title: PDAC_Patient:GEO-PC-103_rep1

description: PDAC tumour RNA, Patient:GEO-PC-103, replicate 1


title: PDAC_Patient:GEO-PC-097_rep1

status: Public on May 05 2014

type: RNA

city: Sydney

first: Jianmin

last: Wu

state: NSW

address: 370 Victoria Street Darlinghurst

department: Cancer Division

country: Australia

institute: Garvan Institute of Medical Research

description: PDAC tumour RNA, Patient:GEO-PC-097, replicate 1

hyb_protocol: Amplified cRNA (750ng) was hybridized onto Illumina human HT-12 arrays (V4) as per manufacturer's instructions

scan_protocol: Arrays were scanned on a Bead Array Reader (Illumina)

data_processing: Expression measurements were extracted using the GenomeStudio (version 2009.1) software (Illumina Inc), using no background correction or normalisation, and exported in one batch. This unnormalised data was Background corrected, log2 transformed, and quantile normalized, using lumi package in R.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: mRNA samples (150ng/sample) were amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) as per manufacturer’s instructions. Amplified RNA was quantified using a NanoDrop (Thermo Scientific) and distribution of the amplified material was analysed in an 2100 Bioanalyzer (Agilent)

growth_protocol: Pancreas tissue was surgically removed from PDAC patients undergoing Whipple surgical resection.

extract_protocol: RNA was extracted from primary tissue using the Qiagen Allprep kit in accordance with the manufacturers instructions.

treatment_protocol: Tissue was immediately snap frozen in liquid nitrogen (for full protocol see APGI website: http://www.pancreaticcancer.net.au/).

tag: tissue

value: Pancreas

tag: disease

value: PDAC


title: PDAC_Patient:GEO-PC-101_rep1

description: PDAC tumour RNA, Patient:GEO-PC-101, replicate 1


title: Quiescent control hepatic stellate cells qHSC4

city: New York

first: Robert

last: Schwabe

state: NY

address: 1150 St. Nicholas Ave, Room 415

country: USA

institute: Columbia University

hyb_protocol: 60 ul (25 ng/ul) of fragemented and labeled cDNA was hybridized to Mouse Genome 1.0ST GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the RMA algorithm as implemented in Bioconductor/R.

organism: Mus musculus

source_name: Quiescent hepatic stellate cells isolated from Balb/c mice

label_protocol: 150 ng RNA was amplified, biotin labeled and fragmented using the Ambion WT Expression kit and GeneChip WT Terminal Labeling and Controls kit.

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated by column purification (Qiagen) and quantification by NanoDrop spectrophotometer.

treatment_protocol: Hepatic stellate cells were isolated from 2 groups of 18 week old male Balb/c mice using density centrifugation and subsequent retinoid autofluorescence-based FACS sorting:  Group 1: Quiescent HSCs were isolated from 18 week old normal Balb/c mice and lysed immediately after FACS sorting. Group 2: Hepatic stellate cells were isolated from 16 week old Balb/c mice that had previously been treated with 4 injections of CCl4 (0.5 ul/g body weight, two injections per week) followed by a rest period of 45 days. Hepatic stellate cells were lysed immediately after FACS sorting.

tag: gender

value: male

tag: strain

value: Balb/c

tag: cell type

value: Quiescent hepatic stellate cells


title: PDAC_Patient:GEO-PC-095_rep1

description: PDAC tumour RNA, Patient:GEO-PC-095, replicate 1


title: PDAC_Patient:GEO-PC-094_rep1

description: PDAC tumour RNA, Patient:GEO-PC-094, replicate 1


title: PDAC_Patient:GEO-PC-090_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-090, replicate 1


title: PDAC_Patient:GEO-PC-088_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-088, replicate 1


title: PDAC_Patient:GEO-PC-096_rep1

description: PDAC tumour RNA, Patient:GEO-PC-096, replicate 1


title: PDAC_Patient:GEO-PC-087_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-087, replicate 1


title: PDAC_Patient:GEO-PC-089_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-089, replicate 1


title: PDAC_Patient:GEO-PC-091_rep1

description: PDAC tumour RNA, Patient:GEO-PC-091, replicate 1


title: genomic DNA from buccal epithelium [F117_P309]

type: genomic

city: Bronx

first: Esther

last: Berko

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

description: YRI and CEU are the HapMap ancestry designations. YRI and CEU units are percent ancestry.

hyb_protocol: standard Illumina protocols for labeling, hybridization, and scanning

data_processing: Raw idat files were preprocessed to obtain normalized M-values in R using the packages *minfi* and *sva*. Three samples in metadata table with NA for YRI/CEU (F136_P369, F83_P209, F134_P361) were removed after preprocessing, prior to running bump-hunting.

molecule: genomic DNA

extract_protocol: DNA was extracted using a modified Qiagen Gentra Puregene buccal cell protocol.

value: TD

value: Female

tag: age at draw (years)

tag: yri

tag: ceu


title: genomic DNA from buccal epithelium [F82_P207]

scan_protocol: standard Illumina protocols for labeling, hybridization, and scanning


title: PDAC_Patient:GEO-PC-093_rep1

description: PDAC tumour RNA, Patient:GEO-PC-093, replicate 1


title: genomic DNA from buccal epithelium [F111_P289]

label_protocol: standard Illumina protocols for labeling, hybridization, and scanning

value: ASD

value: Male


title: genomic DNA from buccal epithelium [F27_P69]


title: genomic DNA from buccal epithelium [F146_P395]


title: genomic DNA from buccal epithelium [F52_P129]


title: genomic DNA from buccal epithelium [F133_P357]


title: PDAC_Patient:GEO-PC-086_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-086, replicate 1


title: PDAC_Patient:GEO-PC-084_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-084, replicate 1


title: PDAC_Patient:GEO-PC-085_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-085, replicate 1


title: genomic DNA from buccal epithelium [F136_P369]


title: genomic DNA from buccal epithelium [F137_P372]


title: genomic DNA from buccal epithelium [F30_P75]


title: PDAC_Patient:GEO-PC-082_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-082, replicate 1


title: PDAC_Patient:GEO-PC-080_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-080, replicate 1


title: PDAC_Patient:GEO-PC-083_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-083, replicate 1


title: genomic DNA from buccal epithelium [F95_P244]


title: genomic DNA from buccal epithelium [F38_P95]


title: genomic DNA from buccal epithelium [F82_P257]


title: genomic DNA from buccal epithelium [F53_P146]


title: PDAC_Patient:GEO-PC-081_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-081, replicate 1


title: genomic DNA from buccal epithelium [F32_P81]


title: genomic DNA from buccal epithelium [F87_P221]


title: PDAC_Patient:GEO-PC-077_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-077, replicate 1


title: PDAC_Patient:GEO-PC-076_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-076, replicate 1


title: genomic DNA from buccal epithelium [F74_P186]


title: genomic DNA from buccal epithelium [F42_P105]


title: genomic DNA from buccal epithelium [F26_P65]


title: PDAC_Patient:GEO-PC-078_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-078, replicate 1


title: PDAC_Patient:GEO-PC-072_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-072, replicate 1


title: PDAC_Patient:GEO-PC-079_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-079, replicate 1


title: genomic DNA from buccal epithelium [F145_P392]


title: PDAC_Patient:GEO-PC-073_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-073, replicate 1


title: PDAC_Patient:GEO-PC-075_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-075, replicate 1


title: PDAC_Patient:GEO-PC-074_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-074, replicate 1


title: PDAC_Patient:GEO-PC-071_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-071, replicate 1


title: genomic DNA from buccal epithelium [F75_P192]

description: YRI and CEU are the HapMap ancestry designations. YRI and CEU units are percent ancestry.


title: genomic DNA from buccal epithelium [F22_P56]


title: PDAC_Patient:GEO-PC-069_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-069, replicate 1


title: 40uM Glutamine Pulse t=368 seconds

first: David

last: Gresham

address: 12 Waverly Place, Rm 203

department: Biology

institute: New York University

description: gene expression in nitrogen limited chemostats

hyb_protocol: Cy3 and Cy5 labeled cRNA was co-hybridized to an Agilent 60-mer DNA microarray at 65C for 16 hours.  DNA microarrays were washed using the standard Agilent wash protocol.

scan_protocol: DNA microarrays were scanned using an Agilent Technologies Scanner G2505B

data_processing: Probe intensities were determined using the Agilent Feature Exractor software and normalized between the Cy5 and Cy3 channel using a linear-loess normalization

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast nitrogen-limited chemostat

label_protocol: cDNA from each sample was generated using MMLV reverse transcriptase primed with a poly-dT primer containing the promoter sequence for T7 RNA polymerase.  Labeled cRNA was generated using T7 RNA polymerase and UTPs labeled with either Cy3 or Cy5.

growth_protocol: Chemostat cultures were maintained in aerobic Sixfors fermentors (Infors) at 30°C using constant stirring at 400rpm

extract_protocol: mRNA was prepared using hot acid phenol exatraction followed by purification using a QIAGEN RNeasy mini kit

treatment_protocol: All nitrogen-limiting media contained 800µM nitrogen regardless of the molecular form of the nitrogen and 1 g/L CaCl2-2H2O, 1 g/L of NaCl, 5 g/L of MgSO4-7H2O, 10 g/L KH2PO4, 2% glucose and trace metals and vitamins

tag: nutrient limitation or pulse

value: 40uM Glutamine

tag: steady-state or pulse

value: pulse

source_name: Ammonium limited chemostat D=0.12

tag: nutrient limitation

value: ammonium

value: steady-state


title: genomic DNA from buccal epithelium [F66_P166]


title: PDAC_Patient:GEO-PC-068_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-068, replicate 1


title: 40uM Glutamine Pulse t= 248 seconds


title: genomic DNA from buccal epithelium [F122_P326]


title: PDAC_Patient:GEO-PC-067_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-067, replicate 1


title: 40uM Glutamine Pulse t= 170 seconds


title: 40uM Glutamine Pulse t=308 seconds


title: genomic DNA from buccal epithelium [F31_P77]


title: PDAC_Patient:GEO-PC-064_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-064, replicate 1


title: 40uM Glutamine Pulse t=120 seconds


title: genomic DNA from buccal epithelium [F26_P64]


title: PDAC_Patient:GEO-PC-066_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-066, replicate 1


title: genomic DNA from buccal epithelium [F137_P373]


title: PDAC_Patient:GEO-PC-065_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-065, replicate 1


title: genomic DNA from buccal epithelium [F102_P265]


title: PDAC_Patient:GEO-PC-063_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-063, replicate 1


title: 40uM Glutamine Pulse t=10 seconds


title: genomic DNA from buccal epithelium [F104_P270]


title: genomic DNA from buccal epithelium [F59_P150]


title: genomic DNA from buccal epithelium [F116_P306]


title: 20uM Glutamine, 40uM Proline Pulse t=120 min

value: 20uM Glutamine + 40uM Proline


title: 20uM Glutamine, 40uM Proline Pulse t=180min


title: 40uM Glutamine Pulse t=40 seconds


title: genomic DNA from buccal epithelium [F142_P383]


