title: mouse lung tissue at week 2, 0 Gy, biological rep3

description: gene expression data from control mouse lung at 2 weeks, replicate 3


title: D431-1: Treatment sensitive glioblastoma stem cells (GSC)

description: untreated clone


title: Tumor 35

value: European-American

tag: tissue type

value: Positive

value: I

tag: tumor grade

tag: node status

value: Alive

tag: hormone-therapy

tag: chemotherapy


title: Tumor 34

tag: survival (months)

tag: survival event

value: Dead

tag: death due to cancer

value: No


title: tumoral tissue specimen PR99

city: Parma

first: Silvia

last: Rossi

state: Parma

address: Viale Usberti, 11/A

department: Genetics, Microbiology, Anthropology ed Evolution

country: Italy

institute: COMT - Centre for Molecular and Translational Oncology, University of Parma

description: tumoral tissue specimen

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using Data Assist software (Applied Biosystems); it were excluded all Ct raw data ≥35 Ct and were exclude outliers among replicates; p-values were adjusted using Benjamini-Hochberg False Discovery Rate.
For the normalization it used the average of all replicates of the 18S housekeeping gene (18S-Hs99999901_s1 assay) and software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data; matrix normalized worksheet reports normalized signal (against housekeeping gene); Fold Change worksheet reports ratios between patients samples and reference sample (HEALTHY).

label: TaqMan assay labels were preloaded on the CARDs

source_name: oral cavity

label_protocol: An equal amount of input cDNA (200 ng) was used per reaction and loaded in one of the eight sample-loading port  on TaqMan Low Density Array (Applied Biosystems) and cards were run on  ABI PRISM 7900 HT Fast Real-Time PCR System (Applied Biosystems Inc., Foster City, CA, USA). For data analysis we used the RQ Manager and Data Assist softwares provided by Applied Biosystem Inc.

extract_protocol: Total RNA from each biopsy was extracted using Trizol® according to the manufacturer’s instructions and in combination with Qiagen RNAeasy Mini Kit (Qiagen). RNA integrity and was verified using Thermo Scientific NanoDropTM spectrophotometers and micro-electrophoresis on a Bioanalyzer 2010 instrument (Agilent). Total RNA (1μg) was reverse-transcribed with the QuantiTect® Reverse Transcription Kit (Qiagen) according to the manufacturer’s instructions and cDNA was quantified

treatment_protocol: All healthy and 119 neoplastic specimens, sampled as fresh tissue, were processed for molecular analyses according to the following scheme: each biopsy was dissected in three 1.5 cm-thick cubes, immersed into RNAlater Solution (Ambion) and frozen at -80°C. One of the three samples was used to extract total RNA for qPCR analyses, whereas the other two samples were used to create a tissue bank.

tag: gender

value: M

tag: tnm grading

tag: lymphonode metastasis

value: N-

tag: tumor stage

tag: grade of differentiation


title: Tumor 02

tag: race

value: African-American

tag: age

tag: estrogen receptor status

tag: triple negative or basal-like subtype

tag: Stage

value: IIIB

value: Yes

tag: neoadjuvant therapy


title: WT-anaerobic-15hrs-rep4

source_name: WT, rep4

tag: genotype/variation

value: WT


title: Tumor 01

tag: tissue type

value: IIA

tag: tumor grade

tag: node status

tag: hormone-therapy


title: tumoral tissue specimen PR98

description: tumoral tissue specimen

value: F

value: N+


title: tumoral tissue specimen PR97

description: tumoral tissue specimen


title: WT-anaerobic-15hrs-rep3

source_name: WT, rep3


title: tumoral tissue specimen PR95

description: tumoral tissue specimen


title: tumoral tissue specimen PR96

description: tumoral tissue specimen


title: tumoral tissue specimen PR94

description: tumoral tissue specimen


title: E14.5 DRG from Bax knockout mice A

city: Baltimore

first: David

middle: D

last: Ginty

address: 725 N. Wolf ST

department: Neuroscience

institute: HHMI/Johns Hopkins Univ

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

source_name: Dissected dorsal root ganglia from E14.5 mouse embryos.

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

growth_protocol:
No cell culture involved.
Please see Growth above

extract_protocol: RNeasy Micro kit (Qiagen).

treatment_protocol:
No treatment involved.
Please see Treatment above

tag: genetic background

tag: Sex

value: mixed

tag: tissue

tag: treatment

value: No treatment involved.

tag: genotype

value: Bax null


title: tumoral tissue specimen PR93

description: tumoral tissue specimen

tag: gender

tag: tnm grading

tag: lymphonode metastasis

tag: tumor stage

tag: grade of differentiation


title: tumoral tissue specimen PR92

description: tumoral tissue specimen

tag: age


title: Tumor 33

tag: race

value: European-American

value: Tumor

tag: estrogen receptor status

value: Negative

tag: triple negative or basal-like subtype

tag: Stage

tag: survival (months)

tag: survival event

tag: death due to cancer

tag: neoadjuvant therapy

tag: chemotherapy


title: tumoral tissue specimen PR91

description: tumoral tissue specimen


title: WT-anaerobic-15hrs-rep1

source_name: WT, rep1

tag: genotype/variation


title: ControlSite_rep4

city: Gainesville

first: Erica

middle: Karin

last: Brockmeier

state: FL

address: 2187 Mowry Road

institute: University of Florida

description:
Econ_L25
Gene expression of fish residing at clean reference site.

hyb_protocol: Hybridization of 600 ng purified cRNA was completed with the Gene Expression hybridization kit (Agilent, Santa Clara, USA). Cy3-labeled cRNA was incubated with blocking agent and fragmentation buffer at 60 C for 30 minutes. Hybridization buffer was then added to the sample and 40 μL of the sample was added to the gasket. The microarray slide was incubated with the gasket for 17 hours at 65 C while spinning at 10 rpm. The slide was then washed and dried, and scanning was conducted at the University of Florida gene expression core by the Microarray Scanner (Agilent, Santa Clara, USA).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted Processed Signal intensities. Normalization was conducted using the LOESS method, and values are reported as Log2 transformed data.

organism: Gambusia holbrooki

source_name: liver, Econfina, control site

label_protocol: The Low RNA Input Amplification Kit for one color (Cy3) (Agilent, Santa Clara, USA) was used to synthesize cRNA. 200 ng RNA and RNA spike-in controls were incubated with T7 primer mix and cDNA synthesis immediately proceeded primer annealing. In vitro transcription and Cy3 incorporation was then conducted and purification of Cy3-labeled cRNA was completed using the RNeasy kit (QIAGEN, Hilden, Germany). cRNA concentrations and specific activities were determined by the Nanodrop (ThermoScientific, Waltham, USA) and a specific activity > 8 was the cut-off value for further processing.

extract_protocol: Liver samples in RNALater were thawed on ice, blotted dry of excess RNAlater, and homogenized in 1mL of TRIzol (Invitrogen, Grand Island, USA). After precipitation in isopropanol and washing with ethanol, RNA was rehydrated with RNAsecure Reagent (Ambion, Grand Island, USA). RNA was DNase treated using Turbo DNase (Ambion, Grand Island, USA). RNA quality and quantity were assessed using the Nanodrop (ThermoScientific, Waltham, USA) and the 2100 BioAnalyzer (Agilent, Santa Clara, USA).

