title: G4-W

description:
S03 G4-R-Cy3 Signal
raw data file:
02_CSU_121662-121207-Chu-G4R+G4W-430-530_Data.xls


title: ChIP-seq Fe65 minus etoposide

status: Public on Mar 29 2017

type: SRA

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

state: CA

address: 9500 Gilman Drive

country: USA

institute: HHMI/UCSD

description: chromatin isolated from DMSO treated cells

library_source: genomic

data_processing:
The ELAND alignment files were converted into BED files for visualization in the genome browser at UCSC.
The peak finding was performed by using MACS and HOMER (homer.ucsd.edu/homer/).
Genome_build: hg18
Supplementary_files_format_and_content: ELAND files, BED files, and PEAK files.

molecule: genomic DNA

organism: Homo sapiens

source_name: SKNSH

growth_protocol: SKNSH were grown in serum supplemented medium at 37C / 5% CO2

extract_protocol:
For ChIP-seq, samples were fixed with 1% formaldehyde for 10 minutes. Fixation was stopped by adding Glycine (0.125M). Chromatin DNA was sheared to 200–500 bp average in size by sonication. Soluble sheared chromatin was immunoprecipitated with Fe65 specific antibody overnight at 4°C. The protein–DNA complex was isolated with agarose beads. Cross-linking was reversed by heating at 65°C o/n. Immunoprecipitated DNA was purified by using QIAGEN PCR purification columns.
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

treatment_protocol: SKNSH were treated with DMSO or 30uM etoposide for 1 h

tag: cell line

value: SKNSH

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: Fe65 polyclonal antibody


title: ChIP-seq Fe65 plus etoposide

description: chromatin isolated from ETOPOSIDE treated cells


title: hippocampus ppi tested C3H HeJ biological replicate 1

status: Public on Mar 30 2017

type: RNA

city: Toronto

first: James

middle: Nicholas

last: Samsom

state: Ontario

address: 544, 155 Dalhousie Street

department: Pharmacology

country: Canada

institute: University of Toronto

description: pooled tissue from 3 mice

hyb_protocol: as per the User Manual: GenChip 3' IVT Express kit: EukGE-WS2v4 of Toronto Centre for Applied Genomics standard hybridization protocol

scan_protocol: as per the User Manual: GenChip 3' IVT Express kit: using Affymetrix Genechip Scanner 3000 as per standard protocol used by Toronto Centre for Applied Genomics

data_processing: The raw array data was investigated for distributional and spatial homogeneity. No artifacts or outliers were detected. The data were loaded into R (v2.6.1) using the affy package (v1.16.0) of the BioConductor open-source project, and pre-processed using the GCRMA variant of the RMA algorithm implemented in the gcrma package (v2.10.0) of BioConductor. Transcriptome-wide correlation analysis between PPI and mRNA relied on Spearman’s rho and linear modelling analysis, simultaneously fitting 18 arrays per tissue to the model: y=b+(m)x(PPI), where y is GCRMA pre-processed signal intensity, b the expression level, PPI  levels for a given strain, and m is the slope. Probesets were annotated using Affymetrix NetAffx (v27)21 and FDR-adjusted p-value (q-value)(Storey and Tibshirani, 2003) using the limma software package (v.2.12.0) and followed by a Bayesian moderation of standard error (Smyth, 2004); correlations and q-values were calculated and candidate genes selected on the combined q-values from the three brain regions: -log|q(Hippocampus) x q(Striatum) x q(Brainstem)|.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: hippocampus, tested

label_protocol: as per the User Manual: GenChip 3' IVT Express kit: Enzo IVT kit as per Toronto Centre for Applied Genomics standard labeling protocol

growth_protocol: Six mouse strains were used: C3H/HeJ; BALB/cJ; C57BLKS/J; C57BL/6J and C57L/J (JAX, Bar Harbor, ME, USA) spanning the range of PPI.19 PND40 mice were housed 6 per cage with a 12 hr light/dark cycle (0700-1900h), at 21±1°C , 50-60% humidity, food and water ad libitum.

extract_protocol: Mice were sacrificed on PND60. RNA was prepared as previously described dissected and snap frozen (-80°C) whole striatum, hippocampus, and brainstem using TRIzol® reagent. RNA quality was determined using the Agilent BioAnalyzer with no RIN <7.7, prepared for hyrbidization and hybridized and scanned at The Centre for Applied Genomics (TCAG) at SickKids, Toronto, Ontario, Canada.

treatment_protocol: PPI testing used 120dB (40ms) startle, prepulses of 75 or 80dB (20ms), 65dB background, prepulse-startle latency of 100ms, and inter-trial-time 15-30s. Scores were averaged across three sessions, PPI calculated as [(PA–PP)/(PA)] × 100, and the mean of 75dB and 80dB trials was used. 6 of 12 mice were tested per strain every other day for 5d at PND50.

tag: Sex

value: male

tag: strain

value: C3H HeJ

tag: tissue

value: hippocampus


title: case110

city: Boston

first: Jarrett

last: Morrow

state: MA

address: 181 Longwood Ave.

department: Channing Division of Network Medicine

institute: Brigham and Women's Hospital

description:
case  FEV1.PP:  26
sample150

hyb_protocol: Total RNA for each sample was hybridized onto a HumanHT-12 Expression BeadChip Array (Illumina, San Diego, CA), based on the manufacturer's protocol.

scan_protocol: The BeadChip Array was scanned using an Illumina BeadArray Reader and quality control analysis was performed using Illumina GenomeStudio software

data_processing: Each of the samples and all probes passed quality control, and the data were background corrected, log2 transformed and quantile normalized.

source_name: lung

label_protocol: standard Illumina protocol

extract_protocol: RNA was extracted from lung tissues using Allprep kit (Qiagen, Valencia, CA).

tag: age

value: F

tag: race

value: AA

tag: bmi

tag: packyears

tag: copd

value: case

tag: ID

value: lung


title: case107

description:
case  FEV1.PP:  30
sample147

value: C


title: case103

description:
case  FEV1.PP:  16
sample143


title: case106

description:
case  FEV1.PP:  27
sample146


title: case108

description:
case  FEV1.PP:  30
sample148

value: M


title: case111

description:
case  FEV1.PP:  43
sample151


title: colon26

city: Okayama

first: Yuka

last: Okusha

state: Okayama

address: shikata-chou

country: Japan

institute: Okayama University

description: Cells were cultured for 3days and total RNA was extracted.

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60℃ for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions.On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0(Agilent) for 17 hours at 65℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1(Agilent) and 1 minute with 37℃ GE Wash buffer2(Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner(G2600D) using one color scan setting for 8x60k array slides(Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Murine colon adenocarcinoma cell line

label_protocol: Cy3 labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer’s instructions, followed by RNeasy column purification(QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from cultured cells by the AGPC method using Trizol (Molecular Research Center, Cincinnati, OH). The concentration and quality (A260/A280) of the total RNA were measured.

treatment_protocol: Colon26, LuM1, and NM11 cells were maintained in RPMI1640 with 10% FBS supplemented with penicillin, streptomycin, and amphotericin B.

