title: CA1 Reconsolidation-impaired, biological rep4


title: CA1 Reconsolidation, biological rep2

status: Public on Sep 25 2015

type: RNA

city: Cardiff

first: Kerrie

middle: L

last: Thomas

state: Wales

address: Maindy Road

department: Neuroscience & Mental Health Research Institute, & Cardiff School of Biosciences

country: United Kingdom

institute: Cardiff University

hyb_protocol: RNA quality was assessed spectrophotometrically on an Agilent Bioanalyser (Agilent Technologies). Only samples with a RNA Integrity Number (RIN) of 8/10 or more went forward for hybridization to Affymetrix GeneChip Rat Genome 230 2.0 Arrays (Agilent Technologies ) according to the manufacturer’s protocol at the Central Biotechnology Service, Cardiff University, UK. No amplification steps were performed before cDNA synthesis before hybridization because RNA extracted form the individual CA1 samples met the 1 to 5 lg total RNA requirement for the reverse transcription step and subsequent hybridization to the Affymetrix array.

scan_protocol: Agilent GeneChip 3000 scanner.

data_processing: Raw intensity data from each microarray were normalized to expression values using MAS5.0. Analysed with Agilent GCOS 1.4.

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: CA1 2 hr Reconsolidation ZIFMSO

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

growth_protocol: In vivo whole organism.

extract_protocol: Total RNA was isolated with RNeasy (Qiagen Ltd).  Approximately 8 microgramsof total RNA per dorsal CA1 was obtained from one rat.

treatment_protocol: Bilateral microinfusions (1 microlitre/hemisphere) of 2 nmol/microlitre Zif268 antisense ODN (ZIFASO, 5’- GGTAGTTGTCCATGGTGG -3’ in PBS, pH 7.4) or Zif268 missense ODN were (ZIFMSO, 5’ - GTGTTCGGTAGGGTGTCA -3’ in PBS, pH 7.4) into the dorsal hippocampus (AP -3.50, relative to bregma) were given 90 min before a 2 min recall of contextual fear memory. Infusions were made in awake rats via previously surgically implanted indwelling stainless steel cannula. The dorsal CA1 was microdissected 2 hr after recall.

tag: strain

value: Lister hooded

tag: gender

value: Male

tag: age

tag: task

value: Contextual fear conditioning (CFC)

tag: interval cfc and recall

value: 48 hours

tag: recall duration

value: 2 minutes

tag: brain region

tag: time after recall

value: 2 hours

tag: treatment

value: ZIFMSO


title: CA1 Reconsolidation-impaired, biological rep2

source_name: CA1 2 hr Reconsolidation Control ZIFASO

value: ZIFASO


title: CA1 Reconsolidation, biological rep8


title: CA1 No extinction (NOR), biological rep5

source_name: CA1 2 hr 10 min CS- No recall CFM

extract_protocol: Total RNA was isolated with RNeasy (Qiagen Ltd).  Approximately 8 micrograms of total RNA per dorsal CA1 was obtained from one rat.

treatment_protocol: Rats habituated to two different contexts were CFC in one of the two contexts. 48hr after CFC rats were either exposed to the conditioned context (CS+) or the other context (CS-) for 10 min. The dorsal CA1 was microdissected 2 hr after context re-exposure.

value: 10 minutes

tag: time after reexposure

value: CS-


title: CA1 Reconsolidation, biological rep4


title: CA1 Reconsolidation-impaired, biological rep6


title: CA1 Reconsolidation, biological rep6


title: CA1 Reconsolidation-impaired, biological rep1


title: WT MG1655

city: New York

first: Gregory

last: Boel

state: NY

address: 1212 Amsterdam Ave.

department: Biological Sciences

country: USA

institute: Columbia University

description: Gene expression data from Escherichia coli in late exponential growth

hyb_protocol: Biotinylated cDNA was hybridized on Affymetrix E. coli 2.0 arrays by the Gene Expression Center at the University of Wisconsin Biotechnology Center.

scan_protocol: standard Affymetrix protocol

label: biotin

organism: Escherichia coli

label_protocol: Biotinylation was performed with Terminal Deoxynucleotidyl Transferase (New England Biolabs) and Biotin-N6-ddATP (Enzo Life Sciences).

growth_protocol: E. coli MG1655 cells were cultured in M9 0.4 % glucose minimum media to a final OD600 of 1.0.

extract_protocol: RNA were extracted using the RNeasy Mini Kit (Qiagen) was reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen) followed by treatment with RNaseH (Invitrogen) and RNaseA (EpiCentre). The resulting cDNA preparation was purified using the MinElute Purification Kit (Qiagen) and then fragmented into 50 200 bp fragments using DNaseI (EpiCentre).

treatment_protocol: Cells were treated with RNA Protect Bacteria Reagent (Qiagen).


title: CA1 Reconsolidation, biological rep3


title: CA1 Reconsolidation-impaired, biological rep7


title: CA1 Reconsolidation-impaired, biological rep8


title: CA1 Reconsolidation, biological rep5


title: CA1 Extinction (EXT), biological rep6

source_name: CA1 2 hr 10 min CS+ Recall CFM

value: CS+


title: CA1 No extinction (NOR), biological rep4


title: CA1 Consolidation, biological rep8

source_name: CA1 2 hr Consolidation BDNFMSO

treatment_protocol: Bilateral microinfusions (1 microlitre/hemisphere) of 2 nmol/microlitre BDNF antisense ODN (BDNFASO, 5’-TCTTCCCCTTTTAATGGT-3’ in PBS, pH 7.4) or BDNF missense ODN (BDNFMSO, 5’ -ATACTTTCTGTTCTTGCC-3’ in PBS, pH 7.4) into the dorsal hippocampus (AP -3.50, relative to bregma) were made 90 min before  3min contextual fear conditioning (CFC) training. Infusions were made in awake rats via previously surgically implanted indwelling stainless steel cannula. The dorsal CA1 was microdissected 2 hr after CFC.

tag: time after cfc

value: BDNFMSO


title: CA1 No extinction (NOR), biological rep2


title: CA1 Extinction (EXT), biological rep5


title: CA1 Extinction (EXT), biological rep3


title: CA1 Extinction (EXT), biological rep4


title: CA1 Extinction (EXT), biological rep2


title: CA1 Extinction (EXT), biological rep1


title: CA1 No extinction (NOR), biological rep1


title: CA1 Consolidation, biological rep7


title: CA1 Consolidation, biological rep6


title: CA1 Consolidation-impaired, biological rep7

source_name: CA1 2 hr Consolidation Control BDNFASO

value: BDNFASO


title: CA1 Consolidation, biological rep1


title: CA1 Consolidation, biological rep2


title: CA1 Consolidation, biological rep5


title: CA1 Consolidation-impaired, biological rep6


title: CA1 Consolidation, biological rep4


title: CA1 Consolidation-impaired, biological rep2


title: CA1 Consolidation-impaired, biological rep3


title: CA1 Consolidation-impaired, biological rep1


title: CA1 Consolidation-impaired, biological rep8


title: CA1 Consolidation-impaired, biological rep5


title: CA1 Consolidation, biological rep3


title: Lung_Squamous_Carcinoma_Survival_Patient63

city: Beijing

first: Ning

last: An

address: NO.17 Pan Jiayuan Nan Li, Chao Yang District

country: China

institute: Chinese academy of medical sciences

description: Gene expression of lung squamous carcinoma survival patient

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Normalized expression data were extracted with R package “limma” using cyclic loess method, and the ComBat algorithm was utilized to eliminate potential batch effects

organism: Homo sapiens

source_name: Lung Squamous Carcinoma Survival Tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from frozen tissues using the TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s specifications. RNA integrity was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). If the RNA integrity number was greater than or equal to 6.5, the total RNA was purified using the RNeasy Mini Kit (Cat No.74106, Qiagen, Germany). The RNA concentration was determined with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, USA).

tag: tissue

value: Cancer survival tissue

tag: smoking index (package*year)

tag: tnm

tag: Stage

tag: survival (year)

tag: events (death = 1, alive = 0)


title: Lung_Squamous_Carcinoma_Survival_Patient67


title: Lung_Squamous_Carcinoma_Survival_Patient62


title: Lung_Squamous_Carcinoma_Survival_Patient69


title: Lung_Squamous_Carcinoma_Survival_Patient59


title: Lung_Squamous_Carcinoma_Survival_Patient57


title: Lung_Squamous_Carcinoma_Survival_Patient56


title: Lung_Squamous_Carcinoma_Survival_Patient58


title: Lung_Squamous_Carcinoma_Survival_Patient60


title: Lung_Squamous_Carcinoma_Survival_Patient68


title: CA1 Consolidation-impaired, biological rep4

tag: strain


title: Lung_Squamous_Carcinoma_Survival_Patient64

tag: gender


title: Lung_Squamous_Carcinoma_Survival_Patient66

tag: age


title: Lung_Squamous_Carcinoma_Survival_Patient65


title: Lung_Squamous_Carcinoma_Survival_Patient61


title: Lung_Squamous_Carcinoma_Survival_Patient55


title: Lung_Squamous_Carcinoma_Survival_Patient54

value: Female


title: Lung_Squamous_Carcinoma_Survival_Patient50


title: Lung_Squamous_Carcinoma_Survival_Patient47


title: Lung_Squamous_Carcinoma_Survival_Patient53


title: Lung_Squamous_Carcinoma_Survival_Patient45


title: Lung_Squamous_Carcinoma_Survival_Patient48


title: Lung_Squamous_Carcinoma_Survival_Patient51


title: Lung_Squamous_Carcinoma_Survival_Patient44


title: Lung_Squamous_Carcinoma_Survival_Patient41


title: Lung_Squamous_Carcinoma_Survival_Patient29


title: Lung_Squamous_Carcinoma_Survival_Patient52


title: Lung_Squamous_Carcinoma_Survival_Patient46


title: Lung_Squamous_Carcinoma_Survival_Patient43


title: Lung_Squamous_Carcinoma_Survival_Patient42


title: Lung_Squamous_Carcinoma_Survival_Patient34


title: CA1 No extinction (NOR), biological rep3

tag: task


title: Lung_Squamous_Carcinoma_Survival_Patient26


title: Lung_Squamous_Carcinoma_Survival_Patient49


title: Lung_Squamous_Carcinoma_Survival_Patient28


title: Lung_Squamous_Carcinoma_Survival_Patient31


title: Lung_Squamous_Carcinoma_Survival_Patient32


title: Lung_Squamous_Carcinoma_Survival_Patient30


title: Lung_Squamous_Carcinoma_Survival_Patient36


title: Lung_Squamous_Carcinoma_Survival_Patient33


title: Lung_Squamous_Carcinoma_Survival_Patient38


title: Lung_Squamous_Carcinoma_Survival_Patient35


title: Lung_Squamous_Carcinoma_Survival_Patient39


title: Lung_Squamous_Carcinoma_Survival_Patient25


title: Lung_Squamous_Carcinoma_Survival_Patient40


title: Lung_Squamous_Carcinoma_Survival_Patient27


title: Lung_Squamous_Carcinoma_Survival_Patient37


title: Lung_Squamous_Carcinoma_Survival_Patient24


title: Lung_Squamous_Carcinoma_Survival_Patient23


title: Lung_Squamous_Carcinoma_Survival_Patient19


title: Lung_Squamous_Carcinoma_Survival_Patient13


title: Lung_Squamous_Carcinoma_Survival_Patient16


title: Lung_Squamous_Carcinoma_Survival_Patient17


title: Lung_Squamous_Carcinoma_Survival_Patient20


title: Lung_Squamous_Carcinoma_Survival_Patient21


title: Lung_Squamous_Carcinoma_Survival_Patient18


title: Lung_Squamous_Carcinoma_Survival_Patient15


title: Lung_Squamous_Carcinoma_Survival_Patient11


title: Lung_Squamous_Carcinoma_Survival_Patient12


title: Lung_Squamous_Carcinoma_Survival_Patient22


title: Lung_Squamous_Carcinoma_Survival_Patient14


title: Nanos2_conditional_overexpression_Germline_stem_cells_treated_with_4-Tamoxifen_1

city: Mishima

first: ZHI

last: ZHOU

address: Yata 1111

department: Division of Mammalian Development

country: Japan

institute: National Institute of Genetics, Japan

description: gene expression after 48hours incubation with DMSO or Tamoxifen

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: cultured Germline stem cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.20 µg RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mouse embryonic fibroblasts (MEFs) derived from C57Bl6 embryos (isolated at day 13.5 post-coitum) were used as feeders for GSC culture. MEF cells treated with mitomycin-C were plated on 0.1% gelatin-coated dishes before GSCs culture. GSCs medium was as previously described. Major growth factors are as followed: rat GDNF (20ng/ml, R&D systems), mouse EGF (20ng/ml, BD Bioscience) and human FGF2 (10ng/ml, Life Technology). For inducing CRE (Rose-CRE-ERT2 knockin mouse) activity in GSCs, 4-Hydroxytamoxifen was added in GSC medium for 48hours.

