title: HSB112_CGE_L [exon-level]

value: CGE


title: HSB112_DFC_R [exon-level]

status: Public on Oct 27 2011

type: RNA

city: New Haven

first: Feng

last: Cheng

state: CT

address: 333 Cedar Street SHM C338

department: Neurobiology

country: USA

institute: Yale University

hyb_protocol: Microarrays were hybridized at 45 °C for 16–24 hours, washed and stained using an Affymetrix FS450 fluidics station, according to manufacturer recommendations. Microarrays were scanned on a GeneChip Scanner 3000 and visually inspected for hybridization artefacts. Exon chip analysis was performed using Affymetrix Power Tools 1.12.0. Probe level data was summarized into probe set level data using the Robust Multichip Average (RMA) background correction algorithm in combination with an R-script. The raw image files (.DAT files) were analyzed using Affymetrix GeneChip Operating Software to generate CEL files.

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing:
Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. These high-quality core probe sets have reliable annotations from RefSeq (www.ncbi.nlm.nih.gov) or Ensembl (www.ensembl.org). Datasets were annotated according to the UCSC human genome hg19 reference sequence (http://genome.ucsc.edu/cgi-bin/hgGateway). 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. The gene and exon expression were evaluated twice, with one evaluation excluding SNP-containing probe sets. The Pearson correlation analysis was performed to compare gene and exon expression levels of the data with and without SNP-containing probe sets. Almost all of the correlation coefficients (98.8%) for all 1,340 samples were within the range of 0.980-0.995 for genes and 0.975-0.995 for exons, suggesting that SNP-containing probe sets have a very minimal effect on measured expression levels (Supplementary Fig.6). Nevertheless, we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values. To filter out low expression signals (including noise or poorly hybridized probes), which may lead to false positives, detection above background (DABG) P-values of exon probe sets and transcript clusters were calculated using Affymetrix power tools (APT, http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx).
The expression level for all core probe sets within an exon were averaged to obtain an expression value for the exon, and the median of all exons within one gene (transcript cluster) was used as the estimate of gene expression.

label: Biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Exon array hybridizations were performed at the Yale Center for Genome Analysis and at Gene Logic Inc. (Gaithersburg, MD). Reverse transcription (RT) was performed to generate cDNA from total RNA using RT primers designed using an oligonucleotide matching algorithm. For the selective cDNA synthesis, the Ambion WT Expression kit (Ambion) was used in combination with the GenechipWT Terminal Labeling and Controls Kit (Affymetrix) for target preparation, according to manufacturer recommendations. PolyA controls were added to the input RNA to measure efficiency of target amplification. Fragmented and labelled second cycle cDNA (5.5 μg) was added to a hybridization cocktail prior to loading of 200 μl onto individual Affymetrix Human Exon 1.0 ST arrays.

extract_protocol: A bead mill homogenizer (Bullet Blender, Next Advance) was used to lyse the pulverized tissue. Each pulverized tissue sample was transferred to a chilled safe-lock microcentrifuge tube (Eppendorf). A mass of chilled stainless steel beads (Next Advance, cat# SSB14B) equal to the mass of the tissue was added to the tube. Two volumes of Buffer RLT (Qiagen) were added to the tissue and beads. Samples were mixed in the Bullet Blender for 1 min at a speed of six. Samples were visually inspected to confirm desired homogenization and then incubated at 37 °C for five min. Buffer RLT was added up to 0.6 ml, and samples were mixed in the Bullet Blender for 1 min. Total RNA was extracted using a non-phenolic procedure (RNeasy Plus Mini Kit, Qiagen), followed by DNase treatment (TURBO DNase, Ambion) as per manufacturers’ instructions. Optical density values of extracted RNA were measured using a NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RNA integrity number (RIN) was determined for each sample using Bioanalyzer RNA 6000 Nano Kit or Bioanalyzer RNA 6000 Pico Kit (Agilent), depending upon the total amount of RNA.

treatment_protocol: This study was conducted using postmortem human brain specimens from tissue collections at the Department of Neurobiology at Yale University School of Medicine and the Clinical Brain Disorders Branch of the National Institute of Mental Health. Additional specimens were procured from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM), the Brain and Tissue Bank for Developmental Disorders at the University of Maryland, the Birth Defects Research Laboratory at the University of Washington, Advanced Bioscience Resources Inc. and the MRC-Wellcome Trust Human Developmental Biology Resource at the Institute of Human Genetics, University of Newcastle, UK. Tissue was collected after obtaining parental or next of kin consent and with approval by the institutional review boards at the Yale University School of Medicine, the National Institutes of Health, and at each institution from which tissue specimens were obtained. Specimens range in age from 5.7 post-conceptual weeks (PCW) to over 80 years. Of 57 post-mortem brain specimens included in this study, 24 were obtained with either left or right hemisphere, and 33 were obtained with both hemispheres. Embryonic and fetal age was extrapolated based on the date of the mother’s last menstruation, characteristics of the fetus noted upon ultrasonographic scanning, foot length of the fetus, and visual inspection.

tag: brain code

tag: region

value: DFC

tag: hemisphere

value: R

tag: Sex

value: M

tag: age

value: 8 PCW

tag: Stage

tag: postmortem interval

tag: ph

tag: rna integrity number


title: HSB112_ITC_R [exon-level]

value: ITC


title: HSB112_HIP_L [exon-level]

value: HIP

value: L


title: HSB113_DFC_L [gene-level]

data_processing:
Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction, quantile normalization, mean probe set summarization, and log2 transformation. Only high-quality core probe sets, as defined by Affymetrix, were included because theyalways have reliable annotations from RefSeq (www.ncbi.nlm.nih.gov) or Ensembl (www.ensembl.org). It is noted that thedatasets were annotated according to the UCSC human genome hg19 reference sequence (http://genome.ucsc.edu/cgi-bin/hgGateway).Besides,105,271 core probes (within 62,448 prob sets) contained common SNPswas removed because SNP-containing probe sets may lead to reduced signal intensity and result in spurious results. These probes were defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is basedon the dbSNPdatabase (version 129, April 2008) andSNPinprobe_1.0 database. Removal of SNP-affected probes was accomplished in Partek program.Probe sets and gene intensities was summarized only on those probes not affected by SNPs.Finally, a total of 17,565 genes (transcript clusters) were surveyed for downstream analysis.
probe group file: HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

value: F

value: 12 PCW


title: HSB113_A1C_R [gene-level]


title: HSB112_DTH_R [exon-level]

value: DTH


title: HSB112_DFC_L [exon-level]


title: HSB112_DTH_L [exon-level]


title: HSB113_A1C_L [gene-level]


title: HSB111_VFC_R [exon-level]

value: VFC


title: HSB111_V1C_R [exon-level]


title: HSB112_VFC_R [gene-level]


title: HSB112_CGE_R [exon-level]


title: HSB111_STR_R [exon-level]

value: STR


title: HSB112_STC_L [gene-level]

value: STC


title: HSB112_OFC_R [gene-level]

value: OFC


title: HSB112_VFC_L [gene-level]


title: HSB112_OFC_L [gene-level]


title: HSB112_PC_L [gene-level]

value: PC


title: HSB112_OC_R [gene-level]

value: OC


title: HSB111_V1C_L [exon-level]


title: HSB112_OC_L [gene-level]


title: HSB111_S1C_R [exon-level]


title: HSB112_PC_R [gene-level]


title: HSB111_STR_L [exon-level]


title: HSB112_STC_R [gene-level]


title: HSB112_MGE_L [gene-level]

value: MGE


title: HSB112_MGE_R [gene-level]


title: HSB112_MSC_R [gene-level]


title: HSB111_STC_L [exon-level]


title: HSB112_MSC_L [gene-level]


title: HSB111_OFC_L [exon-level]


title: HSB111_OFC_R [exon-level]


title: HSB111_S1C_L [exon-level]


title: HSB111_VFC_L [exon-level]


title: HSB111_MD_L [exon-level]

value: MD


title: HSB111_MFC_L [exon-level]

value: MFC


title: HSB111_STC_R [exon-level]

value: R


title: HSB111_MD_R [exon-level]


title: HSB112_MFC_R [gene-level]

value: M

value: 8 PCW


title: HSB111_MFC_R [exon-level]


title: HSB112_LGE_R [gene-level]

value: LGE


title: HSB112_ITC_R [gene-level]

value: ITC


title: HSB112_LGE_L [gene-level]

value: L


title: HSB112_MFC_L [gene-level]


title: HSB112_ITC_L [gene-level]


title: HSB111_M1C_R [exon-level]

value: F


title: HSB111_ITC_R [exon-level]


title: HSB111_M1C_L [exon-level]


title: HSB112_HIP_L [gene-level]

value: HIP


title: HSB112_DFC_R [gene-level]

value: DFC


title: HSB112_DTH_L [gene-level]

value: DTH


title: HSB111_IPC_L [exon-level]

value: IPC


title: HSB112_DTH_R [gene-level]


title: HSB112_CGE_R [gene-level]

value: CGE


title: HSB111_HIP_L [exon-level]


title: HSB112_CGE_L [gene-level]


title: HSB112_HIP_R [gene-level]


title: HSB111_HIP_R [exon-level]


title: HSB111_ITC_L [exon-level]


title: HSB111_DFC_R [exon-level]


title: HSB111_DFC_L [exon-level]


title: HSB112_DFC_L [gene-level]


title: HSB111_IPC_R [exon-level]


title: HSB111_AMY_R [exon-level]

value: AMY


title: HSB112_AMY_R [gene-level]


title: HSB111_AMY_L [exon-level]


title: HSB112_AMY_L [gene-level]


title: HSB111_A1C_L [exon-level]


title: HSB111_V1C_L [gene-level]


title: HSB111_STR_R [gene-level]

value: STR


title: HSB111_V1C_R [gene-level]


title: HSB111_VFC_L [gene-level]

value: VFC


title: HSB107_V1C_L [exon-level]

value: 21 PCW


title: HSB107_STR_L [exon-level]


title: HSB111_STR_L [gene-level]


title: HSB107_VFC_L [exon-level]


title: HSB107_V1C_R [exon-level]


title: HSB111_A1C_R [exon-level]


title: HSB111_VFC_R [gene-level]


title: HSB107_VFC_R [exon-level]


title: HSB111_STC_R [gene-level]

value: STC


title: HSB107_STC_L [exon-level]


title: HSB107_STC_R [exon-level]

value: R


title: HSB107_STR_R [exon-level]


title: HSB107_S1C_R [exon-level]


title: HSB111_S1C_L [gene-level]


title: HSB111_S1C_R [gene-level]


title: HSB111_OFC_R [gene-level]

value: OFC


title: HSB107_MFC_L [exon-level]

value: MFC


title: HSB111_MFC_L [gene-level]


title: HSB107_MFC_R [exon-level]


title: HSB111_MFC_R [gene-level]


title: HSB111_STC_L [gene-level]


title: HSB107_OFC_R [exon-level]


title: HSB107_S1C_L [exon-level]


title: HSB111_M1C_L [gene-level]


title: HSB107_M1C_R [exon-level]


title: HSB111_MD_R [gene-level]

value: MD


title: HSB107_MD_L [exon-level]


title: HSB111_OFC_L [gene-level]


title: HSB107_ITC_R [exon-level]

value: ITC


title: HSB111_M1C_R [gene-level]


title: HSB107_MD_R [exon-level]


title: HSB107_M1C_L [exon-level]

value: L


title: HSB107_OFC_L [exon-level]

value: F


title: HSB107_ITC_L [exon-level]


title: HSB107_IPC_R [exon-level]


title: HSB111_ITC_R [gene-level]


title: HSB111_ITC_L [gene-level]


title: HSB111_IPC_L [gene-level]


title: HSB111_MD_L [gene-level]


title: HSB111_IPC_R [gene-level]


title: HSB107_HIP_R [exon-level]

value: HIP


title: HSB111_HIP_R [gene-level]


title: HSB111_HIP_L [gene-level]


title: HSB107_IPC_L [exon-level]


title: HSB111_AMY_R [gene-level]


title: HSB111_DFC_R [gene-level]

value: DFC


title: HSB107_DFC_R [exon-level]


title: HSB107_HIP_L [exon-level]


title: HSB111_AMY_L [gene-level]


title: HSB111_DFC_L [gene-level]


title: HSB107_DFC_L [exon-level]


title: HSB111_A1C_R [gene-level]


title: HSB106_VFC_R [exon-level]

value: M


title: HSB111_A1C_L [gene-level]


title: HSB107_AMY_R [exon-level]


title: HSB107_VFC_R [gene-level]