treatment_protocol: Wild G. holbrooki were captured from one site downstream of the Buckeye Pulp and Paper Mill (Taylor County, Perry, FL, USA) on the Fenholloway River (GPS coordinates: N 30 058.341’, W 83 588.569’) and from one site in the Econfina conservation area (GPS coordinates: N 30 08.549', W 83 51.962'). One sampling event at the paper mill site was conducted on July 12th, 2012 and two sampling events at Econfina on August 7th and October 4th, 2012. Sexually mature female G. holbrooki were transferred to 5 gallon aerated buckets filled with site water and were processed at the site immediately after collection. Fish were anesthetized using Tricaine-S (Western Chemical, Ferndale, USA) and sacrificed via spinal transection. Livers were removed and stored in RNALater (Qiagen, Hilden, Germany) overnight at 4C before transferred for long-term storage at -80C.

tag: strain

value: wild

tag: tissue

value: liver

value: female

tag: collection site

value: Econfina (control site)


title: ControlSite_rep3

description:
Econ_L23
Gene expression of fish residing at clean reference site.

tag: gender


title: ControlSite_rep2

description:
Econ_L3
Gene expression of fish residing at clean reference site.


title: tumoral tissue specimen PR9

description: tumoral tissue specimen

value: M

tag: tnm grading

tag: lymphonode metastasis

tag: tumor stage

value: IVa


title: PaperMill_rep3

description:
PME_L36
Gene expression of fish residing downstream of pulp and paper mill.

source_name: liver, Fenholloway, paper mill site

value: Fenholloway (paper mill site)


title: tumoral tissue specimen PR90

description: tumoral tissue specimen

value: N-

tag: age

tag: grade of differentiation


title: WT-anaerobic-15hrs-rep2

source_name: WT, rep2

value: WT


title: Normal 01

tag: race

value: African-American

tag: tissue type

value: Non-tumor


title: E14.5 DRG from NGF; Bax double knockout mice A

tag: genetic background

tag: Sex

value: mixed

value: Dissected dorsal root ganglia from E14.5 mouse embryos.

tag: treatment

tag: genotype

value: NGF, Bax null


title: tumoral tissue specimen PR88

description: tumoral tissue specimen

value: N+

value: III


title: tumoral tissue specimen PR85

description: tumoral tissue specimen


title: tumoral tissue specimen PR86

description: tumoral tissue specimen

value: F


title: tumoral tissue specimen PR84

description: tumoral tissue specimen

value: II


title: ControlSite_rep1

description:
Econ_L26
Gene expression of fish residing at clean reference site.

value: wild

value: liver


title: Severe PH Patient Sample

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: Arterial Blood Sample

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 2 to 4 µg total RNA sample, which was 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

growth_protocol: Freshly isolated and processed

extract_protocol: miRNA was isolated from the buffy coats using miRNeasy Mini Kit (Qiagen)

treatment_protocol: Freshly isolated blood was centrifuged to fractionate the buffy coat and miRNA was extracted

tag: disease state

value: Idiopathic PAH

tag: pulmonary artery pressure

value: PAP >53 mm Hg


title: Healthy (Non PH) Control

value: Healthy

value: PAP =20 mm Hg


title: PaperMill_rep1

description:
PME_L42
Gene expression of fish residing downstream of pulp and paper mill.

tag: strain

value: female

value: Fenholloway (paper mill site)


title: del_hnoC-anaerobic-15hrs-rep4

source_name: del_hnoC, rep4

tag: genotype/variation


title: PaperMill_rep2

description:
PME_L6
Gene expression of fish residing downstream of pulp and paper mill.

tag: tissue

tag: collection site


title: E14.5 DRG from NGF; Bax double knockout mice B

value: No treatment involved.


title: tumoral tissue specimen PR83

description: tumoral tissue specimen

tag: gender

value: M

tag: tnm grading

value: IVa


title: PC3 miR-95

city: Toronto

first: Stanley

middle: K

last: Liu

state: Ontario

address: 2075 Bayview Avenue

country: Canada

institute: Sunnybrook Research Institute

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Gene expression array data was normalized using the default parameters in Affymetrix Expression Console Software v 1.2

source_name: PC3 miR-95

label_protocol: Labeling, hybridization, and scanning were performed at The Centre for Applied Genomics (Hospital for Sick Children)

growth_protocol: PC3 prostate cells stably overexpressing miR control or miR-95 were grown in 10% FBS/DMEM media in 37C humidifed incubator

extract_protocol: Total RNA was extracted and purified using the Qiagen RNAeasy mini kit as per manufacturer's instructions

tag: cell line

value: miR-95 overexpression


title: PC3 miR control

source_name: PC3 miR control

value: control


title: guaB- Guo-treated (p)ppGpp0 Cells Replicate 3

city: Houston

first: Jue

middle: D.

last: Wang

state: TX

address: 1 Baylor Plaza, Rm T932

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Biological replicate 3 of 3. guaB- (p)ppGpp0 cells treated with Guo

hyb_protocol: The procedure for hybridization was performed as described previously (Britton et al., 2002).

scan_protocol: Scanned on a GenePix 4000B Scanner (Axon Instruments).

data_processing: GenePix Pro (v 6.1) was used for background subtraction and normalization.

organism: Bacillus subtilis subsp. subtilis str. SMY

source_name: SMY guaB- delta yjbM delta ywaC delta relA

label_protocol: The procedures for reverse transcription and labeling were performed as described previously (Britton et al., 2002).

growth_protocol: Cells were grown in S7 defined medium (Vasantha and Freese, 1980); MOPS was used at 50 mM rather than 100 mM, supplemented with 0.1% glutamate, 1% glucose, and 0.5% casamino acids at 37°C with shaking.

extract_protocol: RNA was extracted using QIAGEN RNeasy Mini Kit following manufacturer's instructions.

treatment_protocol: At OD600~0.3, arginine hydroxamate was added to a final concentration of 0.5mg/ml or guanosine was added to a final concentration of 1mM, cells were collected 20 minutes later.

value: guaB- delta yjbM delta ywaC delta relA

value: 1mM Guo for 20min

source_name: pooled reference RNA

value: Wild-type

tag: reference

value: Pooled RNA from different growth phases and wt backgrounds


title: guaB- Guo-treated (p)ppGpp0 Cells Replicate 1

description: Biological replicate 1 of 3. guaB- (p)ppGpp0 cells treated with Guo


title: guaB- Guo-treated (p)ppGpp0 Cells Replicate 2

description: Biological replicate 2 of 3. guaB- (p)ppGpp0 cells treated with Guo


title: tumoral tissue specimen PR79

description: tumoral tissue specimen

tag: lymphonode metastasis

value: N+

tag: tumor stage

value: III

tag: age

tag: grade of differentiation


title: tumoral tissue specimen PR81

description: tumoral tissue specimen

value: F


title: tumoral tissue specimen PR80

description: tumoral tissue specimen


title: tumoral tissue specimen PR8

description: tumoral tissue specimen


title: tumoral tissue specimen PR77

description: tumoral tissue specimen


title: tumoral tissue specimen PR76

description: tumoral tissue specimen

value: N-

value: II


title: del_hnoC-anaerobic-15hrs-rep1

source_name: del_hnoC, rep1


title: guaB- RHX-treated (p)ppGpp0 Cells Replicate 2

description: Biological replicate 2 of 3. guaB- (p)ppGpp0 cells treated with RHX

value: 0.5mg/ml RHX for 20min


title: tumoral tissue specimen PR74

description: tumoral tissue specimen

value: I


title: guaB- RHX-treated (p)ppGpp0 Cells Replicate 1

description: Biological replicate 1 of 3. guaB- (p)ppGpp0 cells treated with RHX


title: tumoral tissue specimen PR73

description: tumoral tissue specimen


title: guaB- (p)ppGpp0 Cells Replicate 3

description: Biological replicate 3 of 3. guaB- (p)ppGpp0 cells untreated

value: No treatment


title: E14.5 DRG from Bax knockout mice B

tag: genetic background

tag: Sex

value: mixed

value: Dissected dorsal root ganglia from E14.5 mouse embryos.