extract_protocol: Total RNA was extracted with RNeasy mini kit  (QIAGEN, Valencia, CA) according to the manufacture's protocol.

treatment_protocol: Nanos2 cOE GSCs were cultured with DMSO(control) or Tamoxifen (overexpression) for 48 hours. Feeder cells were removed before total RNA extraction.

tag: cell type

value: germline stem cells

value: testis

tag: Sex

value: male


title: Nanos2_conditional_overexpression_Germline_stem_cells_treated_with_DMSO_2


title: Lung_Squamous_Carcinoma_Survival_Patient5

value: Male


title: Lung_Squamous_Carcinoma_Survival_Patient8


title: Lung_Squamous_Carcinoma_Survival_Patient9


title: Lung_Squamous_Carcinoma_Survival_Patient10


title: Lung_Squamous_Carcinoma_Survival_Patient4


title: Lung_Squamous_Carcinoma_Survival_Patient7


title: Nanos2_conditional_overexpression_Germline_stem_cells_treated_with_DMSO_1


title: Nanos2_conditional_overexpression_Germline_stem_cells_treated_with_4-Tamoxifen_2


title: P7_male_testis_Tg-3xFLAG-Nanos2-3'UTR_FLAG IP_1

description: Gene expression E14.5 mouse male gonad Tg-3xFLAG-Nanos2-3'UTR

source_name: postnatal testis

treatment_protocol: Testes were disected in ice-cold PBS and were immeadiately frozen in RNAlater (Ambion). Frozen tissues were stored at -80 degree until total RNA extraction.

tag: postnatal days

tag: genotype

value: Tg-Nanos2 enhancer-3xFLAG-Nanos2-3'UTR


title: P7_male_testis_Tg-3xFLAG-Nanos2-3'UTR_FLAG IP_2


title: Lung_Squamous_Carcinoma_Survival_Patient6


title: P7_male_testis_Tg-3xFLAG-Nanos2-3'UTR_Input_2


title: Lung_Squamous_Carcinoma_Survival_Patient2


title: P7_male_testis_Tg-3xFLAG-Nanos2-3'UTR_Input_1


title: MV411_CA_3hrs_rep3

city: Cambridge

first: Matthew

middle: D.

last: Shair

state: MA

address: 12 Oxford Street

department: Chemistry and Chemical Biology

institute: Harvard University

description: 500,000-800,000 cells were treated with 25nM CA for 3hrs

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G Plus.

data_processing: Arrays were corrected for background, normalized and log2-transformed using the rma function of the affy Bioconductor package.

source_name: MV411 cells, CA, 3hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using the GeneChip 3' IVT Express Kit from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MV4;11 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol: RNA was isolated (RNeasy Plus Microkit, Qiagen or TRIzol, Life Technologies), processed, and hybridized to the Human U133 Plus 2.0 microarray (Affymetrix).

treatment_protocol: Cells were plated (12-well) in triplicate at 500,000 to 800,000 cells/mL and incubated in the presence of DMSO or 25nM CA for 3hrs. Cells were then washed twice with cold PBS, and snap frozen.

tag: cell line

tag: treatment

value: 25nM CA for 3hrs

value: MLL-AF4-rearranged AML


title: Lung_Squamous_Carcinoma_Survival_Patient3


title: Lung_Squamous_Carcinoma_Survival_Patient1


title: MV411_CA_3hrs_rep1


title: MV411_DMSO_3hrs_rep3

description: 500,000-800,000 cells were treated with DMSO for 3hrs

source_name: MV411 cells, DMSO, 3hrs

value: DMSO


title: MOLM14_CA_3hrs_rep2

source_name: MOLM14 cells, CA, 3hrs

growth_protocol: MOLM-14 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

value: MLL-AF9-rearranged AML


title: MV411_DMSO_3hrs_rep1


title: MOLM14_CA_3hrs_rep1


title: MV411_DMSO_3hrs_rep2


title: MOLM14_DMSO_3hrs_rep2

source_name: MOLM14 cells, DMSO, 3hrs


title: MOLM14_CA_3hrs_rep3


title: MOLM14_DMSO_3hrs_rep3


title: MOLM14_CA_24hrs_rep2

description: 500,000-8000,00 cells were treated with 10nM CA for 24hrs

source_name: MOLM14 cells, CA, 24hrs

treatment_protocol: Cells were plated (12-well) in triplicate at 500,000 to 800,000 cells/mL and incubated in the presence of DMSO or 10nM CA for 24hrs. Cells were then washed twice with cold PBS, and snap frozen.

value: 10nM CA for 24hrs


title: MV411_CA_3hrs_rep2


title: MOLM14_DMSO_24hrs_rep3

description: 500,000-8000,00 cells were treated with DMSO for 24hrs

source_name: MOLM14 cells, DMSO, 24hrs


title: MOLM14_DMSO_3hrs_rep1


title: MOLM14_CA_24hrs_rep3


title: 4_MDA-MB-231-FOXC1_(HuGene-1_0-st-v1).plier-gene-default-Signal, biological rep2

city: LOS ANGELES

first: Xiaojiang

last: Cui

state: CA

address: 8700 BEVERLY BLVD

department: SURGERY

institute: CEDARS SINAI MEDICAL CENTER

description:
MDA-MB-231 cells transfected with FOXC1
4_MDA-MB-231-FOXC1_(HuGene-1_0-st-v1).plier-gene-default-Signal

hyb_protocol: Affymetrix GeneChip Human Gene 1.0 ST arrays were hybridized with 10 µg of labeled sense DNA, washed and stained according to the protocol

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip® System.

data_processing: Expression Console software; PLIER algorithm

source_name: FOXC1-overexpressing MDA-MB-231

label_protocol: 100 ng of total RNA were amplified and labeled using the Affymetrix Whole-Transcript Sense Target Labeling Protocol.

growth_protocol: The cells were cultured in DMEM medium, supplemented with 10% FBS, 50IU/ml penicillin, and 50µg/ml streptomycin.

extract_protocol: The total RNA were extracted by RNeasy kit (Qiagen).

treatment_protocol: The cells were transfected with Vector or FOXC1 plasmid using Lipo2000 transfection reagent.

value: Breast cancer cell

tag: transfected with


title: MOLM14_DMSO_24hrs_rep1


title: MOLM14_CA_24hrs_rep1


title: MOLM14_DMSO_24hrs_rep2


title: 3_MDA-MB-231-FOXC1_(HuGene-1_0-st-v1).plier-gene-default-Signal, biological rep1

description:
MDA-MB-231 cells transfected with FOXC1
3_MDA-MB-231-FOXC1_(HuGene-1_0-st-v1).plier-gene-default-Signal


title: K562_CA_3hrs_rep3

source_name: K562 cells, CA, 3hrs

growth_protocol: K562 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

value: chronic myelogenous leukemia (CML)


title: 1_MDA-MB-231-VECTOR_(HuGene-1_0-st-v1).plier-gene-default-Signal, biological rep1

description:
MDA-MB-231 cells transfected with Vector
1_MDA-MB-231-VECTOR_(HuGene-1_0-st-v1).plier-gene-default-Signal

source_name: Vector-expressing MDA-MB-231

value: vector


title: K562_CA_3hrs_rep2


title: 2_MDA-MB-231-VECTOR_(HuGene-1_0-st-v1).plier-gene-default-Signal, biological rep2

description:
MDA-MB-231 cells transfected with Vector
2_MDA-MB-231-VECTOR_(HuGene-1_0-st-v1).plier-gene-default-Signal


title: K562_DMSO_3hrs_rep2

source_name: K562 cells, DMSO, 3hrs


title: K562_CA_3hrs_rep1


title: K562_DMSO_3hrs_rep3


title: K562_DMSO_3hrs_rep1


title: SKBR-3 1uM PF04554878/5uM Lapatinib #2

city: buffalo

first: Dan

last: Wang

address: Elm & Carlton Streets

institute: RPCI

description: DefaultGroup

hyb_protocol: The labeled probes were then mixed with hybridization reagents and hybridized overnight to the HumanHT12 v4 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files are analyzed with Illumina’s GenomeStudio gene expression module (V1.9.0)

source_name: Breast cancer cells treated with FAK inhibitor PF04554878 and Lapatinib

label_protocol: Initially, we converted 250-500 ng total RNA to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA (Illumina TotalPrep RNA Amplification Kit, Ambion Inc., Austin, TX).

extract_protocol: Total RNA was isolated from frozen tissue samples using TRIZOL reagent (Invitrogen).

value: breast cancer


title: SKBR-3 1uM PF04554878/5uM Lapatinib #1

description: DefaultGroup


title: SKBR-3 5uM Lapatinib #2

description: DefaultGroup

source_name: Breast cancer cells treated with HER-2/EGFR kinase inhibitor, Lapatinib


title: SKBR-3 1uM PF04554878 #1

description: DefaultGroup

source_name: Breast cancer cells treated with FAK inhibitor PF04554878


title: SKBR-3 1uM Y15/5uM Lapatinib #3

description: DefaultGroup

source_name: Breast cancer cells treated with FAK inhibitor and Her-2/EGFR inhibitor Lapatinib


title: SKBR-3 untreated #1

description: DefaultGroup

source_name: Breast cancer cells untreated


title: SKBR-3 untreated #2

description: DefaultGroup


title: SKBR-3 1uM Y15 #1

description: DefaultGroup

source_name: Breast cancer cells treated with FAK inhibitor Y15


title: SKBR-3 1uM PF04554878 #2

description: DefaultGroup


title: SKBR-3 1uM Y15 #2

description: DefaultGroup

source_name: Breast cancer cells treated with FAK inhibitor y15


title: SKBR-3 1uM Y15/5uM Lapatinib #1

description: DefaultGroup


title: Vehicle_10_nM_E2_1_05012014_(HTA-2.0)

city: Madison

first: Hao

last: Zeng

state: WI

address: 1111 Highland Ave

department: Department of Oncology

institute: University of Wisconsin Madison

hyb_protocol: According to the standard Affymetrix protocol

data_processing:
Using the Affymetrix Transcriptome Analysis Console software
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

extract_protocol: Qiagen RN easy Plus Kit

value: breast cancer cell line

tag: genotype/variation

tag: pre-treated with

value: none (absence of Dox)

tag: treated with

value: 10 nM E2 for 4 hrs


title: Dox_DMSO_3_05012014_(HTA-2.0)

scan_protocol: According to the standard Affymetrix protocol

value: 500 ng/ml Dox

value: DMSO for 4 hrs


title: Vehicle_DMSO_1_05012014_(HTA-2.0)

label_protocol: According to the standard Affymetrix protocol


title: Dox_DMSO_1_05012014_(HTA-2.0)


title: SKBR-3 5uM Lapatinib #1

description: DefaultGroup


title: Vehicle_10_nM_E2_2_05012014_(HTA-2.0)


title: Vehicle_DMSO_3_05012014_(HTA-2.0)


title: Dox_10_nM_E2_3_05012014_(HTA-2.0)


title: Vehicle_10_nM_E2_3_05012014_(HTA-2.0)


title: Vehicle_DMSO_2_05012014_(HTA-2.0)


title: Dox_DMSO_2_05012014_(HTA-2.0)


title: Dox_10_nM_E2_2_05012014_(HTA-2.0)


title: Dox_10_nM_E2_1_05012014_(HTA-2.0)


title: Cre estradiol sample 5

city: Indianapolis

first: Jeanette

middle: Nance

last: McClintick

state: IN

address: 635 Barnhill Dr.