title: HSB107_A1C_L [exon-level]


title: HSB107_A1C_R [exon-level]


title: HSB107_VFC_L [gene-level]


title: HSB107_AMY_L [exon-level]


title: HSB106_V1C_L [exon-level]


title: HSB107_V1C_R [gene-level]


title: HSB107_V1C_L [gene-level]


title: HSB106_STR_R [exon-level]


title: HSB107_STC_R [gene-level]


title: HSB106_VFC_L [exon-level]


title: HSB106_STR_L [exon-level]


title: HSB107_STR_R [gene-level]


title: HSB107_STC_L [gene-level]


title: HSB106_V1C_R [exon-level]


title: HSB107_S1C_R [gene-level]


title: HSB107_STR_L [gene-level]


title: HSB106_S1C_R [exon-level]


title: HSB107_OFC_R [gene-level]


title: HSB106_S1C_L [exon-level]


title: HSB107_S1C_L [gene-level]


title: HSB106_STC_L [exon-level]


title: HSB106_STC_R [exon-level]


title: HSB107_OFC_L [gene-level]


title: HSB107_MD_R [gene-level]


title: HSB106_MFC_R [exon-level]


title: HSB107_MD_L [gene-level]


title: HSB107_M1C_R [gene-level]


title: HSB107_MFC_R [gene-level]


title: HSB106_OFC_L [exon-level]


title: HSB107_MFC_L [gene-level]


title: HSB107_M1C_L [gene-level]


title: HSB106_MD_R [exon-level]


title: HSB106_MFC_L [exon-level]


title: HSB107_ITC_R [gene-level]


title: HSB107_IPC_R [gene-level]

value: IPC


title: HSB107_ITC_L [gene-level]


title: HSB106_M1C_R [exon-level]


title: HSB106_MD_L [exon-level]


title: HSB107_IPC_L [gene-level]


title: HSB106_ITC_R [exon-level]


title: HSB106_M1C_L [exon-level]


title: HSB107_HIP_R [gene-level]


title: HSB106_HIP_R [exon-level]


title: HSB106_ITC_L [exon-level]


title: HSB106_IPC_L [exon-level]


title: HSB107_DFC_L [gene-level]


title: HSB107_DFC_R [gene-level]


title: HSB107_HIP_L [gene-level]


title: HSB106_OFC_R [exon-level]


title: HSB106_IPC_R [exon-level]


title: HSB107_AMY_R [gene-level]


title: HSB106_HIP_L [exon-level]


title: HSB107_AMY_L [gene-level]


title: HSB106_DFC_L [exon-level]


title: HSB106_DFC_R [exon-level]


title: HSB106_VFC_L [gene-level]


title: HSB106_VFC_R [gene-level]


title: HSB107_A1C_L [gene-level]


title: HSB107_A1C_R [gene-level]


title: HSB106_V1C_R [gene-level]


title: HSB106_V1C_L [gene-level]


title: HSB106_STR_L [gene-level]


title: HSB106_AMY_R [exon-level]


title: HSB106_STC_R [gene-level]


title: HSB106_STR_R [gene-level]


title: HSB106_STC_L [gene-level]


title: HSB106_AMY_L [exon-level]


title: HSB106_S1C_L [gene-level]


title: HSB106_S1C_R [gene-level]


title: HSB105_VFC_R [exon-level]


title: HSB105_VFC_L [exon-level]


title: HSB106_A1C_R [exon-level]


title: HSB106_OFC_R [gene-level]


title: HSB106_OFC_L [gene-level]


title: HSB105_STC_R [exon-level]


title: HSB105_V1C_L [exon-level]


title: HSB105_S1C_R [exon-level]


title: HSB105_S1C_L [exon-level]


title: HSB105_V1C_R [exon-level]


title: HSB106_MFC_R [gene-level]


title: HSB106_A1C_L [exon-level]


title: HSB105_MFC_R [exon-level]


title: HSB105_OFC_L [exon-level]


title: HSB105_STC_L [exon-level]


title: HSB105_M1C_L [exon-level]


title: HSB105_MFC_L [exon-level]


title: HSB105_M1C_R [exon-level]


title: HSB106_MFC_L [gene-level]


title: HSB105_OFC_R [exon-level]


title: HSB106_MD_L [gene-level]


title: HSB106_MD_R [gene-level]


title: HSB106_M1C_R [gene-level]


title: HSB106_M1C_L [gene-level]


title: HSB106_IPC_L [gene-level]


title: HSB106_ITC_R [gene-level]


title: HSB105_IPC_L [exon-level]


title: HSB106_ITC_L [gene-level]


title: HSB106_IPC_R [gene-level]


title: HSB105_ITC_R [exon-level]


title: HSB105_IPC_R [exon-level]


title: HSB105_ITC_L [exon-level]


title: HSB105_HIP_R [exon-level]


title: HSB105_A1C_L [exon-level]


title: HSB105_HIP_L [exon-level]


title: HSB105_AMY_R [exon-level]


title: HSB106_DFC_L [gene-level]


title: HSB106_HIP_L [gene-level]


title: HSB105_DFC_R [exon-level]


title: HSB104_TC_LR [exon-level]

value: TC

value: LR

value: 5.7 PCW


title: HSB106_DFC_R [gene-level]


title: HSB106_HIP_R [gene-level]


title: HSB106_AMY_R [gene-level]

value: AMY


title: HSB104_VF_LR [exon-level]

value: VF


title: HSB105_A1C_R [exon-level]


title: HSB106_A1C_L [gene-level]


title: HSB104_OC_LR [exon-level]

value: OC


title: HSB106_AMY_L [gene-level]


title: HSB104_HIP_LR [exon-level]


title: HSB106_A1C_R [gene-level]

value: R


title: HSB105_DFC_L [exon-level]


title: HSB105_VFC_L [gene-level]

value: VFC


title: HSB104_DIE_LR [exon-level]

value: DIE


title: HSB105_V1C_R [gene-level]


title: HSB105_VFC_R [gene-level]


title: HSB104_FC_LR [exon-level]

value: FC


title: HSB105_STC_R [gene-level]

value: STC


title: HSB105_V1C_L [gene-level]

value: L


title: HSB103_VFC_L [exon-level]

value: 13 PCW


title: HSB103_VFC_R [exon-level]


title: HSB103_V1C_R [exon-level]


title: HSB104_PC_LR [exon-level]

value: PC


title: HSB103_STR_R [exon-level]

value: STR


title: HSB103_V1C_L [exon-level]

value: M


title: HSB105_STC_L [gene-level]


title: HSB103_STR_L [exon-level]


title: HSB105_S1C_R [gene-level]


title: HSB105_S1C_L [gene-level]


title: HSB105_OFC_R [gene-level]

value: OFC


title: HSB103_STC_L [exon-level]


title: HSB103_S1C_R [exon-level]


title: HSB105_MFC_L [gene-level]

value: MFC


title: HSB105_MFC_R [gene-level]


title: HSB103_STC_R [exon-level]


title: HSB105_OFC_L [gene-level]


title: HSB103_S1C_L [exon-level]


title: HSB105_M1C_L [gene-level]


title: HSB103_OFC_L [exon-level]


title: HSB103_OFC_R [exon-level]


title: HSB105_M1C_R [gene-level]


title: HSB105_ITC_R [gene-level]

value: ITC


title: HSB103_MFC_R [exon-level]


title: HSB105_HIP_R [gene-level]

value: HIP


title: HSB105_IPC_R [gene-level]

value: IPC


title: HSB103_MFC_L [exon-level]


title: HSB105_IPC_L [gene-level]


title: HSB103_M1C_R [exon-level]


title: HSB103_M1C_L [exon-level]


title: HSB105_ITC_L [gene-level]


title: HSB105_HIP_L [gene-level]


title: HSB105_DFC_R [gene-level]

value: DFC


title: HSB103_ITC_R [exon-level]


title: HSB103_IPC_R [exon-level]


title: HSB103_ITC_L [exon-level]


title: HSB103_IPC_L [exon-level]


title: HSB103_HIP_R [exon-level]


title: HSB105_DFC_L [gene-level]


title: HSB105_AMY_R [gene-level]

value: AMY


title: HSB103_HIP_L [exon-level]


title: HSB105_A1C_L [gene-level]


title: HSB105_A1C_R [gene-level]

value: R


title: HSB104_VF_LR [gene-level]

value: VF

value: LR

value: 5.7 PCW


title: HSB103_DFC_R [exon-level]


title: HSB103_AMY_R [exon-level]


title: HSB103_AMY_L [exon-level]


title: HSB103_A1C_R [exon-level]


title: HSB103_VFC_R [gene-level]

value: VFC


title: HSB104_FC_LR [gene-level]

value: FC


title: HSB104_DIE_LR [gene-level]

value: DIE


title: HSB104_OC_LR [gene-level]

value: OC


title: HSB104_TC_LR [gene-level]

value: TC


title: HSB102_VFC_R [exon-level]

value: F

value: 21 PCW


title: HSB104_PC_LR [gene-level]

value: PC

value: M


title: HSB102_V1C_L [exon-level]

value: L


title: HSB102_STR_L [exon-level]

value: STR


title: HSB104_HIP_LR [gene-level]

value: HIP


title: HSB103_A1C_L [exon-level]

value: 13 PCW


title: HSB103_V1C_R [gene-level]

value: R


title: HSB103_DFC_L [exon-level]

value: DFC


title: HSB102_V1C_R [exon-level]


title: HSB102_STC_R [exon-level]

value: STC


title: HSB103_VFC_L [gene-level]


title: HSB103_V1C_L [gene-level]


title: HSB102_STR_R [exon-level]


title: HSB102_VFC_L [exon-level]


title: HSB103_STR_R [gene-level]


title: HSB102_S1C_R [exon-level]


title: HSB103_STR_L [gene-level]


title: HSB102_STC_L [exon-level]


title: HSB103_STC_R [gene-level]


title: HSB103_S1C_L [gene-level]


title: HSB103_STC_L [gene-level]


title: HSB103_OFC_R [gene-level]

value: OFC


title: HSB103_M1C_R [gene-level]


title: HSB102_S1C_L [exon-level]


title: HSB103_OFC_L [gene-level]


title: HSB103_MFC_L [gene-level]

value: MFC


title: HSB102_OFC_R [exon-level]


title: HSB103_S1C_R [gene-level]


title: HSB103_ITC_L [gene-level]

value: ITC


title: HSB103_MFC_R [gene-level]


title: HSB103_ITC_R [gene-level]


title: HSB102_MFC_R [exon-level]


title: HSB103_M1C_L [gene-level]


title: HSB103_IPC_R [gene-level]

value: IPC


title: HSB102_ITC_L [exon-level]


title: HSB102_ITC_R [exon-level]


title: HSB102_MD_L [exon-level]

value: MD


title: HSB102_MFC_L [exon-level]


title: HSB102_OFC_L [exon-level]


title: HSB102_IPC_R [exon-level]


title: HSB102_MD_R [exon-level]


title: HSB102_M1C_R [exon-level]


title: HSB103_DFC_R [gene-level]


title: HSB102_M1C_L [exon-level]


title: HSB103_IPC_L [gene-level]


title: HSB102_IPC_L [exon-level]


title: HSB102_HIP_L [exon-level]


title: HSB102_HIP_R [exon-level]


title: HSB102_DFC_R [exon-level]


title: HSB103_HIP_L [gene-level]


title: HSB103_A1C_L [gene-level]


title: HSB103_HIP_R [gene-level]


title: HSB103_A1C_R [gene-level]


title: HSB103_AMY_L [gene-level]

value: AMY


title: HSB103_AMY_R [gene-level]


title: HSB102_VFC_L [gene-level]

value: VFC

value: F


title: HSB102_VFC_R [gene-level]

value: 21 PCW


title: HSB102_A1C_R [exon-level]


title: HSB102_AMY_L [exon-level]


title: HSB103_DFC_L [gene-level]

value: M


title: HSB102_AMY_R [exon-level]


title: HSB102_A1C_L [exon-level]

value: L


title: HSB100_VFC_R [exon-level]

value: 19 PCW


title: HSB100_V1C_R [exon-level]


title: HSB102_V1C_R [gene-level]


title: HSB100_VFC_L [exon-level]


title: HSB100_V1C_L [exon-level]


title: HSB102_V1C_L [gene-level]


title: HSB100_STR_R [exon-level]

value: STR


title: HSB102_DFC_L [exon-level]


title: HSB100_STR_L [exon-level]


title: HSB102_STR_R [gene-level]


title: HSB100_STC_R [exon-level]


title: HSB102_STC_R [gene-level]