value: No treatment involved.

value: Bax null


title: tumoral tissue specimen PR72

description: tumoral tissue specimen

value: M


title: guaB- (p)ppGpp0 Cells Replicate 1

description: Biological replicate 1 of 3. guaB- (p)ppGpp0 cells untreated

tag: genotype

value: guaB- delta yjbM delta ywaC delta relA

tag: treatment


title: guaB- (p)ppGpp0 Cells Replicate 2

description: Biological replicate 2 of 3. guaB- (p)ppGpp0 cells untreated


title: tumoral tissue specimen PR70

description: tumoral tissue specimen


title: tumoral tissue specimen PR7

description: tumoral tissue specimen


title: tumoral tissue specimen PR68

description: tumoral tissue specimen

value: IVa


title: tumoral tissue specimen PR69

description: tumoral tissue specimen


title: guaB- RHX-treated (p)ppGpp0 Cells Replicate 3

description: Biological replicate 3 of 3. guaB- (p)ppGpp0 cells treated with RHX

value: Wild-type


title: Guo-treated ΔcodY (p)ppGpp0 Cells Replicate 2

description: Biological replicate 2 of 3. ΔcodY (p)ppGpp0 cells treated with Guo

source_name: SMY ΔcodY delta yjbM delta ywaC delta relA

value: ΔcodY delta yjbM delta ywaC delta relA

value: 1mM Guo for 20min

value: Pooled RNA from different growth phases and wt backgrounds


title: Guo-treated ΔcodY (p)ppGpp0 Cells Replicate 3

description: Biological replicate 3 of 3. ΔcodY (p)ppGpp0 cells treated with Guo


title: Guo-treated ΔcodY (p)ppGpp0 Cells Replicate 1

description: Biological replicate 1 of 3. ΔcodY (p)ppGpp0 cells treated with Guo


title: tumoral tissue specimen PR66

description: tumoral tissue specimen

value: F


title: RHX-treated ΔcodY (p)ppGpp0 Cells Replicate 2

description: Biological replicate 2 of 3. ΔcodY (p)ppGpp0 cells treated with RHX


title: tumoral tissue specimen PR67

description: tumoral tissue specimen

value: N-


title: tumoral tissue specimen PR65

description: tumoral tissue specimen


title: tumoral tissue specimen PR63

description: tumoral tissue specimen

value: N+


title: tumoral tissue specimen PR62

description: tumoral tissue specimen


title: tumoral tissue specimen PR61

description: tumoral tissue specimen


title: tumoral tissue specimen PR6

description: tumoral tissue specimen


title: RHX-treated ΔcodY (p)ppGpp0 Cells Replicate 1

description: Biological replicate 1 of 3. ΔcodY (p)ppGpp0 cells treated with RHX

value: 0.5mg/ml RHX for 20min


title: ΔcodY (p)ppGpp0 Cells Replicate 2

description: Biological replicate 2 of 3. ΔcodY (p)ppGpp0 cells untreated


title: ΔcodY (p)ppGpp0 Cells Replicate 3

description: Biological replicate 3 of 3. ΔcodY (p)ppGpp0 cells untreated


title: RHX-treated ΔcodY (p)ppGpp0 Cells Replicate 3

description: Biological replicate 3 of 3. ΔcodY (p)ppGpp0 cells treated with RHX


title: Guo-treated (p)ppGpp0 Cells Replicate 3

description: Biological replicate 3 of 3. (p)ppGpp0 cells treated with Guo

source_name: SMY delta yjbM delta ywaC delta relA

value: delta yjbM delta ywaC delta relA


title: RHX-treated (p)ppGpp0 Cells Replicate 3

description: Biological replicate 3 of 3. (p)ppGpp0 cells treated with RHX


title: ΔcodY (p)ppGpp0 Cells Replicate 1

description: Biological replicate 1 of 3. ΔcodY (p)ppGpp0 cells untreated

value: No treatment


title: Guo-treated (p)ppGpp0 Cells Replicate 1

description: Biological replicate 1 of 3. (p)ppGpp0 cells treated with Guo


title: Guo-treated (p)ppGpp0 Cells Replicate 2

description: Biological replicate 2 of 3. (p)ppGpp0 cells treated with Guo


title: tumoral tissue specimen PR59

description: tumoral tissue specimen

source_name: oral cavity

value: I


title: tumoral tissue specimen PR64

description: tumoral tissue specimen

value: II


title: RHX-treated (p)ppGpp0 Cells Replicate 2

description: Biological replicate 2 of 3. (p)ppGpp0 cells treated with RHX


title: PaperMill_rep4

description:
PME_L38
Gene expression of fish residing downstream of pulp and paper mill.

value: wild

value: liver

value: female

value: Fenholloway (paper mill site)


title: tumoral tissue specimen PR56

description: tumoral tissue specimen

value: M


title: tumoral tissue specimen PR55

description: tumoral tissue specimen


title: RHX-treated (p)ppGpp0 Cells Replicate 1

description: Biological replicate 1 of 3. (p)ppGpp0 cells treated with RHX

value: Wild-type


title: tumoral tissue specimen PR54

description: tumoral tissue specimen

value: IVa


title: tumoral tissue specimen PR58

description: tumoral tissue specimen


title: tumoral tissue specimen PR53

description: tumoral tissue specimen


title: (p)ppGpp0 Cells Replicate 1

description: Biological replicate 1 of 3. (p)ppGpp0 cells untreated


title: (p)ppGpp0 Cells Replicate 2

description: Biological replicate 2 of 3. (p)ppGpp0 cells untreated


title: (p)ppGpp0 Cells Replicate 3

description: Biological replicate 3 of 3. (p)ppGpp0 cells untreated


title: Guo-treated Wild-type Cells Replicate 3

description: Biological replicate 3 of 3. WT cells treated with Guo

source_name: SMY

value: 1mM Guo for 20min


title: tumoral tissue specimen PR51

description: tumoral tissue specimen


title: tumoral tissue specimen PR5

description: tumoral tissue specimen


title: tumoral tissue specimen PR57

description: tumoral tissue specimen


title: Guo-treated Wild-type Cells Replicate 1

description: Biological replicate 1 of 3. WT cells treated with Guo

value: Pooled RNA from different growth phases and wt backgrounds


title: RHX-treated Wild-type Cells Replicate 3

description: Biological replicate 3 of 3. WT cells treated with RHX


title: tumoral tissue specimen PR45

description: tumoral tissue specimen

value: III


title: tumoral tissue specimen PR44

description: tumoral tissue specimen

value: F


title: RHX-treated Wild-type Cells Replicate 2

description: Biological replicate 2 of 3. WT cells treated with RHX


title: Wild-type Cells Replicate 3

description: Biological replicate 3 of 3. WT cells untreated


title: tumoral tissue specimen PR43

description: tumoral tissue specimen

value: N+


title: Guo-treated Wild-type Cells Replicate 2

description: Biological replicate 2 of 3. WT cells treated with Guo


title: HBMEC_12h_MBG_rep3

city: College Station

first: Nancy

last: Ing

department: Animal Science

institute: Texas A&M University

description: Sample 6

hyb_protocol: 1.65 ug of labeled cRNA was fragmented and used to hybridize each of the 4 X 44K microarrays prior to washing, as described in Agilent's One Color Microarray-based Gene Expression Analysis protocol.