title: genomic DNA from buccal epithelium [F143_P385]


title: PDAC_Patient:GEO-PC-060_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-060, replicate 1


title: PDAC_Patient:GEO-PC-062_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-062, replicate 1


title: PDAC_Patient:GEO-PC-061_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-061, replicate 1


title: 40uM Glutamine Pulse t=0 seconds


title: genomic DNA from buccal epithelium [F105_P273]


title: 20uM Glutamine, 40uM Proline Pulse t=60 min


title: PDAC_Patient:GEO-PC-058_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-058, replicate 1


title: genomic DNA from buccal epithelium [F147_P397]


title: PDAC_Patient:GEO-PC-056_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-056, replicate 1


title: genomic DNA from buccal epithelium [F136_P368]


title: PDAC_Patient:GEO-PC-057_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-057, replicate 1


title: 20uM Glutamine, 40uM Proline Pulse t=15 min


title: genomic DNA from buccal epithelium [F145_P393]


title: 20uM Glutamine, 40uM Proline Pulse t=5 min


title: 20uM Glutamine, 40uM Proline Pulse t=10 min


title: 20uM Glutamine, 40uM Proline Pulse t=30 min


title: genomic DNA from buccal epithelium [F76_P194]


title: genomic DNA from buccal epithelium [F139_P377]


title: genomic DNA from buccal epithelium [F83_P215]


title: genomic DNA from buccal epithelium [F22_P55]


title: PDAC_Patient:GEO-PC-054_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-054, replicate 1


title: PDAC_Patient:GEO-PC-055_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-055, replicate 1


title: PDAC_Patient:GEO-PC-053_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-053, replicate 1


title: genomic DNA from buccal epithelium [F23_P58]

description: YRI and CEU are the HapMap ancestry designations. YRI and CEU units are percent ancestry.


title: 20uM Glutamine, 40uM Proline Pulse t=2 min

description: gene expression in nitrogen limited chemostats


title: 20uM Glutamine, 40uM Proline Pulse t=0 min


title: genomic DNA from buccal epithelium [F29_P73]


title: genomic DNA from buccal epithelium [F41_P103]


title: 80uM Proline Pulse t=300 seconds

value: 80uM Proline


title: genomic DNA from buccal epithelium [F100_P259]


title: 80uM Proline Pulse t=230 seconds


title: 80uM Proline Pulse t=200 seconds


title: PDAC_Patient:GEO-PC-051_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-051, replicate 1


title: genomic DNA from buccal epithelium [F25_P62]


title: genomic DNA from buccal epithelium [F83_P209]


title: 80uM Proline Pulse t=112 seconds


title: 80uM Proline Pulse t=134 seconds


title: genomic DNA from buccal epithelium [F72_P181]


title: PDAC_Patient:GEO-PC-050_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-050, replicate 1


title: PDAC_Patient:GEO-PC-046_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-046, replicate 1


title: PDAC_Patient:GEO-PC-048_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-048, replicate 1


title: PDAC_Patient:GEO-PC-059_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-059, replicate 1


title: PDAC_Patient:GEO-PC-047_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-047, replicate 1


title: PDAC_Patient:GEO-PC-049_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-049, replicate 1


title: genomic DNA from buccal epithelium [F144_P388]


title: 80uM Proline Pulse t=26 seconds


title: 80uM Proline Pulse t=10 seconds


title: 80uM Proline Pulse t=0 seconds


title: genomic DNA from buccal epithelium [F104_P269]


title: PDAC_Patient:GEO-PC-045_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-045, replicate 1


title: PDAC_Patient:GEO-PC-043_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-043, replicate 1


title: genomic DNA from buccal epithelium [F138_P375]


title: 80uM Proline Pulse t=360 min


title: 80uM Proline Pulse t=240 min


title: genomic DNA from buccal epithelium [F134_P361]


title: 80uM Proline Pulse t=180 min


title: PDAC_Patient:GEO-PC-041_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-041, replicate 1


title: PDAC_Patient:GEO-PC-042_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-042, replicate 1


title: 80uM Proline Pulse t=120 min


title: genomic DNA from buccal epithelium [F107_P278]


title: PDAC_Patient:GEO-PC-040_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-040, replicate 1


title: genomic DNA from buccal epithelium [F114_P301]


title: 80uM Proline Pulse t=60 min


title: PDAC_Patient:GEO-PC-039_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-039, replicate 1


title: PDAC_Patient:GEO-PC-038_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-038, replicate 1


title: genomic DNA from buccal epithelium [F37_P93]


title: PDAC_Patient:GEO-PC-044_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-044, replicate 1


title: 80uM Proline Pulse t=30 min


title: genomic DNA from buccal epithelium [F16_P42]

description: YRI and CEU are the HapMap ancestry designations. YRI and CEU units are percent ancestry.


title: PDAC_Patient:GEO-PC-037_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-037, replicate 1


title: genomic DNA from buccal epithelium [F144_P387]


title: genomic DNA from buccal epithelium [F24_P60]


title: PDAC_Patient:GEO-PC-036_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-036, replicate 1


title: genomic DNA from buccal epithelium [F132_P353]


title: genomic DNA from buccal epithelium [F73_P184]


title: 80uM Proline Pulse t=15 min

description: gene expression in nitrogen limited chemostats


title: PDAC_Patient:GEO-PC-035_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-035, replicate 1


title: 80uM Proline Pulse t=10 min


title: TnfΔARE/+ offspring from a TnfΔARE/+ dam, biological rep4

city: Freising

first: Jana

last: Hemmerling

state: Bavaria

department: ZIEL

country: Germany

institute: Technische Universität München

description: Gene expression data from offspring's ileal epithelium at 8 weeks postnatal under ARE dam conditions

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr on NuGO_Mm1a520177  Genome Array. GeneChips® were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Subsequently to the washing and staining step, gene chips were visually inspected for irregularities and scanned with the GeneChip® Scanner 3000.

data_processing: Data were analyzed using the Affymetrix GCOS Manager software and further using the R- and Bioconductor-based Management and Analysis Database for Multi-platform microArray eXperiments interface (MADMAX, https://madmax.bioinformatics.nl). To extract biologically relevant information normalized data sets were processed with the MADMAX statistical analysis pipeline. The used software and database version were: R version 2.11.1., Bioconductor version 2.6., AnnotationDbi version 1.10.2. Data were normalized using the gc Robust Multichip Average (slow) algorithm.

source_name: Laser microdissected intestinal epithelial cells of 8w offspring ileum

label_protocol: Biotin labeling were performed using the GeneChip® 3’ IVT Express kit (Affymetrix, Santa Clara, USA).

extract_protocol: Total RNA was isolated using Qiagen RNA/DANN AllPrep Micro Kit  according to the manufacturer's instructions.

value: laser microdissected intestinal epithelial cells

tag: genotype

value: TnfΔARE/+, iARE

tag: age

value: murine offspring 8 weeks postnatal

tag: genetic background


title: genomic DNA from buccal epithelium [F134_P360]


title: TnfΔARE/+ offspring from a TnfΔARE/+ dam, biological rep3


title: TnfΔARE/+ offspring from a TnfΔARE/+ dam, biological rep5


title: 80uM Proline Pulse t=5 min


title: PDAC_Patient:GEO-PC-034_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-034, replicate 1

value: Pancreas

value: PDAC


title: PDAC_Patient:GEO-PC-033_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-033, replicate 1


title: TnfΔARE/+ offspring from a TnfΔARE/+ dam, biological rep2


title: 800uM Proline Pulse t=420 min

value: 800uM Proline


title: 80uM Proline Pulse t=0 min


title: PDAC_Patient:GEO-PC-032_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-032, replicate 1


title: genomic DNA from buccal epithelium [F98_P253]


title: genomic DNA from buccal epithelium [F101_P263]


title: PDAC_Patient:GEO-PC-031_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-031, replicate 1


title: genomic DNA from buccal epithelium [F67_P168]


title: 80uM Proline Pulse t=300 min


title: 800uM Proline Pulse t=360 min


title: genomic DNA from buccal epithelium [F74_P188]


title: PDAC_Patient:GEO-PC-052_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-052, replicate 1


title: 800uM Proline Pulse t=300 min


title: Tnf+/+ offspring from a TnfΔARE/+ dam at 17.5 dpc, biological rep4

value: Tnf+/+, iWT


title: Tnf+/+ offspring from a TnfΔARE/+ dam at 17.5 dpc, biological rep5


title: 40uM Glutamine Pulse t=360 min


title: genomic DNA from buccal epithelium [F136_P367]

value: TD


title: TnfΔARE/+ offspring from a TnfΔARE/+ dam, biological rep1


title: genomic DNA from buccal epithelium [F53_P132]

value: Female


title: PDAC_Patient:GEO-PC-028_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-028, replicate 1


title: genomic DNA from buccal epithelium [F57_P283]


title: genomic DNA from buccal epithelium [F130_P344]


title: PDAC_Patient:GEO-PC-030_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-030, replicate 1


title: genomic DNA from buccal epithelium [F118_P312]


title: genomic DNA from buccal epithelium [F7_P16]

value: ASD


title: 40uM Glutamine Pulse t=300 min


title: PDAC_Patient:GEO-PC-025_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-025, replicate 1


title: genomic DNA from buccal epithelium [F115_P303]

value: Male


title: genomic DNA from buccal epithelium [F123_P328]


title: PDAC_Patient:GEO-PC-026_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-026, replicate 1


title: 40uM Glutamine Pulse t=240 min

value: 40uM Glutamine


title: Tnf+/+ offspring from a TnfΔARE/+ dam at 17.5 dpc, biological rep1


title: PDAC_Patient:GEO-PC-027_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-027, replicate 1


title: Tnf+/+ offspring from a TnfΔARE/+ dam at 17.5 dpc, biological rep2


title: TnfΔARE/+ offspring from a Tnf+/+ dam, biological rep5

description: Gene expression data from offspring's ileal epithelium at 8 weeks postnatal under WT dam conditions

value: TnfΔARE/+, ARE


title: Tnf+/+ offspring from a TnfΔARE/+ dam at 17.5 dpc, biological rep3


title: 40uM Glutamine Pulse t=180 min

value: pulse

value: ammonium


title: 40uM Glutamine Pulse t=120 min

value: steady-state


title: genomic DNA from buccal epithelium [F6_P14]

description: YRI and CEU are the HapMap ancestry designations. YRI and CEU units are percent ancestry.