value: BALB/c

tag: gender

value: female


title: case104

description:
case  FEV1.PP:  29
sample144


title: NM11

source_name: Low-metastatic tumor cells


title: case109

description:
case  FEV1.PP:  40
sample149


title: case105

description:
case  FEV1.PP:  30
sample145


title: LuM1

source_name: High-metastatic tumor cells


title: hippocampus ppi untested C57BLKS/J biological replicate 1

description: pooled tissue from 3 mice

source_name: hippocampus, untested


title: case101

description:
case  FEV1.PP:  40
sample141


title: case100

description:
case  FEV1.PP:  38
sample140


title: case102

description:
case  FEV1.PP:  26
sample142


title: case96

description:
case  FEV1.PP:  18
sample135


title: case97

description:
case  FEV1.PP:  18
sample136


title: case98

description:
case  FEV1.PP:  30
sample137


title: cont40

description:
cont  FEV1.PP:  100
sample138

value: cont


title: case93

description:
case  FEV1.PP:  38
sample128


title: cont39

description:
cont  FEV1.PP:  112
sample134


title: cont36

description:
cont  FEV1.PP:  84
sample130


title: cont35

description:
cont  FEV1.PP:  104
sample127


title: cont38

description:
cont  FEV1.PP:  99
sample132


title: case94

description:
case  FEV1.PP:  44
sample129


title: case99

description:
case  FEV1.PP:  24
sample139


title: case95

description:
case  FEV1.PP:  46
sample133


title: cont37

description:
cont  FEV1.PP:  87
sample131


title: case92

description:
case  FEV1.PP:  22
sample125


title: case91

description:
case  FEV1.PP:  19
sample124


title: case90

description:
case  FEV1.PP:  18
sample123


title: case85

description:
case  FEV1.PP:  31
sample118


title: case87

description:
case  FEV1.PP:  23
sample120


title: cont34

description:
cont  FEV1.PP:  92
sample126


title: case86

description:
case  FEV1.PP:  29
sample119


title: case88

description:
case  FEV1.PP:  17
sample121


title: cont31

description:
cont  FEV1.PP:  84
sample113


title: cont33

description:
cont  FEV1.PP:  108
sample115


title: case89

description:
case  FEV1.PP:  18
sample122


title: case84

description:
case  FEV1.PP:  41
sample117


title: case83

description:
case  FEV1.PP:  48
sample116


title: cont30

description:
cont  FEV1.PP:  97
sample112


title: cont29

description:
cont  FEV1.PP:  106
sample111


title: cont32

description:
cont  FEV1.PP:  97
sample114


title: cont26

description:
cont  FEV1.PP:  82
sample106


title: cont24

description:
cont  FEV1.PP:  90
sample103


title: case80

description:
case  FEV1.PP:  20
sample105


title: cont28

description:
cont  FEV1.PP:  105
sample108


title: cont23

description:
cont  FEV1.PP:  95
sample101


title: case81

description:
case  FEV1.PP:  41
sample109


title: cont25

description:
cont  FEV1.PP:  104
sample104


title: cont18

description:
cont  FEV1.PP:  82
sample96


title: case76

description:
case  FEV1.PP:  21
sample90


title: cont16

description:
cont  FEV1.PP:  97
sample94

value: other


title: case77

description:
case  FEV1.PP:  14
sample91


title: cont20

description:
cont  FEV1.PP:  85
sample98


title: cont27

description:
cont  FEV1.PP:  106
sample107


title: cont17

description:
cont  FEV1.PP:  104
sample95


title: cont21

description:
cont  FEV1.PP:  115
sample99


title: case79

description:
case  FEV1.PP:  47
sample102


title: cont15

description:
cont  FEV1.PP:  124
sample93


title: case75

description:
case  FEV1.PP:  19
sample89


title: case82

description:
case  FEV1.PP:  43
sample110


title: case78

description:
case  FEV1.PP:  30
sample92


title: cont14

description:
cont  FEV1.PP:  92
sample87


title: hippocampus ppi tested BalbC/J biological replicate 1

description: pooled tissue from 3 mice

value: BalbC/J


title: cont19

description:
cont  FEV1.PP:  109
sample97


title: cont22

description:
cont  FEV1.PP:  90
sample100


title: case74

description:
case  FEV1.PP:  16
sample88


title: case73

description:
case  FEV1.PP:  36
sample86


title: case70

description:
case  FEV1.PP:  24
sample83


title: case69

description:
case  FEV1.PP:  33
sample82


title: case71

description:
case  FEV1.PP:  26
sample84


title: case67

description:
case  FEV1.PP:  15
sample80


title: case68

description:
case  FEV1.PP:  18
sample81


title: case66

description:
case  FEV1.PP:  32
sample79


title: case63

description:
case  FEV1.PP:  25
sample75


title: case60

description:
case  FEV1.PP:  25
sample72


title: case52

description:
case  FEV1.PP:  30
sample64


title: cont13

description:
cont  FEV1.PP:  113
sample76


title: case56

description:
case  FEV1.PP:  29
sample68


title: case58

description:
case  FEV1.PP:  25
sample70


title: case51

description:
case  FEV1.PP:  22
sample63


title: case53

description:
case  FEV1.PP:  32
sample65


title: case50

description:
case  FEV1.PP:  29
sample62


title: case61

description:
case  FEV1.PP:  13
sample73


title: case57

description:
case  FEV1.PP:  35
sample69


title: case54

description:
case  FEV1.PP:  42
sample66


title: case48

description:
case  FEV1.PP:  20
sample60


title: case49

description:
case  FEV1.PP:  14
sample61


title: case65

description:
case  FEV1.PP:  25
sample78


title: case62

description:
case  FEV1.PP:  17
sample74


title: case47

description:
case  FEV1.PP:  14
sample59


title: case59

description:
case  FEV1.PP:  21
sample71


title: case45

description:
case  FEV1.PP:  32
sample57


title: case64

description:
case  FEV1.PP:  16
sample77


title: case46

description:
case  FEV1.PP:  32
sample58


title: case44

description:
case  FEV1.PP:  34
sample55


title: cont12

description:
cont  FEV1.PP:  87
sample56


title: case43

description:
case  FEV1.PP:  19
sample54


title: case42

description:
case  FEV1.PP:  19
sample53


title: cont11

description:
cont  FEV1.PP:  101
sample46


title: case35

description:
case  FEV1.PP:  22
sample45


title: case38

description:
case  FEV1.PP:  21
sample49


title: case36

description:
case  FEV1.PP:  21
sample47


title: case29

description:
case  FEV1.PP:  23
sample39


title: case33

description:
case  FEV1.PP:  18
sample43


title: case41

description:
case  FEV1.PP:  15
sample52


title: case32

description:
case  FEV1.PP:  13
sample42


title: case39

description:
case  FEV1.PP:  17
sample50


title: case26

description:
case  FEV1.PP:  25
sample36


title: case27

description:
case  FEV1.PP:  38
sample37


title: case30

description:
case  FEV1.PP:  19
sample40


title: case28

description:
case  FEV1.PP:  49
sample38


title: case23

description:
case  FEV1.PP:  33
sample32


title: case34

description:
case  FEV1.PP:  31
sample44


title: case37

description:
case  FEV1.PP:  49
sample48


title: cont10

description:
cont  FEV1.PP:  86
sample33


title: cont9

description:
cont  FEV1.PP:  127
sample31


title: case19

description:
case  FEV1.PP:  34
sample26


title: case24

description:
case  FEV1.PP:  39
sample34


title: case21

description:
case  FEV1.PP:  21
sample29


title: case40

description:
case  FEV1.PP:  22
sample51


title: case25

description:
case  FEV1.PP:  16
sample35


title: case20

description:
case  FEV1.PP:  19
sample28


title: case55

description:
case  FEV1.PP:  17
sample67


title: case22

description:
case  FEV1.PP:  13
sample30


title: case31

description:
case  FEV1.PP:  32
sample41


title: case72

description:
case  FEV1.PP:  9
sample85


title: cont8

description:
cont  FEV1.PP:  82
sample27


title: case17

description:
case  FEV1.PP:  26
sample24


title: cont7

description:
cont  FEV1.PP:  83
sample19


title: case11

description:
case  FEV1.PP:  37
sample16


title: case13

description:
case  FEV1.PP:  20
sample20


title: case10

description:
case  FEV1.PP:  26
sample15


title: case12

description:
case  FEV1.PP:  17
sample18


title: case14

description:
case  FEV1.PP:  22
sample21


title: cont6

description:
cont  FEV1.PP:  85
sample17


title: case15

description:
case  FEV1.PP:  23
sample22


title: case7

description:
case  FEV1.PP:  23
sample12


title: case4

description:
case  FEV1.PP:  29
sample9


title: cont3

description:
cont  FEV1.PP:  107
sample3


title: cont1

description:
cont  FEV1.PP:  106
sample1


title: case3

description:
case  FEV1.PP:  24
sample8


title: case16

description:
case  FEV1.PP:  31
sample23


title: case9

description:
case  FEV1.PP:  23
sample14


title: case6

description:
case  FEV1.PP:  24
sample11


title: case2

description:
case  FEV1.PP:  25
sample6


title: case8

description:
case  FEV1.PP:  38
sample13


title: cont2

description:
cont  FEV1.PP:  120
sample2


title: cont4

description:
cont  FEV1.PP:  85
sample4


title: case1

description:
case  FEV1.PP:  15
sample5


title: case5

description:
case  FEV1.PP:  21
sample10


title: cont5

description:
cont  FEV1.PP:  115
sample7


title: PreM 9 eMSC

city: San Francisco

first: Linda

middle: C.

last: Giudice

address: 499 Illinois St., Sixth Floor

department: Center for Reproductive Health at Mission Bay

institute: UC San Francisco

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing: GeneSpringGX 12.0, Microarray Technology: Affymetrix.ExonExprChip.HuGene-1_0-st-v1, Summarization Algorithm: ExonRMA16, Normalization: Quantile, Baseline Transformation: median of all samples

label: Biotin

source_name: Endometrium

label_protocol: RNA was reverse transcribed/amplified into cDNA using the NuGEN FFPE kit, and sense-strand cDNA targets were created using the NuGEN WT-Ovation Exon Module, followed by fragmentation and labeling using NuGEN Encore Biotin Module for hybridization to Affymetrix Human Gene 1.0 ST arrays.

growth_protocol: eSF and eMSC from Pre-menopause and Peri-menopause subjects were subjected to RNA extraction immediately after sorting by FACS analysis.

extract_protocol: FACS analyzed sorted cell populations were subject to RNA isolation and purification, with DNAse treatment, using Pico Pure RNA Isolation Kit

tag: sample type

value: Fresh Tissue Sample

tag: cell type

value: Endometrial Mesenchymal Stem Cell

tag: group

value: Pre-menopause


title: case18

description:
case  FEV1.PP:  39
sample25


title: PreM 8 eMSC


title: PreM 6 eMSC


title: PreM 5 eMSC


title: PreM 9 eSF

value: Endometrial Stromal Fibroblast


title: PreM 4 eMSC


title: PreM 2 eMSC


title: PreM 8 eSF


title: PreM 2 eSF


title: PeriM 6 eMSC

value: Peri-menopause


title: PeriM 9 eMSC


title: PreM 1 eMSC


title: PreM 1 eSF


title: PeriM 1 eMSC


title: PeriM 5 eMSC


title: PreM 4 eSF


title: PeriM 4 eMSC


title: PeriM 9 eSF


title: PeriM 7 eMSC


title: PeriM 3 eMSC


title: PreM 3 eSF


title: PeriM 8 eSF


title: PreM 7 eSF


title: PreM 6 eSF


title: PreM 5 eSF


title: PeriM 4 eSF


title: PreM 7 eMSC


title: PreM 3 eMSC


title: PeriM 2 eSF


title: PeriM 2 eMSC


title: PeriM 6 eSF


title: PeriM 7 eSF


title: PeriM 1 eSF


title: AC29 Malignant Mesothelioma 13

city: Rotterdam

first: Floris

last: Dammeijer

address: Wytemaweg 80

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus MC

description: Gene expression data from CBA mesothelioma cell line (AC29), sample 13

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 in a GeneChip Hyb Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip Scanner 7G (Affymetrtix)

data_processing: Data were analyzed with BRB-ArrayTools (version3.7.0, National Cancer Institute) using Affymetrix CEL files obtained from GCOS (Affymetrix). To examine the quality of the various arrays, the R package affyQCreport for generating QC reports was run starting from the CEL files. All created plots indicated a high quality of samples and an overall comparability. Raw intensity values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis,MO).

source_name: AC29 murine mesothelioma cell line, sample 13

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

growth_protocol: Cells were grown in T75 flasks in RPMI 1640 (with 2mM L-Glutamine + 25mM HEPES) + 5% Foetal Calf Serum (FCS) and trypsinized using 0.05% Trypsin/EDTA at a confluency of 80%

extract_protocol: Total RNA were extracted using the Rneasy mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Flasks were put on ice and washed once with PBS after which cells were scraped from the bottom and suspended in 350ul Lysisbuffer (RNeasy Kit,Qiagen)

value: CBA

value: 6-8 weeks


title: AC29 Malignant Mesothelioma 15

description: Gene expression data from CBA mesothelioma cell line (AC29), sample 15

source_name: AC29 murine mesothelioma cell line, sample 15


title: AC29 Malignant Mesothelioma 14

description: Gene expression data from CBA mesothelioma cell line (AC29), sample 14

source_name: AC29 murine mesothelioma cell line, sample 14


title: AB1 Malignant Mesothelioma 05

description: Gene expression data from BALB/c mesothelioma cell line (AB1), sample 5

source_name: AB1 murine mesothelioma cell line, sample 5


title: AB1 Malignant Mesothelioma 06

description: Gene expression data from BALB/c mesothelioma cell line (AB1), sample 6

source_name: AB1 murine mesothelioma cell line, sample 6


title: AB1 Malignant Mesothelioma 04

description: Gene expression data from BALB/c mesothelioma cell line (AB1), sample 4

source_name: AB1 murine mesothelioma cell line, sample 4


title: Mob1DKO

city: Fukuoka

first: Kohei

last: Otsubo

address: 3-1-1 Maidashi Higashi-ku

department: Division of Cancer Genetics, Medical Institute of Bioregulation

institute: Kyushu University

description: Gene expression in Mob1DKO lung epithelial cells

hyb_protocol: cRNA was hybridized to a 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with the Bioconductor.

source_name: lung epithelial cell, Mob1 DKO

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: lung epithelial cell


title: Mob1WT

description: Gene expression in WT lung epithelial cells

source_name: lung epithelial cell, wild type


title: AL118

type: genomic

city: Heidelberg

first: Martin

last: Granzow

address: INF 366

country: Germany

institute: University Hospital Heidelberg

description: Hybridized to CytoScanHD array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions using 50ng of DNA.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G and copy number analysis was done with Affymetrix Chromosome Analysis Suite software version 2.1.0.16(r6634) and Annotation Net Affx Build 33. Interpretation was based on human reference sequence GRCh37/hg19, February 2009. The complete data set was visually analyzed. Gains and losses had to meet three criteria to be reported: A minimum of 25 markers per segment, 100 kb minimum genomic length, and less than 50% overlap with known CN variants from the Database of Genomic Variants and/or in-house data obtained from analyzing family trios with a non-cancerous phenotype. Copy number aberrations located at 2p11.2 (IgK@), 14q32.33 (IgH@), and 22q11.22 (IgL@) which might stem from rearrangements of the B-cell receptor gene were excluded from further analysis.