scan_protocol: An Agilent microarray scanner (model 62505C) scanned the miccroarrays at 5 um resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Quartile normalization reduced variability between arrays. On each array, data were normalized to its median expression level.

source_name: HBMEC MBG-treated

label_protocol: RNA was used for reverse transcription and for in vitro transcription of Cy3-labelled cRNA using the Agilent Low-Input Quick Amp labeling kit.Fluorescent cRNA yield was assessed on the Nanodrop.

growth_protocol: HBMEC primary cultures were purchased from ScienCell (Carlsbad, CA) and grown according to their instructions along with an endothelial cell supplement.

extract_protocol: RNA was isolated with TriPure reagent (Roche; Indianapolis, IN). It was analyzed for quality on a Bioanalyzer 2100 and for concentration on a Nanodrop ND-1000.

treatment_protocol: At 80% confluence, 24 h prior to treatment, the medium was changed to low serum (0.5%). At treatment, medium was changed to the original with 10% FBS along with the MBG or DMSO treatment.

tag: cell type

value: human brain microvascular endothelial cells (HBMECs)

tag: treated with

value: 10 nM MBG for 12hr


title: HBMEC_12h_Control_rep3

description: Sample 5

source_name: HBMEC control

value: DMSO (vehicle control) for 12hr


title: HBMEC_12h_Control_rep2

description: Sample 4


title: HBMEC_12h_MBG_rep2

description: Sample 3


title: tumoral tissue specimen PR4

description: tumoral tissue specimen

value: N-

value: I


title: tumoral tissue specimen PR47

description: tumoral tissue specimen


title: RHX-treated Wild-type Cells Replicate 1

description: Biological replicate 1 of 3. WT cells treated with RHX

value: 0.5mg/ml RHX for 20min


title: Wild-type Cells Replicate 2

description: Biological replicate 2 of 3. WT cells untreated

value: No treatment


title: Wild-type Cells Replicate 1

description: Biological replicate 1 of 3. WT cells untreated


title: tumoral tissue specimen PR39

description: tumoral tissue specimen


title: HBMEC_12h_MBG_rep1

description: Sample 2


title: tumoral tissue specimen PR38

description: tumoral tissue specimen


title: tumoral tissue specimen PR34

description: tumoral tissue specimen

value: II


title: tumoral tissue specimen PR37

description: tumoral tissue specimen


title: tumoral tissue specimen PR35

description: tumoral tissue specimen


title: tumoral tissue specimen PR36

description: tumoral tissue specimen


title: HBMEC_12h_Control_rep1

description: Sample 1


title: tumoral tissue specimen PR33

description: tumoral tissue specimen


title: tumoral tissue specimen PR32

description: tumoral tissue specimen


title: tumoral tissue specimen PR31

description: tumoral tissue specimen


title: tumoral tissue specimen PR3

description: tumoral tissue specimen


title: tumoral tissue specimen PR30

description: tumoral tissue specimen


title: HAK-1A HCC clone overexpressing TCF-4J under normoxia

city: Providence

first: Miran

last: Kim

state: RI

address: 55 Claverick St

institute: Liver Research Center, Rhode Island Hospital and Warren Alpert Medical School of Brown University

hyb_protocol: Cy3-labelled cRNA was fragmented and tohybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) using the Gene Expression Hybridization Kit as recommended by Agilent Technologies.

scan_protocol: The slides were scanned using a DNA Microarray Scanner (Agilent Technologies) immediately after washing.

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (Agilent Technologies). The data were subjected to quantile normalization. The normalization was performed using R software (R Development Core Team).

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using Agilent Low-Input Quick Amp Labeling Kit (One-color) (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s instructions.

growth_protocol: HAK-1A cells were maintained in DMEM supplemented with 10% FBS.

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

treatment_protocol: To generate the stable clones overexpressing TCF-4J or TCF-4K, HAK-1A cells were transfected with each plasmid construct by using TransIT-LT1 Reagent (Mirus Bio Co., Madison, WI) according to the manufacturers’ instructions, and selected by G418 (Invitrogen, Carlsbad, CA). Empty vector (EV) clone and HCV Core protein-expressing clones were also prepared by the same method. The expression of exogenous TCF-4 isoform in the established stable clones was confirmed by Western blot analysis. These clones were maintained under either hypoxic (0% Oxgen) or normoxic (20% Oxygen) conditions, and used for the microarray analysis.

value: HAK-1A hepatocellular carcinoma (HCC) cell


title: tumoral tissue specimen PR28

description: tumoral tissue specimen


title: tumoral tissue specimen PR29

description: tumoral tissue specimen


title: HAK-1A HCC clone overexpressing TCF-4K under hypoxia


title: HAK-1A HCC clone overexpressing EV under hypoxia


title: tumoral tissue specimen PR23

description: tumoral tissue specimen

value: M


title: tumoral tissue specimen PR24

description: tumoral tissue specimen


title: tumoral tissue specimen PR20

description: tumoral tissue specimen


title: tumoral tissue specimen PR22

description: tumoral tissue specimen


title: tumoral tissue specimen PR26

description: tumoral tissue specimen


title: HAK-1A HCC clone overexpressing TCF-4K under normoxia


title: tumoral tissue specimen PR2

description: tumoral tissue specimen


title: tumoral tissue specimen PR21

description: tumoral tissue specimen


title: HAK-1A HCC clone overexpressing TCF-4J under hypoxia


title: HAK-1A HCC clone overexpressing HCV Core protein under hypoxia


title: tumoral tissue specimen PR19

description: tumoral tissue specimen


title: tumoral tissue specimen PR18

description: tumoral tissue specimen


title: tumoral tissue specimen PR17

description: tumoral tissue specimen


title: tumoral tissue specimen PR15

description: tumoral tissue specimen


title: HeterotrophicCulture_Heterocyst_rep3

city: East Lansing

first: Claire

last: Vieille

state: MI

address: 567 Wilson Rd

department: Microbiology and Molecular Genetics

institute: Michigan State University

description: This sample is of heterocysts of Anabaena variabilis ATCC 29413 in heterotrophic culture. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Trichormus variabilis ATCC 29413

