source_name: mouse stomach infected with Helicobacter felis; 1 month post infection


title: infected with Helicobacter felis; 9 month post infection B

status: Public on Feb 17 2011

type: RNA

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

country: USA

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v2 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse stomach infected with Helicobacter felis; 9 month post infection

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: Sex

value: unknown

tag: strain

value: FVB/N

tag: disease state

value: infected with Helicobacter felis

tag: tissue

value: stomach


title: P_NY531

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicate mesurements were averaged after removing outliers. After subtracting background signal intensities, data were then normalized using the cubic spline algorithm.

organism: Homo sapiens

source_name: Human hepatocellular carcinoma

extract_protocol: Using formalin-fixed, paraffin-embedded HCC tissues, total RNA was extracted using TRIzol (Invitrogen).

value: hepatocellular carcinoma

tag: vascular invasion

value: No

tag: used for qpcr of microrna in chr19q13.41

value: Yes


title: 2332_Child (GenomeWideSNP_6)

type: genomic

city: Vancouver

first: Tracy

last: Tucker

address: Box 153 4480 Oak Street

country: Canada

institute: University of British Columbia

hyb_protocol: hybridized to GeneChip® Human Mapping 250K Nsp or 250K Sty arrays in an Affymetrix Hybridization Oven 640

scan_protocol: images were obtained using an Affymetrix GeneChip® Scanner 3000 7G and GeneChip® Operating Software version 1.4

data_processing:
CNVs were identified using the Genotyping Console 3.0.1 program.
Since this program cannot perform pair-wise comparisons, we compared the results of each sample to a reference dataset generated by the combined results for the 30 parents in the 15 trios studied on the platform.

label: Biotin

molecule: genomic DNA

source_name: peripheral blood

label_protocol: DNA samples were processed according to the instructions provided in the Affymetrix GeneChip® Mapping 500K Assay Manual

extract_protocol: Genomic DNA was extracted from blood samples using the Puregene DNA kit

tag: developmental state

value: Developmental Delay

value: peripheral blood

tag: phenotype

value: idiopathic MR

tag: family

tag: family member

value: Child

tag: gender

value: Male


title: P_NY547

scan_protocol: Refer to the Illumina beadarray Assay System Manual


title: P_NY539

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: non-infected control timepoint 2 months

source_name: mouse stomach non-infected control timepoint 2 months

value: healthy


title: non-infected control timepoint 4 months

source_name: mouse stomach non-infected control timepoint 4 months


title: P_NY549


title: non-infected control timepoint 0 C

source_name: mouse stomach non-infected control timepoint 0


title: non-infected control timepoint 8 months A

source_name: mouse stomach non-infected control timepoint 8 months


title: P_NY541


title: P_NY537


title: P_NY529


title: 2377_Child (GenomeWideSNP_6)


title: non-infected control timepoint 0 B


title: 1511_Child (GenomeWideSNP_6)


title: keratinocytes exposed to UVB 24 hours A

source_name: Normal human epidermal keratinocytes exposed to UVB 24 hours

tag: cell type

value: epidermal keratinocytes

value: Healthy


title: non-infected control timepoint 0 A


title: keratinocytes exposed to UVB 6 hours B

source_name: Normal human epidermal keratinocytes exposed to UVB 6 hours


title: keratinocytes exposed to UVB 24 hours B


title: keratinocytes exposed to UVB 12 hours A

source_name: Normal human epidermal keratinocytes exposed to UVB 12 hours


title: Spinal cord 7-day time point uninjured C

source_name: Spinal cord 7-day time point uninjured

value: male

tag: age

value: 10 weeks

value: spinal cord


title: keratinocytes exposed to UVB 6 hours A

value: unknown


title: keratinocytes exposed to UVB 12 hours B


title: P_NY525


title: keratinocytes exposed to UVB 0 hours A

source_name: Normal human epidermal keratinocytes exposed to UVB 0 hours


title: keratinocytes exposed to UVB 0 hours B


title: P_NY527


title: P_NY515


title: P_NY501


title: P_NY517


title: P_NY36


title: P_NY523


title: P_NY535


title: P_NY505


title: P_NY511


title: Spinal cord 7-day time point uninjured B


title: P_NY34


title: P_NY521


title: P_NY507


title: P_NY2


title: Spinal cord control timepoint injured C

source_name: Spinal cord control timepoint injured


title: Spinal cord 7-day time point uninjured A


title: P_NY232


title: Spinal cord control timepoint injured B


title: 4821_Child_Father (GenomeWideSNP_6)

value: unaffected

value: Father


title: Spinal cord control timepoint injured A


title: P_M71

value: hepatocellular carcinoma


title: P_NY228


title: P_M75

value: No


title: Spinal cord control timepoint uninjured C

source_name: Spinal cord control timepoint uninjured


title: Spinal cord control timepoint uninjured B


title: Spinal cord 4-day time point injured C

source_name: Spinal cord 4-day time point injured


title: 2894_Child_Father (GenomeWideSNP_6)


title: Spinal cord 7-day time point injured A

source_name: Spinal cord 7-day time point injured


title: 4821_Child (GenomeWideSNP_6)


title: Spinal cord 7-day time point injured B


title: P_NY18

value: Yes


title: Spinal cord 7-day time point injured C


title: Spinal cord 4-day time point injured B


title: Spinal cord 4-day time point injured A


title: P_M77


title: Spinal cord 4-day time point uninjured C

source_name: Spinal cord 4-day time point uninjured


title: Spinal cord control timepoint uninjured A


title: P_M73


title: P_M487


title: Spinal cord 4-day time point uninjured A


title: P_NY208


title: Spinal cord 4-day time point uninjured B


title: P_M479


title: P_M483


title: P_M465


title: P_M461


title: P_M443


title: P_M469


title: cultured chondrocytes; stimulated with IL-1 and L-NMMA

value: chondrocytes


title: cultured chondrocytes; unstimulated (control)


title: P_M421


title: P_M423


title: P_M415


title: Human Chondrocytes: stimulated with IL-1, for 8 days C

value: 45 years


title: Human Chondrocytes: stimulated with IL-1, for 8 days B

value: 59 years


title: cultured chondrocytes; stimulated L-NMMA


title: Human Chondrocytes: stimulated with IL-1, for 8 days A

value: 56 years


title: Human Chondrocytes: unstimulated (control), for 8 days C


title: Human Chondrocytes: unstimulated (control), for 8 days B


title: Human Chondrocytes: stimulated with IL-1 and L-NMMA, for 8 days C


title: P_M407


title: Human Chondrocytes: stimulated with IL-1 and L-NMMA, for 8 days A


title: Human Chondrocytes: stimulated with IL-1 and L-NMMA, for 8 days B


title: P_M431


title: cultured chondrocytes; stimulated with IL-2

source_name: cultured chondrocytes; stimulated with IL-1


title: P_M441

source_name: Human hepatocellular carcinoma


title: Human Chondrocytes: stimulated with L-NMMA, for  8 days A


title: Human Chondrocytes: unstimulated (control), for 8 days A


title: P_M405


title: Human Chondrocytes: stimulated with L-NMMA for 8 days B

source_name: Human Chondrocytes: stimulated with L-NMMA, for  8 days


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 16

value: M

value: schizophrenic

tag: duration of illness

value: 2 yr

value: prefrontal cortex (brain)


title: P_M403


title: P_M395


title: P_M411


title: P_M393


title: P_M409


title: P_M401


title: P_M397


title: P_M383


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 15

value: 3 yr


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 10

value: F

value: 40 yr


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 9

value: 4 yr


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 7

value: 36 yr


title: P_M345


title: P_M381


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 14

value: 65 yr


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 8

value: 28 yr


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 13


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 12

value: 38 yr


title: P_M319

value: hepatocellular carcinoma

value: Yes


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 11

value: 53 yr


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 4


title: P_M377

value: No


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 3


title: P_M367


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 2


title: P_M271


title: P_M309


title: P_M275


title: P_M289


title: P_M293


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 5


title: P_M291


title: P_M375


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 6

value: 33 yr


title: P_M311


title: P_M287


title: P_M285


title: P_M315


title: Prefrontal Cortical region (Brodmann Area) control 16

value: M

value: healthy


title: Prefrontal Cortical region (Brodmann Area) control 11


title: Prefrontal Cortical region (Brodmann Area) control 12


title: P_M269


title: Prefrontal Cortical region (Brodmann Area) control 13


title: Prefrontal Cortical region (Brodmann Area) schizophrenic 1

value: schizophrenic

value: 2 yr


title: Prefrontal Cortical region (Brodmann Area) control 15

value: prefrontal cortex (brain)


title: Prefrontal Cortical region (Brodmann Area) control 14


title: Prefrontal Cortical region (Brodmann Area) control 9


title: Prefrontal Cortical region (Brodmann Area) control 8


title: Prefrontal Cortical region (Brodmann Area) control 10


title: P_M251


title: P_M267


title: P_M235


title: P_M255


title: P_M261


title: P_M225


title: P_M229


title: Prefrontal Cortical region (Brodmann Area) control 6


title: Prefrontal Cortical region (Brodmann Area) control 4


title: Prefrontal Cortical region (Brodmann Area) control 3

value: F


title: Prefrontal Cortical region (Brodmann Area) control 5


title: P_M227


title: Prefrontal Cortical region (Brodmann Area) control 2


title: P_M211


title: P_M217


title: Prefrontal Cortical region (Brodmann Area) control 1


title: P_M219


title: Prefrontal Cortical region (Brodmann Area) control 7


title: B16-OVA melanoma tissue from 11 day tumors C

tag: genotype

value: Female

tag: tissue typ


title: B16-OVA melanoma tissue from 11 day tumors B


title: P_M209


title: B16-OVA melanoma tissue from 11 day tumors A


title: P_M201


title: P_B255


title: B16-OVA melanoma tissue from 6 day tumors C


title: P_B223


title: B16-OVA melanoma tissue from 6 day tumors B


title: P_B213


title: B16-OVA grown in cell culture C

source_name: B16-OVA grown in cell culture

value: B16-OVA grown in cell culture


title: B16-OVA melanoma tissue from 6 day tumors A


title: P_M207


title: P_M203


title: P_B215


title: Normal mouse skin inflamed by treatment with Oxazolone C

source_name: normal skin inflamed by treatment with Oxazolone


title: B16-OVA grown in cell culture A


title: B16-OVA grown in cell culture B


title: P_B221


title: Normal mouse skin inflamed by treatment with Oxazolone A

value: normal skin inflamed by treatment with Oxazolone


title: P_B217


title: P_B219


title: Normal mouse skin C

source_name: normal skin

value: normal skin


title: P_B209


title: Normal mouse skin inflamed by treatment with Oxazolone B


title: P_B203


title: Normal mouse skin B


title: P_B207


title: 4T1 mouse non-metastatic breast cancer :67NRp24 C

source_name: non-metastatic cell line 67NR

tag: cell line

value: non-metastatic

value: breast cancer

tag: passage number


title: P_B205

value: hepatocellular carcinoma


title: P_B175

value: Yes


title: Normal mouse skin A

tag: Sex


title: P_B173


title: P_B179


title: P_B171


title: P_B153


title: P_B157


title: P_B181


title: 4T1 mouse metastatic breast cancer :4T1p32 B

source_name: 4T1 metastatic cell line variant #2

value: metastatic

tag: disease state


title: P_B201

tag: tissue

value: No


title: 4T1 mouse non-metastatic breast cancer :67NRp24 B


title: P_B149

tag: vascular invasion


title: 4T1 mouse metastatic breast cancer :4T1p16-B

source_name: 4T1 metastatic cell line variant #1


title: 4T1 mouse metastatic breast cancer :4T1p16 A


title: 4T1 mouse metastatic breast cancer :4T1p16 C


title: 4T1 mouse metastatic breast cancer :4T1p31 C


title: 4T1 mouse non-metastatic breast cancer:4T07p24 A

source_name: non-metastatic cell lines 4T07


title: 4T1 mouse non-metastatic breast cancer :67NRp24 A


title: P_B211

tag: used for qpcr of microrna in chr19q13.41


title: P_B151


title: 4T1 mouse metastatic breast cancer :4T1p31 A


title: 4T1 mouse non-metastatic breast cancer:4T07p24 B


title: P_B084


title: P_B129


title: P_B082


title: P_B161


title: 4T1 mouse non-metastatic breast cancer:4T07p24 C


title: Thymic Epithelial Cell:Testosterone Treated C

tag: strain

value: thymic epithelia


title: Thymic Epithelial Cell:Testosterone Treated B


title: Thymic Epithelial Cell:Testosterone Treated A


title: P_B080


title: Thymic Epithelial Cell C

source_name: Thymic Epithelial Cell


title: Thymic Epithelial Cell A


title: P_B076


title: Thymic Epithelial Cell B


title: P_B035


title: Gastric cell line co-culture with H. pylori strain B (Low Patogenicity) C

value: strain C


title: Adult brain A

source_name: adult mouse brain

value: BALB/c

value: 30 days

value: healthy

value: brain


title: Adult brain C


title: P7 Brain B

source_name: P7 mouse brain

value: unknown

value: postnatal day 7


title: P7 Brain A


title: Gastric cell line without H. pylori co-culture (control) C


title: Cell line U937, biological rep3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the scrGLYCO-v1GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Human cancer cell line U937