title: HSB102_STR_L [gene-level]


title: HSB102_S1C_L [gene-level]


title: HSB102_S1C_R [gene-level]


title: HSB102_STC_L [gene-level]


title: HSB100_STC_L [exon-level]


title: HSB100_S1C_R [exon-level]


title: HSB102_OFC_R [gene-level]


title: HSB100_S1C_L [exon-level]


title: HSB100_OFC_R [exon-level]


title: HSB100_OFC_L [exon-level]


title: HSB100_MFC_R [exon-level]


title: HSB100_MFC_L [exon-level]


title: HSB102_OFC_L [gene-level]


title: HSB102_MD_L [gene-level]


title: HSB102_MFC_R [gene-level]


title: HSB102_MD_R [gene-level]


title: HSB100_MD_L [exon-level]


title: HSB102_MFC_L [gene-level]


title: HSB102_M1C_R [gene-level]


title: HSB100_MD_R [exon-level]


title: HSB102_M1C_L [gene-level]


title: HSB100_M1C_L [exon-level]


title: HSB100_M1C_R [exon-level]


title: HSB100_ITC_R [exon-level]


title: HSB100_IPC_R [exon-level]


title: HSB102_IPC_L [gene-level]


title: HSB100_ITC_L [exon-level]


title: HSB102_IPC_R [gene-level]


title: HSB102_ITC_R [gene-level]


title: HSB102_ITC_L [gene-level]


title: HSB102_HIP_R [gene-level]

value: HIP


title: HSB100_HIP_L [exon-level]


title: HSB100_IPC_L [exon-level]


title: HSB100_HIP_R [exon-level]

value: R


title: HSB102_HIP_L [gene-level]


title: HSB102_DFC_R [gene-level]

value: DFC


title: HSB102_AMY_L [gene-level]


title: HSB102_AMY_R [gene-level]


title: HSB102_A1C_R [gene-level]


title: HSB100_VFC_R [gene-level]


title: HSB100_DFC_L [exon-level]


title: HSB102_DFC_L [gene-level]


title: HSB100_AMY_R [exon-level]


title: HSB100_DFC_R [exon-level]


title: HSB100_A1C_L [exon-level]


title: HSB100_A1C_R [exon-level]


title: HSB99_VFC_R [exon-level]


title: HSB100_AMY_L [exon-level]


title: HSB99_VFC_L [exon-level]


title: HSB99_V1C_R [exon-level]


title: HSB100_V1C_L [gene-level]


title: HSB102_A1C_L [gene-level]


title: HSB99_V1C_L [exon-level]


title: HSB100_STR_L [gene-level]


title: HSB100_VFC_L [gene-level]


title: HSB99_STR_L [exon-level]


title: HSB100_V1C_R [gene-level]


title: HSB99_STR_R [exon-level]


title: HSB100_STR_R [gene-level]


title: HSB100_STC_L [gene-level]

value: STC


title: HSB100_S1C_R [gene-level]


title: HSB99_STC_L [exon-level]


title: HSB99_STC_R [exon-level]


title: HSB100_S1C_L [gene-level]


title: HSB100_OFC_L [gene-level]

value: OFC


title: HSB99_MSC_R [exon-level]


title: HSB100_STC_R [gene-level]


title: HSB100_OFC_R [gene-level]


title: HSB99_MSC_L [exon-level]


title: HSB100_MFC_R [gene-level]

value: MFC


title: HSB100_MD_L [gene-level]


title: HSB99_MD_R [exon-level]


title: HSB99_MD_L [exon-level]


title: HSB100_M1C_R [gene-level]


title: HSB99_MFC_L [exon-level]


title: HSB99_IPC_R [exon-level]


title: HSB99_MFC_R [exon-level]


title: HSB99_IPC_L [exon-level]


title: HSB100_MFC_L [gene-level]


title: HSB100_MD_R [gene-level]


title: HSB99_HIP_R [exon-level]


title: HSB100_ITC_R [gene-level]

value: ITC


title: HSB100_M1C_L [gene-level]


title: HSB100_DFC_R [gene-level]


title: HSB100_IPC_L [gene-level]

value: IPC


title: HSB99_DFC_R [exon-level]


title: HSB99_HIP_L [exon-level]


title: HSB100_HIP_L [gene-level]


title: HSB100_HIP_R [gene-level]


title: HSB99_DFC_L [exon-level]


title: HSB100_IPC_R [gene-level]


title: HSB99_A1C_L [exon-level]


title: HSB99_A1C_R [exon-level]


title: HSB100_AMY_R [gene-level]


title: HSB100_ITC_L [gene-level]


title: HSB98_VFC_L [exon-level]


title: HSB98_VFC_R [exon-level]


title: HSB100_AMY_L [gene-level]


title: HSB98_STR_R [exon-level]


title: HSB98_V1C_R [exon-level]


title: HSB100_DFC_L [gene-level]


title: HSB98_V1C_L [exon-level]


title: HSB98_STC_L [exon-level]


title: HSB100_A1C_R [gene-level]


title: HSB99_VFC_R [gene-level]


title: HSB99_V1C_R [gene-level]


title: HSB100_A1C_L [gene-level]


title: HSB98_STC_R [exon-level]


title: HSB98_STR_L [exon-level]


title: HSB98_MSC_R [exon-level]


title: HSB98_MFC_R [exon-level]


title: HSB99_V1C_L [gene-level]


title: HSB98_MSC_L [exon-level]


title: HSB98_MD_R [exon-level]

value: MD


title: HSB99_STC_L [gene-level]


title: HSB99_MSC_R [gene-level]


title: HSB99_MSC_L [gene-level]


title: HSB99_VFC_L [gene-level]


title: HSB99_STR_L [gene-level]


title: HSB99_STC_R [gene-level]


title: HSB98_IPC_R [exon-level]


title: HSB98_HIP_L [exon-level]


title: HSB98_DFC_L [exon-level]


title: HSB98_IPC_L [exon-level]


title: HSB99_STR_R [gene-level]


title: HSB98_MD_L [exon-level]


title: HSB99_MFC_L [gene-level]


title: HSB99_MFC_R [gene-level]


title: HSB98_A1C_L [exon-level]


title: HSB98_DFC_R [exon-level]


title: HSB98_HIP_R [exon-level]


title: HSB98_A1C_R [exon-level]


title: HSB98_MFC_L [exon-level]


title: HSB99_HIP_R [gene-level]


title: HSB99_DFC_R [gene-level]


title: HSB99_MD_R [gene-level]


title: HSB99_MD_L [gene-level]


title: HSB99_HIP_L [gene-level]


title: HSB99_DFC_L [gene-level]


title: HSB99_A1C_L [gene-level]


title: HSB97_VFC_R [exon-level]

value: 17 PCW


title: HSB98_VFC_R [gene-level]

value: VFC


title: HSB97_VFC_L [exon-level]

value: F


title: HSB97_V1C_R [exon-level]


title: HSB99_IPC_L [gene-level]

value: 21 PCW


title: HSB98_VFC_L [gene-level]


title: HSB99_IPC_R [gene-level]


title: HSB97_MSC_R [exon-level]


title: HSB97_V1C_L [exon-level]


title: HSB97_STC_R [exon-level]


title: HSB98_V1C_R [gene-level]


title: HSB97_STR_R [exon-level]


title: HSB97_STR_L [exon-level]


title: HSB97_MFC_R [exon-level]


title: HSB97_OFC_R [exon-level]


title: HSB98_STR_R [gene-level]


title: HSB98_STR_L [gene-level]


title: HSB99_A1C_R [gene-level]


title: HSB98_STC_R [gene-level]


title: HSB97_STC_L [exon-level]


title: HSB97_MFC_L [exon-level]


title: HSB98_V1C_L [gene-level]


title: HSB97_MSC_L [exon-level]


title: HSB97_MD_R [exon-level]


title: HSB97_OFC_L [exon-level]


title: HSB97_IPC_R [exon-level]


title: HSB97_MD_L [exon-level]


title: HSB97_HIP_L [exon-level]


title: HSB98_MD_L [gene-level]


title: HSB98_MSC_L [gene-level]


title: HSB98_MD_R [gene-level]


title: HSB97_DFC_R [exon-level]


title: HSB98_STC_L [gene-level]


title: HSB97_IPC_L [exon-level]


title: HSB97_DFC_L [exon-level]


title: HSB98_IPC_R [gene-level]


title: HSB97_HIP_R [exon-level]


title: HSB98_MSC_R [gene-level]


title: HSB98_MFC_L [gene-level]


title: HSB98_HIP_L [gene-level]


title: HSB98_IPC_L [gene-level]


title: HSB98_HIP_R [gene-level]


title: HSB98_MFC_R [gene-level]


title: HSB98_A1C_R [gene-level]


title: HSB98_DFC_R [gene-level]


title: HSB97_VFC_R [gene-level]


title: HSB97_V1C_L [gene-level]


title: HSB98_DFC_L [gene-level]


title: HSB97_A1C_R [exon-level]


title: HSB97_AMY_R [exon-level]

value: AMY


title: HSB96_V1C_R [exon-level]

value: M

value: 16 PCW


title: HSB96_VFC_L [exon-level]

value: L


title: HSB96_STC_R [exon-level]


title: HSB97_AMY_L [exon-level]


title: HSB98_A1C_L [gene-level]

value: 19 PCW


title: HSB96_V1C_L [exon-level]


title: HSB97_V1C_R [gene-level]

value: R


title: HSB96_STR_L [exon-level]

value: STR


title: HSB96_STR_R [exon-level]


title: HSB97_A1C_L [exon-level]


title: HSB97_VFC_L [gene-level]


title: HSB96_STC_L [exon-level]

value: STC


title: HSB97_STR_L [gene-level]


title: HSB97_STR_R [gene-level]


title: HSB96_MSC_R [exon-level]


title: HSB96_MFC_R [exon-level]


title: HSB97_STC_L [gene-level]


title: HSB96_MSC_L [exon-level]


title: HSB96_IPC_L [exon-level]


title: HSB96_MFC_L [exon-level]


title: HSB96_MD_L [exon-level]


title: HSB96_VFC_R [exon-level]


title: HSB97_MSC_R [gene-level]


title: HSB96_MD_R [exon-level]


title: HSB97_OFC_R [gene-level]

value: OFC


title: HSB97_OFC_L [gene-level]


title: HSB97_MFC_R [gene-level]

value: MFC


title: HSB97_MD_L [gene-level]


title: HSB96_DFC_R [exon-level]

value: DFC


title: HSB96_IPC_R [exon-level]

value: IPC


title: HSB96_HIP_R [exon-level]

value: HIP


title: HSB97_MSC_L [gene-level]

value: 17 PCW


title: HSB97_STC_R [gene-level]


title: HSB97_IPC_L [gene-level]


title: HSB97_MFC_L [gene-level]


title: HSB97_MD_R [gene-level]

value: MD


title: HSB96_HIP_L [exon-level]


title: HSB96_A1C_L [exon-level]


title: HSB97_HIP_L [gene-level]

value: F


title: HSB97_AMY_L [gene-level]


title: HSB97_DFC_R [gene-level]


title: HSB92_OFC_R [exon-level]

value: 21 PCW


title: HSB97_A1C_R [gene-level]


title: HSB92_STC_R [exon-level]


title: HSB97_DFC_L [gene-level]


title: HSB97_AMY_R [gene-level]

value: AMY


title: HSB96_VFC_R [gene-level]

value: VFC

value: M


title: HSB97_A1C_L [gene-level]

value: L


title: HSB97_IPC_R [gene-level]


title: HSB96_DFC_L [exon-level]

value: 16 PCW


title: HSB96_A1C_R [exon-level]

value: R


title: HSB92_STR_R [exon-level]

value: STR


title: HSB92_VFC_R [exon-level]


title: HSB92_S1C_R [exon-level]


title: HSB92_MFC_R [exon-level]


title: HSB92_M1C_R [exon-level]


title: HSB97_HIP_R [gene-level]


title: HSB92_ITC_R [exon-level]

value: ITC


title: DP_03

city: Padova

first: Alberto

last: Corradin

state: PD

address: via Tiepolo

department: Dipertimento di Ingegneria dell'Informazione

country: Italy

institute: Università degli Studi di Padova

description: mature miRNA expression data from 3 human thymocytes subsets (DP, CD2+/CD4+/CD8+; SP CD4+, CD2+/CD4+/CD8-; SP CD8+, CD2+/CD4-/CD8+) and from unsorted human thymocytes (CD2+)

hyb_protocol: Labelled total RNA was hybridized for 20 hr at 55C on Agilent Human miRNA microarrays (v2.0) (Agilent Technologies).

scan_protocol: The arrays were scanned at  5 µm resolution using the Agilent Microarray Scanner.

data_processing: The data were extracted with the Feature Extraction Software 9.5.3.1 (Agilent Technologies) and analyzed with BRB Array Tools version 3.6. Spots signalled as absent were excluded; miRNAs absent in more than 75% of chips were excluded from further analyses. No normalization was applied as suggested by Agilent sellers.

source_name: human thymi obtained as surgical tissue discard from pediatric patients

label_protocol: 100 µg of total RNA were dephosphorilated at 5'end and labelled at 3'end with cyanine3–pCp by using the Agilent’s miRNA Complete Labeling and Hyb Kit (Agilent Technologies), following the manufacturer's instructions.