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Anabaena variabilis ATCC 29413 was grown in an eightfold dilution of the medium of Allen and Arnon (Allen and Arnon, Plant Physiol. 30:366) on a shaker at 30°C and 140 rpm. Phototrophic and mixotrophic cultures were grown under continuous illumination by cool white fluorescent lamps (60−70 µmol photons m-2 s-1). Mixotrophic cultures were supplemented with 5 mM fructose. Heterotrophic cultures were grown in the dark in the presence of 5 mM fructose. Cultures were harvested after seven days for phototrophic and heterotrophic cultures, and after four days for mixotrophic cultures

extract_protocol:
separation protocol: Cells pellets from 400-mL cultures were resuspended in 15 mL RNAlater solution (Ambion) and stored at -80°C prior to use. Thawed filament suspensions were sedimented, resuspended in 50 mL of N2-sparged HP buffer (30 mM Hepes/30 mM Pipes/1 mM MgCl2, pH 7.2), and washed three times with HP buffer containing 10 mM Na2EDTA (HP/EDTA). 20% of the filament suspension was used to extract RNA from whole filaments. The rest was used to separate vegetative cell-specific extracts and heterocysts. The washed filaments were resuspended in 40 mL HP/EDTA containing 1 mg mL-1 lysozyme and were shaken at 30°C for 5 min. The lysozyme-treated suspension was sedimented and resuspended in 10 mL HP buffer. The suspension, in a test tube, was subjected to cavitation (Ultrasonic Cleaner bath, Cole-Palmer) for 3 min to destroy a fraction of the vegetative cells. Heterocysts and remaining vegetative cells were sedimented and the supernatant (vegetative cell lysate) was saved on ice for extraction of vegetative cell-specific RNA. The sedimented cells were washed twice with HP/EDTA. The washed cells were resuspended in 1 mL HP/EDTA containing 0.2 mg mL-1 lysozyme and were shaken at 30°C for 25 min. This lysozyme-treated suspension was sedimented and resuspended with 1 mL HP. This suspension was immersed in a 12°C sonic bath for 15 min to destroy all remaining vegetative cells. After centrifugation, the supernatant solution was discarded,  the heterocyst-containing pellet was washed three times with HP and used as the source of heterocyst-specific RNA.
Total RNA was extracted from whole filaments, purified heterocysts, and vegetative cell extracts with the RiboPure-Bacteria kit (Ambion). Extracted RNA was purified with an RNeasy Mini kit (Qiagen) and eluted in 30 µL water. RNA concentration was determined on a NanoDrop ND-1000 spectrophotometer. RNA quality was determined by analysis with an Agilent 2100 bioanalyzer.

value: Wild-type

tag: phenotype

value: heterocyst

tag: accession


title: HeterotrophicCulture_Heterocyst_rep2

description: This sample is of heterocysts of Anabaena variabilis ATCC 29413 in heterotrophic culture. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: HeterotrophicCulture_WholeFilament_rep3

description: This sample is of whole filaments of Anabaena variabilis ATCC 29413 in heterotrophic culture. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

value: whole filament


title: HeterotrophicCulture_Heterocyst_rep1

description: This sample is of heterocysts of Anabaena variabilis ATCC 29413 in heterotrophic culture. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: HeterotrophicCulture_VegetaticeCell_rep3

description: This sample is of vegetative cells of Anabaena variabilis ATCC 29413 in heterotrophic culture. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

value: vegetative cell


title: tumoral tissue specimen PR13

description: tumoral tissue specimen

value: IVa


title: tumoral tissue specimen PR12

description: tumoral tissue specimen

value: F


title: tumoral tissue specimen PR11

description: tumoral tissue specimen

value: N+


title: HeterotrophicCulture_VegetaticeCell_rep2

description: This sample is of vegetative cells of Anabaena variabilis ATCC 29413 in heterotrophic culture. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: tumoral tissue specimen PR102

description: tumoral tissue specimen


title: HeterotrophicCulture_WholeFilament_rep1

description: This sample is of whole filaments of Anabaena variabilis ATCC 29413 in heterotrophic culture. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: tumoral tissue specimen PR100

description: tumoral tissue specimen


title: tumoral tissue specimen PR14

description: tumoral tissue specimen


title: MixotrophicCulture_Heterocyst_rep2

description: This sample is of heterocysts of Anabaena variabilis ATCC 29413 in mixotrophic culture. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: tumoral tissue specimen BS7

description: tumoral tissue specimen


title: tumoral tissue specimen PR10

description: tumoral tissue specimen


title: tumoral tissue specimen PR16

description: tumoral tissue specimen


title: MixotrophicCulture_Heterocyst_rep1

description: This sample is of heterocysts of Anabaena variabilis ATCC 29413 in mixotrophic culture. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: MixotrophicCulture_VegetaticeCell_rep3

description: This sample is of vegetative cells of Anabaena variabilis ATCC 29413 in mixotrophic culture. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: MixotrophicCulture_VegetaticeCell_rep2

description: This sample is of vegetative cells of Anabaena variabilis ATCC 29413 in mixotrophic culture. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: tumoral tissue specimen PR101

description: tumoral tissue specimen


title: MixotrophicCulture_Heterocyst_rep3

description: This sample is of heterocysts of Anabaena variabilis ATCC 29413 in mixotrophic culture. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: HeterotrophicCulture_WholeFilament_rep2

description: This sample is of whole filaments of Anabaena variabilis ATCC 29413 in heterotrophic culture. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: tumoral tissue specimen BS35

description: tumoral tissue specimen


title: tumoral tissue specimen BS37

description: tumoral tissue specimen

value: III


title: tumoral tissue specimen BS36

description: tumoral tissue specimen


title: tumoral tissue specimen BS6

description: tumoral tissue specimen


title: tumoral tissue specimen BS34

description: tumoral tissue specimen


title: MixotrophicCulture_WholeFilament_rep2

description: This sample is of whole filaments of Anabaena variabilis ATCC 29413 in mixotrophic culture. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: MixotrophicCulture_WholeFilament_rep3

description: This sample is of whole filaments of Anabaena variabilis ATCC 29413 in mixotrophic culture. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: MixotrophicCulture_WholeFilament_rep1

description: This sample is of whole filaments of Anabaena variabilis ATCC 29413 in mixotrophic culture. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: PhototrophicCulture_Heterocyst_rep3

description: This sample is of heterocysts of Anabaena variabilis ATCC 29413 in phototrophic culture. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: PhototrophicCulture_Heterocyst_rep2

description: This sample is of heterocysts of Anabaena variabilis ATCC 29413 in phototrophic culture. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: PhototrophicCulture_VegetaticeCell_rep2

description: This sample is of vegetative cells of Anabaena variabilis ATCC 29413 in phototrophic culture. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: PhototrophicCulture_Heterocyst_rep1

description: This sample is of heterocysts of Anabaena variabilis ATCC 29413 in phototrophic culture. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: MixotrophicCulture_VegetaticeCell_rep1

description: This sample is of vegetative cells of Anabaena variabilis ATCC 29413 in mixotrophic culture. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: tumoral tissue specimen BS30

description: tumoral tissue specimen


title: tumoral tissue specimen BS32

description: tumoral tissue specimen


title: tumoral tissue specimen BS29

description: tumoral tissue specimen


title: HeterotrophicCulture_VegetaticeCell_rep1

description: This sample is of vegetative cells of Anabaena variabilis ATCC 29413 in heterotrophic culture. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: PhototrophicCulture_WholeFilament_rep2

description: This sample is of whole filaments of Anabaena variabilis ATCC 29413 in phototrophic culture. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: tumoral tissue specimen BS27

description: tumoral tissue specimen


title: tumoral tissue specimen BS24

description: tumoral tissue specimen


title: PhototrophicCulture_WholeFilament_rep3

description: This sample is of whole filaments of Anabaena variabilis ATCC 29413 in phototrophic culture. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: PhototrophicCulture_VegetaticeCell_rep3

description: This sample is of vegetative cells of Anabaena variabilis ATCC 29413 in phototrophic culture. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: PhototrophicCulture_WholeFilament_rep1

description: This sample is of whole filaments of Anabaena variabilis ATCC 29413 in phototrophic culture. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: tumoral tissue specimen BB52

description: tumoral tissue specimen


title: tumoral tissue specimen BS11

description: tumoral tissue specimen


title: PhototrophicCulture_VegetaticeCell_rep1

description: This sample is of vegetative cells of Anabaena variabilis ATCC 29413 in phototrophic culture. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: E13.5 mouse DRG cultured for 48 hours with NGF 1  chip 1

source_name: Primary explant cultures of dorsal root ganglia dissected from E13.5 mouse embryos.