title: Gastric cell line without H. pylori co-culture (control) A

value: strain A


title: P7 Brain C


title: Cell line U937, biological rep1


title: Gastric cell line co-culture with H. pylori strain B (Low Patogenicity) B

value: strain B


title: P_B031


title: Adult brain B

value: Female


title: Cell line U937, biological rep2


title: Gastric cell line without H. pylori co-culture (control) B


title: P_B072


title: Gastric cell line co-culture with H. pylori strain B (Low Patogenicity) A


title: P_B017


title: P_B029


title: P_B025


title: P_B005


title: P_B007


title: Gastric cell line co-culture with H. pylori strain A (High Patogenicity) C


title: Cell line LS180, biological rep1

source_name: Human cancer cell line LS180


title: Gastric cell line co-culture with H. pylori strain A (High Patogenicity) A


title: Gastric cell line co-culture with H. pylori strain A (High Patogenicity) B


title: Primary chondrocytes treated B

source_name: Primary human chondrocytes treated with TGFß1

value: primary chondrocytes

value: Healthy


title: Cell line LS180, biological rep3


title: Cell line LS180, biological rep2


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 5 ug/ml tunicamycin, 5 hours Replicate A

source_name: ATCC CRL-1904 human adult dermal fibroblasts sample treated with 5 ug/ml tunicamycin, 5 hours

value: Unknown

tag: cell linr

value: ATCC CRL-1904

value: skin fibroblasts


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 5 ug/ml tunicamycin, 5 hours Replicate D


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 5 ug/ml tunicamycin, 5 hours Replicate C


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 100nm Thapsigargin (TG), 30 minutes Replicate C

source_name: ATCC CRL-1904 human adult dermal fibroblasts sample treated with 100nm Thapsigargin (TG), 30 minutes.


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 100nm Thapsigargin (TG), 30 minutes Replicate D


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 100nm Thapsigargin (TG), 30 minutes Replicate A


title: Primary chondrocytes treated A


title: Primary chondrocytes untreated control

source_name: Primary human chondrocytes


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 2 mM Dithiothreitol (DTT), 20 minutes Replicate D

source_name: ATCC CRL-1904 human adult dermal fibroblasts sample treated with 2 mM Dithiothreitol (DTT), 20 minutes


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 100nm Thapsigargin (TG), 30 minutes Replicate B


title: MOZ-TIF2 PL_1

city: Cambridge

first: Nicolas

last: Bonadies

address: Hills Road

department: Haematology

country: United Kingdom

institute: Cambridge Institute for Medical Research

description:
total RNA
replicate 1
4421347032_A

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Bead Station500 scanner

data_processing: Illumina Inc. BeadStudio version 3.3.7, lumi Bioconductor package 23, applying variance-stabilizing transformation and quantile normalization. The non-informative probes were eliminated in the normalized data-set. 24522 of 45281 probes represented on the array were eliminated, due to the fact that they were not expressed or close to background (detection p-value > 0.01).

source_name: MOZ-TIF2 preleukamic cells

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Serially replated MOZ-TIF2 transduced lin-/kit+ bone marrow cells from Bl/6 mice


title: MLL-ENL L_2

description:
total RNA (poor quality)
replicate 2 (omitted because of poor RNA quality)
4421347030_E

source_name: MLL-ENL leukaemic cells

value: Serially transplanted MLL-ENL cells


title: FDCPmix_3

description:
total RNA
replicate 3
4421347032_D

source_name: Factor-Dependent Cells Patterson-Mix cells

value: normal control 2, cell-line


title: WT_1

description:
total RNA
replicate 1
4421347032_F

source_name: lin-/kit+ bone marrow cells from Bl/6 mice

value: normal control 1, primary cells


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 5 ug/ml tunicamycin, 5 hours Replicate B


title: MOZ-TIF2 PL_3

description:
total RNA
replicate 3
4421347030_D


title: MLL-ENL PL_2

description:
total RNA
replicate 2
4421347030_F

source_name: MLL-ENL preleukamic cells

value: Serially replated MLL-ENL transduced lin-/kit+ bone marrow cells from Bl/6 mice


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 2 mM Dithiothreitol (DTT), 20 minutes Replicate C


title: MLL-ENL L_3

description:
total RNA
replicate 3
4421347032_E


title: MOZ-TIF2 L_3

description:
total RNA
replicate 3
4421347032_C

source_name: MOZ-TIF2 leukaemic cells

value: Serially transplanted MOZ-TIF2 cells


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 2 mM Dithiothreitol (DTT), 20 minutes Replicate B


title: WT_3

description:
total RNA
replicate 3
4421347030_C


title: FDCPmix_1

description:
total RNA
replicate 1
4421347032_B


title: WT_2

description:
total RNA
replicate 2
4421347057_F


title: MLL-ENL L_1

description:
total RNA
replicate 1
4421347030_A


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 2 mM Dithiothreitol (DTT), 20 minutes Replicate A


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 0.2 mg/ml castanospermine, 24 hours Replicate D

source_name: ATCC CRL-1904 human adult dermal fibroblasts sample treated with 0.2 mg/ml castanospermine, 24 hours


title: MOZ-TIF2 PL_2

description:
total RNA
replicate 2
4421347030_B


title: FDCPmix_2

description:
total RNA
replicate 2
4421347057_E


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 0.2 mg/ml castanospermine, 24 hours Replicate C


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 0.2 mg/ml castanospermine, 24 hours Replicate B


title: MOZ-TIF2 L_1

description:
total RNA
replicate 1
4421347057_C


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 0.2 mg/ml castanospermine, 24 hours Replicate A


title: MOZ-TIF2 L_2

description:
total RNA
replicate 2
4421347057_B


title: MLL-ENL PL_1

description:
total RNA
replicate 1
4421347057_D


title: ATCC CRL-1904 human adult dermal fibroblasts Untreated control sample Replicate H

source_name: ATCC CRL-1904 human adult dermal fibroblasts (control) sample CON.


title: MLL-ENL PL_3

description:
total RNA
replicate 3
4421347057_A


title: ATCC CRL-1904 human adult dermal fibroblasts Untreated control sample Replicate F


title: 9609_Father (Mapping250K_Nsp)

data_processing:
CNVs were detected using the Copy Number Analysis Tool (CNAT) (release cn-1.5.6_v3.2), which incorporates a Bayesian Robust Linear Model with the Mahalanobis distance classifier (BRLMM) algorithm to perform quantile normalization, followed by regression to reduce the PCR bias due to GC content and fragment length
An HMM-based algorithm implemented in CNAT4 was used to estimate copy number for each SNP in the context of its surrounding SNPs. The Gaussian bandwidth was set to 0 Kb and a minimum of 5 probes was required to detect a CNV. The findings were visualized using GeneChip Genotyping Analysis Software (GTYPE) from Affymetrix.

source_name: peripheral blood

tag: developmental state

value: unaffected

value: peripheral blood

tag: family

value: Father


title: 9609_Child (Mapping250K_Nsp)

value: Developmental Delay

tag: phenotype

value: idiopathic MR

tag: family member

value: Child

tag: gender

value: Male


title: 9390_Mother (Mapping250K_Nsp)

value: Mother


title: 9390_Father (Mapping250K_Nsp)


title: 3921_Mother (Mapping250K_Nsp)


title: ATCC CRL-1904 human adult dermal fibroblasts Untreated control sample Replicate E

value: Unknown

tag: cell type


title: 9609_Mother (Mapping250K_Nsp)


title: ATCC CRL-1904 human adult dermal fibroblasts Untreated control sample Replicate D

value: ATCC CRL-1904


title: ATCC CRL-1904 human adult dermal fibroblasts Untreated control sample Replicate G

value: skin fibroblasts


title: 7581_Child (Mapping250K_Nsp)


title: ATCC CRL-1904 human adult dermal fibroblasts Untreated control sample Replicate C


title: 7581_Mother (Mapping250K_Nsp)


title: 9390_Child (Mapping250K_Nsp)


title: 7581_Father (Mapping250K_Nsp)


title: 7484_Child (Mapping250K_Nsp)


title: 7531_Child (Mapping250K_Nsp)

value: Female


title: ATCC CRL-1904 human adult dermal fibroblasts Untreated control sample Replicate B


title: 7093_Child (Mapping250K_Nsp)


title: 7093_Father (Mapping250K_Nsp)


title: 7484_Mother (Mapping250K_Nsp)


title: 6428_Mother (Mapping250K_Nsp)


title: 7093_Mother (Mapping250K_Nsp)


title: 6428_Father (Mapping250K_Nsp)


title: 5993_Child (Mapping250K_Nsp)


title: 7484_Father (Mapping250K_Nsp)


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 40 nM L-azetidine-2-carboxylate (AZC) 1 hour Replicate D

source_name: ATCC CRL-1904 human adult dermal fibroblasts sample treated with 40 nM L-azetidine-2-carboxylate (AZC) 1 hour


title: ATCC CRL-1904 human adult dermal fibroblasts Untreated control sample Replicate A


title: 7531_Father (Mapping250K_Nsp)


title: 6428_Child (Mapping250K_Nsp)


title: 7531_Mother (Mapping250K_Nsp)


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 40 nM L-azetidine-2-carboxylate (AZC) 1 hour Replicate B


title: 5993_Father (Mapping250K_Nsp)


title: 5993_Mother (Mapping250K_Nsp)


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 40 nM L-azetidine-2-carboxylate (AZC) 1 hour Replicate A


title: Brain C

source_name: Brain

tag: genotype/variation

value: wild type

value: Healthy

tag: age

value: 8 weeks

value: Brain


title: 3519_Child (Mapping250K_Nsp)


title: Brain B


title: 3519_Father (Mapping250K_Nsp)


title: Liver D

source_name: Liver

value: Liver


title: Brain A


title: 3519_Mother (Mapping250K_Nsp)

value: unaffected


title: Liver C


title: 2714_Mother (Mapping250K_Nsp)

value: peripheral blood


title: ATCC CRL-1904 human adult dermal fibroblasts treated with 40 nM L-azetidine-2-carboxylate (AZC) 1 hour Replicate C


title: Testes C

source_name: Testes

value: Testes


title: Liver A


title: 1780_Child (Mapping250K_Nsp)

value: Developmental Delay


title: 1815_Father (Mapping250K_Nsp)

value: Father


title: 3094_Father (Mapping250K_Nsp)


title: 3921_Child (Mapping250K_Nsp)

value: idiopathic MR

value: Child


title: 1815_Child (Mapping250K_Nsp)


title: 2714_Child (Mapping250K_Nsp)

value: Male


title: Testes B


title: Testes A


title: Liver B


title: 1780_Mother (Mapping250K_Nsp)

value: Mother


title: 3921_Father (Mapping250K_Nsp)


title: 9313_Child_Mother (Mapping250_Nsp)


title: Bone Marrow A

source_name: Bone Marrow

value: Bone Marrow


title: Thymus B

source_name: Thymus

value: Thymus


title: 1056_Mother (Mapping250K_Nsp)


title: Bone Marrow C


title: 3094_Mother (Mapping250K_Nsp)


title: Thymus A


title: 9313_Child_Father (Mapping250_Nsp)


title: 8994_Child_Father (Mapping250_Nsp)


title: 1815_Mother (Mapping250K_Nsp)


title: 3094_Child (Mapping250K_Nsp)


title: 1056_Child (Mapping250K_Nsp)

value: Female


title: Thymus C

value: wild type


title: 1056_Father (Mapping250K_Nsp)


title: 8994_Child_Mother (Mapping250_Nsp)


title: Spleen A

source_name: Spleen

value: Healthy

value: Spleen


title: Spleen C

value: 8 weeks


title: 8994_Child (Mapping250_Nsp)


title: Spleen B


title: 2714_Father (Mapping250K_Nsp)


title: 8960_Child_Mother (Mapping250_Nsp)


title: 8960_Child_Father (Mapping250_Nsp)


title: 9313_Child (Mapping250_Nsp)


title: Lymph Node A

source_name: Lymph Node

value: Lymph Node


title: Lymph Node B


title: Lymph Node C


title: Lung B

source_name: Lung

value: Lung


title: Kidney C

source_name: Kidney

value: Kidney


title: Kidney A


title: Rats exposed for 3 months to ultrafine particles 8

city: Los Angeles

first: Boris

middle: Z

last: Simkhovich

address: 1225 Wilshire Boulevard

department: Heart Institute

institute: Good Samaritan Hospital

description: Total RNA was extracted from the hearts of rats exposed for 3 months to filtered air (control) vs. coarse, fine and ultrafine particles.