source_name: CD138+ plasma cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from the sample  aliquot  using  the  Qiagen  AllPrep  DNA/RNA  kit  (Qiagen)  according  to  the  manufacturer’s instructions. RNA was quality‐controlled and quantified using an Agilent 2100 bioanalyzer (Agilent). DNA quality and quantity were assessed using a NanoDrop system (Thermo Scientific).

tag: diagnosis

value: AL amyloidosis

tag: disease type

value: plasma cell dyscrasia

value: CD138+ plasma cells


title: AL117

description: Hybridized to CytoScanHD array


title: AL116

description: Hybridized to CytoScanHD array


title: AL115

description: Hybridized to CytoScanHD array


title: AL114

description: Hybridized to CytoScanHD array


title: gingivaltissue_h_rep4

city: Piracicaba

first: Tiago

last: Taiete

state: São Paulo

address: Avenida Limeira 901

department: Prosthodontics and Periodontics

country: Brazil

institute: Piracicaba Dental School - University of Campinas

description:
This sample is of healthy gingival tissue from edentulous site of patients with no history of periodontitis. It is the fourth of four tissue sample replicate used in this experiment, each from different patient.
547875A12_532

hyb_protocol: Using random assignment, each Cy3-labeled cDNA sample was applied to NimbleGen Human Gene Expression 12 x 135K Arrays (Roche Diagnostics, Mannheim, Germany). Each slide contains 12 independent arrays, each with 135,000 probes covering 45,033 genes, 3 probes per target gene. The array was then hybridized for 16 h at 42 °C, washed, dried, and scanned at 2-µm resolution using a NimbleGen MS 200 Microarray Scanner (Roche NimbleGen).

scan_protocol: The array was then hybridized for 16 h at 42 °C, washed, dried, and scanned at 2-µm resolution using a NimbleGen MS 200 Microarray Scanner (Roche NimbleGen). The NimbleScan v2.6 software (Roche NimbleGen) was used to extract fluorescence intensity signals from the scanned images.

data_processing: The data were analysed using different packages in the software R. All packages were available in the Bioconductor open source software project for analysis of genomic data. Expression data were normalized and summarized using the Robust Multi-Array (RMA) analysis.

molecule: polyA RNA

source_name: heathy gingival tissue - periodontally healthy

label_protocol: Each cDNA sample was random-primer labelled with Cy3-nonamers according to Roche NimbleGen’s standard protocol using NimbleGen One-Color DNA Labelling Kits (Roche Diagnostics, Mannheim, Germany). Where possible, 1 ug of cDNA was used in the labelling reaction. For those samples that did not yield 1 ug of cDNA, the maximal volume (40 uL) of the High Pure column-eluted cDNA was used.

extract_protocol: Tissue specimens were disrupted by a motor pestle (Marconi, Piracicaba, SP, Brazil) and total RNA from the samples was isolated by TRIzol Reagent method (Ambion Inc., Austin, TX, USA) following the manufacturer’s instructions. The remaining DNA was removed using a deoxyribonuclease (Turbo DNA-free, Ambion Inc., Austin, TX, USA).

value: Female

tag: history of periodontal disease

value: No history of periodontitis


title: gingivaltissue_h_rep2

description:
This sample is of healthy gingival tissue from edentulous site of patients with no history of periodontitis. It is the second of four tissue sample replicate used in this experiment, each from different patient.
547875A07_532


title: gingivaltissue_cp_rep4

description:
This sample is of healthy gingival tissue from edentulous site of patients with history of chronic periodontitis. It is the fourth of four tissue sample replicate used in this experiment, each from different patient.
547875A11_532

source_name: heathy gingival tissue - chronic periodontitis

value: Generalized chronic periodontitis


title: gingivaltissue_h_rep1

description:
This sample is of healthy gingival tissue from edentulous site of patients with no history of periodontitis. It is the first of four tissue sample replicate used in this experiment, each from different patient.
547875A01_532

value: Male


title: gingivaltissue_h_rep3

description:
This sample is of healthy gingival tissue from edentulous site of patients with no history of periodontitis. It is the third of four tissue sample replicate used in this experiment, each from different patient.
547875A09_532


title: gingivaltissue_cp_rep3

description:
This sample is of healthy gingival tissue from edentulous site of patients with history of chronic periodontitis. It is the third of four tissue sample replicate used in this experiment, each from different patient.
547875A06_532


title: AL111

description: Hybridized to CytoScanHD array


title: AL113

description: Hybridized to CytoScanHD array


title: AL112

description: Hybridized to CytoScanHD array


title: AL110

description: Hybridized to CytoScanHD array


title: AL109

description: Hybridized to CytoScanHD array


title: gingivaltissue_gagp_rep4

description:
This sample is of healthy gingival tissue from edentulous site of patients with history of generalized aggressive periodontitis. It is the fourth of four tissue sample replicate used in this experiment, each from different patient.
547875A10_532

source_name: heathy gingival tissue - aggressive periodontitis

value: Generalized aggressive periodontitis


title: gingivaltissue_cp_rep2

description:
This sample is of healthy gingival tissue from edentulous site of patients with history of chronic periodontitis. It is the second of four tissue sample replicate used in this experiment, each from different patient.
547875A03_532


title: gingivaltissue_cp_rep1

description:
This sample is of healthy gingival tissue from edentulous site of patients with history of chronic periodontitis. It is the first of four tissue sample replicate used in this experiment, each from different patient.
547875A02_532


title: AL108

description: Hybridized to CytoScanHD array


title: AL107

description: Hybridized to CytoScanHD array


title: AL106

description: Hybridized to CytoScanHD array


title: AML_53

description: Hybridized to CytoScanHD array.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 3000 7G.

data_processing: Copy number analysis was done with Affymetrix Chromosome Analysis Suite (ChAS) software version 2.1.0.16(r6634) and Annotation Net Affx Build 33. Interpretation was based on human reference sequence GRCh37/hg19, February 2009. The complete data set was visually analyzed.

source_name: AML sample

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: DNA were extracted from the sample aliquot using the Qiagen AllPrep DNA/RNA kit (Qiagen) according to the manufacturer’s instructions. RNA was quality‐controlled and quantified using an Agilent 2100 Bioanalyzer (Agilent). DNA quality and quantity were assessed using a NanoDrop system (Thermo Scientific).

tag: disease status

value: acute myeloid leukemia (AML)


title: AL105

description: Hybridized to CytoScanHD array


title: gingivaltissue_gagp_rep1

description:
This sample is of healthy gingival tissue from edentulous site of patients with history of generalized aggressive periodontitis. It is the first of four tissue sample replicate used in this experiment, each from different patient.
547875A04_532


title: gingivaltissue_gagp_rep3

description:
This sample is of healthy gingival tissue from edentulous site of patients with history of generalized aggressive periodontitis. It is the third of four tissue sample replicate used in this experiment, each from different patient.
547875A08_532


title: Nursery non favorable condition

city: PARIS

first: Anne-laure

last: Le gac

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: non favorable growth conditin

hyb_protocol: 1 × 1 Million custom microarray slides were used (Agilent technologies, France).

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Populus nigra x Populus x canadensis

source_name: shoot apical meristem

label_protocol: labeled DNA was generated according to Agilent Technologies recommendations, using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, France).

growth_protocol: Bizet et al., 2015

extract_protocol: Genomic DNA was extracted using CTAB protocol (Doyle & Doyle, 1987)

treatment_protocol: Bizet et al., 2015

tag: genotype

value: P. deltoidesxP.nigra 'ECO28'

value: Dormant shoot apicals meristems

value: Methylated genomic DNA immunoprecipitation

source_name: Reference genomic DNA


title: gingivaltissue_gagp_rep2

description:
This sample is of healthy gingival tissue from edentulous site of patients with history of generalized aggressive periodontitis. It is the second of four tissue sample replicate used in this experiment, each from different patient.
547875A05_532


title: AL103

description: Hybridized to CytoScanHD array


title: AML_95

description: Hybridized to CytoScanHD array.


title: AL102

description: Hybridized to CytoScanHD array


title: AL104

description: Hybridized to CytoScanHD array


title: AML_81

description: Hybridized to CytoScanHD array.


title: AL101

description: Hybridized to CytoScanHD array


title: AML_79

description: Hybridized to CytoScanHD array.


title: AML_13

description: Hybridized to CytoScanHD array.


title: Field plantation Saint-Cyr-en val

description: intermediate favorable growth conditin

value: P. deltoidesxP.nigra 'Dorskamp'


title: AL100

description: Hybridized to CytoScanHD array


title: AML_89

description: Hybridized to CytoScanHD array.


title: AML_82

description: Hybridized to CytoScanHD array.


title: AML_60

description: Hybridized to CytoScanHD array.


title: Field plantation Guenmene

description: non favorable growth conditin


title: AML_94

description: Hybridized to CytoScanHD array.


title: AML_78

description: Hybridized to CytoScanHD array.


title: AML_70

description: Hybridized to CytoScanHD array.


title: AML_66

description: Hybridized to CytoScanHD array.


title: AML_40

description: Hybridized to CytoScanHD array.


title: AML_65

description: Hybridized to CytoScanHD array.


title: AL98

description: Hybridized to CytoScanHD array


title: AL97

description: Hybridized to CytoScanHD array


title: AML_72

description: Hybridized to CytoScanHD array.


title: AML_86

description: Hybridized to CytoScanHD array.


title: AL96

description: Hybridized to CytoScanHD array


title: Nursery optimal condition

description: favorable growth condition


title: AL94

description: Hybridized to CytoScanHD array


title: AL95

description: Hybridized to CytoScanHD array


title: AML_69

description: Hybridized to CytoScanHD array.


title: AL91

description: Hybridized to CytoScanHD array


title: AML_50

description: Hybridized to CytoScanHD array.


title: AML_76

description: Hybridized to CytoScanHD array.


title: AL90

description: Hybridized to CytoScanHD array


title: AML_98

description: Hybridized to CytoScanHD array.


title: AML_49

description: Hybridized to CytoScanHD array.


title: AL92

description: Hybridized to CytoScanHD array


title: AL89

description: Hybridized to CytoScanHD array


title: AL93

description: Hybridized to CytoScanHD array


title: AML_62

description: Hybridized to CytoScanHD array.