growth_protocol:
DRGs were dissected out from 4 litters of E13.5 mouse embryos, and cultured on plates coated with poly-D-lysine and laminin.
Please see Growth above

treatment_protocol:
Cultured for 48 hrs with 50 ng/ml of NGF.
Please see Treatment above

value: mixed

tag: tissue

value: wild type


title: E13.5 mouse DRG cultured for 48 hours with NT3 1 chip 1

treatment_protocol:
Cultured for 48 hrs with 50 ng/ml of NT3.
Please see Treatment above

value: Primary explant cultures of dorsal root ganglia dissected from E13.5 mouse embryos.


title: E13.5 mouse DRG cultured for 48 hours with NGF 2 chip 1

value: Cultured for 48 hrs with 50 ng/ml of NGF.


title: tumoral tissue specimen BB50

description: tumoral tissue specimen

tag: gender


title: tumoral tissue specimen BB49

description: tumoral tissue specimen

tag: tnm grading

value: N-

value: I


title: tumoral tissue specimen BB51

description: tumoral tissue specimen


title: tumoral tissue specimen BS5

description: tumoral tissue specimen

value: II


title: E13.5 mouse DRG cultured for 48 hours with NT3 1 chip 3

value: Cultured for 48 hrs with 50 ng/ml of NT3.


title: E13.5 mouse DRG cultured for 48 hours with NT3 2 chip 1


title: E13.5 mouse DRG cultured for 48 hours with NT3 2 chip 3


title: tumoral tissue specimen BB47

description: tumoral tissue specimen

value: M


title: E13.5 mouse DRG cultured for 48 hours with NGF 2 chip 3


title: E13.5 mouse DRG cultured for 48 hours with NT3 1 chip 2


title: E13.5 mouse DRG cultured for 48 hours with NGF 1  chip 3


title: E13.5 mouse DRG cultured for 48 hours with NT3 2 chip 2


title: tumoral tissue specimen BB43

description: tumoral tissue specimen


title: tumoral tissue specimen BB44

description: tumoral tissue specimen


title: tumoral tissue specimen BB42

description: tumoral tissue specimen


title: tumoral tissue specimen BS13

description: tumoral tissue specimen


title: tumoral tissue specimen BB41

description: tumoral tissue specimen


title: tumoral tissue specimen BB36

description: tumoral tissue specimen

value: IV


title: E13.5 mouse DRG cultured for 48 hours with NGF 2 chip 2


title: tumoral tissue specimen BB46

description: tumoral tissue specimen


title: tumoral tissue specimen BB34

description: tumoral tissue specimen


title: Adult Islets, Replicate 2

city: Perth

first: Munish

last: Mehta

state: WA

address: L6, Rear 50 Murray Street

department: Diabetes Research Unit

country: Australia

institute: Harry Perkin Institute of Medical Reasearch

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Scanning setting: 1.6 for Beadarray reader

data_processing: The data was normalised using RSN (Robust Spline Method). The software used is ' R ' Statistical language and environment.Module Lumi in Bioconductor release 2.13 within R was used for Normalization.

source_name: Pancreas

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit from Ambion

extract_protocol: RNA was extracted with Trizol reagent. Quality check performed with Agilent Bioanalyser 2100

tag: strain

tag: developmental stage

value: Islets (positive control)


title: Adult Islets, Replicate 1


title: tumoral tissue specimen BB33

description: tumoral tissue specimen

tag: lymphonode metastasis


title: tumoral tissue specimen BB28

description: tumoral tissue specimen

tag: tumor stage


title: tumoral tissue specimen BB24

description: tumoral tissue specimen

tag: age


title: tumoral tissue specimen BB40

description: tumoral tissue specimen

tag: grade of differentiation


title: E13.5 mouse DRG cultured for 48 hours with NGF 1  chip 2

tag: genetic background


title: tumoral tissue specimen BB17

description: tumoral tissue specimen


title: tumoral tissue specimen BB23

description: tumoral tissue specimen


title: Islet Progenitors at Day 4 of differentiation, Replicate 1

value: Day 4 of differentiation


title: Islet Progenitors at Day 1 of differentiation, Replicate 1

value: Day 1 of differentiation


title: Islet Progenitors at Day 4 of differentiation, Replicate 2


title: tumoral tissue specimen BB11

description: tumoral tissue specimen


title: Islet Progenitors at Day 1 of differentiation, Replicate 2


title: Islet Progenitors at Day 1 of differentiation, Replicate 3


title: pool of normal oral mucosal tissue HEALTHY

description: pool of normal oral mucosal tissue

value: M/F


title: tumoral tissue specimen BB10

description: tumoral tissue specimen


title: serum_HCV genotype 3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: miRNA expression in HCV genotype 3a infected human serum samples

hyb_protocol: The labeled samples were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water. The hybridization mixture [10X GE blocking agent (4.5 ul), 2X Hi-RPM hybridization buffer (22.5ul)] along with labeled miRNA sample was heated for 5 min at 100 °C and immediately kept on ice. Each 45 ul sample was hybridized onto a microarray at 55 °C for 20 h. Slides were washed 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: miRNA based normalization was done using GeneSpring GX 11.5 Software. 90th Percentile Shift Normalization

source_name: Serum, pooled HCV genotype 3 infected samples

label_protocol: miRNA labeling was performed as described in Agilent miRNA microarray protocol version 2.0 using Agilent miRNA labeling kit. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 7 min and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 hr.

extract_protocol: RNA was prepared using the miRNEasy kit from Qiagen as per manufacturer's protocol using 200 microlitres of each serum sample

tag: sample

value: Serum

tag: age(years)/gender

tag: disease state

value: HCV genotype 3a


title: serum_healthy controls

description: miRNA expression in uninfected human serum samples

source_name: Serum, pooled control healthy samples

value: healthy


title: serum_HCV genotype 1

description: miRNA expression in HCV genotype 1b infected human serum samples

source_name: Serum, pooled HCV genotype 1 infected samples

value: HCV genotype 1


title: Islet Progenitors at Day 0 of differentiation, Replicate 4

value: Day 0 of differentiation


title: Islet Progenitors at Day 0 of differentiation, Replicate 3


title: Embroynic Stem Cells, Replicate 2

value: ESC cells (negative control)


title: Embroynic Stem Cells, Replicate 1


title: Islet Progenitors at Day 0 of differentiation, Replicate 1


title: Islet Progenitors at Day 0 of differentiation, Replicate 2


title: T47D_2D6hr_PDL192_X_2

status: Public on Oct 31 2013

city: Redwood City

first: Josue

last: Samayoa

address: 1500 Seaport BLVD

institute: AbbVie Biotherapeutics Inc.

description: Gene expression data from treated cell line.

hyb_protocol: The biotinylated RNA targets were fragmented, and hybridized to Eos Hu03plus (Internal ID=Hu03Plusa520637F), a customized Affymetrix genechip