title: PDAC_Patient:GEO-PC-023_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-023, replicate 1


title: TnfΔARE/+ offspring from a Tnf+/+ dam, biological rep4


title: TnfΔARE/+ offspring from a Tnf+/+ dam, biological rep3


title: 40uM Glutamine Pulse t=60 min


title: 40uM Glutamine Pulse t=30 min


title: genomic DNA from buccal epithelium [F86_P218]


title: PDAC_Patient:GEO-PC-022_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-022, replicate 1


title: TnfΔARE/+ offspring from a Tnf+/+ dam, biological rep2


title: 40uM Glutamine Pulse t=15 min

description: gene expression in nitrogen limited chemostats


title: Tnf+/+ offspring from a Tnf+/+ dam at 17.5 dpc, biological rep5

value: Tnf+/+, WT


title: TnfΔARE/+ offspring from a Tnf+/+ dam, biological rep1

value: laser microdissected intestinal epithelial cells


title: 40uM Glutamine Pulse t=10 min


title: PDAC_Patient:GEO-PC-021_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-021, replicate 1


title: genomic DNA from buccal epithelium [F108_P280]


title: genomic DNA from buccal epithelium [F14_P37]


title: PDAC_Patient:GEO-PC-020_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-020, replicate 1


title: 40uM Glutamine Pulse t=5 min


title: PDAC_Patient:GEO-PC-018_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-018, replicate 1


title: genomic DNA from buccal epithelium [F57_P284]


title: 40uM Glutamine Pulse t=0 min


title: 40uM Glutamine Pulse t=420 min


title: genomic DNA from buccal epithelium [F65_P163]


title: Tnf+/+ offspring from a Tnf+/+ dam at 17.5 dpc, biological rep4


title: 400uM Glutamine Pulse t=420 min

value: 400uM Glutamine


title: Tnf+/+ offspring from a Tnf+/+ dam at 17.5 dpc, biological rep2

value: murine offspring 8 weeks postnatal


title: genomic DNA from buccal epithelium [F28_P71]


title: PDAC_Patient:GEO-PC-017_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-017, replicate 1

value: Pancreas


title: 400uM Glutamine Pulse t=360 min


title: Tnf+/+ offspring from a Tnf+/+ dam at 17.5 dpc, biological rep3


title: Tnf+/+ offspring from a Tnf+/+ dam at 17.5 dpc, biological rep1


title: 400uM Glutamine Pulse t=300 min


title: PDAC_Patient:GEO-PC-016_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-016, replicate 1

value: PDAC


title: genomic DNA from buccal epithelium [F122_P325]


title: genomic DNA from buccal epithelium [F130_P343]


title: Human UCSC_sample 1

city: Seoul

first: Nayoung

last: Suh

address: 88 Olympic-ro 43-gil, Songpagu

department: Department of Medicine

country: South Korea

institute: Asan Medical Center, University of Ulsan College of Medicine

description: miRNA

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: Human UCSC-1, Passage 5

label_protocol: For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

growth_protocol: All cell lines were cultured in Dulbecco’s modified Eagle’s medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Gibco), 100 units/ml penicillin, and 100 µg/ml streptomycin (Gibco) in 5% CO2 in a humidified incubator at 37°C. All hMSC experiments were performed at passage 3 to 6.

extract_protocol: Total RNA was isolated using Trizol (Life Technologies) according to the manufacturer's instructions.

value: Umbilical cord


title: TnfΔARE/+ fetus from a TnfΔARE/+ dam, biological rep4

description: Gene expression data from 17.5 dpc fetal ileal epithelium under ARE dam conditions

source_name: Laser microdissected intestinal epithelial cells of 17.5 dpc fetal ileum

value: TnfΔARE/+, iARE

value: murine fetus at 17.5 dpc


title: Human UCSC_sample 2

description: miRNA

source_name: Human UCSC-2, Passage 6


title: TnfΔARE/+ fetus from a TnfΔARE/+ dam, biological rep3


title: TnfΔARE/+ fetus from a TnfΔARE/+ dam, biological rep2


title: PDAC_Patient:GEO-PC-013_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-013, replicate 1


title: PDAC_Patient:GEO-PC-014_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-014, replicate 1


title: PDAC_Patient:GEO-PC-019_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-019, replicate 1


title: genomic DNA from buccal epithelium [F64_P161]

value: TD


title: Human BMSC_sample 2

description: miRNA

source_name: Human BMSC-2, Passage 6

value: Bone marrow


title: PDAC_Patient:GEO-PC-024_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-024, replicate 1


title: PDAC_Patient:GEO-PC-015_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-015, replicate 1


title: PDAC_Patient:GEO-PC-012_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-012, replicate 1


title: genomic DNA from buccal epithelium [F39_P97]

value: Male


title: PDAC_Patient:GEO-PC-011_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-011, replicate 1


title: TnfΔARE/+ fetus from a TnfΔARE/+ dam, biological rep5


title: genomic DNA from buccal epithelium [F129_P341]

description: YRI and CEU are the HapMap ancestry designations. YRI and CEU units are percent ancestry.


title: genomic DNA from buccal epithelium [F43_P108]


title: TnfΔARE/+ fetus from a TnfΔARE/+ dam, biological rep1


title: Tnf+/+ fetus from a TnfΔARE/+ dam at 17.5 dpc, biological rep5

value: Tnf+/+, iWT


title: Human ADSC_sample 2

description: miRNA

source_name: Human ADSC-2, Passage 4

value: Adipose


title: Human ADSC_sample 1

description: miRNA

source_name: Human ADSC-1, Passage 5


title: Fibroblast_sample 2

description: miRNA

source_name: MRC5, Passage 9

value: Fibroblast


title: Tnf+/+ fetus from a TnfΔARE/+ dam at 17.5 dpc, biological rep4


title: genomic DNA from buccal epithelium [F98_P254]

value: Female


title: PDAC_Patient:GEO-PC-008_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-008, replicate 1


title: Tnf+/+ fetus from a TnfΔARE/+ dam at 17.5 dpc, biological rep3


title: Tnf+/+ fetus from a TnfΔARE/+ dam at 17.5 dpc, biological rep2


title: Trout injected with NV biological replicate4

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

hyb_protocol: The slides were pre-treated with 1% BSA, fraction V, 5x SSC, 0.1% SDS (30 min at 50 ºC) and washed with 2x SSC (3 min) and 0.2x SSC (3 min) and hybridized overnight in cocktail containing 1.3 x Denhardt’s, 3x SSC 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA

scan_protocol: Signal was captured, processed and segmented using an Agilent scanner (G2565B, Agilent Technologies) by the Agilent Feature Extraction Software (v9.5) with the protocol GE1-v5_95, extended dynamic range and preprocessing by Agilent Feature Extraction.

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent Feature Extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information.

organism: Oncorhynchus mykiss

source_name: Spleen and head kidney, 2d after injection of NV

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore).

growth_protocol: Trout fingerlings were maintained at 18-19 ºC in aquaria with tap-dechlorinated carbon-filtered water provided with biological filters and fed with a commercial feed diet in a 50 l aquarium during two weeks.

extract_protocol: Tissues were homogenized with Tissue Lyser (Qiagen, Hilden, Germany). RNA was extracted using the RNeasy Plus kit (Qiagen, Hilden, Germany).

treatment_protocol: Trouts were intraperitoneally injected with 200 ul of VHSV non-virion (NV) recombinant protein in PBS, 10 ug of protein per trout. Injected trouts were released to containers (1 container per group) immersed in a 50 l aquarium and maintained during 2-days at 14 ºC. Later, trouts were sacrified by decapitation, and spleen and head kidney of each trout were removed and pooled. Tissues were immediately immersed in RNAlater (Qiagen, Hilden, Germany ) at 4 ºC overnight before being frozen at -70 ºC until processed. All trouts were anesthetized by immersion in 50 mg/mL buffered tricaine ethanesulfonate (MS-222, Sigma, Madrid, Spain) prior to handling.

tag: size

value: 10 cm

tag: weight

value: spleen and head kidney

tag: treatment

value: injection of NV recombinant protein


title: Trout injected with NV biological replicate3

tag: tissue


title: Trout injected with NV biological replicate2


title: PDAC_Patient:GEO-PC-010_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-010, replicate 1

tag: disease


title: genomic DNA from buccal epithelium [F88_P223]

value: ASD

tag: gender


title: genomic DNA from buccal epithelium [F20_P51]


title: PDAC_Patient:GEO-PC-005_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-005, replicate 1


title: PDAC_Patient:GEO-PC-006_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-006, replicate 1


title: Fibroblast_sample 1

description: miRNA

source_name: HS68, Passage 13


title: PDAC_Patient:GEO-PC-007_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-007, replicate 1


title: genomic DNA from buccal epithelium [F74_P187]


title: Tnf+/+ fetus from a TnfΔARE/+ dam at 17.5 dpc, biological rep1

value: laser microdissected intestinal epithelial cells


title: Trout injected with NV biological replicate1


title: genomic DNA from buccal epithelium [F3_P7]


title: genomic DNA from buccal epithelium [F33_P84]


title: TnfΔARE/+ fetus from a Tnf+/+ dam, biological rep5

description: Gene expression data from 17.5 dpc fetal ileal epithelium under WT dam conditions

value: TnfΔARE/+, ARE


title: TnfΔARE/+ fetus from a Tnf+/+ dam, biological rep4


title: PDAC_Patient:GEO-PC-004_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-004, replicate 1

value: Pancreas

value: PDAC


title: Human BMSC_sample 1

description: miRNA

source_name: Human BMSC-1, Passage 5


title: TnfΔARE/+ fetus from a Tnf+/+ dam, biological rep3


title: Trout injected with PBS biological replicate4

source_name: Spleen and head kidney, 2d after injection of PBS

treatment_protocol: Trouts were intraperitoneally injected with 100 ul Phosphate buffered salina (PBS) per trout. Injected trouts were released to containers (1 container per group) immersed in a 50 l aquarium and maintained during 2-days at 14 ºC. Later, trouts were sacrified by decapitation, and spleen and head kidney of each trout were removed and pooled. Tissues were immediately immersed in RNAlater (Qiagen, Hilden, Germany ) at 4 ºC overnight before being frozen at -70 ºC until processed. All trouts were anesthetized by immersion in 50 mg/mL buffered tricaine ethanesulfonate (MS-222, Sigma, Madrid, Spain) prior to handling.

value: injection of PBS


title: Trout injected with PBS biological replicate2


title: TnfΔARE/+ fetus from a Tnf+/+ dam, biological rep2

value: murine fetus at 17.5 dpc


title: genomic DNA from buccal epithelium [F19_P49]


title: Trout injected with PBS biological replicate3


title: PDAC_Patient:GEO-PC-001_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-001, replicate 1


title: Batch 400uM Gln pulse t=15 min

description: gene expression in batch cultures

source_name: yeast proline minimal media batch

value: Batch 400uM Gln

value: batch pulse

source_name: Proline batch media

value: proline

value: pulse


title: CD24-shRNA1

city: Birmingham

first: Lizhong

last: Wang

address: 740 20th St S

institute: UAB

description: Gene expression data from cells with transfected CD24-shRNA

hyb_protocol: This analysis is based on Human U133 Plus 2.0 microarrays that were pro-cessed in the microarray facility using the IVT express kit according to the manufacturer's instructions..

scan_protocol: The scanned array images (HG U133 Plus 2.0 chips) were processed with Affymetrix GeneChip Operating software (GCOS).

data_processing:
The linear models were used to the data that are designed specically for microarray analysis (G.K. Smyth. Linear models and empirical Bayes methods for assessing di eren-tial expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, 3: Article 3, 2004.).
The expression values for each gene were calculated using a robust multi-array average (RMA) (Rafael A. Irizarry, Bridget Hobbs, Francois Collin, et al. Exploration, normal-ization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249: 64, 2003). This is a modeling strategy that converts the PM probe values into an expression value for each gene.

source_name: Du145 cells

label_protocol: standard Affymetrix protocol

growth_protocol: Du145 cells were transfected with CD24 shRNAs or scrambel control shRNAs. After drug selection for 3 weeks, the stably transfected cells were used for Affimatrx Human U133 Plus 2.0 microarrays.