title: AL88

description: Hybridized to CytoScanHD array


title: AL87

description: Hybridized to CytoScanHD array


title: AL86

description: Hybridized to CytoScanHD array


title: AL85

description: Hybridized to CytoScanHD array


title: AL84

description: Hybridized to CytoScanHD array


title: AL83

description: Hybridized to CytoScanHD array


title: AL82

description: Hybridized to CytoScanHD array


title: AL80

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 131

city: Würzburg

first: Marcus

last: Dittrich

address: Biozentrum, Am Hubland

department: Biozentrum

institute: University of Würzburg

description: SAMPLE 93

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2, Normalized (dasen and BMIQ) Beta values; the non_normalized.txt contains Unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: DGDM_umbilical cord blood

label_protocol: Standard Illumina Protocol

growth_protocol: Umbilical cord blood from newborns was collected by obstetricians

extract_protocol: Genomic DNA was extracted and purified using Qiagen FlexiGene DNA Kit according to standard instructions

treatment_protocol: After collection it was immediately frozen at -80°C until further use

tag: sample group

value: DGDM

tag: maternal age (yr)

tag: mode of birth

value: ventouse-assisted vaginal birth

tag: gestational week

tag: birth weight (g)

value: female

tag: blood ph

tag: maternal bmi

tag: maternal height (cm)

tag: weight before pregnancy (kg)

tag: weight before birth(kg)

tag: nicotine consumption

tag: placenta weight


title: AL81

description: Hybridized to CytoScanHD array

tag: diagnosis

tag: cell type


title: genomic DNA from umbilical cord blood 132

description: SAMPLE 94

value: unassisted vaginal birth

tag: gender


title: Field plantation Echigey

description: favorable growth condition

tag: tissue

tag: sample type


title: AL78

description: Hybridized to CytoScanHD array

value: AL amyloidosis

tag: disease type


title: AL77

description: Hybridized to CytoScanHD array

value: plasma cell dyscrasia


title: AL76

description: Hybridized to CytoScanHD array

value: CD138+ plasma cells


title: genomic DNA from umbilical cord blood 130

description: SAMPLE 92

tag: sample group

tag: maternal age (yr)

value: male


title: AL99

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 121

description: SAMPLE 83

tag: mode of birth

tag: gestational week


title: AL75

description: Hybridized to CytoScanHD array


title: AL74

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 123

description: SAMPLE 85

tag: birth weight (g)

tag: blood ph


title: AML_80

description: Hybridized to CytoScanHD array.

tag: disease status


title: AL73

description: Hybridized to CytoScanHD array


title: AL72

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 120

description: SAMPLE 82

tag: maternal bmi

tag: maternal height (cm)

tag: weight before pregnancy (kg)

value: Smoker


title: genomic DNA from umbilical cord blood 126

description: SAMPLE 88

tag: weight before birth(kg)

tag: nicotine consumption

tag: placenta weight


title: genomic DNA from umbilical cord blood 127

description: SAMPLE 89

tag: gender


title: genomic DNA from umbilical cord blood 119

description: SAMPLE 81


title: AL79

description: Hybridized to CytoScanHD array

tag: diagnosis

tag: cell type


title: genomic DNA from umbilical cord blood 118

description: SAMPLE 80


title: genomic DNA from umbilical cord blood 128

description: SAMPLE 90


title: genomic DNA from umbilical cord blood 122

description: SAMPLE 84


title: AL70

description: Hybridized to CytoScanHD array

tag: disease type


title: genomic DNA from umbilical cord blood 115

description: SAMPLE 77

tag: sample group

value: Cesarean section


title: AL71

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 124

description: SAMPLE 86

tag: maternal age (yr)


title: genomic DNA from umbilical cord blood 116

description: SAMPLE 78

tag: mode of birth


title: genomic DNA from umbilical cord blood 112

description: SAMPLE 74

tag: gestational week


title: AL69

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 117

description: SAMPLE 79

tag: birth weight (g)


title: genomic DNA from umbilical cord blood 125

description: SAMPLE 87

tag: blood ph


title: genomic DNA from umbilical cord blood 113

description: SAMPLE 75


title: genomic DNA from umbilical cord blood 110

description: SAMPLE 72


title: AL68

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 111

description: SAMPLE 73


title: AL67

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 114

description: SAMPLE 76


title: AL66

description: Hybridized to CytoScanHD array


title: AL65

description: Hybridized to CytoScanHD array


title: AL64

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 108

description: SAMPLE 70

source_name: IGDM_umbilical cord blood

value: IGDM


title: genomic DNA from umbilical cord blood 106

description: SAMPLE 68


title: AL63

description: Hybridized to CytoScanHD array


title: AL62

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 109

description: SAMPLE 71


title: AL61

description: Hybridized to CytoScanHD array


title: AL59

description: Hybridized to CytoScanHD array


title: AL58

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 105

description: SAMPLE 67


title: AL57

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 104

description: SAMPLE 66


title: AL56

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 129

description: SAMPLE 91


title: AL55

description: Hybridized to CytoScanHD array


title: AL54

description: Hybridized to CytoScanHD array


title: AL53

description: Hybridized to CytoScanHD array


title: AL52

description: Hybridized to CytoScanHD array


title: AL51

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 101

description: SAMPLE 63


title: genomic DNA from umbilical cord blood 103

description: SAMPLE 65


title: AL49

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 107

description: SAMPLE 69


title: genomic DNA from umbilical cord blood 102

description: SAMPLE 64


title: AL60

description: Hybridized to CytoScanHD array


title: AL48

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 99

description: SAMPLE 61


title: AL47

description: Hybridized to CytoScanHD array


title: AL50

description: Hybridized to CytoScanHD array


title: AL46

description: Hybridized to CytoScanHD array


title: AL45

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 98

description: SAMPLE 60


title: AL44

description: Hybridized to CytoScanHD array


title: AL43

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 97

description: SAMPLE 59


title: AL42

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 96

description: SAMPLE 58


title: genomic DNA from umbilical cord blood 92

description: SAMPLE 54


title: genomic DNA from umbilical cord blood 93

description: SAMPLE 55


title: genomic DNA from umbilical cord blood 95

description: SAMPLE 57


title: genomic DNA from umbilical cord blood 91

description: SAMPLE 53


title: genomic DNA from umbilical cord blood 82

description: SAMPLE 44

source_name: Non_GDM_umbilical cord blood


title: genomic DNA from umbilical cord blood 94

description: SAMPLE 56


title: genomic DNA from umbilical cord blood 90

description: SAMPLE 52


title: AL39

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 80

description: SAMPLE 42


title: genomic DNA from umbilical cord blood 89

description: SAMPLE 51


title: genomic DNA from umbilical cord blood 84

description: SAMPLE 46


title: AL41

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 88

description: SAMPLE 50


title: AL38

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 76

description: SAMPLE 38


title: AL37

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 87

description: SAMPLE 49


title: genomic DNA from umbilical cord blood 81

description: SAMPLE 43


title: AL36

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 100

description: SAMPLE 62


title: genomic DNA from umbilical cord blood 83

description: SAMPLE 45


title: genomic DNA from umbilical cord blood 86

description: SAMPLE 48


title: AL35

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 77

description: SAMPLE 39


title: genomic DNA from umbilical cord blood 75

description: SAMPLE 37


title: AL29

description: Hybridized to CytoScanHD array


title: AL32

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 85

description: SAMPLE 47


title: AL34

description: Hybridized to CytoScanHD array


title: AL30

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 78

description: SAMPLE 40


title: AL28

description: Hybridized to CytoScanHD array


title: SL1344_Stationary_BR1

type: mixed

city: Dublin

first: Shane

last: Dillon

address: Kevin Street

department: School of Biological Sciences

country: Ireland

institute: Dublin Institute of Technology

description: biological replicate 1

hyb_protocol: Cy3 labeled cDNA and Cy5 labeled control genomic DNAs were co-precipitated using standard sodium acetate/ethanol procedures and resuspended in hybridization buffer (Oxford Gene Technologies), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridiized for 24 hours at 55oC in an Agilent hybiridization oven at 5 rpm. After hybridization, slides were washed according to instructions provided by Oxford Gene Technologies

scan_protocol: The microarray slides were scanned using an Agilent G2505C scanner. Cy3 and Cy5 images were acquired at 5 micron resolution. Scanned images were analyzed using Feature extraction software (Agilent).

data_processing: median normalization of background subtracted Cy3/Cy5 ratios

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SL1344 cells

label_protocol: cDNA synthesis was performed with the Superscript double-stranded cDNA synthesis kit (Invitrogen), following the random-priming method outlined by the manufacturer. Fluorescent labeling of DNA samples for transcriptomic experiments were carried out using the BioPrime Random Labeling kit (Invitrogen) as follows: 60 ml of 2.5 x random primer solution, x* ul DNA, and (70.5-x) ul sterile water were heated at 100oC for 10 minutes, snap chilled on ice and following were then added – 15 ul dNTP mix (1mM dCTP, 2mM dGTP, dTTP, dATP), 1.5 ul 1 mM Cy3/Cy5 labeled dCTP (GE healthcare) and 3 ul Klenow fragment (40 U/ ml). *[1000 ng of cDNA and 1000 ng of sonicated genomic DNA were fluorescently labeled with Cy3 d-CTP and Cy5-dCTP respectively]. The Labeling reactions wereas carried out at 37 oC overnight and 15 ul of stop buffer added to terminate the reaction.

growth_protocol: Cultures of S. Typhimurium SL1344 were inoculated 1:100 into 25 mls fresh Lennox broth and grown at 37oC until OD600 0.2 (Late exponential phase) or OD600 2.0 (Early stationary phase) was reached

extract_protocol: Total RNA was extracted from the cells using the SV total RNA isolation kit from promega as described (www.ifr.ac.uk/safety/molmicro). Sonicated genomic DNA was used as a reference in these experiments and was purified by standard phenol-chloroform extraction followed by sodium acetate/ethanol precipitation.

tag: strain

source_name: SL1344 control DNA


title: genomic DNA from umbilical cord blood 71

description: SAMPLE 33

tag: maternal bmi


title: SL1344_Exponential_BR2

description: biological replicate 2


title: AL27

description: Hybridized to CytoScanHD array


title: AL25

description: Hybridized to CytoScanHD array


title: AL26

description: Hybridized to CytoScanHD array


title: AL40

description: Hybridized to CytoScanHD array


title: SL1344_Exponential_BR1

description: biological replicate 1


title: AL24

description: Hybridized to CytoScanHD array


title: AL23

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 74

description: SAMPLE 36

tag: maternal height (cm)


title: genomic DNA from umbilical cord blood 67

description: SAMPLE 29

tag: weight before pregnancy (kg)


title: genomic DNA from umbilical cord blood 79

description: SAMPLE 41

tag: weight before birth(kg)


title: AL21

description: Hybridized to CytoScanHD array


title: AL20

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 63

description: SAMPLE 25

tag: nicotine consumption


title: genomic DNA from umbilical cord blood 72

description: SAMPLE 34

tag: placenta weight


title: AL31

description: Hybridized to CytoScanHD array


title: SL1344_Stationary_BR2

description: biological replicate 2


title: genomic DNA from umbilical cord blood 73

description: SAMPLE 35

tag: gender


title: AL19

description: Hybridized to CytoScanHD array

tag: diagnosis


title: AL18

description: Hybridized to CytoScanHD array

tag: cell type


title: genomic DNA from umbilical cord blood 68

description: SAMPLE 30


title: AL33

description: Hybridized to CytoScanHD array

tag: disease type


title: genomic DNA from umbilical cord blood 65

description: SAMPLE 27

tag: sample group


title: genomic DNA from umbilical cord blood 61

description: SAMPLE 23

tag: maternal age (yr)