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

description: Sample name: BG01M018

hyb_protocol: each samples was hybridized to a mouse Gene 2.0 array using the standard Affymetrix protocol

scan_protocol: Scanned using the affymetrix GS3000x using Affymetrix Command Console (AGCC)

data_processing:
Cel files were generated by AGCC and imported into Partek Genomics Suite (6.6) RMA (robust multi-array average) signals were generated using the RMA background correction, Quantile normalization and summarization by Median Polish. RMA data was log base 2 transformed.
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

source_name: lung

label_protocol: 100ng of RNA from each sample was labeled using the Ambion WT Expression kit and the Affymetrix WT Terminal Labeling kit

extract_protocol: CMV samples flash frozen, Cre collected in RNAlater, both extracted by Trizol and DNase treated

treatment_protocol: Mice were ovariectomized and Silastic capsules containing either crystalline E2 or cholesterol were implanted sc.  One week later the mice were treated with AdeCre or AdeCMV (empty vector).  Four weeks later the mice were exsanguinated by dissection of the abdominal aorta while under anesthesia and their lungs were harvested

tag: vector

value: AdeCre

value: estradiol


title: Cre estradiol sample 4

description: Sample name: BG01M017


title: Cre control sample 5

description: Sample name: BG01M013

value: Control


title: untreated cells grown in full media [C3]

city: Cleveland

first: Liraz

last: Levi

state: OH

address: 9500 Euclid Avenue

department: Cellular and Molecular Medicine

institute: Lerner Research Institute; Cleveland Clinic

description: Gene expression data from NaF cell in response to different PPARd and RAR treatments

hyb_protocol: Hybridization was done using the standard Affymetrix' WT labeling kit and protocol.

scan_protocol: Hybridized arrays were automatically stained and scanned with the Affymetrix standard GeneTitan protocols.

data_processing: data was processed using Partek-Genomics-Suite (PGS) v6.6 software (Qiagene).

source_name: NaF cells grown in DMEM with 10% FBS

label_protocol: Biotinylated-cRNA was synthesized form total RNA samples and labeled using the Affymetrix IVT labeling protocol.

growth_protocol: NaF cells were grown in full media (DMEM 10% FBS). 48 hours before ligand treatment media was replaced to DMEM containing 10% charcoal-treated FBS. Palmitate treatment was done in full media and samples were compared to full growth-media -grown control (samples C1-C3).

extract_protocol: RNA was extracted using Qiazol than cleaned using RNAeasy columns (Qiagene)

treatment_protocol: Cells were treated with ligands for 6 hours

value: NaF


title: untreated cells grown in full media [C1]


title: Cre estradiol sample 2

description: Sample name: BG01M015


title: cells grown in full media treated with palmitate [PA2]

source_name: NaF cells grown in DMEM with 10% FBS and treated with palmitate (10uM) for 6 hours


title: Cre control sample 4

description: Sample name: BG01M012


title: cells treated with RAR agonist, TTNPB [TTNPB2]

source_name: NaF cells grown in charcoal-treated FBS (10%) DMEM and treated with TTNPB (1uM) for 6 hours


title: cells grown in full media treated with palmitate [PA1]


title: cells treated with RAR agonist, TTNPB [TTNPB3]


title: CMV estradiol sample 4

description: Sample name: BG01M008

value: AdeCMV (empty vector)


title: Cre estradiol sample 1

description: Sample name: BG01M014


title: Cre control sample 3

description: Sample name: BG01M011


title: ZZ_Ko_9_120

status: Public on Sep 24 2015

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

country: Germany

institute: Saarland University

hyb_protocol: The microarrays, that contain 40 replicates of each of the 1,205 miRNAs of miRBase v16 (http://www.mirbase.org/) were hybridized with the labeled miRNA for 20 hours at 55°C and 20rpm.

scan_protocol: Agilent C Scanner, Agilent Scan Control Software

data_processing: Feature Extraction Software, summarizing of technical replicates by median and quantile normalization. Batch effect correction with ComBat R package.

source_name: RNA from plasma

label_protocol: A total of 100 ng total RNA was processed using the miRNA Complete Labeling and Hyb Kit (Agilent, CatNo 5190-0456) to generate fluorescently (cyanine-3) labeled miRNA

extract_protocol: We first treated 100µl plasma with 10µg Heparinase I (Sigma) and 100U RNaseOUTTM (Life Technologies, CatNo 10777-019) and incubated the mixture at 25°C for 1 hour. Nuclease free water (Life Technologies, CatNo AM9932) was added to a final volume of 250µl. A total of 750µl TRIzolLS (Life Technologies, CatNo 10296-028) was added and incubated at RT for 5 min. Then, 20µg glycogen, 5µl spike-in miRNA (miRNA mimic syn-cel-miR-39, 5nM, Qiagen),  and 200µl chloroform were added and incubated for 3 min at RT. After centrifugation at 14000rpm and 4°C, the watery phase was transferred into a new tube and RNA was precipitated with 1,5 volumes of 100% ethanol. RNA was then isolated using the miRNeasy Mini Kit (Qiagen, CatNo 217004) according to manufacturers instructions but with the use of the RNeasy Mini Elute column to allow for a reduced elution volume of 15µl.

treatment_protocol: Blood of lung cancer patients was drawn directly before tumor resection (TP1), ~ two weeks after tumor resection (TP2) and then ~ three months (TP3), six months (TP4), nine months (TP5), 12 months (TP6), 15 months (TP7) and 18 months (TP8) after tumor resection.  Stored at -20 degree

tag: tissue

value: plasma

tag: disease

value: non-cancerous lung disease (control)

tag: patient id

tag: timepoint


title: cells treated with RAR agonist, TTNPB [TTNPB1]


title: cells treated with retinoic acid [RA3]

source_name: NaF cells grown in charcoal-treated FBS (10%) DMEM and treated with all-trans retinoic acid (1uM) for 6 hours


title: ZZ_Ko_6_44


title: cells grown in full media treated with palmitate [PA3]


title: untreated cells grown in full media [C2]


title: Cre control sample 1

description: Sample name: BG01M009


title: CMV control sample 3

description: Sample name: BG01M003


title: CMV estradiol sample 2

description: Sample name: BG01M006


title: cells treated with PPARd agonist, GW1516 [GW3]

source_name: NaF cells grown in charcoal-treated FBS (10%) DMEM and treated with GW1516 (1uM) for 6 hours


title: ZZ_Ko_8_852


title: ZZ_Ko_7_834


title: CMV estradiol sample 3

description: Sample name: BG01M007


title: cells treated with retinoic acid [RA2]


title: CMV control sample 1

description: Sample name: BG01M001


title: cells treated with PPARd agonist, GW1516 [GW1]


title: CMV estradiol sample 1

description: Sample name: BG01M005


title: ZZ_Ko_5_37


title: control charcoal-treated cells [CT1]

source_name: NaF cells grown in charcoal-treated FBS (10%) DMEM


title: ZZ_Ko_3_58


title: control charcoal-treated cells [CT3]


title: CMV control sample 4

description: Sample name: BG01M004


title: ZZ_Ko_2_57


title: cells treated with retinoic acid [RA1]


title: ZZ_Ko_11_113


title: ZZ_Ko_12_184


title: ZZ_Ko_10_208


title: Cre control sample 2

description: Sample name: BG01M010


title: cells treated with PPARd agonist, GW1516 [GW2]


title: Z_5_613

value: lung cancer

value: Z


title: ZZ_Ko_1_30


title: Z_2_454


title: Z_3_501


title: Z_4_558


title: ZZ_Ko_4_71


title: Y_7_719

value: Y


title: Z_1_440


title: Y_4_578


title: Y_5_639


title: CMV control sample 2

description: Sample name: BG01M002


title: Y_6_683


title: Y_3_521


title: X_7_630

value: X


title: Y_1_469


title: Y_2_471


title: Lung_Squamous_Carcinoma_Patient49

description: Gene expression of lung squamous carcinoma precancerous and cancer tissue

hyb_protocol: 600 ng of CTP-Cy3-labelled cRNA (specific activity > 10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µl containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2 x Agilent hybridization buffer were added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief passage in acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides: scan area was 61x21.6 mm, scan resolution 3 µm, dye channel was set to Green, Tiff file dynamic range was 20 bits and Green PMT was set to 100 %.

source_name: Lung Squamous Carcinoma Tissue

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent, version 6.6) according to manufacturer's instructions, followed by RNeasy column purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (Nanodrop ND1000, Labtech) and with the Agilent 2100 Bioanalyser.

value: Cancer tissue obtained from bronchoscopy

tag: status

value: Stage III


title: Cre estradiol sample 3

description: Sample name: BG01M016


title: Z_6_667


title: X_6_574


title: X_5_495


title: control charcoal-treated cells [CT2]


title: X_3_382


title: X_2_310


title: Y_8_753


title: W_6_530

value: W


title: W_7_584


title: W_8_644


title: W_4_423


title: W_3_338


title: W_2_263


title: W_5_483


title: V_8_650

value: V


title: V_7_592


title: V_5_484


title: V_6_540


title: V_2_258


title: V_3_355


title: X_1_289


title: X_4_446


title: V_1_246


title: U_4_692

value: U


title: U_5_729


title: U_6_764


title: U_8_798


title: U_7_783


title: W_1_253


title: U_3_659


title: V_4_422


title: T_8_790

value: T


title: U_2_604


title: T_7_774


title: T_4_679


title: T_5_716


title: T_6_751


title: T_3_635


title: T_2_576


title: S_5_713

value: S


title: T_1_568


title: S_4_674


title: S_3_631


title: S_7_778


title: S_6_750


title: R_8_782

value: R


title: S_2_570


title: S_1_554


title: U_1_596


title: R_7_763


title: R_6_728


title: R_5_691


title: R_4_656


title: R_1_528


title: Q_8_775

value: Q


title: R_3_600


title: R_2_538


title: Q_5_680


title: Q_4_640


title: Q_2_527


title: Q_3_579


title: Q_1_518


title: P_5_676

value: P


title: P_7_745


title: P_4_625


title: Q_7_752


title: Q_6_717


title: P_6_714


title: O_8_765

value: O


title: P_1_511

value: plasma


title: P_2_516


title: P_3_573


title: O_7_730


title: O_4_597


title: O_5_655


title: O_3_546


title: O_6_693


title: P_8_771


title: N_7_706

value: N


title: O_2_487

value: lung cancer


title: N_8_740


title: O_1_478


title: N_6_670


title: N_1_449


title: N_4_564


title: N_2_460


title: N_5_622


title: M_5_608

value: M


title: M_8_733


title: M_7_700


title: M_6_663


title: M_4_555


title: M_2_445


title: M_1_431


title: L_8_793

value: L


title: L_5_724


title: L_4_687


title: M_3_494


title: L_7_780


title: L_6_759


title: L_2_595


title: N_3_504


title: L_1_586


title: L_3_651


title: K_5_500

value: K


title: K_8_665


title: K_7_612


title: K_6_561


title: K_2_320


title: K_4_453


title: J_8_664

value: J


title: J_4_447


title: K_1_315


title: K_3_386


title: J_7_611


title: J_6_557


title: J_3_381


title: J_1_314


title: I_5_499

value: I


title: I_4_452


title: J_2_323


title: I_8_666


title: I_6_559


title: I_1_286


title: I_2_324


title: I_7_614


title: I_3_384


title: H_7_598

value: H


title: H_5_486


title: H_4_429


title: H_6_548


title: H_3_377


title: H_2_303


title: J_5_497


title: H_1_281


title: G_3_354

value: G


title: G_4_419


title: G_5_488


title: G_6_545


title: G_7_599


title: G_1_241


title: G_2_245


title: F_7_542

value: F


title: F_8_593


title: F_6_480


title: G_8_654


title: E_7_615

value: E


title: F_1_238


title: F_2_242


title: E_8_668


title: F_3_293


title: E_5_493


title: E_6_560


title: E_3_379


title: D_8_594

value: D


title: E_4_442


title: D_7_541


title: E_2_301


title: E_1_280


title: F_4_374


title: D_4_372


title: D_6_482


title: F_5_416


title: D_3_297


title: D_1_240


title: D_2_243


title: C_8_653

value: C


title: C_7_601


title: D_5_415


title: C_6_544


title: C_5_481


title: C_3_337


title: C_4_420


title: C_2_264


title: B_8_632

value: B


title: C_1_254


title: B_7_571


title: B_6_512


title: B_5_467


title: B_2_244


title: B_4_391


title: B_1_239


title: A_6_489

value: A


title: A_8_603


title: A_7_547


title: A_5_403


title: A_4_336


title: A_2_237


title: A_3_257


title: A_1_233


title: B_3_292


title: Tibialis anterior muscle from Pip6e-PMO treated mdx mouse 4_microRNA

city: Oxford

first: Thomas

middle: C

last: Roberts

address: South Parks Road

department: Department of Physiology, Anatomy and Genetics

institute: University of Oxford

description:
miRNA expression data from Treated mdx C57/B10 mouse 4, Tibialis anterior muscle
FT4

hyb_protocol: Total labeled RNA was hybridised to the Affymetrix Genechip miRNA array 3.0 using manufacturer's protocols.