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

treatment_protocol: Thymi from two to three patients were pooled for each replicate. Six biological replicates for each sample were hybridized on the arrays.

tag: developmental stage

value: Double Positive T cells


title: DP_02


title: HSB96_VFC_L [gene-level]


title: HSB92_DFC_R [exon-level]


title: HSB96_V1C_R [gene-level]


title: HSB92_V1C_R [exon-level]


title: HSB92_AMY_R [exon-level]


title: HSB92_MD_R [exon-level]


title: Thymus_08

value: Unsorted thymocytes


title: HSB96_STC_R [gene-level]

value: STC


title: Thymus_09


title: Thymus_07


title: HSB96_STC_L [gene-level]


title: HSB96_STR_L [gene-level]


title: DP_01


title: HSB96_STR_R [gene-level]


title: HSB92_HIP_R [exon-level]


title: HSB92_IPC_R [exon-level]

value: IPC


title: HSB92_A1C_R [exon-level]


title: SP_CD8_08

value: Single Positive CD8 T cells


title: Thymus_06


title: SP_CD8_07


title: HSB96_V1C_L [gene-level]


title: SP_CD8_06


title: HSB96_MSC_R [gene-level]


title: HSB96_MD_L [gene-level]


title: SP_CD8_03


title: HSB96_IPC_R [gene-level]


title: HSB96_MSC_L [gene-level]


title: SP_CD8_05


title: SP_CD8_02


title: SP_CD4_06

value: Single Positive CD4 T cells


title: SP_CD4_05


title: SP_CD4_09


title: immunoproteins C.jejuni 5

type: protein

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

hyb_protocol: Fusion proteins were spotted and coupled to the microarray surface for one hour at room temperature with 70% humidity. Slides were washed three times with PBSI (PBS + 0.01% Igepal). Incubation with primary antibody (rabbit polyclonal to C.jejuni) and secondary antibody (goat polyclonal to rabbit, Chromeo-547 conjugated) were performed for 1.5 h each, with washing (three times) with PBSI after each incubation step. Slides were dried with nitrogen and scanned afterwards.

scan_protocol: Fluorescent array images were collected for Cy3 with a Genepix 4200A fluorescent scanner. Image intensity data were extracted and analyzed using Origin Pro 8G.

data_processing: Each protein is printed in duplicate per array. For each protein the median fluorescent intensities of blocks 9-12 representing incubation with only secondary antibody were subtracted from the intensities of block 1-4 representing sample with primary and secondary antibody. The spots representing the cell extract without fusion protein were used to calculate median and standard deviation of the background. Using these values contrast values for each spot were calculated and a cutoff was determined. Contrast values from replicates were used to calculate a mean value and a standard deviation of each sample. If a protein's contrast was greater than the cutoff (using five times the standard deviation) it was considered positive.

molecule: protein

organism: Campylobacter jejuni

source_name: HaloTag-fusion proteins derived from Campylobacter jejuni and expressed in KRX E.coli overexpression strains.

extract_protocol: Fusion proteins were extracted from cultures using EasyLyse Bacterial protein extraction kit (Epicentre)

tag: strain


title: HSB96_MFC_R [gene-level]

value: MFC


title: HSB96_MD_R [gene-level]

value: MD


title: immunoproteins C.jejuni 3


title: HSB96_HIP_R [gene-level]

value: HIP


title: HSB96_DFC_R [gene-level]

value: DFC


title: SP_CD4_04


title: immunoproteins C.jejuni 4


title: Thymus_05


title: immunoproteins C.jejuni 2


title: SP_CD4_08


title: His vs CSN1 48h [0005480017]

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: MACSmolecular Business Unit

institute: Miltenyi Biotec GmbH

description:
His_transfected cells_vs_CSN1_transfected cells_48h_replicate2
CH1: siCSN1 Hela cells transiently transfected with empty His-vector 48h
CH2: siCSN1 Hela cells transiently transfected with His-CSN1-vector 48h

Hybridized to array from batch 747.

hyb_protocol: The fluorescently labeled samples were hybridized overnight to topic-defined PIQORTM Ubiquitin-PS Microarrays Human Antisense using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized PIQOR (TM) Ubiquitin-PS microarrays were done with the ScanArrayLite4000 Microarray Scanner (Packard-Biosciences) and ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned PIQOR (TM) microarrays was done using ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same cDNA was computed. The mean ratios were normalised using the Lowess method. For normalisation only those spots were used for which the fluorescent intensity in one of the two channels was twice the mean background of all unflagged spots. Only genes displaying a net signal intensity 2-fold higher than the mean background were used for further analysis.

source_name: siCSN1 Hela cells_His

label_protocol: 1 µg T7-amplified RNA  was labeled by reverse transcription with Cy3-dCTPs or Cy5-dCTPS as described elsewhere (PMID: 8800675)

growth_protocol: HeLa cells were cultured in RPMI 1640 medium at 37°C and 5% CO2. Hela cells with siCSN1 knockdown were grown in RPMI 1640 medium containing 1 µg/mL puromycin.

extract_protocol: RNA was isolated using a standard RNeasy Mini kit (Qiagen)

treatment_protocol: Cells were transfected using lipofectamine LTX (Invitrogen) for overexpression of His-CSN1 and Flag-CSN2.

tag: transfection protocol

tag: time

source_name: siCSN1 Hela cells_CSN1_48h


title: immunoproteins C.jejuni 1


title: SP_CD4_02


title: DP_07


title: HSB96_A1C_R [gene-level]


title: DP_04


title: HSB96_IPC_L [gene-level]


title: HSB96_MFC_L [gene-level]


title: DP_05


title: HSB96_DFC_L [gene-level]


title: 0h vs 6h Curcumin [0005120074]

description:
Hela cells 0h vs Hela cells treated with Curcumin_6h_replicate 1
CH1: untreated, harvested after 6h
CH2: Hela cells treated for 6h with Curcumin

Hybridized to array from batch 714.

source_name: Hela cells_0h

tag: agent

value: untreated

source_name: Hela cells_6h_Curcumin

value: Curcumin


title: 0h vs 3h Piceatannol [0005120077]

description:
Hela cells 0h vs Hela cells treated with Piceatannol_3h_replicate 1
CH1: untreated, harvested after 3h
CH2: Hela cells treated for 3h with Piceatannol

Hybridized to array from batch 714.

source_name: Hela cells_3h_Piceatannol

value: Piceatannol


title: 0h vs 6h Nr.8 [0005120076]

description:
Hela cells 0h vs Hela cells treated with Nr.8_6h_replicate 1
CH1: untreated, harvested after 6h
CH2: Hela cells treated for 6h with Nr. 8

Hybridized to array from batch 714.

source_name: Hela cells_6h_Nr.8 (Curcumin analogon)

value: Nr. 8


title: 0h vs 6h Piceatannol [0005120078]

description:
Hela cells 0h vs Hela cells treated with Piceatannol_6h_replicate 1
CH1: untreated, harvested after 6h
CH2: Hela cells treated for 6h with Piceatannol

Hybridized to array from batch 714.

source_name: Hela cells_6h_Piceatannol


title: His vs CSN1 24h [0005480016]

description:
His_transfected cells_vs_CSN1_transfected cells_24h_replicate2
CH1: siCSN1 Hela cells transiently transfected with empty His-vector 24h
CH2: siCSN1 Hela cells transiently transfected with His-CSN1-vector 24h

Hybridized to array from batch 747.

source_name: siCSN1 Hela cells_CSN1_24h


title: siGFP vs siCSN1 [0005480014]

description:
siGFP_transfected cells_vs_siCSN1_transfected cells_replicate2
CH1: Hela cells stably transfected with siGFP
CH2: Hela cells stably transfected with siCSN1

Hybridized to array from batch 747.

source_name: Hela cells_siGFP

value: stably transfected with siGFP

source_name: Hela cells_siCSN1

value: stably transfected with siCSN1


title: Thymus_01


title: ppGpp0 strain, dksA-, pGB2, biological rep2

city: Bethesda

first: Katarzyna

last: Potrykus

state: MD

address: 6 Center Drive, 6B rm 316

department: NICHD

institute: NIH

description: Gene expression data from cells at OD~ 0.2

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on E. coli 2.0 arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Mini_prok2v1_450 protocol.

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

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

label: biotin

organism: Escherichia coli

source_name: E.coli ppGpp0 dksA- cells with vector control

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Prokaryotic Traget Preparation in Affymetrix GeneChip® Expression Analysis Technical Manual).

growth_protocol: E.coli cells were grown at 37C, with vigorous shaking, in M9 medium supplemented with amino acids: DFHILQSTV, each at 100ug/ml; IPTG was present at 0.1 mM, and spectinomycin at 15ug/ml.

extract_protocol: at OD460 ~ 0.2, 4 OD units were removed from the culture and immediately added to an equal volume of ice-cold RNAlater reagent (Ambion). Thus treated samples were stored for 20min on ice. Total RNA was extracted with Trizol reagent (Invitrogen) following manufacturer's instructions.

treatment_protocol: IPTG was present since the beginning of the experiment


title: His vs CSN1 48h [0005120071]

description:
His_transfected cells_vs_CSN1_transfected cells_48h_replicate1
CH1: Hela cells transiently transfected with empty His-vector 48h
CH2: Hela cells transiently transfected with His-CSN1-vector 48h

Hybridized to array from batch 714.

source_name: Hela cells_His

source_name: Hela cells_CSN1_48h


title: HSB92_OFC_R [gene-level]

value: OFC

value: R

value: M

value: 21 PCW


title: 0h vs 3h Curcumin [0005120073]

description:
Hela cells 0h vs Hela cells treated with Curcumin_3h_replicate 1
CH1: untreated, harvested after 3h
CH2: Hela cells treated for 3h with Curcumin

Hybridized to array from batch 714.

source_name: Hela cells_3h_Curcumin


title: HSB92_MFC_R [gene-level]


title: His vs CSN1 24h [0005480015]

description:
His_transfected cells_vs_CSN1_transfected cells_24h_replicate1
CH1: siCSN1 Hela cells transiently transfected with empty His-vector 24h
CH2: siCSN1 Hela cells transiently transfected with His-CSN1-vector 24h

Hybridized to array from batch 747.


title: HSB96_A1C_L [gene-level]

value: L

value: 16 PCW


title: ppGpp0 strain, dksA-, pA, biological rep1

source_name: E.coli ppGpp0 dksA- cells overexpressing GreA


title: ppGpp0 strain, dksA-, pA, biological rep2


title: HSB92_VFC_R [gene-level]

value: VFC


title: 0h vs 3h Nr.8 [0005120075]

description:
Hela cells 0h vs Hela cells treated with Nr.8_3h_replicate 1
CH1: untreated, harvested after 3h
CH2: Hela cells treated for 3h with Nr. 8

Hybridized to array from batch 714.

source_name: Hela cells_3h_Nr.8 (Curcumin analogon)


title: HSB92_IPC_R [gene-level]

value: IPC


title: siGFP vs siCSN1 [0005120069]

description:
siGFP_transfected cells_vs_siCSN1_transfected cells_replicate1
CH1: Hela cells stably transfected with siGFP
CH2: Hela cells stably transfected with siCSN1

Hybridized to array from batch 714.


title: HSB96_HIP_L [gene-level]


title: HSB92_ITC_R [gene-level]

value: ITC


title: HSB92_V1C_R [gene-level]


title: Flag vs CSN2 18h [0005120081]

description:
Flag_transfected cells_vs_CSN2_transfected cells_18h_replicate2
CH1: Hela cells transiently transfected with empty Flag-vector 18h
CH2: Hela cells transiently transfected with Flag-CSN2 vector 18h

Hybridized to array from batch 714.