title: genomic DNA from umbilical cord blood 60

description: SAMPLE 22

tag: mode of birth


title: genomic DNA from umbilical cord blood 59

description: SAMPLE 21

tag: gestational week


title: genomic DNA from umbilical cord blood 64

description: SAMPLE 26

tag: birth weight (g)


title: AL17

description: Hybridized to CytoScanHD array


title: AL15

description: Hybridized to CytoScanHD array


title: AL14

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 69

description: SAMPLE 31

tag: blood ph


title: genomic DNA from umbilical cord blood 54

description: SAMPLE 16


title: genomic DNA from umbilical cord blood 70

description: SAMPLE 32


title: AL22

description: Hybridized to CytoScanHD array


title: AL13

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 58

description: SAMPLE 20


title: genomic DNA from umbilical cord blood 56

description: SAMPLE 18


title: AL10

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 66

description: SAMPLE 28


title: genomic DNA from umbilical cord blood 53

description: SAMPLE 15


title: AL9

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 52

description: SAMPLE 14


title: AL8

description: Hybridized to CytoScanHD array


title: AL6

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 49

description: SAMPLE 11


title: AL5

description: Hybridized to CytoScanHD array


title: AL12

description: Hybridized to CytoScanHD array


title: AL7

description: Hybridized to CytoScanHD array


title: AL4

description: Hybridized to CytoScanHD array


title: AL3

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 51

description: SAMPLE 13


title: AL16

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 57

description: SAMPLE 19


title: AL11

description: Hybridized to CytoScanHD array


title: AL2

description: Hybridized to CytoScanHD array


title: genomic DNA from umbilical cord blood 50

description: SAMPLE 12


title: genomic DNA from umbilical cord blood 46

description: SAMPLE 8


title: genomic DNA from umbilical cord blood 45

description: SAMPLE 7


title: genomic DNA from umbilical cord blood 62

description: SAMPLE 24


title: STC Right ind5

city: Barcelona

first: Gerard

last: Muntane

address: Doctor Aiguader 88

department: Biologia Evolutiva

country: Spain

institute: UPF

description: Right hemisphere

hyb_protocol: Hybridization targets were prepared with an Ambion WT Expression Kit (Applied Biosystems/Ambion, Austin, TX) and Affymetrix GeneChip WT Terminal Labeling Kit from total RNA, hybridized to individual GeneChip® Human Gene 2.0 ST arrays in Affymetrix GeneChip® hybridization oven 645, which features comprehensive coverage of the human genome that include probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). Microarrays were washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® hybridization, wash, and stain protocols (Affymetrix, Santa Clara,CA).

scan_protocol: standard Affymetrix protocol

data_processing:
Microarray data were analyzed in R software (R core team, 2014) using packages implemented in Bioconductor. Expression values were normalized using the RMA (Robust Multichip Average) algorithm implemented in the oligo package
RheGene-1_0-st-v1.na34.rhemac2.probeset.csv

organism: Macaca mulatta

source_name: STC Right

label_protocol: standard Affymetrix protocol

growth_protocol: not applicable

extract_protocol: For each specimen, 50–100 mg of tissue were homogenized in 1 mL of TRI reagent in a glass-Teflon tubes and RNA extraction was performed following the manufacturer's protocols. Total RNA was assessed for quality with an Agilent 2100 Bioanalyzer G2939A and Nanodrop 8000 spectrophotometer.

treatment_protocol: not applicable

value: M

tag: age

tag: tissue

value: Brain Right hemisphere


title: genomic DNA from umbilical cord blood 44

description: SAMPLE 6

tag: maternal bmi

tag: maternal height (cm)


title: M1C Right ind5

description: Right hemisphere

source_name: M1C Right


title: STC Left ind5

description: Left hemisphere

source_name: STC Left

value: Brain Left hemisphere


title: VFC Right ind5

description: Right hemisphere

source_name: VFC Right


title: M1C Left ind5

description: Left hemisphere

source_name: M1C Left


title: genomic DNA from umbilical cord blood 39

description: SAMPLE 1

tag: weight before pregnancy (kg)

tag: weight before birth(kg)


title: genomic DNA from umbilical cord blood 42

description: SAMPLE 4

tag: nicotine consumption

tag: placenta weight


title: VFC Left ind5

description: Left hemisphere

source_name: VFC Left

tag: gender


title: M1C Right ind4

description: Right hemisphere


title: genomic DNA from umbilical cord blood 47

description: SAMPLE 9


title: genomic DNA from umbilical cord blood 41

description: SAMPLE 3


title: genomic DNA from umbilical cord blood 37

description: SAMPLE 37

source_name: non_IGDM_umbilical cord blood


title: STC Right ind4

description: Right hemisphere


title: genomic DNA from umbilical cord blood 34

description: SAMPLE 34


title: VFC Right ind4

description: Right hemisphere


title: genomic DNA from umbilical cord blood 33

description: SAMPLE 33


title: genomic DNA from umbilical cord blood 55

description: SAMPLE 17


title: genomic DNA from umbilical cord blood 35

description: SAMPLE 35


title: genomic DNA from umbilical cord blood 29

description: SAMPLE 29


title: genomic DNA from umbilical cord blood 36

description: SAMPLE 36


title: genomic DNA from umbilical cord blood 40

description: SAMPLE 2


title: STC Left ind4

description: Left hemisphere


title: genomic DNA from umbilical cord blood 38

description: SAMPLE 38


title: BALB/c-82

type: protein

city: Hospitalet de Llobregat

first: Rafael

last: Manez

state: Barcelona

address: Feixa Llarga s/n

institute: HUB

description: Analysis of glycan specificities of natural antibodies.

hyb_protocol: Chips were sequentially washed, first with phosphate buffer solution (PBS) plus 0.1% Tween-20 (v/v), followed by PBS plus 0.001% Tween-20 (v/v) and finally with distilled water (Milli-Q grade). Staining of natural antibodies bound to glycans in the chips was achieved in two steps: 1) goat anti-mouse IgG+IgM (H+L) conjugated to biotin and 2) streptavidin labelled with Cy5-dye.

scan_protocol: Chips were scanned using Scanarray GX Plus reader (PerkinElmer) provided with a laser (excitation wavelengths 633 nm).

data_processing:
All data analysis was performed with the ScanArray® Express Microarray Analysis System (PerkinElmer). Binding was expressed in relative fluorescence units (RFU) as median ± median absolute deviation (MAD). Interactive exploration of multidimensional data (heat mapping and agglomerative clustering analysis) was performed with the Hierarchical Clustering Explorer (HCE) application developed by University of Maryland, US (http://www.cs.umd.edu/hcil/hce/).
Sample table represents values of relative fluorescence intensity (RFU) for 419 different glycans (all glycans were printed in 6 replicates). Results for each glycan is expressed as median ± median absolute deviation (MAD).

molecule: protein

source_name: serum

label_protocol: Binding of natural antibodies to glycans printed in the chips was detected using goat anti-mouse IgG+IgM (H+L) conjugated to biotin (Thermo Scientific). Biotinylated antibodies were then determined with streptavidin labelled with Cy5-dye (GE Healthcare).

growth_protocol: BALB/c mice 10 weeks old (Harlan, France), 13 female and 7 male, were maintained in separated cages at IDIBELL animal facility (specific pathogen free, SPF) under controlled conditions of temperature (21 ± 1°C), humidity (55 ± 5%), cycles of light/dark of 12/12 h, and with food and water given ad libitum.

extract_protocol: The chips were incubated for 15 min at 25ºC in incubation chamber with phosphate buffer solution (PBS) plus 0.1% Tween-20 (v/v, Merck) (buffer-3) and then the buffer was carefully removed from the chip surface using a filter paper (Whatman®). BALB/c mouse serum was diluted (1:15) in PBS plus 1% (w/v) of bovine serum albumin (BSA, Sigma-Aldrich) and 1% Tween-20 (v/v) (buffer-1). Diluted serum was spread over the slide surface and incubated in agitation (30 rpm) at 37ºC for 1.5 h. After a round of washing steps with buffer-3, buffer-4 (PBS plus 0.001% Tween-20 v/v) and distilled water (Milli-Q grade), chips were drained by mild centrifugation (1 min, 175xg). The chips were then incubated for 1 h at 37ºC (30 rpm) with goat anti-mouse IgG+IgM (H+L) conjugated to biotin (Thermo Scientific), diluted 200-fold in PBS plus 1% BSA (w/v) and 0.1% Tween-20 (v/v) (buffer-2). The unbound fraction of secondary antibodies was removed by repeating the same round of washing steps. The chips were incubated in darkness at 25ºC for 45 min (30 rpm) with streptavidin labelled with Cy5-dye (GE Healthcare), diluted (1:500) in buffer-2. After another round of washing steps (buffer-3+buffer-4+destiled water), microchips were dried in darkness by airflow. Finally, the chips were scanned using Scanarray GX Plus reader (PerkinElmer) provided with a laser (excitation wavelengths 633 nm).

treatment_protocol: Mice blood extraction was made without the need of anaesthesia by submandibular bleeding. Blood was incubated at room temperature (25ºC) during 45 min and then kept on ice for 1 h. Serum was collected by mild centrifugation (10 min, 1200xg at 4ºC) and stored at -80ºC for further analysis.

tag: strain/background

value: BALB/c

value: 10 weeks

value: serum


title: BALB/c-70


title: genomic DNA from umbilical cord blood 32

description: SAMPLE 32


title: genomic DNA from umbilical cord blood 48

description: SAMPLE 10


title: AL1

description: Hybridized to CytoScanHD array

source_name: CD138+ plasma cells

tag: diagnosis

tag: disease type

tag: cell type


title: BALB/c-65


title: VFC Left ind4

description: Left hemisphere


title: genomic DNA from umbilical cord blood 28

description: SAMPLE 28

tag: sample group

tag: maternal age (yr)

tag: mode of birth


title: M1C Right ind3

description: Right hemisphere

value: F


title: BALB/c-107


title: VFC Right ind3

description: Right hemisphere


title: STC Right ind3

description: Right hemisphere


title: M1C Left ind4

description: Left hemisphere


title: BALB/c-106


title: genomic DNA from umbilical cord blood 30

description: SAMPLE 30

tag: gestational week

tag: birth weight (g)

tag: blood ph


title: BALB/c-104

tag: age

tag: tissue


title: BALB/c-90


title: genomic DNA from umbilical cord blood 31

description: SAMPLE 31

tag: maternal bmi

tag: maternal height (cm)

tag: weight before pregnancy (kg)


title: genomic DNA from umbilical cord blood 26

description: SAMPLE 26

tag: weight before birth(kg)