scan_protocol: Image files from scanning (.dat and .cel files) were generated with Affymetrix Expression Console package.

data_processing: The processing and data analyses were performed in Affymetrix Expression Console Software. The arrays were analyzed using Robust Multichip Analysis (RMA) and DABG (detected above background). In the final analysis we sorted out Mus musculus transcripts only. Transcripts with Absent detection signals in at least three of the four replicates (or two out of the three replicates in the controls) were removed.

label_protocol: 500 ng of total RNA was labeled using the FlashTag Biotin HSR kit (Genisphere).

growth_protocol: Tibialis anterior (TA) muscles were macrodissected and snap frozen in liquid nitrogen-cooled isopentane. 8mm cryosections were prepared from mid-belly of the muscle.

extract_protocol: Samples were extracted using the TRIzol method and DNase I treated with Ambion TURBO DNA-free according to manufacturer's instructions. Samples were re-extracted using acid phenol chloroform and ethanol precipitated. Each RNA sample was analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) to assess RNA quality.

treatment_protocol: Treated animals were injected with a single 12.5mg/kg dose of Pip6e-PMO in sterile saline via the tail vein at 12 weeks of age.

value: Mdx

tag: strain

value: Tibialis anterior muscle

value: Pip6e-PMO treated


title: Tibialis anterior muscle from Pip6e-PMO treated mdx mouse 3_microRNA

description:
miRNA expression data from Treated mdx C57/B10 mouse 3, Tibialis anterior muscle
FT3


title: Tibialis anterior muscle from mdx mouse 4_microRNA

description:
miRNA expression data from Mdx C57/B10 mouse 4, Tibialis anterior muscle
FM4


title: Tibialis anterior muscle from Pip6e-PMO treated mdx mouse 1_microRNA

description:
miRNA expression data from Treated mdx C57/B10 mouse 1, Tibialis anterior muscle
FT1


title: Tibialis anterior muscle from mdx mouse 2_microRNA

description:
miRNA expression data from Mdx C57/B10 mouse 2, Tibialis anterior muscle
FM2


title: Tibialis anterior muscle from Wt mouse 2_microRNA

description:
miRNA expression data from Wt C57/B10 mouse 2, Tibialis anterior muscle
FC2

source_name: Tibialis anterior muscle from C57 mouse 2

value: Wildtype


title: Tibialis anterior muscle from Wt mouse 1_microRNA

description:
miRNA expression data from Wt C57/B10 mouse 1, Tibialis anterior muscle
FC1

source_name: Tibialis anterior muscle from C57 mouse 1


title: Tibialis anterior muscle from mdx mouse 1_microRNA

description:
miRNA expression data from Mdx C57/B10 mouse 1, Tibialis anterior muscle
FM1


title: Tibialis anterior muscle from Pip6e-PMO treated mdx mouse 2_microRNA

description:
miRNA expression data from Treated mdx C57/B10 mouse 2, Tibialis anterior muscle
FT2


title: expression_Placental Tissue_Preeclamptic_Subject_6

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

hyb_protocol: Standard Affymetrix Hyb

scan_protocol: Microarray results were extracted using Agilent Feature Extraction software

data_processing: Data were RMA processed from cell files using Partek. Data were then used for downstream applications

source_name: Human Placental Tissue, Preeclamptic

label_protocol: Standard Affymetrix Labeling

extract_protocol: Trizol

tag: diagnosis

value: preeclamptic

value: placenta

tag: maternal age

tag: race

value: Caucasian

tag: gestational age


title: expression_Placental Tissue_Preeclamptic_Subject_5

value: Hispanic


title: expression_Placental Tissue_Preeclamptic_Subject_18

value: Other


title: expression_Placental Tissue_Preeclamptic_Subject_2

value: African American


title: Tibialis anterior muscle from Wt mouse 3_microRNA

description:
miRNA expression data from Wt C57/B10 mouse 3, Tibialis anterior muscle
FC3

source_name: Tibialis anterior muscle from C57 mouse 3

tag: genotype


title: Tibialis anterior muscle from mdx mouse 3_microRNA

description:
miRNA expression data from Mdx C57/B10 mouse 3, Tibialis anterior muscle
FM3

tag: treatment


title: expression_Placental Tissue_Preeclamptic_Subject_17


title: expression_Placental Tissue_Preeclamptic_Subject_8


title: expression_Placental Tissue_Preeclamptic_Subject_9


title: expression_Placental Tissue_Preeclamptic_Subject_20


title: expression_Placental Tissue_Preeclamptic_Subject_15


title: expression_Placental Tissue_Preeclamptic_Subject_19


title: expression_Placental Tissue_Preeclamptic_Subject_14


title: expression_Placental Tissue_Preeclamptic_Subject_11


title: expression_Placental Tissue_Preeclamptic_Subject_1


title: expression_Placental Tissue_Preeclamptic_Subject_4


title: expression_Placental Tissue_Preeclamptic_Subject_16


title: expression_Placental Tissue_Normotensive_Subject_6

source_name: Human Placental Tissue, Normotensive

value: normotensive


title: expression_Placental Tissue_Normotensive_Subject_9


title: expression_Placental Tissue_Normotensive_Subject_17


title: expression_Placental Tissue_Normotensive_Subject_4


title: expression_Placental Tissue_Preeclamptic_Subject_12


title: expression_Placental Tissue_Preeclamptic_Subject_13


title: expression_Placental Tissue_Normotensive_Subject_5


title: expression_Placental Tissue_Normotensive_Subject_18


title: expression_Placental Tissue_Normotensive_Subject_20


title: expression_Placental Tissue_Normotensive_Subject_14

value: Asian


title: expression_Placental Tissue_Normotensive_Subject_2


title: expression_Placental Tissue_Normotensive_Subject_12


title: expression_Placental Tissue_Normotensive_Subject_15


title: expression_Placental Tissue_Normotensive_Subject_10


title: expression_Placental Tissue_Normotensive_Subject_11


title: expression_Placental Tissue_Normotensive_Subject_16


title: expression_Placental Tissue_Normotensive_Subject_19


title: SKNDZ_miRNA

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

description: miRNA profiling

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. Then, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner G2565BA.

data_processing: The scanned images were analyzed with FeatureExtractor. Intensity values were then processed with AgiMicroRna using default parameters to remove low-quality probes. Signals where then normalized by means of the quantile normalization method.

source_name: Cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA as detailed in the One-color microarray-based gene expression analysis protocol (Agilent). Dye incorporation and cRNA yield were checked with the Biophotometer (Eppendorf).

extract_protocol: miRNAs were isolated according to the manufacturer protocol by using the miRNeasy Micro Kit (Qiagen), then quantified and quality assessed using the Small RNA assay on the 2100 Bioanalyzer (Agilent Technologies): a RIN threshold of 7 was used to select samples for the study. miRNA profiling was performed from 100ng of starting material; samples were hybridized on Human miRNA Microarrays 2.0 (Agilent Technologies) and slides were then scanned using a G2565BA scanner (Agilent Technologies).

value: Neuroblastoma

tag: cell line

value: SKNDZ


title: STANB1_miRNA

description: miRNA profiling


title: STANB7_miRNA

description: miRNA profiling


title: expression_Placental Tissue_Normotensive_Subject_1


title: STANB10_miRNA

description: miRNA profiling


title: expression_Placental Tissue_Preeclamptic_Subject_7


title: SKNBE2_miRNA

description: miRNA profiling


title: expression_Placental Tissue_Preeclamptic_Subject_10


title: LAN1_miRNA

description: miRNA profiling


title: KELLY_miRNA

description: miRNA profiling

value: KELLY


title: IMR32_miRNA

description: miRNA profiling


title: Dorsal_skin_ applied_30%_EtOH, biological rep4

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

hyb_protocol: Labeled cRNAs were hybridized with an Agilent 4×44 K Whole Mouse Genome Microarray.

scan_protocol: Slides were scanned immediately after washing on the Agilent Dual-Laser Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (GE1-v5_91 and Grid:014868_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Dorsal skin, applied 30% ethanol 5 times a week for 2 consecutive weeks after a 10-week UVB irradiation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit, One-color (Agilent Technologies Inc. California, USA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: Total RNA was isolated with Isogen reagent (NIPPON GENE CO., LTD., Tokyo, Japan) and purified with RNAeasy mini kit (QIAGEN, Valencia, CA) according to manufacture's instruction. Total RNA concentration and purity were determined by measuring OD260 and OD 260/280, respectively with NanoDrop spectrophotometer (NanoDrop Technologies Inc., Delaware, USA). The quality of total RNA was assessed by electrophoretic separation on an RNA Nano lab chip, using a 2100 Bioanalyzer (Agilent Technologies Inc.,California, USA) according to the manufactur’s instructions. The 4 total RNA samples of each condition with a 28S/18S band ratio greater than 1.5 were used for microarray analysis.

treatment_protocol: The dorsal region of the mouse was repeatedly irradiated with UVB for 10 weeks. Enalapril maleate treatment was started at 1 week after 10-week irradiation. One hundred microliters of 1% w/v enalapril maleate dissolved in 30 vol % ethanol solution or 30 vol % ethanol (control) was applied 5 times a week for 2 consecutive weeks to the whole dorsal skin of each of the mice.

tag: gender

value: Male

value: dorsal skin

tag: age

value: 19 weeks


title: expression_Placental Tissue_Normotensive_Subject_13


title: Dorsal_skin_ applied_1%_enalapril_maleate_in_30%_EtOH, biological rep4

source_name: Dorsal skin, applied 1% enalapril maleate in 30% ethanol 5 times a week for 2 consecutive weeks after a 10-week UVB irradiation


title: Dorsal_skin_ applied_1%_enalapril_maleate_in_30%_EtOH, biological rep2

value: applied 1% enalapril maleate in 30% ethanol 5 times a week for 2 consecutive weeks after a 10-week UVB irradiation


title: Dorsal_skin_ applied_1%_enalapril_maleate_in_30%_EtOH, biological rep3


title: Dorsal_skin_ applied_30%_EtOH, biological rep3

value: applied 30% ethanol 5 times a week for 2 consecutive weeks after a 10-week UVB irradiation


title: Dorsal_skin_ applied_30%_EtOH, biological rep2


title: Whole blood CONTROL 5786073130_C failed QC

city: Utrecht

first: Femke

middle: NG

last: van 't Hof

address: Heidelberglaan 100

country: Netherlands

institute: University medical center Utrecht

description: failed QC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Sample outliers (gender mismatches, duplicates and PC outliers) and probe outliers (non-autosomal and non-specific probes) were removed. Remaining data were quantile normalized and log2 transformed in R

source_name: CONTROL

label_protocol: tRNA was purified using QIAcube, and quantified with Agilent RNA 6000 nano kit

extract_protocol: PAXgene tubes were frozen at -20 °C after two hours at room temperature, until RNA was isolated using PAXgene extraction kits (Qiagen).