source_name: Hela cells_Flag

source_name: Hela cells_CSN2_18h


title: Flag vs CSN2 14h [0005120080]

description:
Flag_transfected cells_vs_CSN2_transfected cells_14h_replicate2
CH1: Hela cells transiently transfected with empty Flag-vector 14h
CH2: Hela cells transiently transfected with  Flag-CSN2 vector 14h

Hybridized to array from batch 714.

source_name: Hela cells_CSN2_14h


title: HSB92_M1C_R [gene-level]


title: HSB92_STR_R [gene-level]

value: STR


title: HSB92_S1C_R [gene-level]


title: HSB92_MD_R [gene-level]

value: MD


title: HSB92_DFC_R [gene-level]

value: DFC


title: Murine-Leukemia_MeDIP-InversePCR-onArray_Sample6

type: genomic

city: Rotterdam

first: Erdogan

last: Taskesen

address: dr. molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center (EMC)

hyb_protocol: Labeling, hybridization to Affymetrix Mouse Promoter 1.0R arrays, staining, washing and scanning were performed according to the manufacturer’s recommendations.

data_processing: The probe-intensity values are normalized according model-based analysis of tiling-arrays for chip-chip (MAT) using default parameters

label: GeneChip® WT Double-Stranded DNA Terminal Labeling Kit

molecule: genomic DNA

organism: Mus musculus

source_name: Enlarged Spleen, leukemia

growth_protocol: according to protocol animal experimental centre

extract_protocol: Mice were sacrificed, descibed organs were taken out, genomic DNA was extracted using high salt precipitation, followed by isopropanol precipitation and a 70% ethanol wash. DNA methylated viral integration site were captured using MeDIP followed by inverse PCR

treatment_protocol: Injection Gr1.4 MuLV

value: FVB/n

tag: tissue

value: Spleen

value: Adult mouse

tag: disease state

value: Mixed Lineage Leukemia


title: ppGpp0 strain, dksA-, pGB2, biological rep1


title: ppGpp0 strain, pA, biological rep2

source_name: E.coli ppGpp0 cells overexpressing GreA


title: Murine-Leukemia_MeDIP-InversePCR-onArray_Sample5

scan_protocol: Labeling, hybridization to Affymetrix Mouse Promoter 1.0R arrays, staining, washing and scanning were performed according to the manufacturer’s recommendations.

source_name: Enlarged Bone Marrow, leukemia

value: Bone Marrow


title: HSB92_STC_R [gene-level]

value: STC


title: ppGpp0 strain, dksA-, pB, biological rep1

source_name: E.coli ppGpp0 dksA- cells overexpressing GreB


title: ppGpp0 strain, dksA-, pB, biological rep2


title: Flag vs CSN2 14h [0005120064]

description:
Flag_transfected cells_vs_CSN2_transfected cells_14h_replicate1
CH1: Hela cells transiently transfected with empty Flag-vector 14h
CH2: Hela cells transiently transfected with  Flag-CSN2 vector 14h

Hybridized to array from batch 714.


title: untreated (WT) vs Flag [0005120079]

description:
untreated_vs_Flag_transfected cells_replicate2
CH1: untreated
CH2: Hela cells transiently transfected with empty Flag-vector

Hybridized to array from batch 714.

source_name: Hela cells_untreated

value: untransfected


title: Flag vs CSN2 18h [0005120065]

description:
Flag_transfected cells_vs_CSN2_transfected cells_18h_replicate1
CH1: Hela cells transiently transfected with empty Flag-vector 18h
CH2: Hela cells transiently transfected with  Flag-CSN2 vector 18h

Hybridized to array from batch 714.


title: Murine-Leukemia_MeDIP-InversePCR-onArray_Sample4

label_protocol: Labeling, hybridization to Affymetrix Mouse Promoter 1.0R arrays, staining, washing and scanning were performed according to the manufacturer’s recommendations.


title: HSB92_A1C_R [gene-level]

value: R

value: M


title: ppGpp0 strain, pB, biological rep1

source_name: E.coli ppGpp0 cells overexpressing GreB


title: Murine-Leukemia_MeDIP-InversePCR-onArray_Sample3

source_name: Enlarged Lymph node, leukemia

value: Lymph Node


title: HSB92_HIP_R [gene-level]

value: HIP

value: 21 PCW


title: HSB92_AMY_R [gene-level]

value: AMY


title: Murine-Leukemia_MeDIP-InversePCR-onArray_Sample2

source_name: Enlarged Liver, leukemia

value: Liver


title: Murine-Leukemia_MeDIP-InversePCR-onArray_Sample1


title: ppGpp0 strain, pA, biological rep1


title: ppGpp0 strain, pB, biological rep2


title: untreated (WT) vs Flag [0005120063]

description:
untreated_vs_Flag_transfected cells_replicate1
CH1: untreated
CH2: Hela cells transiently transfected with empty Flag-vector

Hybridized to array from batch 714.


title: ppGpp0 strain, pGB2, biological rep2

source_name: E.coli ppGpp0 cells with vector control


title: ppGpp0 strain, pGB2, biological rep1


title: LKOJarid1b_2 (NPC)

city: Copenhagen

first: Sandra

middle: Ursula

last: Schmitz

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research and Innovation Centre

description: SSch-Ext-F10-NPC-2-MoGene-1_0-st-v1-b1.CEL

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: R/Bioconductor. 'affy' package. RMA function. Statistics performed using the 'limma'  package. ANNOTATION: chip library files downloaded from Custom CDF library at bioconductor. vers13 july 6 2010. http://brainarraprefix ”y.mbni.med.umich.edu/”.Brainarray/Database/CustomCDF/CDF_download.asp. Package name mogene10stv1mmentrezg

source_name: neural progenitor cells

label_protocol: samples were processed with the Whole Transcript Assay Kit as recommended by the manufacterer (Affymetrix)

growth_protocol: E14TG2a.4 feeder independent ES cells were cultured on 0.1% gelatin-coated plates in Glasgow medium (Sigma) supplemented with glutamine (Gibco), non-essential amino acids (Gibco), sodium pyruvate (Gibco), 50 µM ß-mercaptoethanol, and 15% foetal bovine serum (HyClone) in the presence of LIF. Recombinant lentiviruses encoding Jarid1b shRNA were produced by standard methods employing co-transfection of PLKO.1 shRNA and packaging vectors in 293FT cells. ESCs were transduced with lentiviral particles for 16 h, and selected with 2 µg/µl Puromycin (Invitrogen) 48 h after transduction. NPCs were generated as described in Bibel et al, (2007), Nat Protoc 2: 1034–1043

extract_protocol: RNAeasy (Qiagen)

treatment_protocol: Cells were transduced with LKO scramble or Jarid1b

tag: shRNA


title: LKOJarid1b_1 (NPC)

description: SSch-Ext-F10-NPC-1-MoGene-1_0-st-v1-a1.CEL


title: LKOJarid1b_3 (NPC)

description: SSch-Ext-F10-NPC-3-MoGene-1_0-st-v1-c1.CEL


title: Rice_wt-water-stress-7

city: Rehovot

first: Zvi

last: Peleg

address: P.O.Box 12

department: Inst. of Plant Sciences

country: Israel

institute: Hebrew University

description: Gene expression data from rice flag leaf RNA hybridized to Affymetrix rice Genome Array

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

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

data_processing: The data were analyzed using JMPGenomics (ver 3) with RMA and quantile normalization and background correction feature.

organism: Oryza sativa

source_name: Flag leaf WT three days of water stress, biological rep1

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

growth_protocol: WT and transgenic plants were grown in controled greenhouse and water stress treatment imposed at preanthesis stage

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

treatment_protocol: Control plants (Well-watered conditions); water deficit (water stress was imposed at pre anthesis stage)

value: Flag leaf

tag: genotype

value: wildtype

value: 10  weeks


title: Rice_wt-water-stress-9

source_name: Flag leaf WT three days of water stress, biological rep3


title: LKOScr_1 (NPC)

description: SSch-Ext-Scr-NPC-1-MoGene-1_0-st-v1-a1.CEL

value: Scrambled


title: LKOJarid1b_2 (ESC)

description: SSch-Ext-F10-d0-2-MoGene-1_0-st-v1-b1.CEL

source_name: embryonic stem cells


title: Rice_5T-water-stress-12

source_name: Flag leaf PSARK::IPT three days of water stress, biological rep3


title: LKOScr_2 (NPC)

description: SSch-Ext-Scr-NPC-2-MoGene-1_0-st-v1-b1.CEL


title: LKOScr_3 (NPC)

description: SSch-Ext-Scr-NPC-3-MoGene-1_0-st-v1-c1.CEL


title: Rice_5T-water-stress-10

source_name: Flag leaf PSARK::IPT three days of water stress, biological rep1


title: Rice_5T-water-stress-11

source_name: Flag leaf PSARK::IPT three days of water stress, biological rep2


title: Rice_5T-well-watered-5

source_name: Flag leaf PSARK::IPT well-watered, control, biological rep2


title: Rice_wt-well-watered-3

source_name: Flag leaf WT well-watered, control, biological rep3


title: LKOJarid1b_1 (ESC)

description: SSch-Ext-F10-d0-1-MoGene-1_0-st-v1-a1.CEL


title: LKOJarid1b_3 (ESC)

description: SSch-Ext-F10-d0-3-MoGene-1_0-st-v1-c1.CEL


title: LKOScr_1 (ESC)

description: SSch-Ext-Scr-d0-1-MoGene-1_0-st-v1-a1.CEL


title: Rice_wt-well-watered-2

source_name: Flag leaf WT well-watered, control, biological rep2


title: Rice_5T-well-watered-4

source_name: Flag leaf PSARK::IPT well-watered, control, biological rep1


title: Rice_wt-water-stress-8

source_name: Flag leaf WT three days of water stress, biological rep2


title: LKOScr_3 (ESC)

description: SSch-Ext-Scr-d0-3-MoGene-1_0-st-v1-c1.CEL


title: Rice_5T-well-watered-6

source_name: Flag leaf PSARK::IPT well-watered, control, biological rep3


title: LKOScr_2 (ESC)

description: SSch-Ext-Scr-d0-2-MoGene-1_0-st-v1-b1.CEL


title: Human Embyronic Neural Stem Cell, Replicate 2

city: Mansoura

first: Hany

middle: El Sayed

last: Marei

state: Dakahlaya

address: Gomhoraya

department: Histology

country: Egypt

institute: Fac. Vet Med

description: Biological replicate 2 of 2.

hyb_protocol: The arrays were hybridized in an ozone-free room. The arrays were loaded into the Agilent SureHyb chamber base. The volume of hybridization sample were slowly dispensed onto the backing. The slide chamber were placed in the hybridization oven set to 65°C. The samples were Rotated at 4 rpm using the 2x Hybridization Buffer, and were hybridized at 65°C for 17 hours.The samples were washed used 1: 6x SSPE, 0.005% NLauroylsarcosine, Triton X102.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: The data were quantile normalized using software R.

source_name: Human embryonic neural stem cells

label_protocol: We used the QuickAmp Labeling Kit Cy3 OneColor to amplify and label target RNA to generate complementary RNA (cRNA) for oligo microroarrays from as little as 200 ng total RNA. The single tube procedure consists of converting mRNA primed with an oligo (d)TT7 primer into dsDNA with MMLVRT, and then generating amplified cRNA using T7 RNA Polymerase.

growth_protocol: Proliferating hENS cells were cultured in DMEM/F12 supplemented with 1% N2 (Invitrogen, Carlsbad CA), 10% BIT-9500 (Stem Cell), 1% penicillin, streptomycin, amphocterin cocktail, EGF (20 ng/ml, Peprotech), and FGF-2 (20 ng/ml, Peprotech). Cells were grown on polyornithine- and laminin-coated dishes and passaged 1:2 with PBS++ (PBS with 1% BSA). All experiments performed with human hENSCs were from passage 1–3.