tag: nicotine consumption

tag: placenta weight


title: genomic DNA from umbilical cord blood 27

description: SAMPLE 27

tag: gender


title: STC Left ind3

description: Left hemisphere


title: BALB/c-87

tag: strain/background


title: M1C Left ind3

description: Left hemisphere


title: VFC Left ind3

description: Left hemisphere


title: BALB/c-88


title: genomic DNA from umbilical cord blood 43

description: SAMPLE 5


title: genomic DNA from umbilical cord blood 24

description: SAMPLE 24


title: BALB/c-53


title: genomic DNA from umbilical cord blood 22

description: SAMPLE 22


title: STC Right ind2

description: Right hemisphere


title: genomic DNA from umbilical cord blood 25

description: SAMPLE 25


title: BALB/c-48


title: VFC Right ind2

description: Right hemisphere


title: BALB/c-56


title: STC Left ind2

description: Left hemisphere


title: M1C Right ind2

description: Right hemisphere


title: BALB/c-45


title: genomic DNA from umbilical cord blood 21

description: SAMPLE 21


title: genomic DNA from umbilical cord blood 23

description: SAMPLE 23


title: BALB/c-42


title: genomic DNA from umbilical cord blood 19

description: SAMPLE 19


title: BALB/c-38


title: genomic DNA from umbilical cord blood 17

description: SAMPLE 17


title: BALB/c-20


title: genomic DNA from umbilical cord blood 18

description: SAMPLE 18


title: VFC Left ind2

description: Left hemisphere


title: VFC Right ind1

description: Right hemisphere


title: BALB/c-37


title: M1C Right ind1

description: Right hemisphere


title: M1C Left ind2

description: Left hemisphere


title: STC Right ind1

description: Right hemisphere


title: STC Left ind1

description: Left hemisphere


title: genomic DNA from umbilical cord blood 14

description: SAMPLE 14

value: ventouse-assisted vaginal birth


title: genomic DNA from umbilical cord blood 15

description: SAMPLE 15


title: BALB/c-19

value: female


title: BALB/c-17


title: genomic DNA from umbilical cord blood 20

description: SAMPLE 20

value: unassisted vaginal birth


title: genomic DNA from umbilical cord blood 11

description: SAMPLE 11


title: genomic DNA from umbilical cord blood 16

description: SAMPLE 16


title: VFC Left ind1

description: Left hemisphere


title: genomic DNA from umbilical cord blood 12

description: SAMPLE 12


title: genomic DNA from umbilical cord blood 9

description: SAMPLE 9


title: GSC11 shCtrl

status: Public on Mar 28 2017

city: New York

first: Sicong

last: Zhang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: GBM

label_protocol: Standard Affymetrix protocol

growth_protocol: GSCs grew in DMEM/F12 medium supplemented with B27, EGF and FGF.

extract_protocol: Total RNA was extracted by Trizol

treatment_protocol: GSCs were transduced with lentivirus and selected by purimycin 2ug/ml. RNA was collected 7 days post transduction.

value: brain

tag: cell type

value: GSC

tag: genotype/variation

value: control


title: genomic DNA from umbilical cord blood 7

description: SAMPLE 7

tag: sample group

tag: maternal age (yr)


title: GSC11 shALKBH5-2

value: ALKBH5 knockdown


title: GSC17 shCtrl


title: BALB/c-44


title: CHOW EPI 3 Hi

city: paris

first: veronique

last: PELLOUX

address: 50-52 bld Vincent Auriol

department: UMR 1166 eq 6

institute: INSERM

description:
SAMPLE 5
101036410004_E

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation and background subtracted with GenomeStudio (Illumina software).

source_name: mouse PDGFRα+ cells with high CD9 expression (CD9high)

label_protocol: Total RNA was amplified and labeled with biotin using Ovation Pico WTA System V2 (NuGEN) and Encore BiotinIL Module (NuGEN) kits according to the manufacturer’s protocol.

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

treatment_protocol: EpiWAT from 3-month-old C3H mice was digested with collagenase. CD9high and CD9low progenitors from the stromal vascular fraction were FACS-sorted with CD45- CD31- Gp38+ PDGFRa+ CD9high and CD45- CD31- Gp38+ PDGFRa+ CD9high.

tag: phenotype

value: lean

value: 3 months

value: epididymal white adipose tissue (EpiWAT)

value: CD45- CD31- Gp38+ PDGFR-alpha-plus CD9high


title: CHOW EPI 4 Lo

description:
SAMPLE 8
101036410016_B

source_name: mouse PDGFRα+ cells with high CD9 expression (CD9low)

value: CD45- CD31- Gp38+ PDGFR-alpha-plus CD9low


title: GSC17 shALKBH5-1


title: CHOW EPI 4 Hi

description:
SAMPLE 7
101036410016_A


title: CHOW EPI 2 Lo

description:
SAMPLE 4
101036410004_D


title: genomic DNA from umbilical cord blood 10

description: SAMPLE 10

value: IGDM

tag: mode of birth

tag: gestational week

tag: birth weight (g)


title: CHOW EPI 3 Lo

description:
SAMPLE 6
101036410004_F

tag: age

tag: tissue


title: genomic DNA from umbilical cord blood 13

description: SAMPLE 13

value: male

tag: blood ph

tag: maternal bmi

tag: maternal height (cm)


title: CHOW EPI 2 Hi

description:
SAMPLE 3
101036410004_C


title: CHOW EPI 1 Lo

description:
SAMPLE 2
101036410004_B


title: TregSplWT#2

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

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: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: Flicr WT

value: 8 Weeks Old

tag: exclusion markers

value: DAPI-/CD11c/CD19/CD8/Cd49b/Ter119 -

tag: genetic background

value: NOD

tag: phenotype markers

value: CD4+ TCRb+ CD25+

tag: separation method

value: FACSAria

tag: Sex

value: Male


title: TregSplWT#1

tag: genotype/variation


title: TregSplKO#1

value: Flicr KO


title: TregSplKO#2


title: TregSplKO#3


title: genomic DNA from umbilical cord blood 4

description: SAMPLE 4

source_name: IGDM_umbilical cord blood

tag: sample group

value: unassisted vaginal birth

tag: gender

value: female

tag: weight before pregnancy (kg)

tag: weight before birth(kg)

tag: nicotine consumption

tag: placenta weight


title: genomic DNA from umbilical cord blood 6

description: SAMPLE 6

tag: maternal age (yr)

tag: mode of birth

value: ventouse-assisted vaginal birth

tag: gestational week

tag: birth weight (g)

value: Smoker


title: CHOW EPI 1 Hi

description:
SAMPLE 1
101036410004_A

tag: strain/background

tag: phenotype

value: lean

tag: age

value: 3 months

tag: tissue

value: epididymal white adipose tissue (EpiWAT)

tag: cell type


title: genomic DNA from umbilical cord blood 5

description: SAMPLE 5

value: IGDM

value: Cesarean section

tag: blood ph

tag: maternal bmi

tag: maternal height (cm)


title: TregSplWT#3

tag: genotype/variation

value: Flicr WT

tag: exclusion markers

tag: genetic background

tag: phenotype markers

tag: separation method

tag: Sex


title: TconvSplWT#2

value: 8 Weeks Old

value: CD4+ TCRb+ CD25-


title: genomic DNA from umbilical cord blood 8

description: SAMPLE 8

tag: sample group

tag: maternal age (yr)

tag: mode of birth

tag: gender

tag: weight before pregnancy (kg)

tag: weight before birth(kg)

tag: nicotine consumption

tag: placenta weight


title: genomic DNA from umbilical cord blood 3

description: SAMPLE 3

tag: gestational week

tag: birth weight (g)

tag: blood ph


title: ANGPTL4-/- mouse 15% SA treated

city: Singapore

first: Terri

last: Phua

state: Singapore

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

description: Comparison of ANGPTL4-/- versus control ANGPTL4+/+ SA sample

hyb_protocol: 2 ug of cDNA were hybridized for 18hrs at 45C on GeneChip Mouse Gene 1.0ST Array inside genechip hybridization oven 640. Genechip fluidics station 450 was used for the washing and staining of the chips.

scan_protocol: Genechips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Partek genomic suite 6.0 with RMA was used to analyze samples

source_name: ANGPTL4-/- mouse 15% SA treated

label_protocol: Further sample processing of the RNA was carried out using Applause® WT-Amp ST System (NuGEN), followed by the NuGEN Encore biotin label kit

growth_protocol: Males 8-10 week-old ANGPTL4+/+ or ANGPTL4-/- littermates were housed at 25 oC with regular light cycles of 12 light/12 dark hours.

extract_protocol: RNA was extracted from the respective treatments with Trizol following the manufacturer’s protocol.

treatment_protocol: Mice are housed in cages of n=2, and are kept on either 5% DSS in drinking water (with changes in DSS every 2 days), or 15% SA (5g of a mixture of 15%SA:85% grounded chow per mouse) for 8 days. Mice were observed for bleeding at the colon, and were euthanized when total change in weight fell below 20% from starting weight.

tag: strain

value: male

tag: genotype/variation

tag: treatment

tag: tissue

value: Fresh whole colon


title: genomic DNA from umbilical cord blood 2

description: SAMPLE 2

tag: maternal bmi

tag: maternal height (cm)


title: TconvSplWT#1

tag: age

tag: exclusion markers

value: DAPI-/CD11c/CD19/CD8/Cd49b/Ter119 -

tag: genetic background

value: NOD

tag: phenotype markers

tag: separation method

value: FACSAria

tag: Sex


title: ANGPTL4+/+ mouse 15% SA treated

source_name: ANGPTL4+/+ mouse 15% SA treated

tag: gender


title: 43540-lo

description:
SAMPLE 14
3998355051_L

source_name: human PDGFRα+ cells with low CD9 expression (CD9low)

label_protocol: Total RNA was amplified and labeled with biotin using Ovation Pico WTA System V2 (NuGEN) and Encore BiotinIL Module (NuGEN) kits according to the manufacturer's protocol.

treatment_protocol: Omental adipose tissue from 7 obese women with mean BMI of 42.9±1.7kg/m2 and mean age of 40.7±3.3 year-old was digested with collagenase. CD9high and CD9low progenitors from the stromal vascular fraction were FACS-sorted with CD45- CD31- CD34+ CD44+ PDGFRa+ CD9high and CD45- CD31- CD34+ CD44+ PDGFRa+ CD9low.