tag: disease status

value: CONTROL

tag: Sex

value: whole blood


title: Whole blood CONTROL 5786073117_J failed QC

description: failed QC

value: Female

tag: tissue


title: Whole blood CONTROL 5786073117_H failed QC

description: failed QC


title: SIMA_miRNA

description: miRNA profiling

value: SIMA


title: Whole blood CASE 5786073036_E failed QC

description: failed QC

source_name: CASE

value: CASE


title: Whole blood CONTROL 5786073032_J failed QC

description: failed QC


title: Whole blood CASE 5786073030_F failed QC

description: failed QC


title: Whole blood CONTROL 5786073032_F failed QC

description: failed QC


title: Whole blood CASE 5786073029_I failed QC

description: failed QC


title: Whole blood CASE 5786073029_E failed QC

description: failed QC


title: Whole blood CONTROL 5786073030_D failed QC

description: failed QC


title: CHP134_miRNA

description: miRNA profiling


title: Dorsal_skin_ applied_1%_enalapril_maleate_in_30%_EtOH, biological rep1


title: Chip-2 Cy5-Hep-11 Cy3-Hep-12

city: Peiking

first: haibo

last: Han

address: 52 Fucheng Road, Haidian District

department: Department of Cell Biology

institute: Peking University School of Oncology

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

scan_protocol: After hybridization detection used fluorescence labeling using tag-specific Cy3 and Cy5 dyes. Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) .
For two color experiments, the ratio of the two sets of detected signals (log2 Hep-12/Hep11 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.

molecule: polyA RNA

label_protocol: RNA was labeled by using LC siences protocol.Briefly,two different tags were used for the two RNA samples in dual-sample experiments.

growth_protocol: Cells were cultured in RPMI1640 containing 10% fetal bovine serum

extract_protocol: Total RNA was extracted by Qiagen kit

tag: sample type

value: 9540468  male  primary

value: 9540468  male  recurrent


title: Whole blood CONTROL 5786073022_D failed QC

description: failed QC


title: Whole blood CASE 5786073030_K failed QC

description: failed QC


title: Whole blood CASE 5786073021_F failed QC

description: failed QC


title: Whole blood CASE 5786073017_F failed QC

description: failed QC


title: CHP212_miRNA

description: miRNA profiling


title: Whole blood CASE 5786073036_D failed QC

description: failed QC


title: ischemic wound edge-1

city: Fort Sam Houston

first: Jaideep

last: Banerjee

state: Texas

address: 3698 Chambers Rd, BHT-1

institute: US Army Inst of Surgical Res.

description:
Test
Mature miRNAs were profiled by real-time PCR using an Applied Biosystems 7900HT real-time PCR instrument equipped with a 384 well reaction plate. RNA (500 ng) was converted to cDNA by priming with a mixture of looped primers (Mega Plex kit, Applied Biosystems, Foster City, CA). Real-time PCR was performed using standard conditions

data_processing:
Normalization of sample was done as per (2^-ΔΔCtischemic)/(2^-ΔΔCtnon-ischemic), where -ΔΔCt = -[ΔCttest -ΔCtcontrol]
Fold Change worksheet reports test/control (i.e., ischemic/non-ischemic) ratios.

label: FAM

source_name: wound edge tissue

extract_protocol: RNA was isolated by miRVana RNA isolation kit.

tag: time

value: 3 days

value: wound edge tissue


title: ischemic wound edge-3


title: ischemic wound edge-2


title: non-ischemic wound edge-4

description:
Control
Mature miRNAs were profiled by real-time PCR using an Applied Biosystems 7900HT real-time PCR instrument equipped with a 384 well reaction plate. RNA (500 ng) was converted to cDNA by priming with a mixture of looped primers (Mega Plex kit, Applied Biosystems, Foster City, CA). Real-time PCR was performed using standard conditions


title: non-ischemic wound edge-2


title: Whole blood CASE 5786073018_J failed QC

description: failed QC


title: non-ischemic wound edge-3


title: Chip-1 Cy3-Hep-11 Cy5-Hep-12

value: 9540467  male  primary

value: 9540467  male  recurrent


title: Dorsal_skin_ applied_30%_EtOH, biological rep1


title: non-ischemic wound edge-1


title: Tibialis anterior muscle from Wt mouse 1_mRNA

description:
Tibialis anterior muscle
FC1

data_processing: The processing and data analyses were performed in Affymetrix Expression Console Software. The arrays were analyzed using Median Polish, RMA background correction and Sketch-Quantile normalization (RMA-Sketch in Affymetrix Expression Console Software). Only the signals from the probe sets in the main category were used. Log2 values have been transformed into linear values. In the final analysis we removed probe set signals that were below 30 in all the groups.

label_protocol: 100 ng of column-purified total RNA was hybridised on to Mouse Gene ST 1.1 Array plates.

extract_protocol: Samples were extracted using the TRIzol method and DNase I treated with Ambion TURBO DNA-free according to manufacturer's instructions. Samples were re-extracted using acid phenol chloroform and ethanol precipitated. The RNA was column-purified (RNeasy Mini kit, Qiagen) before hybridisation. Each RNA sample was analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) to assess RNA quality.

value: wildtype

value: Tibialis anterior muscle


title: Tibialis anterior muscle from mdx mouse 2_mRNA

description:
Tibialis anterior muscle
FM2

hyb_protocol: RNA was hybridised on to Mouse Gene ST 1.1 Array plates.