hyb_protocol: Standard protocol as recommended by Illumina.

data_processing: The data was preprocessed by the Bioconductor lumi package (version 1.5.17). It was vst transformed and quantile normalized.

organism: Rattus norvegicus

source_name: rat heart, ultrafine particles

label_protocol: cRNA synthesis and labeling was carried out by using Illumina Total Prep RNA Amplification Kit (Ambion, Austin, TX). Whole quantity of synthesized cDNA was added to 2.5ul T7 10x reaction buffer, 2.5ul biotinNTP mix, 2.5ul T7 Enzyme mix, and was incubated for 14 hrs at 37C followed by RNeasy column purification (Qiagen, Valencia, CA).

extract_protocol: Surgical tissue was treated with 500ul of TriZol (Invitrogen, Carlsbad, CA) in a 1.5ml Eppendorf tube, and homogenized for 15 seconds. The homogenate was centrifuged for 20 min (4C) at 12,000 x g, and supernatant was transferred to a fresh Eppendorf tube and precipitated by the addition of 100ul of chloroform and vortexed vigorously for 15 seconds.  The sample was incubated for 3 minutes at room temperature and centrifuged for 15 minutes (4C) at 10,000 x g.  The aqueous phase was transferred to a fresh Eppendorf tube and precipitated by the addition of 250l isopropanol.  The precipitate was incubated for 10 min at room temperature and centrifuged for 20 minutes (4C) at 10,000 x g.  The sample was washed once with 0.7 ethanol and the pellet was airdried prior to resuspension in 100ul of DEPC treated water. The RNA was purified by RNeasy Clean Up column (Qiagen, Valencia, CA).

value: Fisher 344

value: male

value: 4 weeks at the beginning of the experiment

value: heart

tag: treatment

value: ultrafine particles (UFP)

tag: treatment duration

value: 3 months


title: Bone Marrow B

tag: Sex

value: Male


title: Lung A

tag: disease state


title: 8327_Child_Father (Mapping250_Nsp)

value: unaffected

tag: tissue

value: peripheral blood

value: Father


title: 8612_Child_Father (Mapping250_Nsp)


title: 8612_Child (Mapping250_Nsp)

value: Developmental Delay

value: idiopathic MR

value: Child

value: Female


title: Rats exposed for 3 months to ultrafine particles 6

scan_protocol: Standard protocol as recommended by Illumina.


title: 8327_Child (Mapping250_Nsp)


title: Rats exposed for 3 months to ultrafine particles 5


title: Rats exposed for 3 months to ultrafine particles 7


title: Kidney B

value: wild type

value: Healthy

value: 8 weeks


title: 8160_Child_Father (Mapping250_Nsp)


title: 8960_Child (Mapping250_Nsp)


title: Rats exposed for 3 months to ultrafine particles 2

value: Fisher 344


title: Rats exposed for 3 months to ultrafine particles 4

value: male


title: 8135_Child_Mother (Mapping250_Nsp)

value: Mother


title: 8160_Child_Mother (Mapping250_Nsp)


title: 1780_Father (Mapping250K_Nsp)


title: 8160_Child (Mapping250_Nsp)


title: 8612_Child_Mother (Mapping250_Nsp)


title: Rats exposed for 3 months to ultrafine particles 3

value: 4 weeks at the beginning of the experiment

value: heart


title: 8135_Child (Mapping250_Nsp)


title: 6942_Child_Father (Mapping250_Nsp)


title: 6942_Child_Mother (Mapping250_Nsp)


title: 8135_Child_Father (Mapping250_Nsp)


title: Rats exposed for 3 months to fine particles 6

source_name: rat heart, fine particles

value: fine particles (FP)

value: 3 months


title: 6932_Child_Mother (Mapping250_Nsp)

value: unaffected


title: 4821_Child_Mother (Mapping250_Nsp)

value: peripheral blood


title: Rats exposed for 3 months to fine particles 4


title: 6932_Child (Mapping250_Nsp)


title: Rats exposed for 3 months to fine particles 5


title: Rats exposed for 3 months to ultrafine particles 1

value: ultrafine particles (UFP)


title: 4821_Child (Mapping250_Nsp)

value: Developmental Delay

value: Male


title: 8327_Child_Mother (Mapping250_Nsp)


title: 2894_Child_Mother (Mapping250_Nsp)


title: 9609_Child_Father (NimbleGen)

hyb_protocol: Two arrays were used for each trio, one in which the child’s DNA was hybridized against the father’s DNA, and another in which the child’s DNA was hybridized against the mother’s DNA. Equal amounts of the child’s and one parent’s DNA were labeled with opposite fluorochromes and hybridized to the array

scan_protocol: The arrays were scanned at 5µm resolution on a GenePix 4000B Scanner.

data_processing:
Data from the hybridizations were analyzed using NimbleScan version 2.4.1 segMNT algorithm
Parameters: 1) the minimum segment difference, which represents the minimum difference in the log2 ratio that two segments must exhibit before they are identified as separate segments, was set at 0.0; 2) the minimum segment length, which represents the minimum number of consecutive probes that must exhibit a change in log2 ratio in order to call a segment, was set at 2; and 3) the acceptance percentile, which represents the stringency with which initial segment boundaries are selected, was set at 0.999. Only segments with a mean absolute log2 ratio of 0.2 or more were considered for further analysis.

label_protocol: DNA was sent to NimbleGen Systems, Inc. (Reykjavik, Iceland), where the hybridizations were performed.

value: idiopathic MR

value: Child

value: Father


title: Rats exposed for 3 months to fine particles 2


title: Rats exposed for 3 months to fine particles 1


title: 9390_Child_Father (NimbleGen)


title: 4821_Child_Father (Mapping250_Nsp)


title: Rats exposed for 3 months to fine particles 3


title: 6932_Child_Father (Mapping250_Nsp)


title: 9609_Child_Mother (NimbleGen)


title: Rats exposed for 3 months to coarse particles 6

source_name: rat heart, coarse particles

value: coarse particles (CP)


title: Rats exposed for 3 months to coarse particles 4


title: Rats exposed for 3 months to coarse particles 5


title: Rats exposed for 3 months to coarse particles 2


title: 2377_Child_Mother (Mapping250_Nsp)


title: Rats exposed for 3 months to coarse particles 1


title: 2894_Child_Father (Mapping250_Nsp)


title: Rats exposed for 3 months to coarse particles 3


title: 2894_Child (Mapping250_Nsp)


title: 9313_Child_Mother (NimbleGen)


title: 9313_Child_Father (NimbleGen)


title: 8994_Child_Mother (NimbleGen)


title: 2377_Child (Mapping250_Nsp)


title: Rats exposed for 3 months to filtered air (control 7)

source_name: rat heart, filtered air

value: filtered air (FA)


title: 2569_Child_Mother (Mapping250_Nsp)


title: 2569_Child_Father (Mapping250_Nsp)


title: 2332_Child_Mother (Mapping250_Nsp)


title: Rats exposed for 3 months to filtered air (control 6)

value: Fisher 344


title: 8960_Child_Father (NimbleGen)


title: 8994_Child_Father (NimbleGen)


title: 2377_Child_Father (Mapping250_Nsp)


title: 2569_Child (Mapping250_Nsp)


title: 8612_Child_Mother (NimbleGen)


title: Rats exposed for 3 months to filtered air (control 5)

value: male


title: Rats exposed for 3 months to filtered air (control 4)


title: 1511_Child_Mother (Mapping250_Nsp)

value: Mother


title: Rats exposed for 3 months to filtered air (control 3)

value: 4 weeks at the beginning of the experiment


title: 6942_Child (Mapping250_Nsp)


title: 8612_Child_Father (NimbleGen)


title: Rats exposed for 3 months to filtered air (control 2)

value: heart


title: Rats exposed for 3 months to filtered air (control 1)


title: Case A CD133neg

city: Heidelberg

first: Aurelie

last: Ernst

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: Labeled, amplified material (700 to 1250 ng per array) was hybridized to the Illumina Human whole genome Sentrix-6 V2 BeadChip® array according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430.

data_processing: Raw data extraction was done using the beadarray R package (svn release 1.7.0) from bioconductor.org. Bead outliers were removed when their expression value dropped below a threshold: the imaging system background, non-specific binding and cross hybridization signal. Individual bead types were flagged as filtered when their bead replicate count dropped below 17. All data was used for the mean expression value calculation within beadarray. Finally, we excluded a bead type when the bead type’s filter flag was set across all samples. Data analysis was done by variance stabilizing and spline normalizing the signals using the algorithms from the lumi R package (release 1.1.0) from bioconductor.org.

source_name: colorectal cancer

label_protocol: Labeling was achieved by use of the incorporation of biotin-16-UTP.

extract_protocol: RNA  was isolated from FACS-sorted cells using the RNeasy kit (Qiagen, Hilden, Germany). RNA quality and concentration were assessed with the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: CD133 negative


title: 2332_Child_Father (Mapping250_Nsp)


title: Case A CD133high

value: CD133 high


title: 2332_Child (Mapping250_Nsp)


title: 8327_Child_Father (NimbleGen)

value: unaffected


title: 8135_Child_Mother (NimbleGen)

value: peripheral blood


title: Case B CD133neg


title: Case B CD133high


title: 8160_Child_Mother (NimbleGen)


title: 8327_Child_Mother (NimbleGen)


title: 9390_Child_Mother (NimbleGen)


title: Case C CD133high


title: 8135_Child_Father (NimbleGen)


title: 7581_Child_Father (NimbleGen)


title: Case C CD133neg


title: squamous cell carcinoma, biological replicate 19

city: Manchester

first: Hui Sun

last: Leong

address: Wilmslow Road

department: The University of Manchester

institute: Cancer Research UK Manchester Institute

description:
V636
0310_CaW(4)30_ExH_nuFFPE_V636.CEL

hyb_protocol: RNA was quantified using a Bioanalyser (Agilent Technologies) and 100 ng amplified using NuGEN WT-Ovation FFPE v2 kit. The WT-Ovation Exon Module V1.0 was used to generate ST-cDNA and 4 µg was hybridised to Affymetrix Human Exon 1.0 ST arrays.

scan_protocol: Affymetrix GeneChip 3000 running GCOS software.

data_processing:
Background adjustment, quantile normalisation and summarisation of probe-level intensity were performed with the Robust Multi-array Average (RMA) algorithm.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: not applicable

source_name: cervix

label_protocol: The RNA was amplified using the WT-Ovation Pico RNA Amplification System, converted using the WT-Ovation Exon Module, and fragmented and labelled using the NuGEN FL-Ovation cDNA Biotin Module v2.

growth_protocol: not applicable

extract_protocol: 3 x 20uM sections of FFPE material was used for all samples. Total RNA was recovered using the Recoverall (Ambion kit) as per manufactures instructions.