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

treatment_protocol: Scramble or CD24 shRNAs were transfected into Du145 cells and the stable transfected cells were used for Affimatrx Human U133 Plus 2.0 microarrays.

value: male

value: prostate

tag: cell line

tag: transfection


title: genomic DNA from buccal epithelium [F93_P238]

value: Male

tag: age at draw (years)


title: Trout injected with PBS biological replicate1

value: 10 cm


title: Tnf+/+ fetus from a Tnf+/+ dam at 17.5 dpc, biological rep5

tag: cell type

value: Tnf+/+, WT


title: CD24-shRNA3


title: TnfΔARE/+ fetus from a Tnf+/+ dam, biological rep1


title: CD24-shRNA4


title: CD24-shRNA2


title: CD24-Scr5

description: Gene expression data from cells with transfected scramble control shRNA

value: scramble control shRNA


title: CD24-shRNA5


title: Batch 400uM Gln pulse t=10 min

description: gene expression in batch cultures


title: Batch 400uM Gln pulse t=7 min

description: gene expression in batch cultures


title: genomic DNA from buccal epithelium [F35_P89]

value: ASD

tag: yri

tag: ceu


title: CD24-Scr4


title: Tnf+/+ fetus from a Tnf+/+ dam at 17.5 dpc, biological rep3

value: laser microdissected intestinal epithelial cells


title: Batch 400uM Gln pulse t=5 min

description: gene expression in batch cultures

tag: nutrient limitation or pulse

tag: steady-state or pulse


title: Batch 400uM Gln pulse t=3 min

description: gene expression in batch cultures

tag: nutrient limitation


title: Tnf+/+ fetus from a Tnf+/+ dam at 17.5 dpc, biological rep4

tag: genotype

tag: age


title: Control 4

status: Public on May 04 2014

city: Jinan

first: Xi

last: Li

state: Shandong

address: 44 Wen Hua West Road

department: School of Medicine

country: China

institute: Shandong University

description: miRCURY LNA Array (version 11.0) system

hyb_protocol: The miRNA expression profiling of the serum samples was performed using the miRCURY LNA Array (version 11.0) system. RNA samples were labeled using the miRCURY Hy3/Hy5 Power labeling kit and hybridized on the miRCURY LNA Array station (version. 11.0).

scan_protocol: Scanning was performed with the Axon GenePix 4000B microarray scanner. GenePix Pro version 6.0 was used to read the raw intensity of the image.

data_processing:
The intensity of the green signal was calculated after background subtraction, and replicated spots in the same slide were averaged to obtain the median intensity. The median normalization method was used to obtain normalized data (foreground minus background divided by median). The median represents the 50th quartile of miRNA intensity which is >50% in all samples after background correction.
Normalized signal intensity. It means the normalized ratio of the microRNA. Median Normalization Method was adopted. Normalized Data=(Foreground-Background)/median*

source_name: serum from peripheral blood

extract_protocol: RNA was isolated using a TRIzol-based miRNA isolation protocol (Sigma Aldrich, St. Louis, MO). Whole blood (5 mL) was separated into serum fractions by centrifugation at 1000g for 10 minutes. Serum RNA was harvested with the TRI Reagent BD (Sigma Aldrich, St. Louis, MO) and the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturers’ instructions.

tag: individual

value: Control

value: serum from peripheral blood

value: 29  years

value: F

tag: number of vessels (cad)

value: N

tag: stable cad for at least 4 months


title: Control 5

description: miRCURY LNA Array (version 11.0) system

label_protocol: The miRNA expression profiling of the serum samples was performed using the miRCURY LNA Array (version 11.0) system. RNA samples were labeled using the miRCURY Hy3/Hy5 Power labeling kit and hybridized on the miRCURY LNA Array station (version. 11.0).

tag: tissue

value: 32  years

value: M


title: Control 2

description: miRCURY LNA Array (version 11.0) system


title: Tnf+/+ fetus from a Tnf+/+ dam at 17.5 dpc, biological rep1

value: murine fetus at 17.5 dpc

tag: genetic background


title: Tnf+/+ fetus from a Tnf+/+ dam at 17.5 dpc, biological rep2


title: Control 3

description: miRCURY LNA Array (version 11.0) system

value: 27  years

tag: gender


title: Patient 9

description: miRCURY LNA Array (version 11.0) system

value: Patient

value: 60  years

value: Y


title: Patient 7

description: miRCURY LNA Array (version 11.0) system

value: 75  years


title: Patient 13

description: miRCURY LNA Array (version 11.0) system

value: 44  years


title: Patient 8

description: miRCURY LNA Array (version 11.0) system

value: 70  years


title: genomic DNA from buccal epithelium [F15_P40]

value: ASD

value: Male


title: PDAC_Patient:GEO-PC-003_rep1 (reanalysis)

description: PDAC tumour RNA, Patient:GEO-PC-003, replicate 1

value: Pancreas

tag: disease

value: PDAC


title: Patient 11

description: miRCURY LNA Array (version 11.0) system

value: serum from peripheral blood

value: 41  years


title: CD24-Scr2

value: male

value: prostate

tag: cell line

tag: transfection

value: scramble control shRNA


title: CD24-Scr1

tag: cell type


title: Patient 4

description: miRCURY LNA Array (version 11.0) system

value: 46  years

value: M


title: CD24-Scr3


title: Patient 12

description: miRCURY LNA Array (version 11.0) system

value: Patient

value: 67  years

value: F


title: Patient 1

description: miRCURY LNA Array (version 11.0) system

value: 65 years

value: Y


title: Patient 2

description: miRCURY LNA Array (version 11.0) system

value: 63  years


title: Patient 3

description: miRCURY LNA Array (version 11.0) system


title: Control 1

description: miRCURY LNA Array (version 11.0) system

value: Control

value: 31  years

value: N


title: Patient 10

description: miRCURY LNA Array (version 11.0) system

value: 62  years


title: Patient 5

description: miRCURY LNA Array (version 11.0) system

value: serum from peripheral blood


title: Patient 6

description: miRCURY LNA Array (version 11.0) system

value: 70  years


title: Batch 400uM Gln pulse t=1 min

description: gene expression in batch cultures

value: Batch 400uM Gln

value: batch pulse

value: proline

value: pulse


title: control D

city: Helsinki

first: Mark

middle: Andrew

last: Screen

address: Biomedicum1, Haartmaninkatu 8

department: Dpt. of Medical Genetics

country: Finland

institute: Folkhälsan Institute of Genetics, University of Helsinki

description:
control D
Control TLU 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalised to the median of all samples using quantile normalisation with Inforsense KDE version 2.0.4. Probes were filtered using a unpaired t-test (p=>0.05) using GeneSpring GX version 11.0

source_name: Vastus lateralis

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 with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: biopsy

value: vastus lateralis control

tag: age at biopsy

tag: Sex

value: M


title: MCF-7_anoxia

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

description: Gene expression data from MCF-7 cells grown in anoxia.

hyb_protocol: Affymetrix GeneChip® expression arrays (GeneChip® Human Gene 2.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA) the arrays were then washed. and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing:
The raw data was normalized in the free software Expression Console provided by Affymetrix (affymetrix.com) using the robust multi-array average (RMA) method using default analysis settings.
we only used the probes designated as 'main', and the controls are removed (e.g. control->affx, control->chip, control->bgp->antigenomic, control->bgp->genomic, normgene->exon, normgene->intron and rescue controls etc.).

source_name: Breast cancer cell line MCF-7

label_protocol: 250 nanograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression. Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

growth_protocol: MCF-7 cells grown in anoxia for 90 hours.

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions.

tag: oxygen condition

value: anoxia


title: control C

description:
control C
Control EVI 1


title: cpxA* vs. WT - Exp 3 - Replicate 2

status: Public on May 03 2014

city: Boston

first: Matthew

middle: K

last: Waldor

state: MA

address: 181 Longwood Ave

department: Division of Infectious Diseases

institute: HHMI/Brigham and Women’s Hospital

hyb_protocol: Slides were prehybridized at 42°C in 5X SSC, 0.1% SDS, 1% BSA, then briefly rinsed with water and isopropanol. Each array was then hybridized simultaneously to two differentially labelled cDNA probes corresponding to RNA from each strain. After hybridization overnight at 42°C, slides were washed sequentially with (i) 2X SSC, 0.1% SDS; (ii) 0.1X SSC, 0.1% SDS; and (iii) 0.1X SSC.

scan_protocol: Slides were scanned using an Axon scanner with the PMT adjusted so that fluorescence from Cy3- and Cy5-labelled probes was balanced. Scans were analysed with GenePix (Axon) to calculate spot intensity and background.

data_processing: The GenePix output was normalized by subtracting the background intensity for each spot before the results were subjected to global means normalization.

organism: Vibrio cholerae

source_name: cpxA* grown to OD600 of 1.0

label_protocol: RNA (10 µg) was reverse transcribed in the presence of 0.5 mM dATP, dCTP and dGTP, 0.2 mM dTTP and 0.3 mM aminoallyl dUTP. RNA was then hydrolysed with NaOH, and cDNAs were purified on Miniprep Spin Prep columns (Qiagen). cDNAs were coupled to monoreactive Cy3 and Cy5 (Amersham), then repurified, dried down and resuspended in hybridization buffer (25% formamide, 5X SSC, 0.1% SDS, 0.1 mg ml-1 salmon sperm DNA, 0.2 mg ml-1 yeast tRNA). Probes were denatured at 95C before hybridization at 42C.

growth_protocol: V. cholerae N16961 WT or cpxA* were grown at 37°C in LB broth with shaking to OD600 of 1.0.