value: Mdx


title: Tibialis anterior muscle from Wt mouse 2_mRNA

description:
Tibialis anterior muscle
FC2


title: Tibialis anterior muscle from Pip6e-PMO treated mdx mouse 2_mRNA

description:
Tibialis anterior muscle
FT2

value: Pip6e-PMO treated


title: Tibialis anterior muscle from mdx mouse 1_mRNA

description:
Tibialis anterior muscle
FM1


title: Tibialis anterior muscle from mdx mouse 4_mRNA

description:
Tibialis anterior muscle
FM4


title: Tibialis anterior muscle from Pip6e-PMO treated mdx mouse 4_mRNA

description:
Tibialis anterior muscle
FT4


title: Whole blood CONTROL 5786073130_H

value: Male


title: Whole blood CONTROL 5786073130_L


title: Whole blood CONTROL 5786073130_I


title: Tibialis anterior muscle from Pip6e-PMO treated mdx mouse 3_mRNA

description:
Tibialis anterior muscle
FT3


title: Tibialis anterior muscle from mdx mouse 3_mRNA

description:
Tibialis anterior muscle
FM3


title: Whole blood CONTROL 5786073130_J


title: Tibialis anterior muscle from Pip6e-PMO treated mdx mouse 1_mRNA

description:
Tibialis anterior muscle
FT1


title: Whole blood CONTROL 5786073130_D


title: Whole blood CONTROL 5786073130_G


title: Tibialis anterior muscle from Wt mouse 3_mRNA

description:
Tibialis anterior muscle
FC3


title: Whole blood CONTROL 5786073130_F


title: Whole blood CONTROL 5786073130_B


title: Whole blood CONTROL 5786073130_K


title: Whole blood CONTROL 5786073117_G


title: Whole blood CONTROL 5786073130_E


title: Whole blood CONTROL 5786073117_L


title: Whole blood CONTROL 5786073130_A


title: Whole blood CONTROL 5786073117_D


title: Whole blood CONTROL 5786073117_I


title: Whole blood CONTROL 5786073117_E


title: Whole blood CONTROL 5786073117_F


title: Whole blood CONTROL 5786073117_K


title: Whole blood CONTROL 5786073117_C


title: Whole blood CONTROL 5786073043_L


title: Whole blood CASE 5786073043_J


title: Whole blood CONTROL 5786073117_A


title: Whole blood CASE 5786073043_I


title: Whole blood CONTROL 5786073043_G


title: Whole blood CONTROL 5786073043_H


title: Whole blood CASE 5786073117_B


title: Whole blood CONTROL 5786073043_D


title: Whole blood CASE 5786073043_F


title: Whole blood CONTROL 5786073043_C


title: Whole blood CASE 5786073043_B


title: Whole blood CASE 5786073039_K


title: Whole blood CONTROL 5786073043_K


title: Whole blood CASE 5786073043_A


title: Whole blood CASE 5786073043_E


title: Whole blood CASE 5786073039_F


title: Whole blood CASE 5786073039_I


title: Whole blood CONTROL 5786073036_K


title: Whole blood CASE 5786073039_G


title: Whole blood CASE 5786073039_J


title: Whole blood CONTROL 5786073039_L


title: Whole blood CONTROL 5786073039_E


title: Whole blood CONTROL 5786073039_A


title: Whole blood CONTROL 5786073039_B


title: Whole blood CASE 5786073039_C


title: Whole blood CASE 5786073036_L


title: Whole blood CONTROL 5786073039_H


title: Whole blood CASE 5786073036_H


title: Whole blood CASE 5786073039_D


title: Whole blood CASE 5786073036_C


title: Whole blood CASE 5786073032_L


title: Whole blood CONTROL 5786073036_A


title: Whole blood CONTROL 5786073036_J


title: Whole blood CONTROL 5786073036_F


title: Whole blood CASE 5786073036_I


title: Whole blood CONTROL 5786073036_G


title: Whole blood CASE 5786073036_B


title: Whole blood CONTROL 5786073032_I


title: Whole blood CASE 5786073032_H


title: Whole blood CASE 5786073032_D


title: Whole blood CASE 5786073032_A


title: Whole blood CASE 5786073030_B


title: Whole blood CASE 5786073030_G


title: Whole blood CASE 5786073032_E


title: Whole blood CONTROL 5786073032_B


title: Whole blood CASE 5786073029_H


title: Whole blood CASE 5786073029_L


title: Whole blood CONTROL 5786073030_C


title: Whole blood CONTROL 5786073030_H


title: Whole blood CASE 5786073029_D


title: Whole blood CONTROL 5786073030_A


title: Whole blood CONTROL 5786073029_G


title: Whole blood CONTROL 5786073032_C


title: Whole blood CASE 5786073029_A


title: Whole blood CONTROL 5786073025_L


title: Whole blood CONTROL 5786073029_K


title: Whole blood CASE 5786073025_J


title: Whole blood CONTROL 5786073030_E


title: Whole blood CONTROL 5786073029_C


title: Whole blood CONTROL 5786073029_B


title: Whole blood CASE 5786073032_K


title: Whole blood CASE 5786073032_G


title: Whole blood CONTROL 5786073025_K


title: Whole blood CONTROL 5786073029_J


title: Whole blood CASE 5786073025_H


title: Whole blood CONTROL 5786073029_F


title: Whole blood CONTROL 5786073030_I


title: Whole blood CASE 5786073025_I


title: Whole blood CASE 5786073022_L


title: Whole blood CONTROL 5786073025_D


title: Whole blood CASE 5786073025_A


title: Whole blood CONTROL 5786073022_G


title: Whole blood CASE 5786073022_C


title: Whole blood CASE 5786073022_F


title: Whole blood CONTROL 5786073022_I


title: Whole blood CASE 5786073025_F


title: Whole blood CONTROL 5786073025_G


title: Whole blood CONTROL 5786073025_C


title: Whole blood CASE 5786073022_J


title: Whole blood CASE 5786073025_E


title: Whole blood CASE 5786073022_B


title: Whole blood CASE 5786073025_B


title: Whole blood CONTROL 5786073021_K


title: Whole blood CONTROL 5786073021_H


title: Whole blood CONTROL 5786073021_D


title: Whole blood CONTROL 5786073022_H


title: Whole blood CASE 5786073022_A


title: Whole blood CONTROL 5786073021_J


title: Whole blood CASE 5786073022_K


title: Whole blood CONTROL 5786073021_L


title: Whole blood CONTROL 5786073021_G


title: Whole blood CASE 5786073022_E


title: Whole blood CONTROL 5786073018_L


title: Whole blood CONTROL 5786073021_C


title: Whole blood CASE 5786073021_A


title: Whole blood CASE 5786073021_E


title: Whole blood CASE 5786073021_B


title: Whole blood CASE 5786073021_I


title: Whole blood CASE 5786073018_G


title: Whole blood CONTROL 5786073018_F


title: Whole blood CASE 5786073018_C


title: Whole blood CASE 5786073017_J


title: Whole blood CONTROL 5786073018_K


title: Whole blood CONTROL 5786073018_D


title: Whole blood CASE 5786073017_K


title: Whole blood CASE 5786073018_B


title: Whole blood CONTROL 5786073018_E


title: Whole blood CASE 5786073017_A


title: Whole blood CONTROL 5786073017_H


title: Whole blood CONTROL 5786073018_I


title: Whole blood CONTROL 5786073018_A


title: Whole blood CASE 5786073018_H


title: Whole blood CONTROL 5786073017_E


title: Whole blood CONTROL 5786073017_I


title: Whole blood CASE 5786073017_C


title: Whole blood CASE 5786073017_B


title: Whole blood CASE 5786073017_L


title: Whole blood CONTROL 5786073015_K


title: Whole blood CASE 5786073017_G


title: Whole blood CONTROL 5786073015_L


title: Whole blood CONTROL 5786073017_D


title: Whole blood CASE 5786073015_J


title: Whole blood CONTROL 5786073015_F


title: Whole blood CASE 5786073015_I


title: Whole blood CONTROL 5786073015_E


title: Whole blood CONTROL 5786073015_H


title: Whole blood CONTROL 5786073013_K


title: Whole blood CASE 5786073013_I


title: Whole blood CASE 5786073013_L


title: Whole blood CASE 5786073015_D


title: Whole blood CASE 5786073015_G


title: Whole blood CASE 5786073015_C


title: Whole blood CONTROL 5786073013_J


title: Whole blood CASE 5786073015_A


title: Whole blood CONTROL 5786073013_H


title: Whole blood CASE 5786073015_B


title: methylation_Placental Tissue_Preeclamptic_Subject_18

type: genomic

hyb_protocol: Standard Illumina Hyb

scan_protocol: Data were processed at Expression Analysis using standard in house processing

data_processing: Data were processed following the Morris et al 2014 pipeline (PMID 24336642).

molecule: genomic DNA

source_name: Placental Tissue

label_protocol: Standard Illumina Labeling

value: preeclamptic

value: placenta

value: Other


title: Whole blood CONTROL 5786073013_G

value: CONTROL

value: whole blood


title: methylation_Placental Tissue_Preeclamptic_Subject_17

value: African American


title: Whole blood CASE 5786073013_F

value: CASE

value: Female


title: Whole blood CONTROL 5786073013_D


title: methylation_Placental Tissue_Preeclamptic_Subject_16

value: Caucasian


title: Whole blood CASE 5786073013_E


title: Whole blood CASE 5786073013_C


title: methylation_Placental Tissue_Preeclamptic_Subject_13


title: methylation_Placental Tissue_Preeclamptic_Subject_19


title: Whole blood CASE 5786073013_B


title: methylation_Placental Tissue_Preeclamptic_Subject_5

value: Hispanic


title: methylation_Placental Tissue_Normotensive_Subject_5

value: normotensive


title: Whole blood CONTROL 5786073011_H


title: Whole blood CONTROL 5786073011_E


title: Whole blood CONTROL 5786073011_L


title: Whole blood CASE 5786073013_A


title: T47D_THZ1_50nM_2

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Samples were prepared for hybridization using 10 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human PrimeView, Affymetrix 901837) were hybridized in a GeneChip Hybridization Oven at 45C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console. A Primeview CDF that included probe information for the ERCC controls (GPL16043), provided by Affymetrix, was used to generate .CEL files.

data_processing: A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf.  The data were analyzed with Bioconductor using the MAS5 normalization method. Then, these data were renormalized to the external spike-ins. See Loven, Orlando et al., Cell, 2012 for additional details.

source_name: MDA-MB-468 cells treated with 50nM THZ1 for 6 hours

label_protocol: For microarray analysis, 100 ng of total RNA containing ERCC RNA Spike-In Mix (see above) was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (30 IVT Express Kit, Affymetrix 901228). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: Human breast cancer cell lines were grown in RPMI-1640, 10% fetal bovine serum, and 1% penicillin/streptomycin

extract_protocol: Total RNA from DMSO or drug –treated cells was extracted using a RNeasy Mini kit with QIAshredder spin column for homogenization and an on-column DNase digestion (79254, Qiagen) following the manufacturer’s instructions and re-suspended in 50 μL nuclease-free water (Ambion, AM9938). Total RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion, 4456740) proportional to cell number (Loven et al., 2012), treated with DNA-freeTM DNase I (Ambion, AM1906), and analyzed on Agilent 2100 Bioanalyzer for integrity.

treatment_protocol: Treated with 50nM THZ1 for 6 hr

tag: cell type

value: ER+/PR+ breast cancer


title: Whole blood CONTROL 5786073011_G


title: T47D_THZ1_50nM_1


title: Whole blood CASE 5786073011_J


title: Whole blood CASE 5786073011_F


title: Whole blood CASE 5786073011_I


title: ZR_75_1_THZ1_250nM_2

source_name: MDA-MB-468 cells treated with 250nM THZ1 for 6 hours

treatment_protocol: Treated with 250nM THZ1 for 6 hr

value: ER+ breast cancer


title: methylation_Placental Tissue_Normotensive_Subject_20


title: T47D_THZ1_250nM_2


title: methylation_Placental Tissue_Preeclamptic_Subject_4


title: T47D_DMSO_2

source_name: MDA-MB-468 cells

treatment_protocol: Treated with DMSO for 6hr


title: Whole blood CASE 5786073011_D


title: T47D_DMSO_1


title: T47D_THZ1_250nM_1


title: methylation_Placental Tissue_Normotensive_Subject_15


title: Whole blood CASE 5786073011_C


title: Whole blood CASE 5786073011_B


title: ZR_75_1_THZ1_250nM_1


title: ZR_75_1_THZ1_50nM_1


title: ZR_75_1_THZ1_50nM_2


title: methylation_Placental Tissue_Preeclamptic_Subject_11


title: Whole blood CONTROL 5786073011_K


title: Patient NP1, Tumor Sample, Location 3

city: Ann Arbor

first: Ana

middle: Rodrigues

last: Grant

state: MI

address: 100 Washtenaw Avenue

department: Computational Medicine & Bioinformatics

institute: University of Michigan

hyb_protocol: Arrays were hybridized overnight (17 hrs). Then the arrays were washed with SSPE-based wash buffers and stained by stacking layers of streptavidin-phycoerithrin and biotinylated antistreptavidin antibody using parallel GeneChip Fluidics 450 stations.

scan_protocol: Oncoscan v3 scanning script, GeneChip Scanner 3000 7G, AGCC software

data_processing:
CEL files are combined by Affymetrix OncoScan Console software to generate OSCHP files, which are analyzed by Nexus Copy Number by BioDiscovery using the TuScan algorithm (which is Affymetrix's version of the ASCAT algorithm)
Probe intensities. B-allele frequency, and Allelic imbalance measurements across 217K probe locations

source_name: Patient NP1, Tumor Sample, Location 3

label_protocol: Samples were labeled with biotin according to the Affymetrix protocol for Oncoscan (P/N 703175 Rev. 1).

extract_protocol: DNA was extracted from frozen tissue, using the Allprep mini kit (Qiagen, Valencia, California) and according to the manufacturer's instructions.

value: male

tag: tumor stage

tag: tumor size (cm)

value: rectum

tag: number of nodes positive

tag: surgery

value: Abdominoperineal Resection of the Rectum


title: methylation_Placental Tissue_Normotensive_Subject_4

tag: diagnosis

tag: maternal age

tag: race


title: Whole blood CONTROL 5786073011_A


title: Whole blood CONTROL 5786073007_H

value: Male


title: BT_549_THZ1_250nM

source_name: BT-549 cells treated with 250nM THZ1 for 6 hours

value: Triple-negative breast cancer


title: Whole blood CONTROL 5786073007_K


title: BT_549_THZ1_50nM

source_name: BT-549 cells treated with 50nM THZ1 for 6 hours


title: MDA_MB_468_THZ1_50nM_2


title: Whole blood CASE 5786073006_K


title: Whole blood CASE 5786073007_J


title: Whole blood CASE 5786073007_G


title: Whole blood CASE 5786073006_L


title: ZR_75_1_DMSO_1


title: Whole blood CONTROL 5786073007_E


title: Whole blood CASE 5786073007_B


title: BT_549_DMSO

source_name: BT-549 cells


title: MDA_MB_468_THZ1_250nM_1


title: Patient NP1, Tumor Sample, Location 2

source_name: Patient NP1, Tumor Sample, Location 2


title: Whole blood CASE 5786073007_L


title: Whole blood CASE 5786073007_F


title: Whole blood CONTROL 5786073007_D


title: Whole blood CONTROL 5786073007_A


title: Whole blood CONTROL 5786073006_J


title: Patient NP1, Tumor Sample, Location 1

source_name: Patient NP1, Tumor Sample, Location 1


title: Whole blood CASE 5786073007_C


title: ZR_75_1_DMSO_2


title: MDA_MB_468_THZ1_50nM_1


title: Patient 204, Tumor Sample, Location 2

source_name: Patient 204, Tumor Sample, Location 2

value: female

value: Low Anterior Resection of the Rectum


title: Patient 204, Tumor Sample, Location 1

source_name: Patient 204, Tumor Sample, Location 1


title: MDA_MB_468_THZ1_250nM_2


title: Patient 20, Tumor Sample, Location 1

source_name: Patient 20, Tumor Sample, Location 1


title: Patient 11, Tumor Sample, Location 3

source_name: Patient 11, Tumor Sample, Location 3

value: Total Proctocolectomy


title: Patient 11, Tumor Sample, Location 2

source_name: Patient 11, Tumor Sample, Location 2


title: Patient 20, Tumor Sample, Location 2

source_name: Patient 20, Tumor Sample, Location 2


title: Patient 11, Tumor Sample, Location 1

source_name: Patient 11, Tumor Sample, Location 1


title: Whole blood CONTROL 5786073006_I

source_name: CONTROL

value: CONTROL

value: whole blood


title: Whole blood CASE 5786073007_I

source_name: CASE

value: CASE


title: Patient 4, Tumor Sample, Location 1

source_name: Patient 4, Tumor Sample, Location 1


title: Patient 1, Tumor Sample, Location 2

source_name: Patient 1, Tumor Sample, Location 2


title: Patient 20, Tumor Sample, Location 3

source_name: Patient 20, Tumor Sample, Location 3


title: MDA_MB_468_DMSO_2

source_name: MDA-MB-468 cells


title: MDA_MB_468_DMSO_1


title: Whole blood CASE 5786073006_H


title: Whole blood CONTROL 5786073006_E

value: Female


title: Whole blood CASE 5786073006_G


title: Whole blood CASE 5786073006_A


title: Whole blood CONTROL 5786073006_B


title: Whole blood CASE 5786073006_F


title: Whole blood CONTROL 5786073003_L


title: Whole blood CASE 5786073006_C


title: Whole blood CONTROL 5786073006_D


title: Patient 4, Tumor Sample, Location 2

source_name: Patient 4, Tumor Sample, Location 2


title: Patient 1, Tumor Sample, Location 1

source_name: Patient 1, Tumor Sample, Location 1


title: Whole blood CASE 5786073003_J


title: Whole blood CASE 5786073003_K


title: Whole blood CASE 5786073003_I


title: Whole blood CASE 5786073003_C


title: H.influenzae R3763-2

city: Oklahoma City

first: Timothy

middle: M

last: VanWagoner

state: OK

address: 940 SL Young Blvd, BMS340

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

description: Biological replicate 2

hyb_protocol: Arrays were pre-hybridized in NimbleGen hybridization chamber at 45°C for two hours with gentle rotation using a buffer containing 100mg/ml herring sperm DNA (Promega Corporation, Madison, WI) 50mM MES, 1M NaCl, 10mM EDTA, 0.005% Tween-20 for fifteen minutes. The prehybe solution was replaced with a 350ml volume of the same composition as the pre-hybridization buffer but supplemented with 4mg of labeled prokaryotic cDNA and 1nM labeled control oligonucleotide. The array was hybridized overnight at 45°C with gentle rotation. Following hybridization, the arrays were removed from the hybridization and washed three times, at room temperature, in a buffer containing 6X SSPE, 0.01% (v/v) Tween-20 and then six times in a buffer containing 100mM MES, 26mM NaCl, 0.01% (v/v) Tween-20 at 45°C. Arrays were stained) in a buffer containing 50mM MES, pH 6.6, 1M NaCl, 0.005% Tween-20, and 1:1000 dilution of Streptavidin-Cy3 (GE Healthcare) for ten minutes with gentle agitation, then washed twice in 6X SSPE, 0.01% (v/v) Tween-20 at room temperature, dried under argon and stored desiccated.