treatment_protocol: not applicable

value: squamous cell carcinoma

tag: age of ffpe block (years)

tag: p63 staining status


title: adenocarcinoma, biological replicate 8

description:
V505
0909_CaW(2)92_nuExH_FFPE_V505.CEL

value: adenocarcinoma


title: 7581_Child_Mother (NimbleGen)

source_name: peripheral blood

value: Developmental Delay


title: 7531_Child_Mother (NimbleGen)

value: idiopathic MR


title: adenocarcinoma, biological replicate 9

description:
V669-2
0310_CaW(4)33_ExH_nuFFPE_V669-2.CEL


title: Case D CD133neg


title: 7531_Child_Father (NimbleGen)

value: Child


title: adenocarcinoma, biological replicate 7

description:
V615
0709_CaW(2)81_nuExH_FFPE_V615.CEL


title: adenocarcinoma, biological replicate 6

description:
V594
0709_CaW(2)79_nuExH_FFPE_V594.CEL


title: Case D CD133high


title: Case E CD133neg


title: 7484_Child_Mother (NimbleGen)


title: Case E CD133high


title: 7093_Child_Father (NimbleGen)

value: Father


title: 7093_Child_Mother (NimbleGen)


title: squamous cell carcinoma, biological replicate 18

description:
V590
0310_CaW(4)22_ExH_nuFFPE_V590.CEL


title: 6932_Child_Mother (NimbleGen)


title: 6942_Child_Father (NimbleGen)


title: 8160_Child_Father (NimbleGen)


title: adenocarcinoma, biological replicate 3

description:
V545
0909_CaW(2)95_nuExH_FFPE_V545.CEL


title: adenocarcinoma, biological replicate 4

description:
V548
0909_CaW(2)83_nuExH_FFPE_V548.CEL


title: adenocarcinoma, biological replicate 1

description:
V420
0310_CaW(4)18_ExH_nuFFPE_V420.CEL


title: HESC1

city: Taipei

first: Pin-hsun

last: Chen

address: 128 Academia Road, Section 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academia Sinica

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

scan_protocol: Chips were scanned with Affymetrix GeneChip Scanner 7G

data_processing: Raw data were analyized by Genespring GX, normalized by RMA (Robust Multichip Average) and the weakly expressed signals (<20% of total samples) were excluded.

source_name: Human embryonic stem cell line, H9

extract_protocol: Total RNA was isolated from cells with TRI Reagent (Molecular Research Center) and treated with DNase I according to manufacturer’s instruction.

value: HES


title: PompD-iPSC-CMLC B03

data_processing: Raw data were analyized by Genespring GX, normalized by RMA (Robust Multichip Average) and the weakly expressed signals (<20% of total samples) were excluded

source_name: PompD-iPSC B03 cell line derived cardiomyocyte-like cells

value: PomD-iPSC-CMLC


title: HESC2

source_name: Human embryonic stem cell line, NTU1


title: 1511_Child (Mapping250_Nsp)

value: Male


title: HES2-CMLC

source_name: HES2 cell line derived cardiomyocyte-like cells

extract_protocol: Total RNA was isolated from cells with TRI Reagent (Molecular Research Center) and treated with DNase I according to manufacturer’s instruction

value: HES-CMLC


title: 6942_Child_Mother (NimbleGen)

value: Mother


title: 1511_Child_Father (Mapping250_Nsp)


title: 7484_Child_Father (NimbleGen)


title: PomD-iPSC A25

source_name: Human iPSC(Pompe desease, Case no.778)-25

value: PomD-iPSCs


title: 6428_Child_Mother (NimbleGen)


title: PompD-iPSC-CMLC A10

source_name: PompD-iPSC A10 cell line derived cardiomyocyte-like cells


title: squamous cell carcinoma, biological replicate 17

description:
V668
0310_CaW(4)32_ExH_nuFFPE_V668.CEL


title: 6428_Child_Father (NimbleGen)


title: 6932_Child_Father (NimbleGen)


title: squamous cell carcinoma, biological replicate 16

description:
V629
0310_CaW(4)29_ExH_nuFFPE_V629.CEL


title: 4821_Child_Mother (NimbleGen)


title: adenocarcinoma, biological replicate 5

description:
V588
0709_CaW(2)78_nuExH_FFPE_V588.CEL


title: PomD-iPSC B03

source_name: Human iPSC(Pompe desease, Case no.826)-03


title: 8960_Child_Mother (NimbleGen)


title: PompD-iPSC-CMLC A17

source_name: PompD-iPSC A17 cell line derived cardiomyocyte-like cells


title: PomD-iPSC A17

source_name: Human iPSC(Pompe desease, Case no.778)-17


title: 5993_Child_Father (NimbleGen)


title: 5993_Child_Mother (NimbleGen)


title: 4821_Child_Father (NimbleGen)


title: squamous cell carcinoma, biological replicate 11

description:
V604
0310_CaW(4)24_ExH_nuFFPE_V604.CEL


title: Human fibroblast, Pompe desease, Case no. 826

source_name: Skin biopsy

value: HF, Pompe disease


title: squamous cell carcinoma, biological replicate 12

description:
V611B
0310_CaW(4)26_ExH_nuFFPE_V611B.CEL


title: 3519_Child_Mother (NimbleGen)


title: squamous cell carcinoma, biological replicate 13

description:
V618
0310_CaW(4)27_ExH_nuFFPE_V618.CEL


title: RT4_Aza_rep3 (repeated)

city: Sheffield

first: James

middle: W

last: Catto

state: South Yorks

address: Beech Hill Road

department: Institute for Cancer Studies

institute: University of Sheffield

description: MicroRNA gene expression with 5-azacytidine (2uM) treatment

hyb_protocol: Hybridization was performed with 10x GE Blocking Agent and 2x Hi-RPM Hybridization Buffer according to the Agilent microRNA protocol in a Agilent SureHyb chamber loaded into a hybridization oven at 55°C rotating at 20 rpm for 20 hours

scan_protocol: Microarrays were scanned immediately to reduce the impact of environmental oxidants on signal intensities using a High-resolution Agilent microarray scanner (Scan sitting: Values for 8×15k Formats, Scan region: Scan Area (61×21.6mm), Sac resolution (μm): 5,5μm scanning mode: Single Press, eXtended dynamic range (XDR): Selected, Dye channel: Green, Green photo-multiplier tube (PMT): XDR High 100%, XDR Low 5%).

data_processing: Fluorescence intensity was calculated using Feature Extraction software (Vsn. 10.5.1.1, Agilent) and analysis performed using Genespring GX (Agilent) and Excel (Microsoft, WA). GeneSpring defaults with the percentile shift to the 50th percentile; hence raw signal to 1.0, normalisation by percentile shift to the 50th percentile, and no baseline transformation.

source_name: Bladder cancer cell line

label_protocol: 2 μl (100ng) of diluted total RNA was added to a 1.5ml Eppendorf tube and kept on ice. 2 μl of Calf Intestinal Alkaline Phosphatase (CIP) master mix was to total RNA. The reaction mixture was incubated in a heat block at 37 oC for 30 minutes.  After that 2.8μl of 100% DMSO was added to each sample and incubated at 100 oC for 7 minutes.  Samples were then immediately transferred to an ice-water bath, and 4.5μl of ligation master mix was added according to the protocol

growth_protocol: Bladder cancer cell lines (RT4, RT112 and EJ ) were grown in Dulbecco’s medium with 10% fetal calf serum. NHU cells were grown in keratinocyte serum-free medium containing bovine pituitary extract, epidermal growth factor and cholera toxin. The cultures were incubated at 37 ºC in a with 5% CO2.

extract_protocol: Total RNA was extracted using the mirVanaTM kit (Ambion, TX) according to manufacturer’s protocol from each cell line before and after 5-azacytidine treatment.

treatment_protocol: Bladder cancer cell lines were treated with DNA Methyltransferase inhibition (2uM) 5-azacytidine for 5-7 days (added on alternate days).

tag: cell line

value: Bladder cancer

tag: agent

value: 5-azacytidine (2uM)


title: squamous cell carcinoma, biological replicate 14

description:
V622
0709_CaW(2)82_nuExH_FFPE_V622.CEL


title: PomD-iPSC A10

source_name: Human iPSC(Pompe desease, Case no.778)-10


title: Human fibroblast, Pompe desease, Case no. 778


title: EJ_Aza_rep3 (repeated)

value: EJ


title: 3921_Child_Mother (NimbleGen)

tag: developmental state

value: peripheral blood

value: unaffected


title: 3519_Child_Father (NimbleGen)

tag: family


title: squamous cell carcinoma, biological replicate 8

description:
V573
0709_CaW(2)77_nuExH_FFPE_V573.CEL

value: squamous cell carcinoma


title: squamous cell carcinoma, biological replicate 15

description:
V624
0310_CaW(4)28_ExH_nuFFPE_V624.CEL


title: knockdown at 8 hrs, males, samples from pooled experiments (DS003014)

city: RTP

first: Sheetal

last: Shah

state: NC

address: 3054E Cornwallis Road

institute: Syngenta

description:
Gene expression data from adults treated for 8 hours
DS003014

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA. 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in an Affymetrix Fluidics Station.

data_processing: data was processed using RMA in GeneData Refiner

organism: Drosophila melanogaster

source_name: 2-3 day old adults

growth_protocol: Drosophila melanogaster flies were cultured according to standard methods, and  maintained on a rich diet (10L water, 100g agar (USP #7060 Bio-serve), 350g Brewer’s dried yeast (Sunshine Health), 300g black treacle (Lyles), 150g sucrose (Tate & Lyle), 300g Difco dextrose (Becton Dickinson), 150g cornmeal (#1151, Bioserve), 100g wheatgerm (#1659, Bioserve), 200g soya bean flour (#S9633 Sigma Aldrich), 10g methyl-4-hydroxybenzoate (#H3647 Sigma Aldrich) in 10ml ethanol, 50ml proprionic acid (#P5561  Sigma Aldrich)).

extract_protocol: RNA from the frozen flies per treatment was extracted using RNAwiz (Ambion) according to the manufacturer's instructions.

treatment_protocol: 0.75 mls of a 5%sucrose:1%agar mix was set in each well of a 24-well plate. 20 ul of an ethanol-acetone solvent was spread uniformly on the surface of the sucrose-agar base in a well (this solvent was considered to be inert in our assays here, but was included as a type of control for future experiments where insecticide might also be applied in the solvent).   10 (2-3 day old) adult flies of appropriate genotype & sex were infested per well, with ≥3 replicates per 'treatment', i.e. per sex-genotype-timepoint. The plates were sealed with a breatheable film (BEM1, Web Scientific), and incubated under standard conditions (25oC, 70-75% humidity). Each experiment was repeated 2-3 times to provide independent replication.  The adult flies were recovered from the assay plates at the pre-defined timepoints, transferred into eppendorf tubes and immediately frozen on dry ice and then stored in a -80oC freezer.

value: Males

tag: developmental stage

value: 2-3 day old adults

value: whole animal

tag: number

value: 3 independent tests (pooled equivalent amount of RNA from each test)

tag: time

value: 8 hours


title: control at 8 hrs, males, samples from pooled experiments (DS003013)

description:
Gene expression data from adults treated for 8 hours
DS003013

scan_protocol: 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in an Affymetrix Fluidics Station.