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

tag: cell type

value: human embryonic neural stem cells (hENSCs)


title: Dopaminergic Neurons from Human Substantia nigra, Replicate 1

description: Biological replicate 1 of 2.

source_name: Dopaminergic neurons from human substantia nigra

value: substantia nigra (brain)

value: dopaminergic neurons


title: Dopaminergic Neurons from Human Substantia nigra, Replicate 2

description: Biological replicate 2 of 2.


title: Human Embyronic Neural Stem Cell, Replicate 1

description: Biological replicate 1 of 2.


title: Rice_wt-well-watered-1

source_name: Flag leaf WT well-watered, control, biological rep1


title: MH63-Rs105, biological replicate 2

status: Public on Oct 26 2011

city: Beijing

first: Jie

last: Zhao

address: No. 2 Yuan Ming Yuan West Street

country: China

institute: Institute of Plant Protection, Chinese Academe of Agricultural Sciences

description: Gene expression data from MH63 inoculated with rice leaf streak disease pathogen of Xanthomonas oryzae pv. oryzicola Rs105 strain

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 h at 45°C using an Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained at Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip® Scanner 3000 7G.

source_name: MH63 seedlings

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

growth_protocol: Rice seeds were surface-disinfected and then soaked in distilled sterile water for germination at 28°C for 2 days. Rice seedlings were grown in pots fertilized with half-strength of basal macro- and micro-salt nutrition components of MS medium (Murashige and Skoog, 1962) in a controlled climate chamber at 16-h-light (30°C)/8-h-dark (26°C) cycle.

treatment_protocol: At the age of 30-day, 60-day, 75-day and 90-day old, seedling samples were collected; seedlings, at the age of 30-day old, were treated with high-temperature (45°C) and low-temperature (12°C) respectively at climate chambers, and samples were collected 6 hours after treatment; Seedlings were inoculated respectively with rice leaf blight disease pathogen of Xanthomonas oryzae pv. oryzae JxoI and  Pxo99 strains, rice leaf streak disease pathogen of Xanthomonas oryzae pv. oryzicola Rs105 strain and rice non-host pathogen of Xanthomonas compestris pv. vesicatoria Xv5 strain at the age of 75-day old.

value: leaves

tag: cultivar

value: Minghui 63

tag: genotype/variation


title: HH1-Xv5, biological replicate 1

description: Gene expression data from HH1 inoculated with non-host pathogen of Xanthomonas compestris pv. vesicatoria Xv5 strain

source_name: HH1 seedlings

tag: age


title: MH63-Xv5, biological replicate 3

description: Gene expression data from MH63 inoculated with non-host pathogen of Xanthomonas compestris pv. vesicatoria Xv5 strain


title: MH63-Pxo99, biological replicate 2

description: Gene expression data from MH63 inoculated with rice leaf blight disease pathogen of Xanthomonas oryzae pv. oryzae Pxo99


title: HH1-Xv5, biological replicate 3

value: non-host pathogen of Xanthomonas compestris pv. vesicatoria Xv5 strain


title: MH63-Rs105, biological replicate 1

value: rice leaf streak disease pathogen of Xanthomonas oryzae pv. oryzicola Rs105 strain


title: HH1-Rs105, biological replicate 3

description: Gene expression data from HH1 inoculated with rice leaf streak disease pathogen of Xanthomonas oryzae pv. oryzicola Rs105 strain


title: MH63-Pxo99, biological replicate 3

value: rice leaf blight disease pathogen of Xanthomonas oryzae pv. oryzae Pxo99


title: MH63-Xv5, biological replicate 2


title: MH63-JxoI, biological replicate 2

description: Gene expression data from MH63 inoculated with rice leaf blight disease pathogen of Xanthomonas oryzae pv. oryzae JxoI


title: HH1-Pxo99, biological replicate 3

description: Gene expression data from HH1 inoculated with rice leaf blight disease pathogen of Xanthomonas oryzae pv. oryzae Pxo99


title: HH1-Rs105, biological replicate 2


title: HH1-Pxo99, biological replicate 2


title: MH63-JxoI, biological replicate 3

value: rice leaf blight disease pathogen of Xanthomonas oryzae pv. oryzae JxoI


title: MH63-Rs105, biological replicate 3


title: HH1-Pxo99, biological replicate 1


title: HH1-Rs105, biological replicate 1


title: HH1-Xv5, biological replicate 2


title: MH63-Xv5, biological replicate 1


title: MH63-JxoI, biological replicate 1


title: MH63-LT, biological replicate 3

description: Gene expression data from MH63 treated with low-temperature (12°C) for 6 h

tag: condition

value: low-temperature (12°C) for 6 h


title: HH1-JxoI, biological replicate 3

description: Gene expression data from HH1 inoculated with rice leaf blight disease pathogen of Xanthomonas oryzae pv. oryzae JxoI


title: HH1-JxoI, biological replicate 2


title: MH63-Pxo99, biological replicate 1


title: HH1-JxoI, biological replicate 1


title: MH63-LT, biological replicate 2


title: HH1-LT, biological replicate 3

description: Gene expression data from HH1 treated with low-temperature (12°C) for 6 h


title: MH63-LT, biological replicate 1


title: Lung tumor (Dnmt3a KO vs. WT) rep 10

city: Cambridge

first: Qing

last: Gao

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description: Biological replicate 10

hyb_protocol: Agilent (mouse 4x44k) array. The hybridization cocktail consisted of 825 ng cy-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60C in an Agilent rotor oven set to maximum speed. The arrays were treated with Wash Buffer #1 (6X SSPE / 0.005% n-laurylsarcosine) on a shaking platform at room temperature for 2 minutes, and then Wash Buffer #2 (0.06X SSPE) for 2 minutes at room temperature. The arrays were then dipped briefly in acetonitrile before a final 30 second wash in Agilent Wash 3 Stabilization and Drying Solution, in the hood using a stir plate and stir bar at room temperature.

scan_protocol: Arrays were scanned using an Agilent scanner G2565BA and the data was extracted using Agilent’s Feature Extraction software v10.1.1.1 set to the default two-color gene expression protocol.

data_processing: Using spot-quality weights, arrays were normalizated across channels by loess and across arrays with Aquantile.  Differential expression was assayed by moderated t-test, corrected for FDR.  Analysis was performed using limma.

source_name: Lung tumor (WT) rep 10

label_protocol: Cy-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 2 µg total RNA. Briefly, first and second strand cDNA are generated using MMLV-RT enzyme and an oligo-dT based primer. In vitro transcription is performed using T7 RNA polymerase and either cyanine 3-CTP or cyanine 5-CTP, creating a direct incorporation of dye into the cRNA.

growth_protocol: K-ras LSL-G12D mice were crossed with the Dnmt3a conditional KO mice. After adenoviral Cre recombinase –mediated recombination, mice were generated with lung cells that carried the K-ras G12D mutation and were homozygous (KO) and WT at the Dnmt3a locus. Tumors were flash-frozen in liquid nitrogen and stored at -80°C.

extract_protocol: Total RNA was isolated with AllPrep DNA/RNA mini kit (Qiagen).

treatment_protocol: adenoviral Cre recombinase  was delivered to mice of 6-12 weeks old via intratracheal or intranosal approach

tag: gender

value: F

value: WT

source_name: Lung tumor (Dnmt3a KO) rep 10

value: M

value: KO


title: HH1-LT, biological replicate 1


title: Lung tumor (Dnmt3a KO vs. WT) rep 5

description: Biological replicate 5

source_name: Lung tumor (WT) rep 5

source_name: Lung tumor (Dnmt3a KO) rep 5


title: Lung tumor (Dnmt3a KO vs. WT) rep 11

description: Biological replicate 11

source_name: Lung tumor (Dnmt3a KO) rep 11

source_name: Lung tumor (WT) rep 11


title: Lung tumor (Dnmt3a KO vs. WT) rep 2

description: Biological replicate 2

source_name: Lung tumor (Dnmt3a KO) rep 2

source_name: Lung tumor (WT) rep 2


title: MH63-HT, biological replicate 3

description: Gene expression data from MH63 treated with high-temperature (45°C) for 6 h

value: wildtype

value: high-temperature (45°C) for 6 h


title: Lung tumor (Dnmt3a KO vs. WT) rep 12

description: Biological replicate 12

source_name: Lung tumor (Dnmt3a KO) rep 12

source_name: Lung tumor (WT) rep 12


title: Lung tumor (Dnmt3a KO vs. WT) rep 4

description: Biological replicate 4

source_name: Lung tumor (Dnmt3a KO) rep 4

source_name: Lung tumor (WT) rep 4


title: Lung tumor (Dnmt3a KO vs. WT) rep 9

description: Biological replicate 9

source_name: Lung tumor (WT) rep 9

source_name: Lung tumor (Dnmt3a KO) rep 9


title: HH1-HT, biological replicate 3

description: Gene expression data from HH1 treated with high-temperature (45°C) for 6 h


title: MH63-90, biological replicate 2

description: Gene expression data from MH63 at the age of 90-day old


title: Lung tumor (Dnmt3a KO vs. WT) rep 8

description: Biological replicate 8

source_name: Lung tumor (Dnmt3a KO) rep 8

source_name: Lung tumor (WT) rep 8


title: HH1-HT, biological replicate 2

source_name: HH1 seedlings


title: HH1-LT, biological replicate 2


title: Lung tumor (Dnmt3a KO vs. WT) rep 3

description: Biological replicate 3

source_name: Lung tumor (WT) rep 3

source_name: Lung tumor (Dnmt3a KO) rep 3


title: Lung tumor (Dnmt3a KO vs. WT) rep 6

description: Biological replicate 6

source_name: Lung tumor (Dnmt3a KO) rep 6

source_name: Lung tumor (WT) rep 6


title: Lung tumor (Dnmt3a KO vs. WT) rep 1

description: Biological replicate 1

source_name: Lung tumor (WT) rep 1

source_name: Lung tumor (Dnmt3a KO) rep 1


title: MH63-HT, biological replicate 2

source_name: MH63 seedlings


title: HH1-HT, biological replicate 1


title: WT pretumor mouse 7213

city: Chicago

first: Kathryn

last: Bieging

state: IL

address: 303 East Chicago Ave

department: Microbiology-Immunology

institute: Northwestern University

hyb_protocol: standard Illumina protocol

scan_protocol: An Illumina iScan was used to scan the arrays.

data_processing: GeneSpring analysis software, version GX (Agilent Technologies, Santa Clara, CA) was used for data analysis.  The quantile normalization method was used for preprocessing, and the baseline was set to the median of all samples.  The detection p-value was used to eliminate probes which were not significantly expressed in any sample.  Probes were excluded from the analysis if none of the samples had a detection p-value greater than 0.95.  To identify significant probes, the Benjamini-Hochberg false discovery rate (FDR) was used for the multiple testing correction p-value.  Probes with p<0.05 and a fold change of >1.5 were considered significant.

source_name: B cells purified from the spleen of 3 week old WT mouse

label_protocol: RNA samples were amplified, labeled, and hybridized at the Genomics Core Facility at the Center for Genetic Medicine at Northwestern University according to Illumina protocols.

growth_protocol: Mice were sacrificed when cervical lymph node tumors could be observed externally and the mice were moribund.  Pretumor samples were collected at 3 weeks of age.  All animals were maintained at Northwestern University’s Center for Comparative Medicine, in accordance with University animal welfare guidelines.

extract_protocol: Total RNA was isolated from tumor or pretumor cells using RNeasy RNA extraction kit from QIAGEN (Valenica, CA).  RNA preps were evaluated for quality using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Only samples with an RNA integrity number (RIN) greater than 8.0 were used for microarray analysis.

treatment_protocol: Pretumor B cells were purified from the spleens of 3 week old transgenic mice using magnetic-activated cell sorting (MACS) with CD19 positive selection according to manufacturer protocols (Miltenyi).  Purity of >90% was confirmed by analyzing B220 expression by flow cytometry.  Tumors were dissociated between frosted glass slides.  Red blood cells were lysed using 155 mM ammonium chloride, and filtered through nytex to remove debris.