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

treatment_protocol: The cultures were not treated.

tag: strain/background

tag: genotype/variation

value: cpxA*

source_name: WT grown to OD600 of 1.0

value: WT


title: cpxA* vs. WT - Exp 2 - Replicate 2


title: DM2 E

description:
sample E
80239

value: DM2 vastus lateralis


title: cpxA* vs. WT - Exp 3 - Replicate 1


title: DM2 D

description:
sample D
80243

value: F


title: DM2 B

description:
sample B
2648


title: control A

description:
control A
Control ATO 1


title: DM2 F

description:
sample F
61003


title: DPSC 50mM 48hr_rep 1

city: Los Angeles

first: Yong

last: Kim

state: CA

address: 10833 Le Conte Ave, 73-022 CHS

institute: UCLA

description: EtOH treatment

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

label: Biotin

source_name: dental pulp stem cells

label_protocol: Biotin

growth_protocol: Established human dental pulp stem cells were cultured in vitro

extract_protocol: Total RNA was extracted by using Qiagen Rneasy kit

treatment_protocol: Different concentrations (0, 1, 5, 10 and 20mM) were mixed with culture medium and the cells were exposed to EtOH for 24 or 48hrs

value: adult mesenchymal stem cells


title: cpxA* vs. WT - Exp 1 - Replicate 2


title: MCF-7_hypoxia

description: Gene expression data from MCF-7 cells grown in Hypoxia.

growth_protocol: MCF-7 cells grown in Hypoxia for 90 hours.

value: hypoxia


title: DM2 A

description:
sample A
903


title: DPSC 50mM 48hr_rep 2

description: EtOH treatment


title: MCF-7_normoxia_1

description: Gene expression data from MCF-7 cells grown in normoxia.

growth_protocol: MCF-7 cells grown in normoxia for 90 hours.

value: normoxia


title: ∆cpxR (pBAD33-cpxR) vs ∆cpxR (pBAD33) -1h inducing conditions - Exp 2 - Replicate 2

scan_protocol: Slides were scanned using a Packard Scanarray 4000 with the PMT adjusted so that fluorescence from Cy3- and Cy5-labelled probes was balanced. Scans were analysed with QUANTARRAY (Packard) to calculate spot intensity and background.

data_processing: The Quantarray output was normalize by substracting the background intensity for each spot before the results were subjected to global means normalization.

organism: Vibrio cholerae O1 biovar El Tor str. N16961

source_name: ∆cpxR (pBAD33) -1h inducing conditions

label_protocol: RNA (10 µg) was reverse transcribed in the presence of 0.5 mM dATP, dCTP and dGTP, 0.2 mM dTTP and 0.3 mM aminoallyl dUTP. RNA was then hydrolysed with NaOH, and cDNAs were purified on Miniprep Spin Prep columns (Qiagen). cDNAs were coupled to monoreactive Cy3 and Cy5 (Amersham), then repurified, dried down and resuspended in hybridization buffer (25% formamide, 5X SSC, 0.1% SDS, 0.1 mg ml-1 salmon sperm DNA, 0.2 mg ml-1 yeast tRNA). Probes were denatured at 95∞C before hybridization at 42∞C.

growth_protocol: V. cholerae N16961 ∆cpxR harboring (pBAD33-cpxR) or (pBAD33) were grown at 37°C in LB+glucose until mid-logarithmic phase.

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

treatment_protocol: Cells were washed, resuspended in LB+arabinose to induce transcription from the PBAD promoter and harvested after 1h of growth at 37°C.

tag: strain

value: Vibrio cholerae N16961∆cpxR (pBAD33)

source_name: ∆cpxR (pBAD33-cpxR) -1h inducing conditions

value: Vibrio cholerae N16961∆cpxR (pBAD33-cpxR)


title: DM2 C

description:
sample C
80244


title: ∆cpxR (pBAD33-cpxR) vs ∆cpxR (pBAD33) -1h inducing conditions - Exp 2 - Replicate 1


title: DPSC 20mM 48hr_rep 2

description: EtOH treatment


title: cpxA* vs. WT - Exp 1 - Replicate 1


title: control B

description:
control B
Control PLE 1


title: MCF-7 normoxia_2


title: DPSC 20mM 48hr_rep 1

description: EtOH treatment


title: ∆cpxR (pBAD33-cpxR) vs ∆cpxR (pBAD33) -1h inducing conditions - Exp 1 - Replicate 1


title: DPSC 10mM 48hr_rep 2

description: EtOH treatment


title: DPSC 10mM 48hr_rep 1

description: EtOH treatment


title: ∆cpxR (pBAD33-cpxR) vs ∆cpxR (pBAD33) -1h inducing conditions - Exp 1 - Replicate 2


title: cpxA* vs. WT - Exp 2 - Replicate 1


title: DPSC 5mM 48hr_rep 2

description: EtOH treatment


title: DPSC 1mM 48hr_rep 2

description: EtOH treatment


title: Data_274_area_4

city: Isfahan

first: Sayyed Morteza

last: Hosseini

address: Royan Street

department: Embryology

country: Iran

institute: Royan Institute

description: Biological replicats 4 of 4. SCNT_TSA blastocysts at day 7 after reconstitution were compared to IVF as reference.

hyb_protocol: Antisense RNA (825 ng per replicate) was hybridized on the Agilent-manufactured EmbryoGENE® slides in a two-color dye-swap design. The microarray chip used, EmbryoGENE®, covers almost of the bovine pre-attachment transcriptome and hence allows analyzing most forms of gene expression in bovine blastocysts.

scan_protocol: After 17 h of hybridization at 65 °C, microarray slides were washed for 1 min in gene expression wash buffer 1 (RT), 3 min in gene expression wash buffer 2 (42 °C), 10 sec in 100% acetonitrile (RT) and 30 sec in Stabilization and Drying Solution (Agilent). Slides were scanned with Power Scanner (Tecan) and features extraction was done with Array-pro6.3 (MediaCybernetics).

data_processing: Intensity files were analyzed with FlexArray 1.6.1 (Michal Blazejczyk, Mathieu Miron, Robert Nadon (2007), FlexArray: statistical Data analysis software for gene expression microarrays. Genome Quebec, Montreal, Canada, URL:http://genomequebec.mcgill.ca/FlexArray). Specifically, raw Data were corrected by background subtraction, and then normalized within and between each array (Loess and quantile, respectively). Statistical comparison between treatments (CTR-NT vs. IVF and TSA-NT vs. IVF) was done with the Limma algorithm. In pairwise comparisons among transcripts with a p-value < 0.01, a false discovery rate (FDR) of 20%, and a fold change >2.0 were considered differentially expressed.

organism: Bos taurus

label_protocol: Amplified RNA was labeled with Cy3 and Cy5 using the ULS Fluorescent Labeling Kit (Kreatech).

growth_protocol: Embryo production protocol: The method of SCNT was perfomed according to our previously published paper: Jafari et al. 2011,Mol Reprod Dev. 78:576-84.

extract_protocol:
Total RNA from each replicate was extracted and purified using the PicoPure RNA Isolation Kit (Life Science). After DNase digestion (Qiagen), quality and concentration of extracted RNA was analyzed by bioanalyzer (Agilent). All extracted samples showed good quality with an RNA integrity number ≥7.0.
Purified RNA was amplified by in vitro transcription by T7 RNA amplification using the RiboAmp HSPlus RNA Amplification Kit (Life Science).

tag: time of embryo collection

value: 7 dpIVF (days post-in-vitro fertilization)

tag: sex known

tag: cloning

value: No

value: 7 dpSCNT (days post-somatic cell nuclear transfer)

value: Female

value: Yes


title: DPSC 1mM 48hr_rep 1

description: EtOH treatment


title: Data_274_area_1

description: Biological replicats 1 of 4. SCNT_TSA blastocysts at day 7 after reconstitution were compared to IVF as reference.

value: 7 dpIVF(days post-in-vitro fertilization)


title: DPSC No TX-48hr_rep 2

description: EtOH treatment


title: DPSC 5mM 48hr_rep 1

description: EtOH treatment


title: Data_274_area_2

description: Biological replicats 2 of 4. SCNT_TSA blastocysts at day 7 after reconstitution were compared to IVF as reference.


title: DPSC No TX-48hr_rep 1

description: EtOH treatment


title: DPSC 20mM 24hr_rep 2

description: EtOH treatment


title: DPSC 50mM 24hr_rep 1

description: EtOH treatment


title: DPSC 50mM 24hr_rep 2

description: EtOH treatment


title: Data_273_area_3

description: Biological replicats 3 of 4. IVF blastocysts at day 7 after fertilzation were used as reference.

source_name: TSA-SCNT


title: Mouse 1805 late bx

city: Madison

first: Terrah

middle: Jean

last: Paul Olson

state: WI

address: 600 Highland Ave.

department: Surgery

institute: University of Wisconsin School of Medicine and Public Health

description:
Sample name: 379
Gene expression data from tumor late in mouse lifespan with final pathology
F1 (SWR x C57BL/6) Apc^Min/+

hyb_protocol: After fragmentation, all samples were hybridized to Mouse Gene 1.0 ST arrays at 45C for 16 hours overnight following all procedures outlined in the Gene Chip WT terminal Labeling and Hybridization User manual.  GeneChips were post-processed on AFX Fluidics 450 Station according to all AFX protocols and procedures defined for the Mouse Gene 1.0 ST Array.

scan_protocol: GeneChips scanned on GC3000 G7 scanner.

data_processing: Data extracted and processed using Affymetrix Command Console.  Chips were normalized by robust multiarray averaging using the XPS system.  Following preliminary analyses involving per gene analysis of variance, differential expression between adenomas and intramucosal carcinomas was measured by Student's t-test and fold change.  We screened by fold change exceeding 2 and by unadjusted p-value less than 0.05.  The false discovery rate was determined by the q-value method, and could not be reduced below 51% given sample size.

source_name: colon tumor, biopsy late timepoint

label_protocol: Ambion GeneChip WT Expression kit was used for labeling according to manufacturer's instructions.  300ng of RNA input used for each sample.  Poly-A RNA controls included at 300ng.

growth_protocol: Mice were generated by crossing SWR females with C57BL/6 Apc^Min/+ males.  F1 Apc^Min/+ hybrids were identified by genotyping at Apc.  Mice were housed in climate controlled rooms with 12-hour light-dark cycles and given food and water ad libitum except as described in "treatment protocol".

extract_protocol: Biopsies were stabilized in either RLT buffer with beta-mercaptoethanol or RNALater, and then stored at -80 degrees C until processing.  RNA was extracted using RNAEasy Micro Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: At or within 1 week of weaning, mice were treated with a 4% solution of dextran sodium sulfate (average M.W. 500,000) in drinking water for 4 days, followed by 17 days of regular water, then a second cycle of 4% dextran sodium sulfate for 4 days.  After allowing 30 days for tumor initiation, mice were examined by colonoscopy under general anesthesia with inhaled isoflurane every 14 days.  They underwent biopsy of tumors during colonoscopy every 28 days.

tag: generation

value: SWR x C57BL/6

value: Apc^Min/+

value: Male

tag: treatment

value: two treatments of 4% dextran sodium sulfate in drinking water at weaning

tag: age

value: 395 days

tag: timepoint

value: late in mouse lifespan

tag: disease state (final pathology)

value: adenoma


title: DPSC 20mM 24hr_rep 1

description: EtOH treatment

value: adult mesenchymal stem cells


title: Mouse 1803 late bx

description:
Sample name: 368
Gene expression data from tumor late in mouse lifespan with final pathology
F1 (SWR x C57BL/6) Apc^Min/+

tag: gender

value: 369 days


title: Data_273_area_2

description: Biological replicats 2 of 4. IVF blastocysts at day 7 after fertilzation were used as reference.


title: Mouse 3413 late bx

description:
Sample name: 365
Gene expression data from tumor late in mouse lifespan with final pathology
F1 (SWR x C57BL/6) Apc^Min/+

value: 200 days

value: intramucosal carcinoma


title: Data_273_area_1

description: Biological replicats 1 of 4. IVF blastocysts at day 7 after fertilzation were used as reference.