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

tag: gender

value: w;Act-GAL4/CyO;+/TM3 Sb


title: 3094_Child_Father (NimbleGen)

value: Developmental Delay

tag: phenotype

value: idiopathic MR

tag: family member

value: Child

value: Father


title: Patient 446B DCIS (microRNA)

city: Boston

first: Bethany

last: Hannafon

state: MA

address: 650 Albany Street

department: Medicine/Section of Hematology and Oncology

institute: Boston University School of Medicine

description: Single-stranded cDNA was synthesized from 800ng of total RNA, reverse transcription reaction was diluted combined with master mix and loaded onto the TaqMan Low Density array.

scan_protocol: RT-PCR data was aquired on the 7900 Real-Time PCR System  (Applied Biosystems)

data_processing: All probes with cycle threshold (Ct)=40 in >2/3 PRM or >6/8 HN and >6/8 DCIS samples were considered non-expressed and removed. Remaining Ct values for 232/365 probes were global-median normalized by transforming all expression values by re-scaling to a target value of 12.

source_name: ductal carcinoma in situ epithelium

label_protocol: 800ug of total RNA was reverse-transcribed in 8 multiplex RT reactions (100ng/reaction) using the TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems), according to manufacturer's protocol. Each multiplex reaction was diluted, combined with Universal PCR Master Mix (No AmpErase UNG), loaded onto array, centrifuged, and sealed, according to manufacturer's protocol.

extract_protocol: On average, ~50 10 um-thick cryostat sections were prepared for the extraction of total RNA by laser-capture microdissection from normal or DCIS epithelial regions, which were identified by a surgical pathologist (AdlM) using every 7th section stained by Hematoxylin and Eosin. Total RNA was extracted from the captured epithelium using the RNAqueous miRNA Isolation Kit (Ambion, Austin, TX) according to manufacturer's protocol with additional DNAse treatment step.

treatment_protocol: Primary patient breast tissue was snap-frozen in liquid nitrogen, embedded in optimal cutting temperature compound and stored at -80C

tag: tissue source

value: Primary breast cancer

value: female

tag: age

value: ductal carcinoma in situ epithelium


title: RT112_Control_rep3

description: MicroRNA gene expression without 5-azacytidine

value: Bladder cancer


title: RT112_Aza_rep3

value: 5-azacytidine (2uM)


title: squamous cell carcinoma, biological replicate 6

description:
V568
0909_CaW(2)93_nuExH_FFPE_V568.CEL


title: NHU_rep4

source_name: Normal urothelium cells

value: NHU

value: Normal bladder


title: squamous cell carcinoma, biological replicate 10

description:
V601A
0310_CaW(4)23_ExH_nuFFPE_V601A.CEL

source_name: cervix

value: squamous cell carcinoma


title: control at 8 hrs, males, samples from pooled experiments (DS003012)

description:
Gene expression data from adults treated for 8 hours
DS003012

value: Males

value: 2-3 day old adults

tag: genotype/variation


title: squamous cell carcinoma, biological replicate 7

description:
V572
0310_CaW(4)19_ExH_nuFFPE_V572.CEL

tag: disease state


title: 2894_Child_Mother (NimbleGen)

source_name: peripheral blood

tag: tissue

value: peripheral blood

value: unaffected

value: Mother


title: NHU_rep3


title: Patient 405 DCIS (microRNA)


title: Patient 444 DCIS (microRNA)


title: Patient 380 DCIS (microRNA)


title: control at 5 hrs, males, samples from pooled experiments (DS003010)

description:
Gene expression data from adults treated for 5 hours
DS003010

value: whole animal

value: 3 independent tests (pooled equivalent amount of RNA from each test)

value: w;Act-GAL4/CyO;+/TM3 Sb

value: 5 hours


title: NHU_rep1


title: NHU_rep2


title: squamous cell carcinoma, biological replicate 5

description:
V562
0909_CaW(2)89_nuExH_FFPE_V562.CEL

tag: age of ffpe block (years)


title: 2569_Child_Mother (NimbleGen)

value: Developmental Delay

value: idiopathic MR

value: Child


title: squamous cell carcinoma, biological replicate 9

description:
V577
0310_CaW(4)20_ExH_nuFFPE_V577.CEL

tag: p63 staining status


title: squamous cell carcinoma, biological replicate 4

description:
V558
0909_CaW(2)90_nuExH_FFPE_V558.CEL


title: RT4_Control_rep2

tag: cell line

value: Bladder cancer


title: RT4_Control_rep3

tag: agent


title: Patient 258 DCIS (microRNA)

value: Primary breast cancer

value: female

value: ductal carcinoma in situ epithelium


title: Patient 274 DCIS (microRNA)


title: control at 2 hrs, males, samples from pooled experiments (DS003007)

description:
Gene expression data from adults treated for 2 hours
DS003007

value: 2 hours


title: control at 2 hrs, males, samples from pooled experiments (DS003006)

description:
Gene expression data from adults treated for 2 hours
DS003006

value: Males


title: control at 5 hrs, males, samples from pooled experiments (DS003009)

description:
Gene expression data from adults treated for 5 hours
DS003009

value: 2-3 day old adults


title: 2714_Child_Father (NimbleGen)

tag: developmental state

value: peripheral blood

value: Father


title: Patient 248 DCIS (microRNA)


title: RT112_Control_rep2


title: squamous cell carcinoma, biological replicate 1

description:
V509
0909_CaW(2)84_nuExH_FFPE_V509.CEL

value: squamous cell carcinoma


title: RT112_Control_rep1


title: 3921_Child_Father (NimbleGen)

tag: family

value: unaffected


title: 3094_Child_Mother (NimbleGen)

value: Mother


title: control at 0 hrs, males, sample from pooled experiments (DS003005)

description:
Gene expression data from adults treated for 0 hours
DS003005

tag: developmental stage

value: whole animal

value: 2 independent tests (pooled equivalent amount of RNA from each test)

value: w;Act-GAL4/CyO;+/TM3 Sb

value: 0 hours


title: Patient 446B HN (microRNA)

source_name: histologically normal breast epithelium

value: histologically normal breast epithelium


title: knockdown at 0 hrs, females, single experiment sample (DS003003)

description:
Gene expression data from adults treated for 0 hours
DS003003

value: Females

tag: number

value: 1 test


title: Patient 405 HN (microRNA)

value: Primary breast cancer

value: female


title: squamous cell carcinoma, biological replicate 3

description:
V554
0909_CaW(2)87_nuExH_FFPE_V554.CEL


title: control at 0 hrs, males, samples from pooled experiments (DS003004)

description:
Gene expression data from adults treated for 0 hours
DS003004

tag: time


title: knockdown at 5 hrs, males, samples from pooled experiments (DS003011)

description:
Gene expression data from adults treated for 5 hours
DS003011

tag: gender

value: 3 independent tests (pooled equivalent amount of RNA from each test)

value: 5 hours


title: 2377_Child_Father (NimbleGen)

value: Developmental Delay

tag: phenotype

value: idiopathic MR

value: Child


title: RT112_Aza_rep2

value: Bladder cancer

value: 5-azacytidine (2uM)


title: 2714_Child_Mother (NimbleGen)

value: peripheral blood

tag: family member

value: unaffected

value: Mother


title: RT4_Aza_rep2


title: Patient 379 DCIS (microRNA)

tag: tissue source

value: ductal carcinoma in situ epithelium


title: Patient 444 HN (microRNA)

tag: age


title: CskKO/Csk_biological rep2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description:
CskKO/Csk-rep2
Csk-/- mouse embryonic fibroblasts (Csk-/- MEFs) expressing Csk.

hyb_protocol: Refer to Agilent miRNA hybridisation protocol. Probes were hybridized at 55°C for 20 hours with rotation. Then the slides were washed by Gene expression wash buffer 1 at room temperature for 5 minutes and by Gene expression wash buffer 2 at 37°C for 5 minutes.

scan_protocol: After hybridization and washing, the slides were scanned using an Agilent scanner (G2505B). Images were extracted using Agilent Feature Extraction software (ver. 9.5.3.1) and Agilent GeneSpring GX software (ver. 10.0.2).

data_processing: Data were processed by the Agilent GeneSpring GX software. Total gene signal from GeneView data files extracted with default settings in Agilent Feature Extraction, which summarized the measurements of all probes for each gene on an array, was used as signal for miRNAs. To avoid missing values after log-transformation, any signal which was still less than 1 was reset to be equal to 1. Differences in miRNA expressions between the 4 pairs was determinate if the fold change of expression values was >2.0 and the p value was <0.05 using Student's t test for further analysis.

source_name: Csk-/- C57BL/6J MEFs expressing Csk

label_protocol: One hundred nanograms of aliquots of total RNA was used for making miRNA probes according to the Agilent protocol (ver. 1.6). Briefly, total RNA was dephosphorylated with calf intestine alkaline phosphatase (Takara Bio, Shiga, Japan), denatured with dimethyl sulfoxide, and labeled with pCp-Cy3 using T4 RNA ligase (Takara Bio, Shiga, Japan) using the miRNA Labeling Reagent and Hybridization Kit (5190-0408, Agilent).

extract_protocol: Total RNA was extracted with Sepazol (Nacalai Tesque, Kyoto, Japan) according to the manufacturer’s instructions. RNA yield and A260/280 ratio were monitored with a NanoDropND-100 spectrometer (Thermo Scientific, Wilmington, DE), and RNA integrity numbers were assessed with the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only RNA extracts with RNA integrity number values >9 were included in further analyses.

tag: strain

tag: genotype

value: Csk-/-

tag: cell type

value: mouse embryonic fibroblasts (MEFs)

tag: transfection

value: Csk


title: 2332_Child_Mother (NimbleGen)

tag: tissue


title: RT112_Aza_rep1

tag: cell line


title: knockdown at 0 hrs, males, single experiment sample (DS003002)

description:
Gene expression data from adults treated for 0 hours
DS003002

value: Males

value: 2-3 day old adults

value: whole animal

value: 1 test

tag: genotype/variation

value: 0 hours


title: 2569_Child_Father (NimbleGen)

tag: developmental state

value: Developmental Delay

value: Father


title: Patient 379 HN (microRNA)

value: Primary breast cancer

value: female

value: histologically normal breast epithelium


title: RT4_Aza_rep1

description: MicroRNA gene expression with 5-azacytidine (2uM) treatment

value: Bladder cancer

tag: agent

value: 5-azacytidine (2uM)


title: Patient 380 HN (microRNA)


title: ARV1 mutant, rep 3

city: New York

first: Stephen

middle: L

last: Sturley

state: NY

address: 630 West 168th Street, PH1512 East

department: Department of Pediatrics

institute: Columbia University

description:
Yeast_ARV1-3
YG_S98 array format

hyb_protocol: The biotin-labeled and fragmented cRNA was hybridized to the YE6100 or S98 Yeast GeneChip arrays (Affymetrix), washed, and stained according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the Hewlett-Packard Gene Array Scanner (Affymetrix) at a wavelength of 570 nm.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Saccharomyces cerevisiae

source_name: Yeast ARV1 mutant strain

label_protocol: Synthesis of biotin-labeled cRNA was carried out by in vitro transcription using Enzo Bioarray RNA transcript labeling kit (Enzo Diagnostics), according to the manufacturer's instructions.

growth_protocol: Cells grown to mid-logarithmic stage (A600=0.5-0.6) in YEPD.

extract_protocol: Total RNA was extracted and poly(A)+ RNA was purified from total RNA by Oligotex oligo(dT) selection according to manufacturer's instructions (Qiagen).

tag: mating type

value: MATa

value: ARV1 mutant


title: 1815_Child_Father (NimbleGen)

value: peripheral blood

value: idiopathic MR

tag: family

value: Child

value: unaffected


title: 2377_Child_Mother (NimbleGen)

value: Mother


title: CskKO/Csk+Src_biological rep2

description:
CskKO/Csk+Src-rep2
Csk-/- mouse embryonic fibroblasts (Csk-/- MEFs) expressing Csk and c-Src.

source_name: Csk-/- C57BL/6J MEFs expressing Csk and c-Src

value: Csk-/-

value: mouse embryonic fibroblasts (MEFs)

value: Csk+Src


title: CskKO/Src_biological rep2

description:
CskKO/Src-rep2
Csk-/- mouse embryonic fibroblasts (Csk-/- MEFs) expressing c-Src.

source_name: Csk-/- C57BL/6J MEFs expressing c-Src

value: Src


title: CskKO/mock_biological rep2

description:
CskKO/mock-rep2
Csk-/- mouse embryonic fibroblasts (Csk-/- MEFs).

source_name: Csk-/- C57BL/6J MEFs

value: mock


title: 2332_Child_Father (NimbleGen)

value: Developmental Delay

value: Father


title: 1780_Child_Mother (NimbleGen)


title: 2894_Child_Father (NimbleGen)


title: squamous cell carcinoma, biological replicate 2

description:
V553
0909_CaW(2)88_nuExH_FFPE_V553.CEL

tag: disease state

value: squamous cell carcinoma

tag: age of ffpe block (years)

tag: p63 staining status


title: Patient 258 HN (microRNA)

description: Single-stranded cDNA was synthesized from 800ng of total RNA, reverse transcription reaction was diluted combined with master mix and loaded onto the TaqMan Low Density array.