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing:
Raw data files were obtained after analysis of scanned images with GCOS (GeneChip Operating Software, Affymetrix). Gene expression data was generated according to the method described by Henshall et al.
Henshall SM, Afar DE, Hiller J, Horvath LG, Quinn DI, Rasiah KK, Gish K, Willhite D, Kench JG, Gardiner-Garden M, et al. Survival analysis of genome-wide gene expression pro?les of prostate cancers identi?es new prognostic targets of disease relapse. Cancer Res 2003;63:4196?4203

source_name: T47D, treated with PDL192, 6h, rep 1

label_protocol: cDNA was prepared from the RNA template, and used for in vitro transcription in the presence of biotinylated nucleoside triphosphates

extract_protocol: RNA was isolated and purified with RNeasy Micro kits (Qiagen) and analyzed using an Agilent 2100 Bioanalyzer RNA 6000

tag: cell line

tag: treatment

tag: time point

value: 6 hrs


title: BT549_2D6h_PDL192_X_2

source_name: BT549, treated with PDL192, 6h, rep 1


title: T47D_2D48hr_MSL109_X_1

source_name: T47D, treated with MSL109, 48h, rep 2

value: 48 hrs


title: BT549_2D6h_PDL192_X_1

source_name: BT549, treated with PDL192, 6h, rep 2


title: T47D_2D24hr_PDL192_X_2

source_name: T47D, treated with PDL192, 24h, rep 1

value: 24 hrs


title: BT549_2D6h_MSL109_X_2

source_name: BT549, treated with MSL109, 6h, rep 1


title: T47D_2D6hr_MSL109_X_1

source_name: T47D, treated with MSL109, 6h, rep 2


title: T47D_2D3d_MSL109_X_2

source_name: T47D, treated with MSL109, 72h, rep 1

value: 72 hrs


title: T47D_2D3d_PDL192_X_2

source_name: T47D, treated with PDL192, 72h, rep 1


title: BT549_2D6h_MSL109_X_1

source_name: BT549, treated with MSL109, 6h, rep 2


title: T47D_2D48hr_PDL192_X_2

source_name: T47D, treated with PDL192, 48h, rep 1


title: T47D_2D48hr_PDL192_X_1

source_name: T47D, treated with PDL192, 48h, rep 2


title: T47D_2D3d_PDL192_X_1

source_name: T47D, treated with PDL192, 72h, rep 2


title: BT549_2D48h_MSL109_X_2

source_name: BT549, treated with MSL109, 48h, rep 1


title: T47D_2D48hr_MSL109_X_2

source_name: T47D, treated with MSL109, 48h, rep 1


title: T47D_2D6hr_PDL192_X_1

source_name: T47D, treated with PDL192, 6h, rep 2


title: BT549_2D48h_PDL192_X_1

source_name: BT549, treated with PDL192, 48h, rep 2


title: T47D_2D24hr_PDL192_X_1

source_name: T47D, treated with PDL192, 24h, rep 2


title: BT549_2D48h_MSL109_X_1

source_name: BT549, treated with MSL109, 48h, rep 2


title: T47D_2D6hr_MSL109_X_2

source_name: T47D, treated with MSL109, 6h, rep 1


title: T47D_2D24hr_MSL109_X_2

source_name: T47D, treated with MSL109, 24h, rep 1


title: BT549_2D3d_PDL192_X_2

source_name: BT549, treated with PDL192, 72h, rep 1


title: T47D_2D3d_MSL109_X_1

source_name: T47D, treated with MSL109, 72h, rep 2


title: BT549_2D48h_PDL192_X_2

source_name: BT549, treated with PDL192, 48h, rep 1


title: T47D_2D24hr_MSL109_X_1

source_name: T47D, treated with MSL109, 24h, rep 2


title: BT549_2D3d_MSL109_X_2

source_name: BT549, treated with MSL109, 72h, rep 1


title: BT549_2D24h_PDL192_X_1

source_name: BT549, treated with PDL192, 24h, rep 2


title: BT549_2D24h_MSL109_X_1

source_name: BT549, treated with MSL109, 24h, rep 1


title: BT549_2D24h_MSL109_L_2

source_name: BT549, treated with MSL109, 24h, rep 2


title: BT549_2D24h_PDL192_X_2

source_name: BT549, treated with PDL192, 24h, rep 1


title: tumoral tissue specimen BB29

description: tumoral tissue specimen

source_name: oral cavity

value: N+


title: male WT, replicate C

status: Public on Oct 29 2013

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

description: Total RNA from Male WT (p38a-f/f) macrophages; pooled from 2-3 samples from individual mice, biological replicate 3

hyb_protocol: Samples were injected into arrays and placed in the Affymetrix Genechip® Hybridization Oven 640 at 45° C and 60 RPM for 16-18 hours overnight.

scan_protocol: Arrays were stained using the Affymetrix Genechip® Fluidics Station 450 and scanned with the Affymetrix Genechip® Scanner 3000.

data_processing:
The signal intensity for each probe on each chip was calculated from scanned images using GeneChip Operating Software (Affymetrix), and signal intensities were analyzed using BioConductor (http://www.bioconductor.org).  Probe intensities were background corrected, normalized, and summarized using the Robust Multichip Average method described by Speed and coworkers (Bolstad et al., 2003; Irizarry et al., 2003).  An alternative normalization method based on housekeeping genes did not significantly change the results.  Probe sets were considered differentially expressed when the signed fold change was ≥ 1.5, and the P-value was < 0.05.
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

source_name: TGC-induced peritoneal macrophage

label_protocol: Approximately 4ug of cDNA generated using the Ovation® Pico WTA System V2 was fragmented and labeled using the Encore® Biotin Module from NuGEN. Efficiency of the biotin labeling reaction was verified using NeutrAvidin (10mg/mL) with a gel-shift assay.

growth_protocol: macrophages were isolated on D4 post thioglycolate injection, adhered to plates overnight

extract_protocol: RNA was isolated using the RNEasy kit (Qiagen) according to manufacturer’s instructions. Microarray was performed on 3 biological replicates for each condition (e.g. female KO). To create each replicate, equal amounts of RNA from 2-3 different mice were pooled. An RNA input of 25ng was used to generate cDNA through the First Strand and Second Strand synthesis reactions of the Ovation® Pico WTA System V2 from NuGEN. The cDNA samples were then purified using an Agencourt® RNAClean® XP magnetic bead protocol.  Following purification, samples were amplified using SPIA reagents from the Ovation® Pico WTA System V2 from NuGEN. A final cDNA purification is performed using an Agencourt® RNAClean® XP magnetic bead protocol.

treatment_protocol: all samples were stimulated for 4 hrs with heat killed mycobacterium tuberculosis

value: male

tag: genotype

value: WT

tag: cell type

value: macrophage

value: C57BL/6 background, p38 floxed mice (Mapk14tm1.2Otsu) crossed with Lysm-Cre mice


title: male KO, replicate C

description: Total RNA from Male CKO (p38a-f/f-Lysm-Cre) macrophages; pooled from 2-3 samples from individual mice, biological replicate 3

tag: gender

value: p38 KO


title: male KO, replicate A


title: male WT, replicate B

description: Total RNA from Male WT (p38a-f/f) macrophages; pooled from 2-3 samples from individual mice, biological replicate 2


title: Female WT, replicate C

description: Total RNA from Female WT (p38a-f/f) macrophages; pooled from 2-3 samples from individual mice, biological replicate 3

value: female


title: BT549_2D3d_MSL109_X_1

source_name: BT549, treated with MSL109, 72h, rep 2


title: Female WT, replicate B

description: Total RNA from Female WT (p38a-f/f) macrophages; pooled from 2-3 samples from individual mice, biological replicate 2