title: Mouse 3407 late bx

description:
Sample name: 370
Gene expression data from tumor late in mouse lifespan with final pathology
F1 (SWR x C57BL/6) Apc^Min/+

value: 215 days


title: Mouse 2201 late bx

description:
Sample name: 346
Gene expression data from tumor late in mouse lifespan with final pathology
F1 (SWR x C57BL/6) Apc^Min/+

value: 267 days


title: Data_274_area_3

description: Biological replicats 3 of 4. SCNT_TSA blastocysts at day 7 after reconstitution were compared to IVF as reference.

value: 7 dpIVF (days post-in-vitro fertilization)

value: No

value: 7 dpSCNT (days post-somatic cell nuclear transfer)


title: Data_237_area_4

description: Biological replicats 4 of 4. SCNT blastocysts at day 7 after reconstitution were compared to IVF as reference.

source_name: SCNT

value: Female

value: Yes


title: DPSC 10mM 24hr_rep 2

description: EtOH treatment

tag: cell type


title: DPSC 10mM 24hr_rep 1

description: EtOH treatment


title: 437_CreER: mutant mouse 3

city: Incheon

first: Young Jae

last: Lee

address: 155, Gaetbeol-ro, Yeonsu-gu

department: Lee Gil Ya cancer and Diabetes Institute

institute: Gachon University

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each mouse-8 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)).   Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05).    Selected gene signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test sample and control sample was carried out using fold-change.   Go-ontology analysis for significant probe list was performed using PANTHER (http://www.pantherdb.org/panther/ontologies.jsp), using text files containing Gene ID list and accession number of illumina probe ID.   All data analysis and visualization of differentially expressed genes was conducted using R 2.4.1(www.r-project.org).

source_name: mouse lung, tamoxifen-treated Tmem1002loxP/2loxP;ROSA26+/CreER

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Three control mice and three mutant mice were treated with tamoxifen (two consecutive intraperitoneal injections, 0.1 mg/g of body weight) to activate CreER recombinase.

tag: tissue

value: lung


title: Mouse 1755 late bx

description:
Sample name: 319
Gene expression data from tumor late in mouse lifespan with final pathology
F1 (SWR x C57BL/6) Apc^Min/+

value: SWR x C57BL/6

value: Apc^Min/+

value: 234 days


title: Mouse 3407 early bx

description:
Sample name: 325
Gene expression data from tumor early in mouse lifespan
F1 (SWR x C57BL/6) Apc^Min/+

source_name: colon tumor, biopsy early timepoint

value: two treatments of 4% dextran sodium sulfate in drinking water at weaning

value: 87 days

value: early in mouse lifespan

value: unknown


title: Mouse 3413 early bx

description:
Sample name: 336
Gene expression data from tumor early in mouse lifespan
F1 (SWR x C57BL/6) Apc^Min/+

value: Male

value: 117 days


title: Mouse 2201 early bx

description:
Sample name: 255
Gene expression data from tumor early in mouse lifespan
F1 (SWR x C57BL/6) Apc^Min/+

value: 95 days


title: DPSC 5mM 24hr_rep 2

description: EtOH treatment

value: adult mesenchymal stem cells


title: Data_237_area_3

description: Biological replicats 3 of 4. SCNT blastocysts at day 7 after reconstitution were compared to IVF as reference.

value: 7 dpIVF (days post-in-vitro fertilization)


title: 434_CreER: mutant mouse 1


title: Data_236_area_4

description: Biological replicats 4 of 4. IVF blastocysts at day 7 after fertilzation were used as reference.

value: No


title: Data_237_area_2

description: Biological replicats 2 of 4. SCNT blastocysts at day 7 after reconstitution were compared to IVF as reference.

value: 7 dpSCNT (days post-somatic cell nuclear transfer)


title: Data_237_area_1

description: Biological replicats 1 of 4. SCNT blastocysts at day 7 after reconstitution were compared to IVF as reference.

value: Female


title: DPSC 5mM 24hr_rep 1

description: EtOH treatment


title: 438: control mouse 3

source_name: mouse lung, tamoxifen-treated Tmem1002loxP/2loxp


title: 431: control mouse 2


title: Mouse 1805 early bx

description:
Sample name: 157
Gene expression data from tumor early in mouse lifespan
F1 (SWR x C57BL/6) Apc^Min/+

value: 86 days


title: DPSC No TX-24hr_rep 2

description: EtOH treatment


title: hBMSC after 7-day osteogenic induction

city: Shanghai

first: Jiawen

last: Si

address: 639, Zhizaoju Road

department: Department of Oral and Maxillofacial Surgery

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

description: BMSC D7

hyb_protocol: The microarray hybridization was performed based on the manufacturer’s standard protocols.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000(Affymetrix)

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Then the gene expression analysis and alternative splice analysis proceeded separately. [1] Gene expression analysis: Genesrping software (version 12.5; Agilent Technologies) was employed  to finish the basic analysis. Differentially expressed genes were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 1.5 [2]  Alternative splice analysis: Alternative splice analysis was conducted by Transcriptome Analysis Console (version1.0, Affymetrix). Differential exon or junction identified through splicing index. The threshold was splicing index >= 2.0 or < = -2.0 .

source_name: hBMSC after 7-day osteogenic induction

label_protocol: The sample labeling was performed based on the manufacturer’s standard protocols.

growth_protocol: The hAECs, hBMSCs and hAFMSCs were cultured in the expansion culture medium (ECM) with regular passaging. The ECM for hAECs was prepared with DMEM/F12 medium (Invitrogen, China) supplemented with 2 mM L-Glutamine (Invitrogen, China), 10 ng/ml rhEGF (Invitrogen, China), 20% fetal bovine serum (Gibco, China) and 1% antibiotic-antimycotic (Gibco, China). The ECM for hBMSCs and hAFMSCs was prepared with DMEM/F12 medium (Invitrogen, China) supplemented with 2 mM L-Glutamine (Invitrogen, China), 10 ng/ml rhFGF (Invitrogen, China), 20% fetal bovine serum (Gibco, China) and 1% antibiotic-antimycotic (Gibco, China).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNAs integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The hAECs, hBMSCs and hAFMSCs were cultured in a classical osteogenic induction medium [α-MEM (Invitrogen, China) supplemented with 10% FBS (Gibico, China), 0.1 mM ascorbic acid (Sigma-Aldrich, USA), 10 mM β-glycerophosphate (Sigma-Aldrich, USA), 10-5 mM dexamethasone (Sigma-Aldrich, USA)]. After the 7-day osteogenic induction, total RNA was extracted with RNAiso Plus reagent (Takara, Japan).

value: Human bone marrow mesenchymal stem cells (hBMSCs)

tag: time point

value: after 7-day osteogenic induction


title: Mouse 1755 early bx

description:
Sample name: 155
Gene expression data from tumor early in mouse lifespan
F1 (SWR x C57BL/6) Apc^Min/+

value: SWR x C57BL/6

value: Apc^Min/+

value: 94 days


title: 430: control mouse 1

value: lung


title: Data_236_area_2

description: Biological replicats 2 of 4. IVF blastocysts at day 7 after fertilzation were used as reference.

value: Yes


title: DPSC 1mM 24hr_rep 2

description: EtOH treatment


title: Data_236_area_3

description: Biological replicats 3 of 4. IVF blastocysts at day 7 after fertilzation were used as reference.


title: Mouse 1803 early bx

description:
Sample name: 156
Gene expression data from tumor early in mouse lifespan
F1 (SWR x C57BL/6) Apc^Min/+

value: two treatments of 4% dextran sodium sulfate in drinking water at weaning

value: 87 days

value: early in mouse lifespan

value: unknown


title: hAFSC after 7-day osteogenic induction

description: AFSC D7

source_name: hAFSC after 7-day osteogenic induction

value: Human amniotic fluid stem cells (hAFSC)


title: hAEC before osteogenic induction

description: AEC D0

source_name: hAEC before osteogenic induction

value: human amniotic epithelial cells (hAEC)

value: before osteogenic induction


title: hAEC after 7-day osteogenic induction

description: AEC D7

source_name: hAEC after 7-day osteogenic induction


title: DPSC No TX-24hr_rep 1

description: EtOH treatment

value: adult mesenchymal stem cells


title: hAFSC before osteogenic induction

description: AFSC D0

source_name: hAFSC before osteogenic induction


title: Data_273_area_4

value: 7 dpSCNT (days post-somatic cell nuclear transfer)

value: Female

value: 7 dpIVF (days post-in-vitro fertilization)

value: No


title: 4FBMIFNg#3

status: Public on May 02 2014

city: San Francisco

first: Joseph

last: McCune

state: California

address: 1001 Potrero Ave

institute: UCSF

hyb_protocol: 600 ng of each aRNA hybridized to custom Agilent 4x44k microarrays as per manufacturer's instructions

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.6 software

data_processing: Custom in-house scripts and the Bioconductor Limma package were used for filtering and normalization.  Control features were removed.  Probe intensities were log2 transformed and quantile normalized.  Genes determined to be not expressed were filtered out (expressed genes = log2 intensity >= 7 across all samples within a group).  Arrays were median centered, followed by median centering of genes.

source_name: fetal_bone marrow_IFNg stimulated

label_protocol: 1.5 ug of aRNA coupled to Cy3 as per standard protocols

growth_protocol: Cells were isolated, frozen immediately, thawed, left in media or stimulated with IFNg for 4 hours, and then sorted into lysis buffer.

extract_protocol: Dissociated cells isloated by FACS. Up to 2-5K cells sorted into Ambion RNAqueous Micro kit lysis buffer. RNA isolated as per manufacturer's instructions.  RNA amplified in two rounds with Ambion Aminoallyl MessageAmp II kit.

tag: developmental stage

value: Fetal

tag: tissue source

value: Bone marrow

value: Classical monocytes

tag: stimulated with

value: IFNg for 4 hrs


title: 4FBMIFNg#4


title: Data_236_area_1

description: Biological replicats 1 of 4. IVF blastocysts at day 7 after fertilzation were used as reference.

value: Yes


title: dRIM2 +/-, biological replicate 1 (Heterozygous-101)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

country: Italy

institute: University of Padova

description: Gene expression of dRIM2 +/- larvae (Hetero-101).

hyb_protocol: 1.65 μg of labeled cRNA were used in each reaction and the hybridization was carried out at 65°C for 17 hours in an hybridization oven rotator (Agilent Technologies, Palo Alto, CA). The arrays were washed by Agilent Gene expression washing buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) and Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Inter-array normalization of expression levels was performed with quantile to correct possible experimental distortions. Normalization function was applied to expression data of all experiments and then values of spot replicates within arrays were averaged. Furthermore, Feature Extraction Software provides spot quality measures in order to evaluate the quality and the reliability of the hybridization. In particular, flag glsFound (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as null. So, in order to make more robust and unbiased statistical analyses, probes with a high proportion of null values were removed from the dataset. 40% of null was used as threshold in the filtering process, obtaining a total of 25,349  available Drosophila transcripts.