value: Primary breast cancer

tag: gender

value: female

value: histologically normal breast epithelium


title: knockdown at 2 hrs, males, samples from pooled experiments (DS003008)

description:
Gene expression data from adults treated for 2 hours
DS003008

value: Males

tag: developmental stage

value: 2-3 day old adults

value: whole animal

tag: number

value: 3 independent tests (pooled equivalent amount of RNA from each test)

tag: time

value: 2 hours


title: EJ_Aza_rep2

value: EJ

value: Bladder cancer

value: 5-azacytidine (2uM)


title: RT4_Control_rep1

description: MicroRNA gene expression without 5-azacytidine


title: EJ_Aza_rep1


title: CskKO/Csk+Src_biological rep1

description:
CskKO/Csk+Src-rep1
Csk-/- mouse embryonic fibroblasts (Csk-/- MEFs) expressing Csk and c-Src.

tag: strain

tag: genotype

value: Csk-/-

value: mouse embryonic fibroblasts (MEFs)

value: Csk+Src


title: EJ_Control_rep3


title: Control, rep 3

description:
Yeast_Control-3
YG_S98 array format

source_name: Yeast control strain

value: MATa

value: control


title: 1780_Child_Father (NimbleGen)

value: Developmental Delay

value: peripheral blood

tag: phenotype

value: idiopathic MR

tag: family member

value: Child

value: unaffected

value: Father


title: Pooled RM 3 (microRNA)

description: Pooled sample was prepared by combining 400ng total RNA from each of 9 RM epithelial samples

source_name: pooled sample of fresh-frozen micro-dissected normal breast epithelium from 9 reduction mammoplasty samples

tag: tissue source

value: Reduction mammoplasty

value: female

tag: age

tag: tissue

value: pooled normal breast epithelium


title: Patient 248 HN (microRNA)

value: Primary breast cancer

value: histologically normal breast epithelium


title: CskKO/Csk_biological rep1

description:
CskKO/Csk-rep1
Csk-/- mouse embryonic fibroblasts (Csk-/- MEFs) expressing Csk.

tag: cell type

tag: transfection

value: Csk


title: control at 0 hrs, males, single experiment sample (DS003001)

description:
Gene expression data from adults treated for 0 hours
DS003001

value: Males

value: 2-3 day old adults

value: whole animal

value: 1 test

tag: genotype/variation

value: w;Act-GAL4/CyO;+/TM3 Sb

value: 0 hours


title: CskKO/Src_biological rep1

description:
CskKO/Src-rep1
Csk-/- mouse embryonic fibroblasts (Csk-/- MEFs) expressing c-Src.

value: Csk-/-

value: mouse embryonic fibroblasts (MEFs)

value: Src


title: EJ_Control_rep1

tag: cell line

value: EJ

value: Bladder cancer

tag: agent


title: Pooled RM 2 (microRNA)

value: Reduction mammoplasty


title: EJ_Control_rep2


title: BDV PvsGFP biological replicate 2 dyeswap

description: BDV P(cy3)vsGFP(cy5) biological replicate 2 dyeswap

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. The values were inversed/obtained by using Agilent Genespring 7.3.1 software according to manufacturer's instructions.

source_name: C6 rat glioma cell line expressed with GFP

label_protocol: 500 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: C6 cells are seeded on 6-well plates and transfected with GFP/BDV P plasmid for 3 days.

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

treatment_protocol: no teatment

value: GFP

source_name: C6 rat glioma cell line expressed with BDV P

value: BDV P


title: Pooled RM 1 (microRNA)

description: Pooled sample was prepared by combining 400ng total RNA from each of 9 RM epithelial samples. Single-stranded cDNA was synthesized from 800ng of pooled RNA, reverse transcription reaction was diluted combined with master mix and loaded onto the TaqMan Low Density array.

value: female

value: pooled normal breast epithelium


title: 1815_Child_Mother (NimbleGen)

tag: developmental state

value: Developmental Delay

value: peripheral blood

value: idiopathic MR

tag: family

value: Child

value: unaffected

value: Mother


title: BDV PvsGFP biological replicate 1 dyeswap

description: BDV P(cy3)vsGFP(cy5) biological replicate 1 dyeswap


title: SCC_N24_1Mb_aCGH

status: Public on Feb 16 2011

first: Ian

last: Roberts

department: Cancer Cell Unit

institute: Hutchison MRC Research Centre

description: Dye swapped hybridisations. Filename suffix (e.g. Cy3 or Cy5) indicates Test gDNA dye. Ratios are always Test / Ref. Average Log 2 ratios were computed by inverting dye swapped values.

hyb_protocol: aCGH probes were hybridised to template slides according to Centre for Microarray Resources (Cambridge University, Pathology Department) methods

scan_protocol: Stringency washed array slides were scanned using an Axon 4100B microarray scanner

data_processing:
R using snapCGH bioconductor package
Mean pixel values are background subtracted, median normalized, with replicate spots averaged. Dye swapped experiments were inverted prior to combining, and averaging.

label: Cy3, Cy5

source_name: Test, cervical carcinoma tissue, minimum 95% tumour

label_protocol: gDNA was labelled using Invitrogen Bioprime aCGH labelling kit, according to manufactures protocols

extract_protocol: Following mechanical disaggregation, gDNA was extracted using proteinase K phenol / choloroform method.

value: cervix

tag: histopathological diagnosis

value: squamous cell carcinoma

tag: histopathological tumour grade

value: grade III / late stage

label: Cy5, Cy3

source_name: Ref, peripheral blood lymphocytes

tag: pbl

value: pooled random donor samples


title: SCC_N34_1Mb_aCGH


title: 1511_Child_Father (NimbleGen)

value: Father


title: SCC_N8_1Mb_aCGH


title: SCC_N82_1Mb_aCGH


title: SCC_N98_1Mb_aCGH


title: SCC_G31_1Mb_aCGH


title: CskKO/mock_biological rep1

description:
CskKO/mock-rep1
Csk-/- mouse embryonic fibroblasts (Csk-/- MEFs).

tag: strain

value: Csk-/-

value: mouse embryonic fibroblasts (MEFs)

value: mock


title: GFPvsBDV P biological replicate 2

description: GFP(cy3)vsBDV P(cy5) biological replicate 2

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.

value: BDV P

value: GFP


title: SCC_N44a_1Mb_aCGH


title: SCC_N14_1Mb_aCGH


title: SCC_N44_1Mb_aCGH


title: SCC_N10_1Mb_aCGH


title: SCC_N12_1Mb_aCGH


title: SCC_N58_1Mb_aCGH


title: SCC_N57_1Mb_aCGH


title: SCC_N55_1Mb_aCGH


title: SCC_G30_1Mb_aCGH


title: GFPvsBDV P biological replicate 1

description: GFP(cy3)vsBDV P(cy5) biological replicate 1


title: SCC_G29_1Mb_aCGH


title: SCC_N11_1Mb_aCGH


title: SCC_N22_1Mb_aCGH


title: SCC_N21_1Mb_aCGH


title: SCC_G24_1Mb_aCGH


title: SCC_G26_1Mb_aCGH


title: SCC_G23_1Mb_aCGH


title: SCC_G19_1Mb_aCGH


title: SCC_G15_1Mb_aCGH


title: SCC_G10_1Mb_aCGH


title: SCC_G22_1Mb_aCGH


title: 1056_Child_Father (NimbleGen)


title: SCC_G12_1Mb_aCGH


title: SCC_G14_1Mb_aCGH


title: SCC_G12r_1Mb_aCGH


title: SCC_G06_1Mb_aCGH


title: SCC_G16_1Mb_aCGH


title: SCC_G03_1Mb_aCGH


title: SCC_G17_1Mb_aCGH


title: SCC_G09_1Mb_aCGH


title: CELL_LINE_SW756_1Mb_aCGH

hyb_protocol: aCGH probes were hybridised to template slides according to Pennsylvania

data_processing:
R using snapCGH bioconductor package
Mean pixel values are background subtracted, median normalized, with replicate spots averaged. Dye swapped experiments were inverted prior to combining, and averaging.
Dye swapped hybridisations. Filename suffix (e.g. Cy3 or Cy5) indicates Test gDNA dye. Ratios are always Test / Ref. Average Log 2 ratios were computed by inverting dye swapped values.

source_name: Test, cervical squamous cell carcinoma

growth_protocol: SCC cell lines were grown in 10% FCS + 90% GMEM + antibiotics

extract_protocol: gDNA was extracted using proteinase K phenol / choloroform method.

tag: hpvtype

tag: reference

value: pooled random donor samples peripheral blood lymphocytes


title: SCC_G08_1Mb_aCGH


title: SCC_G18_1Mb_aCGH


title: SCC_G11_1Mb_aCGH


title: 1056_Child_Mother (NimbleGen)

value: Developmental Delay

tag: phenotype

tag: family member


title: CELL_LINE_MS751_1Mb_aCGH


title: SCC_G01_1Mb_aCGH


title: CELL_LINE_SiHa_1Mb_aCGH


title: CELL_LINE_CaSki_1Mb_aCGH


title: SCC_G20_1Mb_aCGH


title: CELL_LINE_HT3_1Mb_aCGH

value: negative


title: SCC_G02_1Mb_aCGH


title: Patient 274 HN (microRNA)

tag: tissue source

value: Primary breast cancer

tag: gender

value: female

tag: age

value: histologically normal breast epithelium


title: CELL_LINE_C4I_1Mb_aCGH

tag: tissue


title: CELL_LINE_C33A_1Mb_aCGH


title: SIL_S99660_1Mb_aCGH

source_name: Test, microdissected cervical squamous intraepithelial lesion

value: high grade squamous intraepithelial lesion


title: CELL_LINE_C4II_1Mb_aCGH

value: cervix


title: CELL_LINE_ME180_1Mb_aCGH

value: squamous cell carcinoma


title: SIL_S99385_1Mb_aCGH


title: SIL_S99175_1Mb_aCGH

value: low grade squamous intraepithelial lesion

value: other


title: SIL_S99382_1Mb_aCGH


title: BM-3

city: Phoenix

first: Julianna

last: Ross

state: AZ

department: Cancer and Cell Biology

institute: Translational Genomics Research Institute

description: FFPE tumor sample from a lung cancer patient with no detetcted brain metastasis.

hyb_protocol: All hybridization was performed in automated hybridization stations with slow mixing mechanism. GenoExplorer microRNA arrays - human (GenoSensor Corporation, Tempe, AZ; containing probes in triplicate for 678 validated human mature miRNAs with an additional 473 validated human pre-miRNAs along with positive and negative control probes) were used for hybridization. One miRNA microarray chip hybridization was performed per patient sample. The reaction was incubated at 42oC for 16 hours. The array was then stained by streptavidin-Cy5 dye. After washes, the arrays were dried and scanned. Each miRNA was represented by 3 probes.

scan_protocol: Array was scanned using Axon 4000B. Raw data with signal intensity was analyzed by GenePix software.

data_processing: Raw intensity values for each of the three probes for every miRNA were averaged and standard deviation was also calculated. To calculate the fold change, the averaged miRNA intensities were compared to the signal threshold [Threshold was determined by array background + 2x background SD (standard deviation)] for the respective arrays, and if these averaged miRNA intensities were higher than the signal threshold, then these were divided by the average of the intensities for 5srRNA2 and PC-hu5S for data normalization. All the normalized values were further divided by a factor of 10 for scaling down the normalized data.

source_name: FFPE lung cancer sample, brain metastasis negative

label_protocol: Total RNA (a minimum of 1µg) was labeled using GenoExplorer microRNA labeling kit (GenoSensor, Tempe, AZ). Briefly, a biotinylated adaptor is labeled at the 5'end of miRNA and other non-capped small non-coding RNA. The reaction was incubated at 20oC for 2 hours. The labeled samples were then used for hybridization.

extract_protocol: RNA was extracted from all FFPE NSCLC tumor specimens by manually scraping (macrodissection) the tumor tissue from the slides followed by de-paraffinization with xylene at 50oC. Three to six sections per tumor sample were used for RNA extraction. The pellet obtained after centrifugation was washed in 100% ethanol and digested with digestion buffer (RecoverAll Total Nucleic Acid Isolation, Part # 8788G, Ambion) and proteinase K solution at 50°C for 3 hours. Total RNA was extracted following standard protocols using phenol and guanidine thiocyanate. The concentration and purity of isolated RNA was estimated using the ND-1000 micro-spectrophotometer (NanoDrop Technologies, Wilmington, DE).