title: Tmod3 KO-2

city: La jolla

first: Velia

last: Fowler

address: 10550 North Torrey Pines Road

department: Department of Cell and Molecular Biology

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA Express using the default CDFRME file and settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: mouse fetal liver at E14.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: phenotype

value: small fetal liver, anemia


title: male WT, replicate A

description: Total RNA from Male WT (p38a-f/f) macrophages; pooled from 2-3 samples from individual mice, biological replicate 1


title: male KO, replicate B


title: Tmod3 KO-3

tag: strain


title: Tmod3 WT-1

value: normal


title: Tmod3 WT-2


title: Tmod3 WT-3


title: Female WT, replicate A

description: Total RNA from Female WT (p38a-f/f) macrophages; pooled from 2-3 samples from individual mice, biological replicate 1


title: Female KO, replicate C

description: Total RNA from Female CKO (p38a-f/f-Lysm-Cre) macrophages; pooled from 2-3 samples from individual mice, biological replicate 3


title: Female KO, replicate A

description: Total RNA from Female CKO (p38a-f/f-Lysm-Cre) macrophages; pooled from 2-3 samples from individual mice, biological replicate 1


title: Tmod3 KO-1


title: Female KO, replicate B

description: Total RNA from Female CKO (p38a-f/f-Lysm-Cre) macrophages; pooled from 2-3 samples from individual mice, biological replicate 2


title: Royan_B4_R2i

status: Public on Oct 21 2013

city: Tehran

first: Hossein

last: Baharvand

address: Hafez St., Bani Hashem St.

country: Iran

institute: Royan Institute for Stem Cell Biology and Technology

description:
Strain C57BL/6
7469653032_A

hyb_protocol: Illumina BeadStation (Illumina)

scan_protocol: Illumina BeadStation (Illumina)

data_processing: The raw signal intensities of regular and control probes were extracted from Illumina® GenomeStudio software and used for normexp (Ritchie et al., 2007) background correction followed by quantile normalization using the limma (Smyth and Ritchie, 2011) package. For most of the bioinformatics analysis, we developed several scripts in R statistical language (R Core Team, 2012).

label: Biotin

source_name: Royan B4 mESC line cultured in R2i condition

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: mESC lines, Royan B20 and Royan B18, were generated from C57BL/6 mouse strains blastocysts in N2B27 medium supplemented with PD0325901 (PD)+SB431542 (SB)+LIF and mainteined as the same for more than 10 passages

extract_protocol: RNeasy Mini Kit

treatment_protocol: mESC lines, Royan B20 and Royan B18, were passaged simultaneously in N2B27 medium supplemented with PD+LIFor SB+LIF or 2i (PD+CHIR99021)+LIF for 10 passages.

tag: culture condition

value: Embryonic Stem Cell (ESC)


title: Royan_C17_R2i

description:
Strain BALB/c
7469653032_D

source_name: Royan C17 mESC line cultured in R2i condition

value: BALB/c


title: Royan_B20_R2i_R3

description:
Replicate 3 of 3
7991003089_F

source_name: Royan B20 mESC line cultured in R2i condition


title: Royan_C17_SB

description:
Strain BALB/c
7469653032_F

source_name: Royan C17 mESC line cultured in SB condition

value: SB


title: Royan_B18_R2i_R2

description:
Replicate 2 of 3
7539439008_E

source_name: Royan B18 mESC line cultured in R2i condition


title: Royan_B20_R2i_R2

description:
Replicate 2 of 3
7991003089_E


title: Royan_B20_PD_R3

description:
Replicate 3 of 3
7991003089_C

source_name: Royan B20 mESC line cultured in PD condition

value: PD


title: Royan_B20_R2i_R1

description:
Replicate 1 of 3
7991003089_D


title: Royan_C17_PD

description:
Strain BALB/c
7469653032_E

source_name: Royan C17 mESC line cultured in PD condition


title: Royan_B20_PD_R2

description:
Replicate 2 of 3
7991003089_B


title: Royan_B4_SB

description:
Strain C57BL/6
7469653032_C

source_name: Royan B4 mESC line cultured in SB condition


title: Royan_B18_R2i_R1

description:
Replicate 1 of 3
7539439008_D


title: Royan_B4_PD

description:
Strain C57BL/6
7469653032_B

source_name: Royan B4 mESC line cultured in PD condition


title: Royan_B18_R2i_R3

description:
Replicate 3 of 3
7539439008_F


title: Royan_B20_PD_R1

description:
Replicate 1 of 3
7991003089_A


title: BT549_2D3d_PDL192_X_1

source_name: BT549, treated with PDL192, 72h, rep 2


title: Royan_B18_PD_R3

description:
Replicate 3 of 3
7539439008_C

source_name: Royan B18 mESC line cultured in PD condition


title: Royan_B18_PD_R2

description:
Replicate 2 of 3
7539439008_B


title: Royan_B18_PD_R1

description:
Replicate 1 of 3
7539439008_A


title: Royan_B20_2i_R2

description:
Replicate 2 of 2
7991003089_H

source_name: Royan B20 mESC line cultured in 2i condition


title: Royan_B18_2i_R2

description:
Replicate 2 of 2
7539439008_H

source_name: Royan B18 mESC line cultured in 2i condition


title: Royan_B18_2i_R1

description:
Replicate 1 of 2
7539439008_G


title: Nasal_DNA_Methylation_Nonsmoker4

status: Public on Oct 01 2013

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description:
Nasal epithelial cells extracted from human volunteers not exposed to cigarette smoke
Gene methylation data from nonsmokers

hyb_protocol: Samples were hybridized to IlluminaMethylation BeadChips array

scan_protocol: BeadChips were coated and then imaged on an Illumina iScan Reader

data_processing: Data were analyzed with GenomeStudio software (version 3.2) methylation module

label: Bisulfite converted DNA

source_name: nasal epithelial cells, nonsmoker

label_protocol: IlluminaHumanMethylation27 BeadChip bisulfite conversion with Zymo EZ DNA Methylation kit

growth_protocol: Primary human nasal epithelial cells were expanded to passage 2 in bronchial epithelial growth medium and then plated on collagen-coated filter supports with a 0.4 uM pore size, and cultured in a 1:1 mixture of bronchial epithelial cell basic medium and DMEM-H with SingleQuot supplements, bovine pituitary extracts (13mg/ml), bovine serum albumin (BSA, 1.5 ug/ml), and nystatin (20 units). Upon confluency, all-trans retinoic acid was added to the medium and air liquid interface culture conditions (removal of the apical medium) were created to promote differentiation.

extract_protocol: TRIzol DNA Extraction

treatment_protocol: DNA was extracted from human blood samples

value: Nasal epithelial cells

tag: agent

tag: dose

value: no exposure

value: healthy


title: Nasal_DNA_Methylation_Nonsmoker2


title: Nasal_DNA_Methylation_Smoker3

description:
Nasal epithelial cells extracted from human volunteers chronically exposed to cigarette smoke
Gene methylation data from smokers

source_name: nasal epithelial cells, smoker

treatment_protocol: Nasal epithelial cells were extracted from volunteers and grown until fully differentiated. DNA was then extracted.

value: tobacco smoke

value: exposure


title: Nasal_DNA_Methylation_Nonsmoker5


title: Nasal_DNA_Methylation_Nonsmoker3


title: Nasal_DNA_Methylation_Nonsmoker6


title: Nasal_DNA_Methylation_Smoker6


title: Nasal_DNA_Methylation_Smoker4