tag: disease status

value: morbid obesity without diabetes or glucose intolerance

value: omental white adipose tissue (oWAT)

tag: cell type

value: CD45- CD31- CD34+ CD44+ PDGFR-alpha-plus CD9low

tag: individual identifier


title: ANGPTL4+/+ mouse 5% DSS treated

description: Comparison of ANGPTL4-/- versus control ANGPTL4+/+ DSS sample

source_name: ANGPTL4+/+ mouse 5% DSS treated

value: 5% DSS


title: 43679-lo

description:
SAMPLE 12
3998355051_H

value: female


title: ANGPTL4+/+ mouse Vehicle Control

description: Comparison of ANGPTL4-/- versus control ANGPTL4+/+ Veh sample

source_name: ANGPTL4+/+ mouse Vehicle Control

value: Vehicle Control


title: 43540-hi

description:
SAMPLE 13
3998355051_K

source_name: human PDGFRα+ cells with high CD9 expression (CD9high)

value: CD45- CD31- CD34+ CD44+ PDGFR-alpha-plus CD9high


title: 43523-lo

description:
SAMPLE 10
3998355051_D


title: ANGPTL4-/- mouse Vehicle Control

source_name: ANGPTL4-/- mouse Vehicle Control


title: 43523-hi

description:
SAMPLE 9
3998355051_C


title: 43679-hi

description:
SAMPLE 11
3998355051_G


title: genomic DNA from umbilical cord blood 1

description: SAMPLE 1

tag: sample group

value: IGDM

tag: maternal age (yr)

tag: mode of birth

value: unassisted vaginal birth

tag: gestational week

tag: birth weight (g)

tag: blood ph

tag: weight before pregnancy (kg)

tag: weight before birth(kg)

tag: nicotine consumption

tag: placenta weight


title: 42977-hi

description:
SAMPLE 5
3998355043_I

tag: tissue


title: 43492-hi

description:
SAMPLE 7
3998355043_K


title: 43549-hi

description:
SAMPLE 1
3998355043_E


title: 43329-hi

description:
SAMPLE 3
3998355043_G


title: 43492-lo

description:
SAMPLE 8
3998355043_L


title: 42977-lo

description:
SAMPLE 6
3998355043_J


title: 43329-lo

description:
SAMPLE 4
3998355043_H


title: M1C Left ind1

description: Left hemisphere

source_name: M1C Left

value: F

tag: age

value: Brain Left hemisphere


title: ANGPTL4-/- mouse 5% DSS treated

source_name: ANGPTL4-/- mouse 5% DSS treated

tag: strain

tag: genotype/variation

tag: treatment


title: EAE-Th17_EPB06P1_wt mouse_spinal cords_1_3A

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive, Health Sciences Research Bldg E170

department: Coulter Department of Biomedical Engineering

institute: Georgia Tech and Emory Univ

hyb_protocol: The Biotin-labeled cRNA was used to probe Mouse MG_430_PM array, comprising of 45,037 probe sets and representing more than 20,000 mouse genes.

scan_protocol: Biotin-labeled cRNA was generated from cDNA and used to probe Mouse MG_430_PM array, comprising of 45,037 probe sets and representing more than 20,000 mouse  genes, using the Gene Titan MC instrument (Affymetrix, West Sacramento, CA).

data_processing: The data were analyzed with the BMS Xpress functional genomics data warehouse (internal BMS system) and were processed to RMA intensities.

source_name: wild type mouse spinal cord

label_protocol: Total RNA was treated with DNase I and cleaned up with Qiagen RNeasy MiniElute Cleanup Kit (Cat. # 74204). The RNA concentrations were determined by NanoDrop and RNA quality was evaluated using Experion (Bio-Rad). All target labeling reagents were purchased from Affymetrix (West Sacramento CA). Double-stranded cDNAs were synthesized from 1 ?g of total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA.

extract_protocol: Total RNA was isolated from the cells with Qiagen RNeasy Mini Kit (Cat. # 74104).

treatment_protocol: Act1-deficient or wild-type control mice were injected with 3.0 x 107 polarized MOG35-55-specific Th1 or Th17 cells/mouse 4 hours after 500 Rad sublethal-irradiation. To prepare MOG specific polarized T cell populations, drain lymph node cells were prepared from mice immunized with MOG35-55(200ug/mouse emulsified with complete Freund Adjuvant)  10 days after immunization.  Cells were cultured for 5 days with MOG35-55 at a concentration of 25 μg/ml under Th1 (20ng/ml rmIL-12[R&D], 2μg/ml αIL-23p19[eBioscience]) polarizing conditions or (20ng/ml rmIL-23[R&D]) as a Th17 polarizing condition. The spinal cords were collected at the onset of EAE disease symptoms.

tag: mouse strain

value: wild type

tag: challenge

value: Passive transfer of MOG35-55 specific Th17 cells

value: spinal cords


title: 43549-lo

description:
SAMPLE 2
3998355043_F

tag: disease status

tag: gender

tag: cell type

tag: individual identifier


title: Unchallenged_EPC04P1_wt mouse_spinal cords_2_7B

value: Unchallenged


title: Unchallenged_EPH04P1_Act1 ko mouse_spinal cords_4_8D

source_name: Act1 ko mouse spinal cord

value: Act1 ko


title: EAE-Th1_EPE03P1_wt mouse_spinal cords_1_1I

value: Passive transfer of MOG35-55 specific Th1 cells


title: PHLC312

city: Toronto

first: Ming

last: Tsao

address: 610 University Avenue

department: Ontario Cancer Institute

institute: University of Toronto

description: patient derived xenograft

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: patient derived xenograft_non-engrafter

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

growth_protocol: piece of primary tumor was implanted subcutaneously into SCID mouse to form xenograft tumors

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

treatment_protocol: no treatment

tag: host strain

value: non-obese diabetic severe combined immune deficient (NODSCID) mouse

tag: tissue type

value: xenograft

tag: tissue implanted

value: patient-derived non-small cell lung carcinoma (NSCLC)

tag: egfr mutaion status

value: EGFR mutant

tag: engraftment status

value: non-engrafter


title: EAE-Th17_EPE06P1_Act1 ko mouse_spinal cords_4_4D


title: Unchallenged_EPE02P1_wt mouse_spinal cords_5_7E


title: Unchallenged_EPB05P1_Act1 ko mouse_spinal cords_2_8B


title: PHLC278

description: patient derived xenograft


title: EAE-Th17_EPE05P1_wt mouse_spinal cords_2_3B


title: PHLC315

description: patient derived xenograft

source_name: patient derived xenograft_engrafter

value: engrafter


title: EAE-Th1_EPD03P1_wt mouse_spinal cords_5_5I


title: Unchallenged_EPH01P1_Act1 ko mouse_spinal cords_3_8C


title: EAE-Th1_EPG03P1_wt mouse_spinal cords_4_4I


title: PHLC316

description: patient derived xenograft


title: PHLC301

description: patient derived xenograft


title: PHLC269

description: patient derived xenograft


title: PHLC244

description: patient derived xenograft


title: Unchallenged_EPB02P1_Act1 ko mouse_spinal cords_1_8A


title: PHLC289

description: patient derived xenograft


title: EAE-Th17_EPG04P1_Act1 ko mouse_spinal cords_3_4C


title: PHLC282

description: patient derived xenograft


title: EAE-Th17_EPD04P1_wt mouse_spinal cords_3_3C


title: PHLC232

description: patient derived xenograft


title: Unchallenged_EPF05P1_wt mouse_spinal cords_4_7D


title: PHLC214

description: patient derived xenograft


title: PHLC213

description: patient derived xenograft


title: PHLC285

description: patient derived xenograft


title: EAE-Th17_EPG01P1_Act1 ko mouse_spinal cords_1_4A


title: Unchallenged_EPA06P1_wt mouse_spinal cords_3_7C


title: EAE-Th17_EPF02P1_wt mouse_spinal cords_5_3E


title: PHLC192

description: patient derived xenograft


title: PHLC233

description: patient derived xenograft


title: PHLC208

description: patient derived xenograft


title: PHLC148

description: patient derived xenograft


title: Unchallenged_EPF06P1_Act1 ko mouse_spinal cords_5_8E


title: EAE-Th1_EPB03P1_wt mouse_spinal cords_3_3I


title: EAE-Th1_EPA07P1_wt mouse_spinal cords_2_2I


title: Unchallenged_EPD01P1_wt mouse_spinal cords_1_7A


title: PHLC137

description: patient derived xenograft


title: EAE-Th17_EPC01P1_wt mouse_spinal cords_4_3D


city: Munich

first: Matjaz

last: Rokavec

address: Thalkirchner Str. 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University Munich

description: genomic DNA from parental DLD1 colorectal cancer cell line

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: GenomeStudio software

source_name: epithelial, parental

growth_protocol: Colorectal cancer cell line DLD1 and its derivatives were maintained in McCoy`s 5A Medium (Invitrogen) containing 10% fetal bovine serum (FBS, Invitrogen), 100 units/ml penicillin and 0.1 mg/ml streptomycin.

extract_protocol: Genomic DNA from cell lines was isolated using the DNeasy Blood & Tissue Kit (Qiagen)

tag: cell line

value: colorectal cancer


description: genomic DNA from SPH (mesenchymal-like DLD1 derivative)  colorectal cancer cell line

source_name: mesenchymal, derived from colonospheres


description: genomic DNA from METS (metastasis-derived DLD1 derivative)  colorectal cancer cell line

source_name: epithelial, derived from xenograft lung metastasis


description: genomic DNA from SA (mesenchymal-like DLD1 derivative) colorectal cancer cell line

source_name: mesenchymal, derived from soft agar colonies


title: PHLC170

description: patient derived xenograft


title: PHLC97

description: patient derived xenograft


title: PHLC14

description: patient derived xenograft


title: PHLC160

description: patient derived xenograft


title: L5 dorsal horn of spinal cord_21days_WTD_WTD3

city: Beijing

first: Yanqiong

address: No 16, Nanxiaojie, Dongzhimennei

country: China

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description: Gene expression after 3ws of WTD (12.60 g/kg, p.o.) treatment of dorsal horn of L5 spinal cord

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: L5 dorsal horn of spinal cord, 21days, WTD, WTD3,  replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Male ICR mice (8 weeks old) were obtained from Experimental Animal Center of Beijing University, Beijing, China (License No: SCXK-2012-0004). They were kept in a temperature controlled environment (23±1℃), 55±5 % relative humidity with a 12h:12h light-dark cycle and with free access to food and water.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: 24 hours after sham or SNL operation, ICR mice were orally given with vehicle (10 ml/kg) or WTD (12.60 g/kg) once a day for consecutive 21 days.

tag: tissue

value: L5 dorsal horn of spinal cord

value: male


title: PHLC164

description: patient derived xenograft


title: PHLC29

description: patient derived xenograft


title: L5 dorsal horn of spinal cord_21days_WTD_WTD2

source_name: L5 dorsal horn of spinal cord, 21days, WTD, WTD2,  replicate 1

tag: age


title: L5 dorsal horn of spinal cord_21days_vehicel_sham3

description: Gene expression after 3ws of vehicle treatment of dorsal horn of L5 spinal cord

source_name: L5 dorsal horn of spinal cord, 21days, vehicel, sham3,  replicate 1


title: 20081126 4.08 54

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

hyb_protocol: The neutralized color reaction was purified and combined with the appropriate competitive sample in hybridization buffer containing SSC and HEPES buffer with poly(dA)-poly(dT) (Sigma) for blocking and 0.1% for overnight hybridization at 65º C.

scan_protocol: After hybridization arrays were scanned (Axon 4000B: Axon Instruments) using Genepix 5.0 software (Axon Instruments) matching laser power and PMT to roughly normalize the two chanels.

data_processing: Data were filtered for feature quality and diameter, high background intensity, and low feature intensity. Features with demonstrated effects of sequence divergence (poor gDNA hybridization) were also filtered out.

organism: Xenotilapia leptura

source_name: whole brain

label_protocol: 2µg of total RNA from whole brain was reverse transcribed and labeled according to Renn et al. (2004): Briefly, amino-allyl dUTP (Sigma) was incorporated to the cDNA using oligo-dT(12 -18) with SuperScript II (Invitrogen) according to the manufacturer’s protocol, dye-coupling with Cy3 or Cy5 (CyDye Post-Labeling Reactive Dye Pack, Amersham) following RNA hydrolyzation and purification.

growth_protocol: adult

extract_protocol: RNA was extracted with standard trizol protocol

treatment_protocol: brains were extracted from animals captured in the wild. Animals were euthanized as quickly as possible after capture and brains were rapidly removed and stored in RNAlater solution.