value: non-small cell lung cancer (NSCLC) tumor

tag: brain metastasis

value: no

tag: histology

value: adenocarcinoma

tag: stage at diagnosis

tag: # months follow-up

value: male


title: BM-5


title: SIL_S9866_1Mb_aCGH


title: SIL_S99228_1Mb_aCGH


title: SIL_S99211_1Mb_aCGH


title: SIL_S99353_1Mb_aCGH


title: SIL_S98296_1Mb_aCGH

value: no abnormality detected


title: CELL_LINE_DoTc2_1Mb_aCGH


title: BM-6


title: BM-4


title: SIL_S99183_1Mb_aCGH


title: BM+5

description: FFPE tumor sample from a lung cancer patient with brain metastasis.

source_name: FFPE lung cancer sample, brain metastasis positive

value: yes

tag: # months between diagnosis and bm development

value: metastasis present at diagnosis


title: BM-1


title: BM+6


title: BM+7


title: BM+3


title: BM+4


title: SIL_S97703_1Mb_aCGH

value: pooled random donor samples peripheral blood lymphocytes


title: BM+2


title: SIL_S97689_1Mb_aCGH


title: BM+1


title: SIL_M0212_1Mb_aCGH


title: SIL_M0211_1Mb_aCGH

value: negative


title: SIL_M0167_1Mb_aCGH


title: SIL_M0159_1Mb_aCGH


title: 1511_Child_Mother (NimbleGen)

source_name: peripheral blood

tag: developmental state

value: Developmental Delay

value: peripheral blood

value: idiopathic MR

tag: family

value: Child

value: unaffected

value: Mother


title: SIL_M0156_1Mb_aCGH

value: cervix

tag: histopathological tumour grade

value: high grade squamous intraepithelial lesion


title: SIL_M0236_1Mb_aCGH


title: SIL_S97275_1Mb_aCGH


title: SIL_M0099_1Mb_aCGH

value: low grade squamous intraepithelial lesion


title: SIL_M0095_1Mb_aCGH


title: SIL_S97574_1Mb_aCGH

value: other


title: SIL_M0090_1Mb_aCGH


title: SIL_M0081_1Mb_aCGH


title: miRNA expression in 1G flight control for 8d

city: Sendai

first: Atsushi

last: Higashitani

address: Katahira

department: Graduate School of Life Sciences

institute: Tohoku University

hyb_protocol: After pre-hybridization for 60 min at 37C with 6 x SSPE, 1% SDS, 0.2% BSA, hybridization was performed at 37C for 4 hr hybridization in Hybridization Buffer (6xSSPE, 0.8% BSA, 12% DI-Formamide, 2.5% SDS). Array was washed 4 times with 6 x SSPE, 0.05% Tween-20 （25C） for 3 min, 3 x SSPE, 0.05% Tween-20 （25C） for 3 min, 0.5 x SSPE, 0.05% Tween-20 （25C） for 3 min and 0.5 x SSPE, 0.05% Tween-20 （25C） for 3 min.

scan_protocol: GenePix® 4000B scanner (Molecular Devices)

data_processing: Array-Pro Analyzer® Ver.4.5 （Media Cｙbernetics, Inc.）

organism: Caenorhabditis elegans

source_name: Adult hermaphrodites

label_protocol: Total RNA (17 micro-g) was purified by flash PAGE^TM system. Label IT® miRNA Labeling Kit (Mirus Bio Corp., cat.#MIR8305) was used for probe label with Cｙ5.

growth_protocol: A full description of the experimental procedures and flight hardware, including illustrations, employed on this experiment can be found in (Higashitani et al., 2010, Biol. Sci. Space, 23, 183-187). All experiments were carried out under temperature controlled conditions in the Cell Biology Experiment Facility (CBEF) within the KIBO module.Cultures for microRNA expression analysis were grown for 4 d and 8 d. Experiments were stopped by first observing the animals by light microscopy and then by freezing with subsequent storage at -80°C in MELFI. Flight samples were thawed on ice with M9 buffer containing 0.05% gelatine, and approximately 10^3 adult hermaphrodites were collected in each experimental condition by picking under stereo microscopy.

extract_protocol: Total RNA was isolated with TRIzol Reagent (Invitrogen).

treatment_protocol: FilgenArray miRNA Caenorhabditis elegans V15 <CombiMatrix Co. Ltd> was used in each experiment.

tag: condition

value: 1G flight control for 8d


title: miRNA expression in ground control for 4 d

value: ground control for 4 d


title: miRNA expression in ground control for 8 d

value: ground control for 8 d


title: miRNA expression in 1G flight control for 4d

value: 1G flight control for 4d


title: SIL_M0082_1Mb_aCGH

tag: hpvtype


title: 4hr sham partial hepatectomy old replicate 2

city: Houston

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Gene expression data from liver 4h after sham partial hepatectomy in old mice.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C to Affymetrix GeneChip Mouse Expression U74Av2 arrays.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: Raw signal intensites were normalized using the RMA algorithm implemented with R and BioC (justRMA function).

source_name: liver

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

growth_protocol: Male mice of the CB6F1 hybrid strain at 5-6 months of age, and at 25-27 months of age were obtained from Jackson Laboratories, and the National Institute on Aging, respectively.

extract_protocol: Total RNA was isolated using the RNeasy mini columns from Qiagen.

treatment_protocol: Mice were anesthetized by use of an intraperitoneal injection of avertin followed by supplementary inhalation of isoflurane.  Partial hepatectomy was performed by surgical removal of 70% of the liver mass.  Liver tissue was collected at  0, 0.5, 1, 2 and 4 hour(s) following surgery.

value: 25-27 months

tag: strain

value: male

tag: treatment

value: sham partial hepatectomy

tag: time (hours)


title: 4hr sham partial hepatectomy young replicate 2

description: Gene expression data from liver 4h after sham partial hepatectomy in young mice.

value: 5-6 months


title: 4hr sham partial hepatectomy old replicate 1


title: 4hr sham partial hepatectomy young replicate 1


title: SIL_M0059_1Mb_aCGH

tag: reference

value: pooled random donor samples peripheral blood lymphocytes


title: SIL_M0076_1Mb_aCGH


title: SIL_M0041_1Mb_aCGH


title: 2hr sham partial hepatectomy old replicate 2

description: Gene expression data from liver 2h after sham partial hepatectomy in old mice.

tag: gender


title: SIL_M0063_1Mb_aCGH


title: SIL_M0080_1Mb_aCGH


title: SIL_M0039_1Mb_aCGH


title: SIL_M0045_1Mb_aCGH


title: SIL_M0034_1Mb_aCGH


title: 2hr sham partial hepatectomy old replicate 1

tag: age


title: 2hr sham partial hepatectomy young replicate 2

description: Gene expression data from liver 2h after sham partial hepatectomy in young mice.


title: SIL_M0024_1Mb_aCGH

tag: tissue


title: miRNA expression in micro gravity for 8 d

value: micro gravity for 8 d


title: miRNA expression in micro gravity for 4 d

value: micro gravity for 4 d


title: 1hr sham partial hepatectomy old replicate 2

description: Gene expression data from liver 1h after sham partial hepatectomy in old mice.


title: SIL_M0016_1Mb_aCGH


title: 2hr sham partial hepatectomy young replicate 1


title: 1hr sham partial hepatectomy old replicate 1


title: 1hr sham partial hepatectomy young replicate 2

description: Gene expression data from liver 1h after sham partial hepatectomy in young mice.


title: SIL_M0001_1Mb_aCGH


title: 0.5hr sham partial hepatectomy old replicate 2

description: Gene expression data from liver 0.5h after sham partial hepatectomy in old mice.


title: BDC into NOD.RAG-/- (48 hrs.) 3

city: Saint Louis

first: Emil

last: Unanue

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

hyb_protocol: Affymetrix GeneChip® Fluidics Station 450

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G, GCOS

data_processing:
GCOS, Expression Console, and DNAStar Arraystar 4.0
affymetrix-algorithm-name = RMA
affymetrix-algorithm-version = 1.0
affymetrix-algorithm-param-Background correction method = RMA Background Correction
affymetrix-algorithm-param-Normalization method = Quantile
affymetrix-algorithm-param-Summarization method = Median polish

source_name: pancreatic islets of Langerhans, BDC T cell transfer into NOD.RAG-/- strain, 48 hrs.

label_protocol: Affymetrix® GeneChip® WT Sense Target Labeling

extract_protocol: Ambion RNAqeuous Micro Kit

tag: genotype/variation

value: RAG-/-

value: NOD

tag: organ

value: Pancreas


title: 1hr sham partial hepatectomy young replicate 1


title: BDC into NOD.IFNGR-/- (48 hrs.) 2

source_name: pancreatic islets of Langerhans, BDC T cell transfer into NOD.IFNGR-/- strain, 48 hrs.

value: IFNGR-/-


title: 0.5hr sham partial hepatectomy young replicate 1

description: Gene expression data from liver 0.5h after sham partial hepatectomy in young mice.


title: 0.5hr sham partial hepatectomy young replicate 2


title: 48h partial hepatectomy old replicate 2

description: Gene expression data from liver 48h after partial hepatectomy in old mice.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C to Affymetrix GeneChip Mouse Expression Array 4302. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

treatment_protocol: Mice were anesthetized by use of an intraperitoneal injection of avertin followed by supplementary inhalation of isoflurane.  Partial hepatectomy was performed by surgical removal of 70% of the liver mass or animals underwent sham surgeries whereby animals were subjected to similar surgical conditions, however their livers were not resected but merely manipulated.  Liver tissue was collected at  0, 24,38 and 48 hour(s) following surgery.

value: partial hepatectomy


title: 48h partial hepatectomy old replicate 1


title: 0.5hr sham partial hepatectomy old replicate 1


title: 4hr partial hepatectomy old replicate 3

description: Gene expression data from liver 4h after partial hepatectomy in old mice.


title: BDC into NOD.RAG-/- (48 hrs.) 2


title: BDC into NOD.RAG-/- (24 hrs.)

source_name: pancreatic islets of Langerhans, BDC T cell transfer into NOD.RAG-/- strain, 24 hrs.


title: 38h partial hepatectomy old replicate 2

description: Gene expression data from liver 38h after partial hepatectomy in old mice.


title: BDC into NOD.RAG-/- (48 hrs.) 1


title: 48h partial hepatectomy old replicate 3


title: 38h partial hepatectomy old replicate 1


title: 4hr partial hepatectomy old replicate 1


title: 4hr partial hepatectomy old replicate 2


title: B6.g7 splenocytes into NOD.RAG (24 hrs.)

source_name: pancreatic islets of Langerhans, B6.g7 splenocytes transfer into NOD.RAG-/- strain, 24 hrs.


title: 48h partial hepatectomy young replicate 1

description: Gene expression data from liver 48h after partial hepatectomy in young mice.


title: 24h partial hepatectomy old replicate 3

description: Gene expression data from liver 24h after partial hepatectomy in old mice.


title: 24h partial hepatectomy old replicate 2


title: 48h partial hepatectomy young replicate 2


title: 38h partial hepatectomy old replicate 3


title: BDC into NOD.IFNGR-/- (48 hrs.) 1


title: untreated purified beta cells

source_name: purified beta cells, NOD.RAG-/- strain, untreated


title: 24h partial hepatectomy old replicate 1


title: untreated NOD.RAG 3

source_name: pancreatic islets of Langerhans, NOD.RAG-/- strain, untreated


title: 38h partial hepatectomy young replicate 3

description: Gene expression data from liver 38h after partial hepatectomy in young mice.


title: BDC into NOD.IFNGR-/- (24 hrs.)

source_name: pancreatic islets of Langerhans, BDC T cell transfer into NOD.IFNGR-/- strain, 24 hrs.


title: untreated NOD.RAG 1


title: untreated NOD.RAG 2


title: 48h partial hepatectomy young replicate 3


title: 38h partial hepatectomy young replicate 2


title: 24h partial hepatectomy young replicate 3

description: Gene expression data from liver 24h after partial hepatectomy in young mice.


title: 4hr partial hepatectomy young replicate 3

description: Gene expression data from liver 4h after partial hepatectomy in young mice.