scan_protocol: Scanning was done with NimbleScan version=2.4.31

data_processing: Software for data normalization were tools from the Bioconductor project. Data was normalized using quantile normalization as described by Bolstad (2003), and gene calls generated using the RMA algorithm as described by Irizarry (2003).

organism: Haemophilus influenzae R2866

source_name: H. influenzae R3763 grown in sBHI_ replicate 2

label_protocol: Total prokaryotic RNA is converted to cDNA by random primed reverse transcription with SuperScript II (Invitrogen Corporation, Carlsbad, CA) in a reaction containing 10mg RNA, 1mg random hexamer, 1200U SuperScript II, 1X SuperScript first strand buffer, 20mM DTT, 500mM dNTPs in a total volume of 60ml. Following incubation, residual RNA was enzymatically degraded with the addition of 1U RNase H and 1mg RNase A. Reactions were purified by extraction with phenol:chloroform:isoamyl alcohol (25:24:1) followed by ethanol precipitation.in the presence of 1ml of Pellet Paint Co-Precipitant (EMD Biosciences, Madison WI). cDNA was enzymatically fragmented with 0.2U Dnase I in a 40ml reaction volume for 15 minutes at 37°C. Dnase I was inactivated by incubation at 99°C for ten minutes. Fragmented cDNA was end-labeled by the catalytic addition of 3’ biotin-N6-ddATP (Perkin-Elmer, Boston, MA) with terminal deoxynucleotidyl transferase (Promega Corporation, Madison, WI). The biotin-labeled reaction products were purified by centrifugal concentration through a Centricon YM-10 Concentrator (Millipore Corporation, Billerica, MA).

growth_protocol: H. influenzae were grown in brain heart infusion broth (BHI) containing 10ug/ml NAD and 2.0ug/ml hemin or RPMI 1640 with L-glutamine and 25mM HEPES, 0.87mM MEM sodium pyruvate, .775mM uracil, 6.5 mM inosine, pH 7.56

extract_protocol: RNA was prepared using Trizol (as described by the manufacturer). Residual genomic DNA was removed by treatment with RNase-free DNase (Invitrogen) as directed by the manufacturer and confirmed by q-rt-PCR analysis. RNA samples were then precipitated using LiCl and samples resolved by PAGE to ensure sample integrity.

treatment_protocol: 25 ml samples were taken after once cultures reached OD600 of 0.3 to 0.4 and transfered into an equal volume of RNAProtect reagent.

tag: strain

value: Strain R2866 modA10::Rb

tag: protocol

value: supplemented brain heart infusion broth


title: H.influenzae R3790-1

description: Biological replicate 1

source_name: H. influenzae R2866 grown in chemically defined media_ replicate 1

value: Strain R2866

value: chemically defined media


title: H.influenzae R3791-2

description: Biological replicate 2

source_name: H. influenzae R3763 grown in chemically defined media_ replicate 2


title: H.influenzae R3791-1

description: Biological replicate 1

source_name: H. influenzae R3763 grown in chemically defined media_ replicate 1


title: H.influenzae R3790-3

description: Biological replicate 3

source_name: H. influenzae R2866 grown in chemically defined media_ replicate 3


title: Whole blood CASE 5786073003_G


title: Whole blood CONTROL 5786073003_E


title: H.influenzae R3763-1

description: Biological replicate 1

source_name: H. influenzae R3763 grown in sBHI_ replicate 1


title: Whole blood CONTROL 5786073003_B


title: Whole blood CONTROL 5786073003_A


title: Whole blood CASE 5786073003_H


title: Whole blood CONTROL 5786073003_F


title: H.influenzae R2866-2

description: Biological replicate 2

source_name: H. influenzae R2866 grown in sBHI_ replicate 2


title: Whole blood CASE 5786073003_D


title: H.influenzae R2866-3

description: Biological replicate 3

source_name: H. influenzae R2866 grown in sBHI_ replicate 3


title: H.influenzae R3790-2

description: Biological replicate 2

source_name: H. influenzae R2866 grown in chemically defined media_ replicate 2


title: H.influenzae R2866-1

description: Biological replicate 1

source_name: H. influenzae R2866 grown in sBHI_ replicate 1


title: Rrm3 binding sml1D rad53D 150mM HU 90 minutes from G1 release (related to Figure S1A)

city: Milano

first: Michele

last: Giannattasio

state: Italy

address: Via Adamello, 16

department: Genome stability

institute: IFOM

description: sml1D rad53D Rrm3-myc cells were arrested in G1 and released in 150 mM of HU. Pif1 binding profiles were determined at 90 minutes from the G1 release.

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

organism: Saccharomyces cerevisiae

source_name: sml1D rad53D Rrm3 binding 90 min 150mM HU

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in YP+glucose 2% at 28°C

extract_protocol: ssDNA-BrdU-IP on chip profiles were determined as described in (Katou et al 2003). Binding profiles by ChIP on chip were determined as described in (Bermejo et al., 2009).

treatment_protocol: G1 synchronization was performed in YP+glucose 2% at 28°C with 4 μg/ml final alpha facfor concentration.G1-arrested cells were released in YP+glucose 2% supplemented either with 150 mM or 25 mM of hydroxyurea (HU).For ChIP on chip binding profiles cells were fixed with 1% Formaldehyde for 30 minutes. For BrdU incorporation profiles cells were released in HU with 200 ug/ml of BrdU and fixed with 0.1% Sodium Azide on ice for 30 minutes at the indicated times.

tag: antibody

value: anti-Myc clone 9E10

tag: genotype

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, CAN1, GAL, PSI+, sml1::TRP1, rad53::KANMX6, RRM3-13MYC-HIS3 (W303 derivative RAD5 locus wild type)

tag: growth protocol

value: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) for 2h and 15 minutes and released in YP+2% glucose with 150 mM hydroxyurea (HU).

tag: treatment

value: 150 mM hydroxyurea (HU) 90 minutes. Cell were fixed with 1% Formaldehyde for 30 minutes.

source_name: input DNA

value: input DNA


title: Pol1 binding sml1D rad53D rrm3D pif1-m2 150mM HU 60 minutes from G1 release (related to Supplemental Figure S2)

description: sml1D rad53D rrm3D pif1-m2 Pol1-FLAG cells were arrested in G1 and released in 150 mM of HU. Pol1 binding profiles were determined at 60 minutes from the G1  release.

source_name: sml1D rad53D Pol1 binding 60 min 150 mM HU

value: anti-FLAG M2 F1804 (SIGMA)

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, CAN1, GAL, PSI+, POL1-6HIS-3FLAG-NATMX, sml1::TRP1, rad53::KANMX6, rrm3::HIS3, pif1-m2 (W303 derivative RAD5 locus wild type)

value: 150 mM hydroxyurea (HU) 60 minutes. Cell were fixed with 1% Formaldehyde for 30 minutes.


title: Rrm3 binding sml1D 150mM HU 90 minutes from G1 release (related to Figure S1A)

description: sml1D Rrm3-myc cells were arrested in G1 and released in 150 mM of HU. Pif1 binding profiles were determined at 90 minutes from the G1 release.

source_name: sml1D Rrm3 binding 90 min 150mM HU

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, CAN1, GAL, PSI+, sml1::TRP1, RRM3-13MYC-HIS3 (W303 derivative RAD5 locus wild type)


title: Pol1 binding sml1D rad53D 150mM HU 60 minutes from G1 release (related to Supplemental Figure S2)

description: sml1D rad53D Pol1-FLAG cells were arrested in G1 and released in 150 mM of HU. Pol1 binding profiles were determined at 60 minutes from the G1  release.

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, CAN1, GAL, PSI+, POL1-6HIS-3FLAG-NATMX, sml1::TRP1, rad53::KANMX6 (W303 derivative RAD5 locus wild type)


title: Rrm3 binding  sml1D rad53D 25mM HU 45 minutes from G1 release (related to Figure 2A)

description: sml1D rad53D RRM3-MYC cells were arrested in G1 and released in 25 mM of HU. Rrm3 binding profiles were determined at 45 minutes from the G1  release.

source_name: sml1D rad53D Rrm3 binding 45 min 25 mM HU

value: anti-MYC antibody

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, CAN1, GAL, PSI+, sml1::TRP1, rad53::KANMX6, RRM3-13MYC-HIS3(W303 derivative RAD5 locus wild type)

value: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) for 2h and 15 minutes and released in YP+2% glucose with 25  mM hydroxyurea (HU).

value: 25 mM hydroxyurea (HU) 45 minutes. Cell were fixed with 1% Formaldehyde for 30 minutes.


title: Pif1 binding  sml1D rad53D 25mM HU 45 minutes from G1 release (related to Figure 2A)

description: sml1D rad53D Pif1-FLAG cells were arrested in G1 and released in 25 mM of HU. Pif1 binding profiles were determined at 45 minutes from the G1  release.

source_name: sml1D rad53D Pif1 binding 45 min 25 mM HU

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, can1-100, GAL, PSI+, sml1::TRP1, rad53::KANMX6, PIF1-6HIS-3FLAG-NATMX (W303 derivative RAD5 locus wild type)


title: Pol1 binding  sml1D rad53D 25mM HU 45 minutes from G1 release (related to Figure 2A)

description: sml1D rad53D Pol1-FLAG cells were arrested in G1 and released in 25 mM of HU. Pol1 binding profiles were determined at 45 minutes from the G1  release.

source_name: sml1D rad53D Pol1 binding 45 min 25 mM HU


title: hESC_EB6_shKBTBD8_replicate2

city: Berkeley

first: Michael

last: Rape

address: 330F Li Ka Shing Center

department: Molecular and Cell Biology

institute: UC Berkeley

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on HUMAN GENE 1.0 ST ARRAY Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the G7 GeneChip Scanner.

data_processing: The data were analyzed with Bioconducter/R GCRMA. The trimmed mean target intensity of each array was arbitrarily set to 6.

source_name: Embryoid bodies, sh KBTBD8, differentiation for 6 days

label_protocol: Biotinylated cRNA were prepared according to the standard NuGen's protocol from >50ng of total RNA

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, # 74104) according to the manufacturer's insructions

tag: cell line

value: hESC H1

tag: lentiviral infection

value: lentiviral infection with shRNA targeting KBTBD8

tag: differentiation state

value: Embroyid bodies, 6 days

value: differentiation in AggrewellTM800 plates (#27865, StemCell Technologies Inc.) and APEL medium (#05210, StemCell Technologies Inc.) following the guidelines of the manufacturer’s technical manual (#29146).