organism: Drosophila melanogaster

source_name: Whole body of third instar larvae

label_protocol: 800 ng of total RNA were labeled with “Agilent One-Color Microarray-Based Gene Expression protocol” according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labeled with Cy3-dCTP. Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurements (Nanodrop, Wilmington, DE).

extract_protocol: Total RNA was extracted from approximately 10  larvae for each genotype using Trizol (Life Technologies) according to the manufacter's instructions and further purified with LiCl 8M. All RNA samples were checked for quality by capillary electrophoresis (RNA 6000 Nano LabChip, Agilent Bioanalyzer 2100, Agilent Technologies).

value: Whole body of third instar larvae

tag: genotype

value: dRIM2 +/-


title: DPSC 1mM 24hr_rep 1

description: EtOH treatment


title: dRIM2 +/-, biological replicate 3 (Heterozygous-4)

description: Gene expression of dRIM2 +/- larvae (Hetero-4).


title: dRIM2 +/-, biological replicate 2 (Heterozygous-102)

description: Gene expression of dRIM2 +/- larvae (Hetero-102).


title: 4FBMIFNg#1


title: 3FBMUnstim#4

source_name: fetal_bone marrow_unstimulated


title: dRIM2 -/-, biological replicate 1 (Homozygous-101)

description: Gene expression of dRIM2 -/- larvae (Homo-101).

value: dRIM2 -/-


title: dRIM2 -/-, biological replicate 3 (Homozygous-103)

description: Gene expression of dRIM2 -/- larvae (Homo-103).


title: dRIM2 -/-, biological replicate 2 (Homozygous-102)

description: Gene expression of dRIM2 -/- larvae (Homo-102).


title: 3FBMUnstim#3


title: dRIM2 -/-, biological replicate 4 (Homozygous-104)

description: Gene expression of dRIM2 -/- larvae (Homo-104).


title: hBMSC before osteogenic induction

description: BMSC D0

source_name: hBMSC before osteogenic induction

value: Human bone marrow mesenchymal stem cells (hBMSCs)


title: 3FBMUnstim#2


title: 2ABMIFNg#4

source_name: adult_bone marrow_IFNg stimulated

value: Adult


title: 2ABMIFNg#2


title: 3FBMUnstim#1


title: 2ABMIFNg#3


title: 1ABMUnstim#1

source_name: adult_bone marrow_unstimulated


title: 1ABMUnstim#2


title: 1ABMUnstim#3


title: 1ABMUnstim#4


title: 2ABMIFNg#1


title: 435_CreER: mutant mouse 2

value: lung

tag: genotype/variation


title: Mock_LAI_SupT1_28hr_3

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing.  250ng of each RNA sample was hybridized to one Agilent 4X44K mouse array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The T lymphoblastic leukemia cell line SUP-T1 was obtained from American Type Cell Culture collection (Manassas, VA; CRL-1942) and cultured in RPMI 1640 supplemented with penicillin (100 U/ml), streptomycin (100 µg/ml), GlutaMAX-I (Invitrogen, Carlsbad, CA) and 10% Fetal Bovine Serum (HyClone, Logan, UT). HIV-1 LAI strain was obtained from NIH AIDS Research & Reference Reagent Program (Germantown, MD) and propagated in SUP-T1 cells. Viral titers were measured in U373-MAGI-CXCR4CEM cells obtained through the AIDS Research and Reference Reagent Program following a protocol by M. Emerman (Vodicka et al., 1997).

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: 1x10^6 homo sapien were infected with LAI/lab strain at MOI giving infection of almost 100% of cells; this was visible in a QC step in which cells 24 hours after infection were stained for p24 antigen.  MOI (2.5) was set so that this infection rate was achieved after 1 hour incubation of cells with virus.  Mock, UV-inactivated virus, and live virus infections were carried out in three (each) separate tubes and infected cells were maintained in separate suspensions (9 samples each).  Time point aliquots were then collected in 4-hr intervals from each suspension, cells were pelleted, and lysed in 1 ml Trizol.

tag: infection

value: Mock


title: UV_LAI_SupT1_12hr_2

value: UV-Inactivated Virus


title: HIV_LAI_SupT1_20hr_3

value: HIV


title: HIV_LAI_SupT1_4hr_3


title: UV_LAI_SupT1_24hr.2_3


title: HIV_LAI_SupT1_32hr_1


title: HIV_LAI_SupT1_12hr_3


title: Mock_LAI_SupT1_28hr_1


title: Mock_LAI_SupT1_12hr_3


title: HIV_LAI_SupT1_24hr.2_3


title: HIV_LAI_SupT1_28hr_1


title: Mock_LAI_SupT1_16hr_2


title: HIV_LAI_SupT1_32hr_3


title: Mock_LAI_SupT1_12hr_1


title: 4FBMIFNg#2


title: Mock_LAI_SupT1_8hr_2


title: Mock_LAI_SupT1_8hr_3


title: Mock_LAI_SupT1_4hr_2


title: Mock_LAI_SupT1_12hr_2


title: UV_LAI_SupT1_12hr_3


title: Mock_LAI_SupT1_20hr_2


title: HIV_LAI_SupT1_4hr_1


title: HIV_LAI_SupT1_16hr_1


title: HIV_LAI_SupT1_24hr.2_2


title: Mock_LAI_SupT1_28hr_2


title: Mock_LAI_SupT1_24hr.2_3


title: Mock_LAI_SupT1_4hr_3


title: HIV_LAI_SupT1_16hr_2


title: UV_LAI_SupT1_12hr_1


title: UV_LAI_SupT1_4hr_1


title: Mock_LAI_SupT1_20hr_1


title: HIV_LAI_SupT1_4hr_2


title: Mock_LAI_SupT1_32hr_3


title: HIV_LAI_SupT1_28hr_2


title: HIV_LAI_SupT1_20hr_1


title: HIV_LAI_SupT1_24hr.2_1


title: Mock_LAI_SupT1_16hr_3


title: Fetal bone marrow classical mono unstimulated 8

hyb_protocol: Hybridizations were performed for 17 hrs, according to the manufacturers protocol.

data_processing: This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003).  No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization. A one-way ANOVA linear model was fit to the comparison to estimate the mean M values and calculated moderated t-statistic, B statistic, false discovery rate and p-value for each gene for the comparison of interest. Adjusted p-values were produced by the method proposed by Holm (1979). All procedures were carried out using functions in the R package limma in Bioconductor [Smyth (2004), Gentleman (2004)].

label_protocol: Cy3-CTP labeling was performed using NimbleGen one-color labeling kits. Labeled Cy3-cDNA was assessed using Nanodrop ND-8000 and equal amounts of Cy3 labeled target were hybridized to Agilent array

growth_protocol: Cells were isolated, frozen immediately, thawed, and sorted into lysis buffer.

extract_protocol: Dissociated cells isolated by FACS. Between 200K and 1 million cells sorted into RLT Buffer (Qiagen) and isolated via Qiagen Rneasy Mini kit


title: Adult bone marrow classical mono unstimulated 1


title: Fetal bone marrow classical mono unstimulated 10


title: Adult bone marrow classical mono unstimulated 5


title: HEPG2 control rep 2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: Gene expression profiling of Human hepatocellular cancer cell line

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Human Whole Genome Array.

scan_protocol: Scanning were performed per recommended specifications

data_processing: Raw data obtained in .cel format were analyzed using GeneSpring GX v 12.0. RMA method was used for probe summarization and normalization was done to median of tissue specific samples.

source_name: HEPG2 control

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

growth_protocol: Cancer cell lines were grown in 10 % DMEM and Lymphocytes in 10 % RPMI in a CO2 incubator.

treatment_protocol: Cancer cell lines and lymphocytes were grown in in a CO2 incubator and PST-Dox nanoparticles were administered for 24 hr for the treatement groups and total RNA was isolated using Trizol extration protocols.

tag: cell line

value: HEPG

value: hepatocellular cancer


title: HEPG2 PST-Dox treated rep 2

description: Gene expression profiling of treated Human hepatocellular cancer cell line

source_name: HEPG2 PST-Dox treated


title: Adult bone marrow classical mono unstimulated 4


title: A549 PST-Dox treated rep 1

description: Gene expression profiling of Human adenocarcinoma cancer cell line

source_name: A549 PST-Dox treated

value: adenocarcinoma


title: A549 control rep 1

source_name: A549 control


title: Fetal bone marrow classical mono unstimulated 7

value: Fetal


title: Fetal bone marrow classical mono unstimulated 9

value: Bone marrow


title: A375 control rep 2

description: Gene expression profiling of Human melanoma cancer cell line

source_name: A375 control

value: melanoma


title: A549 control rep 2


title: HEPG2 control rep 1


title: HEPG2 PST-Dox treated rep 1


title: A375 PST-Dox treated rep 1

description: Gene expression profiling of treated Human melanoma cancer cell line

source_name: A375 PST-Dox treated


title: A375 control rep 1


title: A549 PST-Dox treated rep 2

description: Gene expression profiling of treated Human adenocarcinoma cancer cell line


title: Lymphocyte PST-Dox treated rep 1

description: Gene expression profiling of treated Isolated normal lymphocytes

source_name: Lymphocyte PST-Dox treated

value: Isolated normal lymphocytes


title: Lymphocyte PST-Dox treated rep 2


title: A375 PST-Dox treated rep 2


title: Adult bone marrow classical mono unstimulated 3

value: Classical monocytes


title: IGTB419.14

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: healthy individual_monocytes from PBMCs

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: age (yrs)

tag: Sex

value: Male

value: monocytes from peripheral blood mononuclear cells (PBMCs)

tag: batch

tag: inclusion markers

tag: exclusion markers

tag: phenotype markers

tag: separation method

value: Aria Sorter


title: Lymphocyte control rep 1

description: Gene expression profiling of Isolated normal lymphocytes

source_name: Lymphocyte control

tag: cell type


title: iPS-derived neurons_uninfected + NaB 3

city: Pittsburgh

first: Leonardo

last: D'Aiuto

state: PA

address: 3811 O’Hara Street

institute: UPMC

description: iPS-derived neurons

hyb_protocol: Labeled RNA was hybridized for 17 hr at 65C on Agilent gene expression array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8X60K array slides

data_processing: Agilent Feature Extraction v10.7.3.1 default parameters and further analyzed by  a cyclic loess algorithm authored in the R programming environment using the Bioconductor suite of tools, and only probes with Entrez gene IDs are selected for further analysis (in total 38804).

source_name: iPS-derived neurons_uninfected + NaB

label_protocol: Cy3-CTP  labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA.