title: 4hr partial hepatectomy young replicate 2


title: 4hr partial hepatectomy young replicate 1


title: 2hr partial hepatectomy old replicate 1

description: Gene expression data from liver 2h after partial hepatectomy in old mice.


title: 2hr partial hepatectomy old replicate 3


title: 24h partial hepatectomy young replicate 1


title: 48h sham partial hepatectomy old replicate 1

description: Gene expression data from liver 48h after sham partial hepatectomy in old mice.


title: 24h partial hepatectomy young replicate 2


title: 3A9 into IP-HEL (24 hrs.) 2

source_name: pancreatic islets of Langerhans, 3A9 T cell transfer into insulin promoter HEL transgenic strain, 24 hrs.

value: insulin promoter HEL transgenic


title: 24h sham partial hepatectomy old replicate 1

description: Gene expression data from liver 24h after sham partial hepatectomy in old mice.


title: 3A9 into IP-HEL (24 hrs.) 3


title: 48h sham partial hepatectomy old replicate 2


title: 38h sham partial hepatectomy old replicate 1

description: Gene expression data from liver 38h after sham partial hepatectomy in old mice.


title: 2hr partial hepatectomy young replicate 3

description: Gene expression data from liver 2h after partial hepatectomy in young mice.


title: 3A9 into IP-HEL (8 hrs.)

source_name: pancreatic islets of Langerhans, 3A9 T cell transfer into insulin promoter HEL transgenic strain, 8 hrs.


title: 2hr partial hepatectomy young replicate 2


title: 2hr partial hepatectomy old replicate 2


title: 24h sham partial hepatectomy young replicate 1

description: Gene expression data from liver 24h after sham partial hepatectomy in young mice.


title: 3A9 into IP-HEL (24 hrs.) 1


title: untreated IP-HEL islets 1

source_name: pancreatic islets of Langerhans, insulin promoter HEL transgenic strain, untreated


title: 24h sham partial hepatectomy young replicate 2


title: 38h sham partial hepatectomy young replicate 1

description: Gene expression data from liver 38h after sham partial hepatectomy in young mice.


title: 38h sham partial hepatectomy old replicate 2


title: 2hr partial hepatectomy young replicate 1


title: 48h sham partial hepatectomy young replicate 1

description: Gene expression data from liver 48h after sham partial hepatectomy in young mice.


title: 3A9 into B10.BR (24 hrs.)

source_name: pancreatic islets of Langerhans, 3A9 T cell transfer into B10.BR strain, 24 hrs.

value: wildtype


title: untreated IP-HEL islets 2


title: 24h sham partial hepatectomy old replicate 2


title: 48h sham partial hepatectomy young replicate 2


title: 0hr control old replicate 2

description: Gene expression data from liver of 0h control old mice.


title: 1hr partial hepatectomy old replicate 2

description: Gene expression data from liver 1h after partial hepatectomy in old mice.


title: 0hr control old replicate 1


title: 0hr control young replicate 2

description: Gene expression data from liver of 0h control young mice.


title: 1hr partial hepatectomy old replicate 1


title: 0hr control young replicate 1


title: 1hr partial hepatectomy old replicate 3


title: 1hr partial hepatectomy young replicate 3

description: Gene expression data from liver 1h after partial hepatectomy in young mice.


title: Tg-3

city: Little Rock

middle: Allen

last: Helms

state: AR

address: 4301 W. Markham

department: Reynolds Center on Aging

institute: University of Arkansas for Medical Sciences

hyb_protocol: Each pair of wild-type and transgenic heart samples were hybridized to a miRCURY LNA mouse microRNA Array (version 10.0), which held 578 mature microRNA probes, as well as perfectly matched and mismatched probes for quality control.

scan_protocol: Agilent Microarray Scanner (Model G2565B)

data_processing: After signal amplification, the background was subtracted and normalized using LOWESS (Locally Weighted Scatter plot Smoothing) regression algorithm.

source_name: cardiac ventricles

label_protocol: Each pair of wild-type and transgenic heart samples were labeled with Hy3 and Hy5 fluorescent dyes.

growth_protocol: The wild-type FVB mice and the transgenic mice on FVB background ranged from age at 7 days to 6 months.

extract_protocol: All RNA samples were first isolated from the mouse cardiac ventricles using UltraSpec RNA Isolation Reagent. To clean mouse DNA contamination and enrich the small RNA fraction, the total RNA samples were purified using miRNeasy Mini kit (Qiagen) and RNase-free DNase I.

treatment_protocol: To study the effect of SRF level on cardiac gene expression and function in the mouse heart, we employed the cardiac-specific transgenic approach to increase the SRF protein level in one mouse model. The ventricular tissue samples used for the microRNA array analysis were obtained from 6-month-old wild-type mice and age-matched SRF-Tg mice. The RNA sample isolation and microRNA array were performed in triplets for both wild-type and transgenic mice.

value: SRF-Tg

value: FVB


title: Colon with SB1117 infection at 4day biological rep2

city: Rochester

first: Jun

last: Sun

state: MN

address: 575 Elmwood Ave

institute: university of rochester

description: Gene expression data from colon mucosa with salmonella SB1117 infection at 4day

hyb_protocol: Mouse cDNA was hybridized to the Mouse Gene 1.0 ST array, a microarray chip containing 28,000 sequenced mouse genes

scan_protocol: the array was washed and stained with streptavidin-phycoerythrin, and scanned in a proprietary Affymetrix scanner, according to the GeneChip® Whole Transcript Sense Target Labeling Assay manual.

data_processing: The data were processed with Expression Console (Affymetrix) using the PLIER algorithm.

source_name: colon mucosa with salmonella SB1117 infection at 4days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Animal experiments were performed using specific-pathogen-free female C57BL/6 mice (Taconic, Hudson, NY) that were 6-7 weeks old.  Water and food were withdrawn 4 h before oral gavage with 7.5 mg/mouse of streptomycin. Afterwards, animals were supplied with water and food. Twenty hours after streptomycin treatment, water and food were withdrawn again for 4 hours before the mice were infected with 1x107 CFU of S. Typhimurium (100µl suspension in HBSS) or treated with sterile HBSS (control) by oral gavage as previously described

tag: sex

value: female

value: intestinal colon mucosa


title: 0hr control old replicate 3

value: 25-27 months

value: male


title: Tg-1


title: Tg-2


title: 1hr partial hepatectomy young replicate 2

value: 5-6 months


title: 1hr partial hepatectomy young replicate 1


title: Colon with SL1344 infection at 4day biological rep3

description: Gene expression data from colon mucosa with salmonella SL1344 infection at 4day

source_name: colon mucosa with salmonella SL1344 infection at 4days


title: 0.5hr partial hepatectomy old replicate 3

description: Gene expression data from liver 0.5h after partial hepatectomy in old mice.


title: Colon with SB1117 infection at 4day biological rep1


title: nTg-2

value: wild type


title: 0hr control young replicate 3


title: 0.5hr partial hepatectomy old replicate 2


title: Control at 4day biological rep3

description: Gene expression data from colon mucosa at 4day

source_name: colon mucosa at 4day


title: A549 GFP Control Replicate 2

description:
Biological replicate 2 of 2.  Control cells.
A549 GFP Control Replicate 2_LogRatio

hyb_protocol: Approximately 800ng of both Cy5-labeled experimental cRNA and Cy3-labeled universal reference RNA were hybridized to each microarray (adjusting for labeling efficiency).

scan_protocol: Images were captured using an Agilent DNA microarray scanner set at default settings for gene expression.

data_processing: Scanned images were processed using Feature Extractor v. 10.5.1.1. By applying a LOWESS (locally weighted linear regression) correction for dye-bias, background noise was subtracted from spot intensities. To filter the preprocessed data, genes with a background signal higher than feature signal were removed.

source_name: A549 cells with GFP control vector

label_protocol: A quick-amplification kit (Agilent, Santa Clara, CA) was used to amplify and label 500 ng target mRNA species to complementary RNA (cRNA) for oligo microarrays according to the manufacturer’s protocol. For each array, experimental samples were run in duplicate along with a commercial universal reference RNA (Stratagene, La Jolla, CA) were labeled with cyanine 5-CTP and cyanine-3-CTP (Perkin Elmer, Boston, MA), respectively. cRNA concentration and labeling efficiency was measured spectrophotometrically.

growth_protocol: For each experimental sample, 3 x 10^5 cells were seeded in duplicate using standard growth conditions and grown for 24 hours before total RNA isolation.

extract_protocol: Total RNA was isolated according to manufacturer’s protocol (mirVana miRNA Isolation Kit, Ambion, Austin, TX). Total RNA yield was assessed using a NanoDrop 2000c (Thermo Scientific, Wilmington, DE), and quality was assessed on a BioAnalyzer 2400 using a BioAnalyzer RNA 6000 Nano LabChip Kit (Agilent Technologies, Palo Alto, CA).

tag: cell line

value: NSCLC Cell Line A549

tag: protocol

value: CTRL

source_name: Universal reference RNA

value: Universal reference RNA


title: A549 miR-328 Replicate 1

description:
Biological replicate 1 of 2.  miR-328 overexpressing cells.
A549 miR-328 Replicate 1_LogRatio

source_name: A549 cells with miR-328 vector

value: miR-328 overexpression


title: nTg-3


title: A549 GFP Control Replicate 1

description:
Biological replicate 1 of 2.  Control cells.
A549 GFP Control Replicate 1_LogRatio


title: Colon with SL1344 infection at 4day biological rep1


title: 38h partial hepatectomy young replicate 1

description: Gene expression data from liver 38h after partial hepatectomy in young mice.

source_name: liver


title: nTg-1


title: 0.5hr partial hepatectomy old replicate 1


title: Colon with SL1344 infection at 4day biological rep2


title: 0.5hr partial hepatectomy young replicate 3

description: Gene expression data from liver 0.5h after partial hepatectomy in young mice.


title: Control at 4day biological rep2


title: Control at 4day biological rep1


title: Spr_biol_repl2

city: Basel

first: Robert

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: Biological replicate 2 of 3.

hyb_protocol: Following fragmentation, 7.5 ug of single-stranded DNA was hybridized for 16 hr at 45C on  Affymetrix GeneChip® Mouse Tiling 2.0R B Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Sequences of the 25 nt long probes were aligned to the chromosomal positions (UCSC genome build mm9) using MUMmer(http://mummer.sourceforge.net/). Only probes with one perfect match and no near-match (match of 23 or 24 nts) were left. We also filtered out the probes arising from the reverse strand and/or matching chromosomes other than X,Y,2 or the mitochondrial genome. Intensities of remaining probes were quantile normalized and analyzed using R (http://www.r-project.org/). Chromosomal localizations of individual probes with normalized log2 intensities are in the resulting BED files. LogFC values of Spr v. B6 comparison together with P values were calculated using limma package from Biconductor (www.bioconductor.org). The P values were adjusted using Benjamini & Hochberg correction. Chromosomal localizations of the probes together with logFC and adjusted P values are in the Spr_v_B6.bed file, which is linked to the Series GSE19633 record as a supplementary file.

organism: Mus spretus

source_name: spretus

label_protocol: 2 ug total RNA was used to prepare biotinylated single-stranded target by modification of the Affymetrix protocol (Whole Transcript (WT) Double-Stranded Target Assay Manual, 702179 Rev. 3, Affymetrix), where the synthesis of second-strand cDNA was omitted in the final step.

extract_protocol: Total RNA was isolated from the testes of individual mice using the RNeasy Mini kit (Qiagen) according to manufacturer's instructions.

value: 2 months

value: testes


title: Spr_biol_repl3

description: Biological replicate 3 of 3.


title: 0.5hr partial hepatectomy young replicate 2

value: partial hepatectomy


title: Colon with SB1117 infection at 8hr biological rep3

description: Gene expression data from colon mucosa with salmonella SB1117 infection at 8hr


title: 0.5hr partial hepatectomy young replicate 1


title: Spr_biol_repl1

description: Biological replicate 1 of 3.


title: Colon with SB1117 infection at 8hr biological rep2

source_name: colon mucosa with salmonella SB1117 infection at 8hr


title: 0hr control old replicate 2


title: Colon with SB1117 infection at 8hr biological rep1


title: 0hr control old replicate 1


title: B6_biol_repl3

description: Biological replicate 3 of 3.

organism: Mus musculus domesticus


title: 0hr control old replicate 3