tag: Sex

tag: mating type

value: monogamous

tag: ID

organism: Xenotilapia tenuidentata

value: polygynous


title: 20081209 4.08 57

organism: Xenotilapia flavipinnis


title: L5 dorsal horn of spinal cord_21days_vehicel_sham1

source_name: L5 dorsal horn of spinal cord, 21days, vehicel, sham1,  replicate 1


title: L5 dorsal horn of spinal cord_21days_WTD_WTD1

source_name: L5 dorsal horn of spinal cord, 21days, WTD, WTD1,  replicate 1


title: EAE-Th17_EPA05P1_Act1 ko mouse_spinal cords_2_4B

tag: mouse strain


title: 2008125 4.08 55


title: L5 dorsal horn of spinal cord_21days_vehicel_SNL3

source_name: L5 dorsal horn of spinal cord, 21days, vehicel, SNL3,  replicate 1


title: L5 dorsal horn of spinal cord_21days_vehicel_SNL1

source_name: L5 dorsal horn of spinal cord, 21days, vehicel, SNL1,  replicate 1


title: PHLC5

description: patient derived xenograft


title: L5 dorsal horn of spinal cord_21days_vehicel_SNL2

source_name: L5 dorsal horn of spinal cord, 21days, vehicel, SNL2,  replicate 1


title: 2008125 4.08 56


title: 20081210 4.08 94


title: 2008129 4.08 52

organism: Xenotilapia ochrogenys


title: 2008125 4.08 49


title: 20081217 4.08 53


title: 2008124 4.08 48


title: 20081210 4.08 58


title: 20081126 4.08 51


title: 20081125 4.08 47


title: L5 dorsal horn of spinal cord_21days_vehicel_sham2

source_name: L5 dorsal horn of spinal cord, 21days, vehicel, sham2,  replicate 1


title: 2008124 4.08 46


title: 2008122 4.08 42


title: 2008122 4.08 45


title: 2008122 4.08 44


title: 2008122 4.08 43

value: monogoamous


title: 2008122 4.08 36


title: 2008122 4.08 37


title: 2008122 4.08 39


title: 20090108 4.08 81 Xo117 vs Xf126

value: female


title: 20081125 4.08 35


title: 2008124 4.08 40


title: 20090108 4.08 82 Al114f vs Mt108f


title: 20081125 4.08 31


title: 20081107 4.08 93 Al116f vs Mt107f 3 me


title: 2008122 4.08 34


title: 20081125 4.08 27


title: 200916 4.08 87 Mt107f vs Al112f


title: 200917 4.08 79 Xo114f vs Xf127f


title: 200917 4.08 80 Xf127f vs Xo115f


title: 20081023 4.08 90 Al2 vs Mt111f 3b me


title: 20081030 4.08 91 Mt110f vs Al2 2b me


title: 20081017 4.08 89 Al2 vs Xo117f 2b me


title: 20090107 4.08 24 Xf126 vs Xo116


title: 200916 4.08 85 Mt109f vs Al116f


title: 200917 4.08 88 Xo113f vs Mt109f


title: 20071215 4.08 73 Xf127f vs Mt110f fine


title: 2008122 4.08 38


title: 200917 4.08 25 Xf123 vs Xo117


title: 2008115 4.08 92 Mt108f vs Al1 2 me


title: 20071215 4.08 76 Xo117f vs Mt111f fine


title: 20071219 4.08 78 Xo113f vs Xf129f fine


title: 20071219 4.08 77 Xf128f vs Xo113f fine


title: 20071215 4.08 70 Mt108f vs Xf126f fine


title: 20071215 4.08 71 Al116f vs Xo113f fine


title: Adjacent normal tissue from patient 19

city: Nanjing

first: chenyu

last: lin

address: Longmian Road No.639

department: Life science

institute: China Pharmaceutical University

hyb_protocol: The labled RNA were hybridized for 16 hr at 48C on Affymetrix miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with miRNA QCTool using Affymetrix default analysis settings and quantile as normalization method.

source_name: Adjacent normal tissue from patient 19

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit. This kit can be used to label any RNA sample, including total RNA, severely degraded RNA, plant RNA, and low molecular weight RNA.

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

treatment_protocol: collect pairs of ESCC tissues and adjacent nontumor tisssues

tag: subject status/id

value: esophageal squamous cell carcinoma (ESCC)  patient 19

value: normal esophageal tissue


title: Adjacent normal tissue from patient 16

source_name: Adjacent normal tissue from patient 16

value: esophageal squamous cell carcinoma (ESCC)  patient 16


title: Cancer and normal tissue from patient 19

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

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

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Cancer tissue from patient 19

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

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

value: Esophageal squamous carcinoma tissue


title: Adjacent normal tissue from patient 18

source_name: Adjacent normal tissue from patient 18

value: esophageal squamous cell carcinoma (ESCC)  patient 18


title: Cancer and normal tissue from patient 15

source_name: Cancer tissue from patient 15

value: esophageal squamous cell carcinoma (ESCC)  patient 15

source_name: Adjacent normal tissue from patient 15


title: 20071211 4.08 68 Mt111f vs Al114f fine


title: Adjacent normal tissue from patient 14

source_name: Adjacent normal tissue from patient 14

value: esophageal squamous cell carcinoma (ESCC)  patient 14


title: Adjacent normal tissue from patient 15


title: Cancer and normal tissue from patient 16

source_name: Cancer tissue from patient 16


title: Adjacent normal tissue from patient 9

source_name: Adjacent normal tissue from patient 9

value: esophageal squamous cell carcinoma (ESCC)  patient 9


title: Cancer tissue from patient 19


title: Adjacent normal tissue from patient 17

source_name: Adjacent normal tissue from patient 17

value: esophageal squamous cell carcinoma (ESCC)  patient 17


title: 20071206 4.08 64 Xo115f vs Xf123f fine

source_name: whole brain


title: 20071211 4.08 69 Xf126f vs Al114f fine


title: Cancer and normal tissue from patient 17

source_name: Cancer tissue from patient 17


title: 20071206 4.08 65 Al112f vs Mt110f fine


title: Cancer and normal tissue from patient 18

source_name: Cancer tissue from patient 18


title: 20071205 4.08 63 Xo116f vs Xf128f fine


title: Cancer tissue from patient 17


title: Cancer and normal tissue from patient 9

source_name: Cancer tissue from patient 9


title: Cancer tissue from patient 18


title: 20071215 4.08 72 Al112f vs Xf127f fine


title: Cancer tissue from patient 14

source_name: Cancer tissue from patient 14


title: Cancer tissue from patient 15


title: 2008122 4.08 41


title: Cancer and normal tissue from patient 14


title: Cancer tissue from patient 16


title: Health Control 4

city: Kensington

first: Daniel

middle: D

last: Murray

state: NSW

address: The Kirby Institute, Wallace Wurth Building, UNSW Australia

department: Immunovirology and pathogenesis program

country: Australia

institute: Kirby Institute

data_processing:
Raw data was analysed to see which miRNAs were detectable in serum of HIV infected individuals. No further processing was performed. A miRNA was deemed as 'dectable' if the miRNA was expressed <35CT in more 3 or more samples.
Please note that undetermined values were replaced with a blank in the sample data table.

label: FAM

source_name: HIV Negative_serum

label_protocol: cDNA was reversed transcribed and pre-amplified according to manufacturers instructions.

extract_protocol: Total RNA extracted using Trizol methodology

tag: hiv status

value: HIV Negative

value: serum


title: Health Control 3


title: SPH (mesenchymal-like DLD1 derivative) colorectal cancer cell line, replicat 1

hyb_protocol: Standard Agilent Protocol

scan_protocol: Standard Agilent Protocol

data_processing: Quantile normalization was performed using the preprocessCore package with R version 3.2.0

source_name: colorectal cancer cell line

label_protocol: Standard Agilent Protocol for Cy3 labeling

extract_protocol: Total RNA from cell lines was isolated using the miRNeasy Kit (Qiagen).

tag: parental cell type

value: colorectal cancer cell line DLD1

tag: cell characteristics

value: mesenchymal, derived from colonospheres


title: Health Control 1


title: Chronic HIV 3

source_name: HIV Positive_serum

value: HIV Positive


title: Chronic HIV 4


title: Chronic HIV 2


title: SPH (mesenchymal-like DLD1 derivative) colorectal cancer cell line, replicat 2


title: RNA of Transected hippocampus tissue-7d (C3O)

city: Nantong

first: cheng

last: xiang

address: Qixiu Road NO.19

institute: Nantong University

description:
Sample C3O
The raw data for former sample is in Row 1 to 155, and the latter is in Row 156 to 349, and between is the space for empty and QC probe.

hyb_protocol: The microarrays were prehybridized for 1 h at  37℃ based on the designed probe, removed the liquid and hybriedized with 4 ug denatured reversed-transcribed RNA for 16h at the same tempreture.

scan_protocol: Imaging was performed using a laser scanner GenePix4000B (Molecular Device)

data_processing: Normalized intensities were transformed into gene expression log2 values. The ratio and log2 ratio of normalized spot intensities between the test and control samples were calculated. P values were calculated using the analysis of variance (ANOVA) method.

organism: Rattus norvegicus

source_name: Transected hippocampus tissue-7d

label_protocol: 2 mg of total RNA was reverse-transcribed using Amino Allyl messageAmp II kit(Life Technologies) and labeled with ULS-Cy5. Labelling efficiency was calculated by the concentration of CyDye and RNA, as measured by spectrophotometry.

extract_protocol: RNA isolated using TRIZOL

tag: strain

value: Sprague-Dawley

tag: protocol

value: transection

value: hippocampus


title: RNA of normal hippocampus tissue (N3P)

description:
Sample N3P
The raw data for former sample is in Row 1 to 155, and the latter is in Row 156 to 349, and between is the space for empty and QC probe.

source_name: normal hippocampus tissue

value: control


title: METS (metastasis-derived DLD1 derivative)  colorectal cancer cell line, replicat 2

value: epithelial, derived from xenograft lung metastasis


title: Cancer tissue from patient 9


title: METS (metastasis-derived DLD1 derivative)  colorectal cancer cell line, replicat 3


title: RNA of Transected hippocampus tissue-7d (C1B)

description:
Sample C1B
The raw data for former sample is in Row 1 to 155, and the latter is in Row 156 to 349, and between is the space for empty and QC probe.


title: RNA of Transected hippocampus tissue-7d (C2G)

description:
Sample C2G
The raw data for former sample is in Row 1 to 155, and the latter is in Row 156 to 349, and between is the space for empty and QC probe.


title: SA (mesenchymal-like DLD1 derivative) colorectal cancer cell line, replicat 3

value: mesenchymal, derived from soft agar colonies


title: SA (mesenchymal-like DLD1 derivative) colorectal cancer cell line, replicat 1


title: SA (mesenchymal-like DLD1 derivative) colorectal cancer cell line, replicat 2


title: METS (metastasis-derived DLD1 derivative)  colorectal cancer cell line, replicat 1


title: parental DLD1 colorectal cancer cell line, replicat 2

value: epithelial, parental