tag: genetic background

value: B cells


title: Lung tumor (Dnmt3a KO vs. WT) rep 7

description: Biological replicate 7

source_name: Lung tumor (WT) rep 7

source_name: Lung tumor (Dnmt3a KO) rep 7


title: MH63-HT, biological replicate 1


title: WT pretumor mouse 7320


title: MH63-90, biological replicate 3


title: MH63-90, biological replicate 1


title: HH1-90, biological replicate 3

description: Gene expression data from HH1 at the age of 90-day old


title: HH1-90, biological replicate 2


title: λ-MYC pretumor mouse 7023

source_name: B cells purified from the spleen of 3 week old λ-MYC mouse

value: λ-MYC


title: WT pretumor mouse 7022


title: MH63-75, biological replicate 3

description: Gene expression data from MH63 at the age of 75-day old


title: λ-MYC pretumor mouse 7227


title: MH63-75, biological replicate 2


title: HH1-75, biological replicate 3

description: Gene expression data from HH1 at the age of 75-day old


title: LMP2A pretumor mouse 7330

source_name: B cells purified from the spleen of 3 week old LMP2A mouse


title: LMP2A pretumor mouse 7144


title: λ-MYC pretumor mouse 7326


title: LMP2A/λ-MYC pretumor mouse 7222

source_name: B cells purified from the spleen of 3 week old LMP2A/λ-MYC mouse


title: LMP2A pretumor mouse 7323


title: λ-MYC pretumor mouse 7224


title: MH63-75, biological replicate 1


title: MH63-60, biological replicate 2

description: Gene expression data from MH63 at the age of 60-day old


title: HH1-90, biological replicate 1


title: LMP2A/λ-MYC pretumor mouse 7225


title: MH63-60, biological replicate 3


title: λ-MYC pretumor mouse 7223


title: HH1-75, biological replicate 1


title: HH1-75, biological replicate 2


title: MH63-60, biological replicate 1


title: HH1-60, biological replicate 3

description: Gene expression data from HH1 at the age of 60-day old


title: HH1-60, biological replicate 2


title: LMP2A/λ-MYC pretumor mouse 7221


title: LMP2A/λ-MYC pretumor mouse 7028


title: MH63-30, biological replicate 3

description: Gene expression data from MH63 at the age of 30-day old


title: λ-MYC cervcial lymph node tumor mouse 5851

source_name: λ-MYC cervcial lymph node

tag: age at tumor

value: 123 days

value: λ-MYC cervcial lymph node tumor


title: MH63-30, biological replicate 2

value: leaves


title: LMP2A/λ-MYC pretumor mouse 7146


title: λ-MYC cervcial lymph node tumor mouse 5577

value: 116 days


title: MH63-30, biological replicate 1

value: Minghui 63


title: HH1-30, biological replicate 3

description: Gene expression data from HH1 at the age of 30-day old


title: λ-MYC cervcial lymph node tumor mouse 5933

value: 63 days


title: λ-MYC cervcial lymph node tumor mouse 3000


title: LMP2A/λ-MYC cervcial lymph node tumor mouse 6038

source_name: LMP2A/λ-MYC cervcial lymph node

value: 43 days

value: LMP2A/λ-MYC cervcial lymph node tumor


title: LMP2A/λ-MYC cervcial lymph node tumor mouse 5662

value: 50 days


title: LMP2A/λ-MYC cervcial lymph node tumor mouse 5935

value: 40 days


title: HH1-30, biological replicate 1


title: LMP2A/λ-MYC cervcial lymph node tumor mouse 5660

value: 46 days


title: LMP2A/λ-MYC cervcial lymph node tumor mouse 5930


title: LMP2A/λ-MYC cervcial lymph node tumor mouse 5646

value: 48 days


title: HH1-30, biological replicate 2


title: KMD, biological replicate 3

description: Gene expression data from KMD

source_name: KMD seedlings

value: Xiushui 11

value: KMD


title: XS11, biological replicate 2

description: Gene expression data from XS11

source_name: XS11 seedlings

value: wildtype


title: λ-MYC cervcial lymph node tumor mouse 5860

value: 114 days


title: XS11, biological replicate 3

description: Gene expression data from XS11


title: XS11, biological replicate 1

description: Gene expression data from XS11


title: KMD, biological replicate 2

description: Gene expression data from KMD


title: LMP2A/λ-MYC cervcial lymph node tumor mouse 5850


title: KMD, biological replicate 1

description: Gene expression data from KMD


title: Epi.Exo.Scl._Maturation zone_V_rep2

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

description:
RXP4001_035
Gene expression of Epidermis/Exodermis/Sclerenchyma at 10-20 mm region from basal side.

hyb_protocol: At least 1,100 ng Cy3-labeled cRNA was fragmented and hybridized on a slide of rice 4x44K microarray RAP-DB (Agilent; G2519F#15241) at 65℃ for 17 hours. Hybridization and washing of the hybridized slide were performed according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75th percentile normalization and log2 transformation with GeneSpring GX11 (Agilent).

organism: Oryza sativa Japonica Group

source_name: Epidermis/Exodermis/Sclerenchyma_10-20 mm from basal side

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction, and labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the modified manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by the RNeasy Mini Kit (Qiagen), and the cRNA yield was determined using the NanoDrop ND-1000 UV-VIS spectrophotomer (NanoDrop).

growth_protocol: Rice seeds were sterilized with 70% (v/v) ethanol solution and 1% (v/v) sodium hypochlorite solution, imbibed in distilled water in the dark at 25°C for 2 days, and transferred onto a nylon net floated in distilled water in a growth chamber (60% humidity; 14 h light period at 30°C and 10 h dark period at 25°C). After 3 days of germination, the seedlings were transferred to a nutrient solution (based on Yoshida nutrient solution; pH 5.5) and allowed to grow for another 7 days. The pH of the nutrient solution was adjusted using 1N NaOH and maintained using MES (buffer), and the solution was renewed every 2 days.

extract_protocol: Total RNA was extracted from each sample with a Pico-Pure RNA isolation kit (Arcturus) according to the manufacturer’s protocol. The quantity and quality of the obtained RNAs were checked with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: The crown roots of 10-day-old seedlings with length more than 5 cm were used for the gene expression profiling. The samples were fixed in 99.5% cold ethanol or 100% cold acetone. Sample fixation and paraffin-embedding were performed using the Microwave Processor (Energy Beam Sciences, East Granby, CT). The paraffin-embedded samples were cut into 12-20 µm thick sections using a microtome (Leica RM2255) and used for laser microdissection with the Veritas Laser Microdissection System LCC1704 (Arcturus).

value: Nipponbare

value: root

tag: tissue type

value: epidermis/exodermis/sclerenchyma

tag: developmental stage

value: maturation zone V


title: N 5 rep1 -

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cross-correlation normalisation in R or Matlab

source_name: normal donor

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

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

value: lung normal donor CD166-


title: End.Per.Ste._Maturation zone_V_rep1

description:
RXP4001_037
Gene expression of Endodermis/Pericycle/Stele at 10-20 mm region from basal side.

source_name: Endodermis/Pericycle/Stele_10-20 mm from basal side

value: endodermis/pericycle/stele


title: Epi.Exo.Scl._Maturation zone_V_rep3

description:
RXP4001_036
Gene expression of Epidermis/Exodermis/Sclerenchyma at 10-20 mm region from basal side.


title: N 6 rep1 -

description: replicate 1


title: End.Per.Ste._Elongation zone/Maturation zone_I_rep2

description:
RXP4001_032
Gene expression of Endodermis/Pericycle/Stele at 1-3 mm region from root tip.

source_name: Endodermis/Pericycle/Stele_1-3 mm from root tip

value: elongation zone, maturation zone I


title: End.Per.Ste._Elongation zone/Maturation zone_I_rep3

description:
RXP4001_033
Gene expression of Endodermis/Pericycle/Stele at 1-3 mm region from root tip.


title: N 7 rep1 +

description: replicate 2

value: lung normal donor CD166+


title: N 6 rep1 +

description: replicate 1


title: Cortex_Elongation zone/Maturation zone_I_rep2

description:
RXP4001_029
Gene expression of Cortex at 1-3 mm region from root tip.

source_name: Cortex_1-3 mm from root tip

value: cortex


title: N 7 rep1 -

description: replicate 2


title: P 1-3 rep2 -

description: replicate 2

source_name: primary tumor

value: lung primary tumor CD166-


title: N 5 rep2 -

description: replicate 2


title: P 1-3 rep1 -

description: replicate 1


title: N 5 rep1 +

description: replicate 1


title: Epi.Exo.Scl._Elongation zone/Maturation zone_I_rep3

description:
RXP4001_027
Gene expression of Epidermis/Exodermis/Sclerenchyma at 1-3 mm region from root tip.

source_name: Epidermis/Exodermis/Sclerenchyma_1-3 mm from root tip


title: Cortex_Elongation zone/Maturation zone_I_rep1

description:
RXP4001_028
Gene expression of Cortex at 1-3 mm region from root tip.


title: End.Per.Ste._Elongation zone/Maturation zone_I_rep1

description:
RXP4001_031
Gene expression of Endodermis/Pericycle/Stele at 1-3 mm region from root tip.


title: N 5 rep2 +

description: replicate 2


title: End.Per.Ste._Maturation zone_V_rep2

description:
RXP4001_038
Gene expression of Endodermis/Pericycle/Stele at 10-20 mm region from basal side.


title: P 1-3 rep2 +

description: replicate 2

value: lung primary tumor CD166+


title: Epi.Exo.Scl._Maturation zone_V_rep1

description:
RXP4001_034
Gene expression of Epidermis/Exodermis/Sclerenchyma at 10-20 mm region from basal side.


title: Cortex_Elongation zone/Maturation zone_I_rep3

description:
RXP4001_030
Gene expression of Cortex at 1-3 mm region from root tip.


title: mesocarp_woolly_Juicy_S2R1

city: Santiago

first: Leonardo

middle: Ignacio

last: Pavez

state: Santiago

address: Av Manuel Montt #948

country: Chile

institute: Universidad de Las Américas

hyb_protocol: Prehybridizations were carried out by soaking whole glass slides in a solution containing 5 x SSC, 0.1% SDS, and BSA 0.1% at 55 ÂºC for at 90 minutes. Then the slides were washed five times with distilled water, and dried by centrifuging for 2 min at 2000 rev. min_1. Hybridizations were carried out in 50 ÂµL of hybridization solution (5 x SSC, 0.1% SDS, 20 % formamide) containing 90-100 pmol of Cy3- and Cy5-labelled target cDNAs. The glass slides were placed in a hybridization chamber and incubated at 49 ÂºC on a thermal bath for 16 h. Then the slides were washed with 2x SSC 0.1% SDS 4 times for 10 min. Six additional washes (three with 0.1 x SSC 0.1% SDS and three with 0.1 x SSC, for 10 min each) at room temperature were performed before drying the glass slides with a brief centrifugation.

scan_protocol: The slide images were quantified using ScanArray Express software (Perkin-Elmer).

data_processing: Array data were analyzed using the R statistical language and environment (http://www.r-project.org), specifically with the microarray analysis tools available from the Bioconductor Project (http://www.bioconductor.org). Spots that showed qcom<0.5 (Wang et al.,2001) were considered low-quality spots and were removed. Data were background-subtracted and normalized using the LIMMA Bioconductor package (Smyth, 2004). Lists of regulated significant genes were determinated using Significant Analysis of Microarrays (SAM) (Tusher et al., 2001) FDR<3.

organism: Prunus persica

source_name: Mesocarp, mature woolly fruits

label_protocol: Total RNA (20 Âµg) from peach fruits was converted into target cDNA by reverse transcription using the SuperScript Indirect cDNA Labelling System (Invitrogen, USA) following the manufacturerâs instructions.

extract_protocol: Total RNA was isolated from fruit as described by Meisel et al, A Rapid and Efficient Method for Purifying High Quality Total RNA from Peaches (Prunus persica) for Functional Genomics Analyses. Biol Res 38: 83-88, 2005

value: Venus x Venus

value: Mesocarp, mature woolly fruits

source_name: Mesocarp, mature juicy fruits

value: Mesocarp, mature juicy fruits


title: mesocarp_woolly_Juicy_S3R1


title: P 1-3 rep1 +

description: replicate 1


title: mesocarp_woolly_Juicy_S1R1


title: Maturation zone_V_rep3

description:
RXP4001_024
Gene expression of 10-20 mm region from basal side corresponding to maturation zone.

source_name: Maturation zone_10-20 mm from basal side


title: mesocarp_woolly_Juicy_S4R2


title: mesocarp_woolly_Juicy_S2R2


title: mesocarp_woolly_Juicy_S1R2


title: X 3 rep2 -

description: replicate 2

source_name: tumor xenograft

value: lung tumor xenograft CD166-


title: Epi.Exo.Scl._Elongation zone/Maturation zone_I_rep2

description:
RXP4001_026
Gene expression of Epidermis/Exodermis/Sclerenchyma at 1-3 mm region from root tip.


title: mesocarp_woolly_Juicy_S4R1


title: mesocarp_woolly_Juicy_S3R2


title: R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 - singlet oxygen conditions - replicate 2

city: Giessen

middle: Harald Michael

last: Metz

address: Heinrich-Buff-Ring 26-32

department: Institut für Mikro- und Molekularbiologie

institute: Justus-Liebig-Universität Giessen

description:
Lov2 singlet oxygen stress
biological sample 4-6

hyb_protocol: The RNA of three independent experiments of Rhodobacter sphaeroides wild type and the Δlov deletion mutant were pooled and hybridized to one array. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

scan_protocol: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: R with Limma package was used for data evaluation. LOWESS normalized and background subtracted.

organism: Cereibacter sphaeroides 2.4.1

source_name: R. sphaeroides Δlov total cells

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation

growth_protocol: R. sphaeroides strains of the wild type 2.4.1 and the Δlov mutant were diluted to an OD660 of 0.2 and gassed to adjust aerobic conditions (≈ 170 µM O2). 0.2 µM of methylene blue was added to the cultures to act as photosensitizer. After one doubling time of growth in the darkness cells were illuminated with 800 W m-2 of white light for 7 min.