extract_protocol: RNA was extracted using RNeasy kits (Qiagen)

treatment_protocol: Neuronal cultures were either infected with HSV-1 in triplicate or uninfected, with each individual sample harvested separately to provide biological replicates for expression analysis. Microarray analysis was performed on i) uninfected neurons; ii) neurons infected with HSV-1 at an MOI of 0.3 in the presence or absence of (E)-5-(2-bromovinyl)-2'-deoxyuridine along with interferon (IFN)-α; iii) neuron quiescent cultures treated with sodium butyrate (NaB, 5 mM);  iv) uninfected neurons treated with E)-5-(2-bromovinyl)-2'-deoxyuridine and interferon IFN-α; v) uninfected neurons treated with NaB

value: human skin biopsy samples

tag: cells

value: glutamatergic neurons

value: human iPS-derived neurons

tag: gender

value: male


title: iPS-derived neurons_uninfected + 5BVdU + IFN-alpha 2

description: iPS-derived neurons


title: iPS-derived neurons_HSV-1 reactivation 2

description: iPS-derived neurons

source_name: iPS-derived neurons_HSV-1 reactivation

value: female


title: iPS-derived neurons_HSV-1 quiescient infection 2

description: iPS-derived neurons


title: iPS-derived neurons_HSV-1-infected 1

description: iPS-derived neurons

source_name: iPS-derived neurons_HSV-1-infected


title: iPS-derived neurons_uninfected + NaB 2

description: iPS-derived neurons


title: IGTB1009.F4 [CD4]

source_name: healthy individual_CD4 T-Cells from PBMCs

value: T4 Naive cells from human peripheral blood mononuclear cells (PBMCs)

value: CD3+ CD4+ CD62L+


title: Lymphocyte control rep 2

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


title: iPS-derived neurons_HSV-1 reactivation 3

description: iPS-derived neurons


title: iPS-derived neurons_uninfected + 5BVdU + IFN-alpha 3

description: iPS-derived neurons


title: iPS-derived neurons_HSV-1 quiescient infection 1

description: iPS-derived neurons


title: iPS-derived neurons_HSV-1-infected 2

description: iPS-derived neurons


title: iPS-derived neurons_uninfected + 5BVdU + IFN-alpha 1

description: iPS-derived neurons


title: iPS-derived neurons_HSV-1 reactivation 1

description: iPS-derived neurons


title: iPS-derived neurons_uninfected + NaB 1

description: iPS-derived neurons


title: iPS-derived neurons_uninfected 2

description: iPS-derived neurons

source_name: iPS-derived neurons_uninfected


title: iPS-derived neurons_HSV-1-infected 3

description: iPS-derived neurons


title: iPS-derived neurons_uninfected 1

description: iPS-derived neurons


title: Ezh2_Delete_2day_2

first: William

last: Hwang

address: Lim Lab - Box 0525, 35 Medical Center Way

department: Neurosurgery

description: replicate 2

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

source_name: Differentiated NSCs

label_protocol: Biotinylated cRNA was generated from total RNA using an Ambion Illumina RNA amplification kit (Ambion)

growth_protocol: SVZ NSCs were passaged 5 times in proliferation medium(DMEM/F12/N2 – Invitrogen, 5% FCS - Hyclone, 20 ng ml-1 EGF, 20 ng ml-1 bFGF, 35 μg ml-1 bovine pituitary extract – Peprotech) before switching to differentiation media (same as proliferation media except with 2% FCS and no EGF or bFGF) for the specified time.

extract_protocol: Total RNA was isolated by Trizol (Life Technologies), purified using the RNeasy Plus Mini Kit (Qiagen) and quantified using the NanoDrop spectrophotometer. Samples were checked for quality using an Agilent TapeStation

treatment_protocol: Ezh2 was acutely deleted by the addition of 4-hydroxytamoxifen (4OHT) to SVZ NSC cultures generated from UBC-CreERT2;Ezh2F/F from P3-4

tag: age

tag: tissue

value: SVZ


title: Ezh2_Delete_4day_3

description: replicate 3


title: Ezh2_Delete_1day_1

description: replicate 1


title: Ezh2_Delete_4day_2

description: replicate 2


title: Ezh2_Delete_4day_1

description: replicate 1


title: Ezh2_Delete_0day_2

description: replicate 2


title: Ezh2_Delete_2day_3

description: replicate 3


title: Ezh2_Delete_7day_1

description: replicate 1


title: Ezh2_Delete_0day_3

description: replicate 3


title: Ezh2_Delete_1day_2

description: replicate 2


title: Control_4day_2

description: replicate 2


title: iPS-derived neurons_HSV-1 quiescient infection 3

description: iPS-derived neurons

tag: tissue source


title: Control_7day_1

description: replicate 1


title: Ezh2_Delete_0day_1

description: replicate 1


title: Control_1day_2

description: replicate 2


title: Control_2day_3

description: replicate 3


title: Control_1day_1

description: replicate 1


title: Control_2day_1

description: replicate 1


title: Control_0day_2

description: replicate 2


title: Control_2day_2

description: replicate 2


title: Control_4day_3

description: replicate 3


title: Control_4day_1

description: replicate 1


title: Control_0day_3

description: replicate 3


title: Postnatal day 7 DORSAL spinal cord Aldh1l1-GFP negative NON-astrocytes, biological rep. 3

first: David

last: Rowitch

address: 35 Medical Center Way, RMB 932D

department: Institute for Regenerative Medicine

institute: University of California-San Francisco

hyb_protocol: please contact UCSF genomics core for details

data_processing: data preprocessed in R using Bioconductor suite- oligo package/RMA algorithm used to background correct, normalize, and summarize, Limma package/treat algorithm used to assess differential expression

source_name: Aldh1L1-GFP+ flow sorted DORSAL spinal cord

label_protocol: purified RNA was amplified and biotin labeled (WT ovation, NuGen)

growth_protocol: mouse spinal cords from postnatal day 7 Aldh1l1-GFP transgenic mice on a swiss-webster background

extract_protocol: RNA was trizol purified with glycogen as a carrier molecule, DNAse digested, and further purified on an RNAeasy mini column (Qiagen)

treatment_protocol: papain dissociated and flow sorted on a BD facs aria II to isolate astrocytes (aldh1l1-GFP positive) and non-astrocytes (Aldh1l1-GFP negative),

tag: spinal cord region

value: DORSAL

value: NON-astrocytes


title: Postnatal day 7 VENTRAL spinal cord Aldh1l1-GFP negative NON-astrocytes, biological rep. 2

scan_protocol: please contact UCSF genomics core for details

source_name: Aldh1L1-GFP+ flow sorted VENTRAL spinal cord

value: VENTRAL


title: Control_0day_1

description: replicate 1


title: Postnatal day 7 DORSAL spinal cord Aldh1l1-GFP negative NON-astrocytes, biological rep. 1


title: Postnatal day 7 VENTRAL spinal cord Aldh1l1-GFP negative NON-astrocytes, biological rep. 1


title: Postnatal day 7 DORSAL spinal cord Aldh1l1-GFP negative NON-astrocytes, biological rep. 2


title: hom_rep4

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: replicate 4

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using quantile normalisation with Illumina Genomestudio 2011.1

source_name: eye

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 with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain

tag: genotype/variation

value: homozygote

tag: allele

value: Pxdn

tag: mouse id

value: unknown


title: Postnatal day 7 VENTRAL spinal cord Aldh1l1-GFP positive astrocytes, biological rep. 3

value: astrocytes


title: Postnatal day 7 DORSAL spinal cord Aldh1l1-GFP positive astrocytes, biological rep. 3


title: wt_rep4

description: replicate 4

value: wild type

tag: Sex


title: hom_rep2

description: replicate 2


title: Postnatal day 7 VENTRAL spinal cord Aldh1l1-GFP negative NON-astrocytes, biological rep. 3


title: Postnatal day 7 VENTRAL spinal cord Aldh1l1-GFP positive astrocytes, biological rep. 1


title: hom_rep1

description: replicate 1


title: hom_rep3

description: replicate 3


title: Postnatal day 7 DORSAL spinal cord Aldh1l1-GFP positive astrocytes, biological rep. 2


title: wt_rep2

description: replicate 2


title: wt_rep3

description: replicate 3


title: Pancreatic islets from IKK2-CApdx-1 mice 5

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

description: Gene expression data from pancreatic islets of diabetic IKK2-CApdx-1 mice

hyb_protocol: Labeled ssDNA was hybridized to Mouse Gene 1.0 ST  Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were scanned with a Affymetrix GeneChip Scanner 3000 according to the Affimetrix protocol.

data_processing: Affymetrix® Expression Console™ Software for normalization, BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) and GeneSifter software (http://www.geospiza.com) for further analysis

source_name: Pancreatic islets isolated from diabetic IKK2-CApdx-1 mice that express constitutively active IKK2 in β-cells via Pdx-1-tTA

label_protocol: The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com).

growth_protocol: Mice were housed under specific pathogen-free conditions at the animal facility of the University of Ulm and fed ad libitum.

extract_protocol: Total RNA was isolated from pancreatic islet with RNeasy mini kit (QIAGEN)

treatment_protocol: Mice were left untreated prior to islet isolation.

value: Mouse pancreatic islets

value: C57BL/6 and NMRI (1:1)


title: wh fat_het_rep4

description:
SAMPLE 24
replicate 4

hyb_protocol: Standard Illumina hybridization protocol

source_name: wh fat_het

value: heterozygote

value: Endra

value: white adipose tissue

value: 117 days


title: Pancreatic islets from Pdx-1+/- mice 4

description: Gene expression data from pancreatic islets of Pdx-1+/- mice

source_name: Pancreatic islets isolated from Pdx-1+/- mice (Pdx-1-tTA is generating Pdx-1 haploinsufficiency)


title: Postnatal day 7 VENTRAL spinal cord Aldh1l1-GFP positive astrocytes, biological rep. 2


title: wh fat_het_rep2

description:
SAMPLE 22
replicate 2

value: male


title: wh fat_het_rep3

description:
SAMPLE 23
replicate 3


title: Pancreatic islets from IKK2-CApdx-1 mice 4


title: Postnatal day 7 DORSAL spinal cord Aldh1l1-GFP positive astrocytes, biological rep. 1


title: Pancreatic islets from control mice 5

description: Gene expression data from pancreatic islets of control mice

source_name: Pancreatic islets isolated from control mice


title: wh fat_wt_rep4

description:
SAMPLE 20
replicate 4

source_name: wh fat_wt


title: Pancreatic islets from Pdx-1+/- mice 3


title: wh fat_het_rep1

description:
SAMPLE 21
replicate 1


title: Pancreatic islets from control mice 3


title: Pancreatic islets from IKK2-CApdx-1 mice 2


title: wh fat_wt_rep3

description:
SAMPLE 19
replicate 3


title: Pancreatic islets from IKK2-CApdx-1 mice 3


title: wh fat_wt_rep2

description:
SAMPLE 18
replicate 2


title: Pancreatic islets from Pdx-1+/- mice 2


title: Pancreatic islets from control mice 4


title: bone_het_rep4

description:
SAMPLE 16
replicate 4

value: bone


title: wh fat_wt_rep1

description:
SAMPLE 17
replicate 1


title: Pancreatic islets from control mice 2


title: Pancreatic islets from Pdx-1+/- mice 1


title: bone_het_rep2

description:
SAMPLE 14
replicate 2


title: wt_rep1

description: replicate 1


title: Pancreatic islets from IKK2-CApdx-1 mice 1