title: hESC_H1_shcontrol_replicate3

source_name: hESC plurpotent, sh control

value: lentiviral infection with control shRNA

value: pluripotent

value: feeder-free culture on matrigel-coated plates (#354277, BD Biosiences) in mTeSRTM1, (#05871/05852, 30 StemCell Technologies Inc,)


title: hESC_EB6_shcontrol_replicate3

source_name: Embryoid bodies, sh control, differentiation for 6 days


title: hESC_H1_shKBTBD8_replicate3

source_name: hESC plurpotent, sh KBTBD8


title: hESC_EB6_shKBTBD8_replicate1


title: hESC_H1_shKBTBD8_replicate1


title: hESC_EB6_shcontrol_replicate1


title: hESC_H1_shKBTBD8_replicate2


title: hESC_H1_shcontrol_replicate2


title: hESC_EB6_shKBTBD8_replicate3


title: BrdU incorporation sml1D rad53D 25mM HU 45 minutes from G1 release (related to Figure 2A)

description: sml1D rad53D cells carrying the TK repeats were arrested in G1 and released in 25 mM of HU with 200 ug/ml of BrdU. BrdU incorporation profiles were determined at 45 minutes from the G1  release.

source_name: sml1D rad53D BrdU 45 min 25 mM HU

value: anti-BrdU MI-11-3 (MBL)

value: MAT a ade2-1 ura3-1 his3-11,15 leu2-3,112, trp1-1 CAN1, GAL, PSI+, sml1::TRP1, rad53::KANMX4, ura3::7x-TKs-URA3 (W303 derivative RAD5 locus wild type)

value: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) for 2h and 15 minutes and released in YP+2% glucose with 25  mM hydroxyurea (HU) and 200ug/ml BrdU.

value: 25 mM hydroxyurea (HU) 90 minutes with 200ug/ml BrdU. Cell were fixed with 0.1% sodium azide 40 minutes in ice.

tag: sample type

value: input DNA


title: hESC_H1_replicate3

source_name: hESC plurpotent


title: hEB6_H1_replicate2

source_name: Embryoid bodies, differentiation for 6 days


title: hESC_H1_replicate2


title: hESC_EB6_shcontrol_replicate2


title: hEB6_H1_replicate3


title: Pif1 binding  sml1D 25 mM HU 45 minutes from G1 release (related to Figure 2A)

description: sml1D Pif1-FLAG cells were arrested in G1 and released in 25 mM of HU. Pif1 binding profiles were determined at 45 minutes from the G1  release.

source_name: sml1D Pif binding 45 min 25 mM HU

value: anti-FLAG M2 F1804 (SIGMA)

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, can1-100, GAL, PSI+, sml1::TRP1, PIF1-6HIS-3FLAG-NATMX (W303 derivative RAD5 locus wild type)


title: Rrm3 binding  sml1D 25 mM HU 45 minutes from G1 release (related to Figure 2A)

description: sml1D RRM3-MYC cells were arrested in G1 and released in 25 mM of HU. Rrm3 binding profiles were determined at 45 minutes from the G1  release.

source_name: sml1D Rrm3 binding 45 min 25 mM HU

value: anti-MYC antibody

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, CAN1, GAL, PSI+, sml1::TRP1, RRM3-13MYC-HIS3 (W303 derivative RAD5 locus wild type)

value: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) for 2h and 15 minutes and released in YP+2% glucose with 25  mM hydroxyurea (HU).


title: Pol1 binding sml1D 25 mM HU 45 minutes from G1 release (related to Figure 2A)

description: sml1D Pol1-FLAG cells were arrested in G1 and released in 25 mM of HU. Pol1 binding profiles were determined at 45 minutes from the G1  release.

source_name: sml1D Pol1 binding 45 min 25 mM HU

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, can1-100, GAL, PSI+, POL1-6HIS-3FLAG-NATMX, sml1::TRP1 (W303 derivative RAD5 locus wild type)

value: 25 mM hydroxyurea (HU) 45 minutes. Cell were fixed with 1% Formaldehyde for 30 minutes.


title: Pol1 binding sml1D rad53D 150mM HU 90 minutes from G1 release (related to Figure 1B)

description: sml1D rad53D POL1-FLAG cells were arrested in G1 and released in 150 mM of HU. Pol1 Binding profiles were determined at 90 minutes from the G1  release.

source_name: sml1D rad53D Pol1 binding 90 min 150mM HU

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, CAN1, GAL, PSI+, POL1-6HIS-3FLAG-NATMX, sml1::TRP1, rad53::KANMX6 (W303 derivative RAD5 locus wild type)

value: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) for 2h and 15 minutes and released in YP+2% glucose with 150 mM hydroxyurea (HU).

value: 150 mM hydroxyurea (HU) 90 minutes. Cell were fixed with 1% Formaldehyde for 30 minutes.


title: hESC_H1_replicate1

value: hESC H1

value: pluripotent


title: hEB6_H1_replicate1

value: Embroyid bodies, 6 days

value: differentiation in AggrewellTM800 plates (#27865, StemCell Technologies Inc.) and APEL medium (#05210, StemCell Technologies Inc.) following the guidelines of the manufacturer’s technical manual (#29146).


title: Pif1 binding  sml1D 150mM HU 90 minutes from G1 release (related to Figure 1B)

description: sml1D PIF1-FLAG cells were arrested in G1 and released in 150 mM of HU. Pif1 binding profiles were determined at 90 minutes from the G1  release.

source_name: sml1D Pif1 binding 90 min 150mM HU

source_name: input DNA


title: Pol1 binding sml1D 150mM HU 90 minutes from G1 release (related to Figure 1B)

description: sml1D POL1-FLAG cells were arrested in G1 and released in 150 mM of HU. Pol1 binding profiles were determined at 90 minutes from the G1  release.

source_name: sml1D Pol1 binding 90 min 150mM HU


title: BrdU incorporation sml1D rad53D 150mM HU 90 minutes from G1 release (related to Figure 1B)

description: sml1D rad53D cells carrying the TK repeats were arrested in G1 and released in 150 mM of HU with 200 ug/ml of BrdU.BrdU incorporation profiles have been determined at 90 minutes from the G1  release.

source_name: sml1D rad53D BrdU 90 min 150mM HU

value: anti-BrdU MI-11-3 (MBL)

value: MAT a ade2-1 ura3-1 his3-11,15 leu2-3,112, trp1-1 CAN1, GAL, PSI+, sml1::TRP1, rad53::KANMX4, ura3::7x-TKs-URA3 (W303 derivative RAD5 locus wild type)

value: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) for 2h and 15 minutes and released in YP+2% glucose with 150 mM hydroxyurea (HU)  and 200ug/ml BrdU.

value: 150 mM hydroxyurea (HU) 90 minutes with 200ug/ml BrdU. Cell were fixed with 0.1% sodium azide 40 minutes in ice.


title: Rrm3 binding rad53-k227a 150mM HU 90 minutes from G1 release (related to Figure 1A)

description: RRM3-MYC rad53-k227a cells were arrested in G1 and released in 150 mM of HU.Rrm3 binding profiles have been determined at 90 minutes from the G1  release

source_name: rad53-k227a Rrm3 binding 90 min 150mM HU

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, CAN1, GAL, PSI+, rad53-K227A-KANMX6, RRM3-13MYC-HIS3 (W303 derivative RAD5 locus wild type)

value: input DNA


title: hESC_H1_shcontrol_replicate1

value: lentiviral infection with control shRNA

value: feeder-free culture on matrigel-coated plates (#354277, BD Biosiences) in mTeSRTM1, (#05871/05852, 30 StemCell Technologies Inc,)


title: BrdU incorporation sml1D 25mM HU 45 minutes from G1 release (related to Figure 2A)

description: sml1D cells carrying the TK repeats were arrested in G1 and released in 25 mM of HU with 200 ug/ml of BrdU. BrdU incorporation profiles were determined at 45 minutes from the G1  release.

source_name: sml1D BrdU 45 min 25 mM HU

value: MAT a ade2-1 ura3-1 his3-11,15 leu2-3,112, trp1-1 CAN1, GAL, PSI+, sml1::TRP1, ura3::7x-TKs-URA3 (W303 derivative RAD5 locus wild type)

value: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) for 2h and 15 minutes and released in YP+2% glucose with 25  mM hydroxyurea (HU)  and 200ug/ml BrdU.

value: 25 mM hydroxyurea (HU) 45 minutes with 200ug/ml BrdU. Cell were fixed with 0.1% sodium azide 40 minutes in ice.


title: Pif1 binding sml1D rad53D 150mM HU 90 minutes from G1 release (related to Figure 1B)

description: sml1D rad53D PIF1-FLAG cells were arrested in G1 and released in 150 mM of HU. Pif1 Binding profiles were determined at 90 minutes from the G1  release.

source_name: sml1D rad53D Pif1 binding 90 min 150mM HU

value: anti-FLAG M2 F1804 (SIGMA)

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, can1-100, GAL, PSI+, sml1::TRP1, rad53::KANMX6, PIF1-6HIS-3FLAG-NATMX (W303 derivative RAD5 locus wild type)

value: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) for 2h and 15 minutes and released in YP+2% glucose with 150 mM hydroxyurea (HU).


title: Activated neutrophil rep3

city: Bronx

first: Dachuan

last: Zhang

address: 1301 Morris Park Avenue, Price Center 113

department: Cell Biology

institute: Albert Einstein College of Medicine

description: gene expression data from neutrophils with CD45.1 allele

hyb_protocol: Labeled cRNA was hybridized to Mouse Gene ST 1.0 microarrays (Affymetrix).

scan_protocol: Gene chips were scanned by GeneChip Scanner 3000 7G system (Affymetrix).

data_processing: Raw data were normalized by RMA algorithm and analysed using the Gene Pattern analysis platform (Broad Institute).

source_name: neutrophils 2 hours after TNF-α injection

label_protocol: Amplified cRNA was labelled with the GeneChip WT terminal labelling kit (Affymetrix).

growth_protocol: Control and aged neutrophils were derived by adoptive transfer for 10 min and 6 h, respectively. Activated neutrophils were harvested from mice injected with 0.5 μg TNF-α for 2 hours.

extract_protocol: Total RNA from sorted neutrophils was extracted using RNeasy Plus Micro Kit (Qiagen). RNA was amplified using Ovation One-Direct System (NuGEN).

treatment_protocol: 2000 neutrophils were directly sorted from mouse blood using fluorescence-activated cell sorting (FACS).

tag: tissue

value: Blood

tag: cell type

value: neutrophil

value: activated


title: Activated neutrophil rep2


title: Aged neutrophil rep3

source_name: neutrophils 6 hours after adoptive transfer

value: aged


title: BrdU incorporation sml1D 150mM HU 90 minutes from G1 release (related to Figure 1B)

description: sml1D cells carrying the TK repeats were arrested in G1 and released in 150 mM of HU with 200 ug/ml of BrdU. BrdU incorporation profiles were determined at 90 minutes from the G1  release.

source_name: sml1D BrdU 90 min 150mM HU

value: anti-BrdU MI-11-3 (MBL)


title: Not tag profile generated using anti-my antibody 150 mM HU 90 minutes (related to figure 1A)

description: wild type cells (no tag)  were arrested in G1 and released in 150 mM of HU. Binding profiles have been determined at 90 minutes from the G1  release.

source_name: No tag profile anti-MYC antibody 90 min 150 mM HU

value: anti-MYC antibody

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, CAN1, GAL, PSI+ (W303 derivative RAD5 locus wild type)

value: 150 mM hydroxyurea (HU) 90 minutes. Cell were fixed with 1% Formaldehyde for 30 minutes.


title: Pol1 binding rad53-k227a 150mM HU 90 minutes from G1 release (related to Figure 1A)

description: POL1-MYC rad53-k227a cells were arrested in G1 and released in 150 mM of HU.Pol1 binding profiles have been determined at 90 minutes from the G1  release.

source_name: rad53-k227a Pol1 binding 90 min 150mM HU

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, CAN1, GAL, PSI+, POL1-9MYC-TRP1, rad53-K227A-KANMX6 (W303 derivative RAD5 locus wild type)

value: input DNA


title: Aged neutrophil rep1


title: Aged neutrophil rep2


title: Control neutrophil rep2

source_name: neutrophils 10 min after adoptive transfer

value: control


title: Not tag profile generated using anti-FLAG antibody 150 mM HU 90 minutes (related to figure 1B)

source_name: No tag profile anti-FLAG antibody 90 min 150 mM HU