extract_protocol: Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.

value: Δlov

tag: growth protocol

value: singlet oxygen stress, aerobic conditions

source_name: R. sphaeroides 2.4.1 total cells

value: wild type


title: R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 - singlet oxygen conditions - replicate 1

description:
Lov1 singlet oxygen stress
biological sample 1-3


title: Maturation zone_V_rep2

description:
RXP4001_023
Gene expression of 10-20 mm region from basal side corresponding to maturation zone.

value: Nipponbare

value: root


title: Epi.Exo.Scl._Elongation zone/Maturation zone_I_rep1

description:
RXP4001_025
Gene expression of Epidermis/Exodermis/Sclerenchyma at 1-3 mm region from root tip.

value: epidermis/exodermis/sclerenchyma


title: R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 - blue light conditions - replicate 2

description:
Lov2 blue light
biological sample 4-6

growth_protocol: R. sphaeroides strains grown semiaerobically (90 µM O2) under blue light illumination (20 µmol m-2 s-1).

value: blue light, semiaerobic conditions


title: Maturation zone_V_rep1

description:
RXP4001_022
Gene expression of 10-20 mm region from basal side corresponding to maturation zone.

value: maturation zone V


title: X 3 rep1 -

description: replicate 1


title: X 2 rep1 -

description: replicate 1


title: R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 - blue light conditions - replicate 1

description:
Lov1 blue light
biological sample 1-3


title: X 2 rep2 -

description: replicate 2


title: R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 - microaerobic conditions - replicate 2

description:
LOV2 micro
Biologial sample 4-6

hyb_protocol: A total of two arrays were hybridized to RNA from a total of six 2.4.1 cultures. In the same way two arrays were hybridized to RNA from a total of six 2.4.1Δlov cultures. 2 µg of the pooled RNA were incubated with Cy3 dye (2.4.1Δlov) or Cy5 dye (2.4.1) for 15 min at 85°C in the dark. Labeled RNAs were purified using KREApure columns, and the dye incorporation was measured using the nanodrop. Equal quantities of Cy3/Cy5 incorporated RNAs were mixed and incubated with fragmentation buffer for 30 min at 60°C. The samples were mixed with hybridization buffer (Agilent), hybridized onto microarray glass slides, and incubated overnight (17 hrs) at 65°C in a hybridization oven.

scan_protocol: Scanned on an Genepix 3100 scanner. Images were quantified using GenePix Pro 7 Acquisition and Analysis Microarray Software.

data_processing: R with the LIMMA package was used for data evaluation. LOWESS normalized, background subtracted.

source_name: R. sphaeroides Δlov (total cells)

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech, Amsterdam, Netherlands) was used for RNA labeling and fragmentation. 2 µg of the pooled RNA were incubated with Cy3 dye (2.4.1Δlov) or Cy5 dye (2.4.1) for 15 min at 85°C in the dark. Labeled RNAs were purified using KREApure columns, and the dye incorporation was measured using the nanodrop.

growth_protocol: Cells grown to an OD660=0,8 under microaerobic conditions and isolated with Hot Phenol

extract_protocol: Total RNA was extracted by the hot phenol method (Gabain et al., 1983; Janzon et al., 1986). Genomic DNA contamination from RNA samples was removed by DNaseI treatment (Invitrogen, Carlsbad, USA). After DNA digestion, RNA was purified on RNeasy® MinElute™ spin columns (QIAGEN, Hilden, Germany).

value: microaerobic conditions

source_name: R. sphaeroides 2.4.1


title: Maturation zone_IV_rep1

description:
RXP4001_019
Gene expression of 12-15 mm region from root tip corresponding to maturation zone.

source_name: Maturation zone_12-15 mm from root tip

value: maturation zone IV


title: Tgfb48.2

first: Swati

last: Bhattacharyya

address: 240 E Huron st, McGAW, M230

department: Medicine

description: Primary fibroblasts incubated with Tgfb1 for 48h.

hyb_protocol: Hybridization to Illumina Human Ref-8 version 2 Expression Microarray Chips (Illumina, San Diego, CA) using the standard protocolas recommended by Illumina.

scan_protocol: Standard protocol as recommended by Illumina.

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.5.9). It was vst transformed and rsn normalized.

source_name: Cultures of primary fibroblasts from neonatal foreskin, Tgfb1, 48h

label_protocol: cDNA was labeled using an Ambion labeling kit (Ambion).

value: neonatal foreskin

value: primary fibroblasts

tag: treatment

tag: time


title: SOX2 Sup

city: ChiaYi

first: Chin

last: Li

address: 168 University Road, Minhsiung

department: Life Science

country: Taiwan

institute: National Chung Cheng University

hyb_protocol: Phalanx HOA v5 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 10 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer in duplicate.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 500; 532nm power10, PMT460) and quantify the fluoresence intensity.

data_processing: Signals passed the filter (at least one probe which Flag=0 in all slides) were input into Rosetta Resolver® error model to calculate the normalized intensity (median shifting), technical reproducebility (R>0.99), and pairwise conparison (log2 ratio and p-value).

source_name: Unbound RNA SOX2

label_protocol: Total RNA (>0.4 µg) was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

extract_protocol: RNA extraction by Chin Li using TRIZOL reagent. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

tag: cell line


title: Maturation zone_III_rep3

description:
RXP4001_018
Gene expression of 6-9 mm region from root tip corresponding to maturation zone.

source_name: Maturation zone_6-9 mm from root tip

tag: tissue

value: maturation zone III


title: X 3 rep1 +

description: replicate 1

value: lung tumor xenograft CD166+


title: Maturation zone_IV_rep2

description:
RXP4001_020
Gene expression of 12-15 mm region from root tip corresponding to maturation zone.


title: X 1 rep2 -

description: replicate 1


title: Tgfb48.1

extract_protocol: Standard protocol as recommended by Illumina.


title: SOX2 Matrix

source_name: matrix-associated RNA from SOX2 pull down


title: Tgfb24.1

description: Primary fibroblasts incubated with Tgfb1 for 24h.

source_name: Cultures of primary fibroblasts from neonatal foreskin, Tgfb1, 24h


title: Tgfb24.2


title: Maturation zone_III_rep1

description:
RXP4001_016
Gene expression of 6-9 mm region from root tip corresponding to maturation zone.


title: X 3 rep2 +

description: replicate 1


title: X 1 rep1 -

description: replicate 2


title: Egr1m48.2

description: Primary fibroblasts infected by Egr1 mutated adenoviral recombinant and incubated for 48h.

source_name: Cultures of primary fibroblasts from neonatal foreskin, Egr1, 48h


title: Maturation zone_IV_rep3

description:
RXP4001_021
Gene expression of 12-15 mm region from root tip corresponding to maturation zone.


title: Maturation zone_III_rep2

description:
RXP4001_017
Gene expression of 6-9 mm region from root tip corresponding to maturation zone.


title: Egr1m48.1


title: R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 - microaerobic conditions - replicate 1

description:
LOV1 micro
Biologial sample 1-3


title: X 2 rep2 +

description: replicate 2


title: GST Sup

source_name: Unbound RNA GST


title: Maturation zone_II_rep3

description:
RXP4001_015
Gene expression of 3-6 mm region from root tip corresponding to maturation zone.

source_name: Maturation zone_3-6 mm from root tip

value: maturation zone II


title: X 2 rep1 +

description: replicate 1


title: Egr1m24.2

description: Primary fibroblasts infected by Egr1 mutated adenoviral recombinant and incubated for 24h.

source_name: Cultures of primary fibroblasts from neonatal foreskin, Egr1, 24h


title: Maturation zone_II_rep2

description:
RXP4001_014
Gene expression of 3-6 mm region from root tip corresponding to maturation zone.


title: Rice plant leaves at inflorescence-forming stage under drought stress, rep4

city: Shanghai

first: Zaochang

last: Liu

address: 2901 Beidi Rd., Minhang District

department: Lab

institute: SAAS

hyb_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100ul of 6× SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34C. After hybridization, detection used fluorescence labelling employing tag-specific Cy3 and Cy5 dyes.

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

data_processing: Data were analysed by first subtracting the background and then normalizing the signals using a LOWESS filter (locally weighted regression) (Bolstad et al., 2003).

source_name: control leaf, 6 DAW

label_protocol: Performed by LC Sciences (http://www.lcsciences.com).

extract_protocol: Total RNA was extracted at 6 DAW using TRIzol Total RNA Reagent according to the manufacturer's instructions.

value: leaf

value: inflorescence forming

value: normal watering

value: 6 DAW

source_name: drought-stressed leaf, 6 DAW

value: drought stress


title: Egr1m24.1


title: Maturation zone_II_rep1

description:
RXP4001_013
Gene expression of 3-6 mm region from root tip corresponding to maturation zone.

value: Nipponbare


title: Rice plant leaves at inflorescence-forming stage under drought stress, rep2

source_name: drought-stressed leaf, 5 DAW

extract_protocol: Total RNA was extracted at 5 DAW using TRIzol Total RNA Reagent according to the manufacturer's instructions.

value: 5 DAW

source_name: control leaf, 5 DAW


title: C48.2

description: Primary fibroblasts infected with control adenovirus for 48h used as a control.

source_name: Cultures of primary fibroblasts from neonatal foreskin, control, 48h


title: C24.1

description: Primary fibroblasts infected with control adenovirus for 24h used as a control.

source_name: Cultures of primary fibroblasts from neonatal foreskin, control, 24h


title: Rice plant leaves at tillering stage under drought stress, rep6

source_name: control leaf, 14 DAW

extract_protocol: Total RNA was extracted at 14 DAW using TRIzol Total RNA Reagent according to the manufacturer's instructions.

value: tillering

value: 14 DAW

source_name: drought-stressed leaf, 14 DAW


title: X 1 rep2 +

description: replicate 2

source_name: tumor xenograft


title: S 3 rep1

description: replicate 1

source_name: tumor sphere

value: lung tumor sphere


title: C48.1


title: Maturation zone_I_rep3

description:
RXP4001_012
Gene expression of 2-3 mm region from root tip corresponding to maturation zone.

source_name: Maturation zone_2-3 mm from root tip

value: root

value: maturation zone I


title: S 4 rep2

description: replicate 2


title: S 2 rep3

description: replicate 3


title: X 1 rep1 +

description: replicate 1


title: C24.2

value: neonatal foreskin


title: S 3 rep2

description: replicate 2


title: S 4 rep1

description: replicate 1


title: Maturation zone_I_rep1

description:
RXP4001_010
Gene expression of 2-3 mm region from root tip corresponding to maturation zone.


title: Rice plant leaves at inflorescence-forming stage under drought stress, rep3


title: Maturation zone_I_rep2

description:
RXP4001_011
Gene expression of 2-3 mm region from root tip corresponding to maturation zone.


title: Rice plant leaves at tillering stage under drought stress, rep5


title: Elongation zone_rep1

description:
RXP4001_007
Gene expression of 1-2 mm region from root tip corresponding to elongation zone.

source_name: Elongation zone_1-2 mm from root tip

value: elongation zone


title: Rice plant leaves at tillering stage under drought stress, rep3

source_name: drought-stressed leaf, 12 DAW

extract_protocol: Total RNA was extracted at 12 DAW using TRIzol Total RNA Reagent according to the manufacturer's instructions.

value: 12 DAW

source_name: control leaf, 12 DAW


title: Rice plant leaves at tillering stage under drought stress, rep4


title: S 2 rep1

description: replicate 1


title: Elongation zone_rep2

description:
RXP4001_008
Gene expression of 1-2 mm region from root tip corresponding to elongation zone.


title: S 2 rep2

description: replicate 2


title: Rice plant leaves at tillering stage under drought stress, rep2

source_name: drought-stressed leaf, 10 DAW

extract_protocol: Total RNA was extracted at 10 DAW using TRIzol Total RNA Regent according to the manufacturer's instructions.

value: 10 DAW

source_name: control leaf, 10 DAW


title: Rice plant leaves at tillering stage under drought stress, rep1


title: Rice plant leaves at inflorescence-forming stage under drought stress, rep1


title: Division zone_rep2

description:
RXP4001_005
Gene expression of division zone.

source_name: Division zone

value: division zone


title: Division zone_rep1

description:
RXP4001_004
Gene expression of division zone.


title: S 1 rep3

description: replicate 3


title: Division zone_rep3

description:
RXP4001_006
Gene expression of division zone.