title: YG51N

city: Seoul

first: Jae Yun

last: Lim

address: 211 Eonju-ro, Gangnam-gu

department: Medical Oncology

country: South Korea

institute: Gangnam Severance Hospital, Yonsei University

hyb_protocol: Labeled, material (15ul per array) was hybridized to the Illumina Human v2 MicroRNA expression BeadChip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Chips were scanned with an Illumina BeadArray Reader (Illumina)

data_processing: Signal intensity values were analyzed using BeadStudio version 3.1.3. We set a cut-off detection p-value of 0.01 to determine whether a probe was significantly detected. Thereafter the data of 410 probes was analyzed . The data were normalized using quantile normalization in the R language environment and log2 transformed.

source_name: surrounding non-cancer tissue

label_protocol: 200 ng of total RNA was converted to cDNA. A single miRNA-specific oligo (MSO) was used to assay each miRNA. All MSOs were hybridized to the sample in parallel, and followed by a solid-phase primer extension step. The universal PCR step created fluorescently labeled products identifiable by their unique MSO sequence. The address sequence from each MSO was used to hybridize specific miRNA products to specific locations on the BeadArrayTM substrate for readout.

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

value: M

tag: histology

value: Normal

tag: Stage


title: YG45N

status: Public on Sep 01 2013

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: gender

tag: age


title: YG54N


title: stimulated subject 100

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description: Sample 200

hyb_protocol: Biotin-labeled, amplified material was hybridized to Illumina Human-HT-12 v3 BeadChips, according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA; 11322355 Rev. A, 11286331 Rev. A).

scan_protocol: Microarrays were scanned on the Illumina Bead Array Reader (Illumina, Inc., San Diego, CA) with default outlier detection according to the manufacturer's instructions and summarized raw probe intensities were exported using Illumina’s GenomeStudio v2011.1 Gene Expression module.

data_processing: Microarray expression analysis was performed in R (http://www.r-project.org/). Summarized raw probe intensities (48,750 probes) were first filtered by an Illumina detection P value of 0.01 in at least 10% of the samples, leaving 14,168 expressed probes for further analysis. Second, each transcript was transformed and normalized through variance stabilization and normalization.  Third, technical batches were adjusted using ComBat (http://jlab.byu.edu/ComBat/Abstract.html) with fixed effects of amplification round.

source_name: whole blood

label_protocol: Sample labeling was performed using the Illumina TotalPrep RNA Amplification Kit (Ambion, TX, USA) according to the manufacturer's instructions.

extract_protocol: RNA was extracted from whole blood collected in PAXgene Blood RNA tubes using the PAXgene Blood RNA Kit (PreAnalytiX GmbH, Hombrechtikon, Switzerland).

value: male

tag: stimulus

value: stimulated

tag: status

value: case

tag: bmi


title: YG55N


title: YG73N

value: F


title: 196-29628-E

city: Chicago

first: Joseph

middle: C

last: Maranville

state: IL

address: 920 E. 58th Street

country: USA

institute: 920 E. 58th Street

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalized and variance transformed using LUMI package in R

source_name: PBMCs

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

extract_protocol: RNA was extracted with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: treatment

value: vehicle (EtOH) + phytohemagglutinin

tag: in vitro lymphocyte gc sensitivity (lgs - %inhibition by dex)


title: YG42N


title: baseline subject 99

description: Sample 197

value: baseline


title: stimulated subject 99

description: Sample 198


title: baseline subject 98

description: Sample 196


title: YG76T

source_name: primary gastric adenocarcinoma

value: Intestinal


title: YG40N


title: 193-29623-D

value: dexamethasone + phytohemagglutinin


title: YG35N


title: stimulated subject 98

description: Sample 195


title: 192-29554-E


title: YG75T

value: Diffuse


title: 191-29554-D


title: UT0102L [Methylation]

type: genomic

city: Ube

first: Ryo

last: Maekawa

address: Minami-Kogushi 1-1-1

department: Department of Obstetrics and Gynecology

country: Japan

institute: Yamaguchi University School of Medicine

description: uterine leiomyoma obtained from same case as UT0102M

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

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

data_processing: GenomeStudio Methylation Module

label: Alexa555 and Alexa647

molecule: genomic DNA

source_name: Leiomyoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from frozen tissue of myometrium and leiomyoma obtained from the woman who underwent hysterectomy using Qiagen DNeasy Kit according to standard instructions

value: Female

tag: tissue

value: frozen tissue of uterine leiomyoma

tag: disease state

value: leiomyoma


title: UT0103M [Methylation]

description: myometrium tissue obtained from same case as UT0103L

source_name: Myomet

value: frozen tissue of myometrium with leiomyoma

value: myometrium tissue obtained from uterus with leiomyoma


title: UT0103L [Methylation]

description: uterine leiomyoma obtained from same case as UT0103M

value: frozen tissue ofuterine leiomyoma


title: 189-29536-D


title: UT0102M [Methylation]

description: myometrium tissue obtained from same case as UT0102L


title: baseline subject 97

description: Sample 193


title: 185-29524-E


title: YG74T

value: M


title: stimulated subject 96

description: Sample 192

value: control


title: baseline subject 96

description: Sample 191

value: male


title: 212-29786-E


title: Myomet0103 [Methylation]

description: control myometrium tissue to compare with myometrium with leiomyoma

source_name: Control

value: frozen tissue of myometrium without leiomyoma

value: normal myometrium


title: YG70T


title: UT0101L [Methylation]

description: uterine leiomyoma obtained from same case as UT0101M


title: UT0101M [Methylation]

description: myometrium tissue obtained from same case as UT0101L


title: 183-29523-E


title: 184-29524-D


title: Myomet0101 [Methylation]


title: stimulated subject 95

description: Sample 190

value: stimulated


title: 187-29536-E

value: vehicle (EtOH) + phytohemagglutinin


title: 182-29523-D


title: Myomet0102 [Methylation]


title: baseline subject 95

description: Sample 189

value: baseline


title: YG67T


title: 180-29401-D


title: YG68T

value: Intestinal


title: baseline subject 94

description: Sample 187


title: stimulated subject 97

description: Sample 194

value: case


title: stimulated subject 94

description: Sample 188


title: lqz342 Uterus_P1pos_4

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: normal

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with RMA as implemented in  Partek Genomics Suite 6.6

label: Biotin

organism: Mus musculus

source_name: UTERUS

label_protocol: standard Affymetrix protocol

growth_protocol: A small chuck of normal or tumor tissue was collected and frozen on dry ice immediately after animal was euthanized. For Prom1+ and Prom1- cells isolation, tissues were dissociated into single cells and  sorted using anti-Prom1 MicroBeads (Miltenyi Biotec).

extract_protocol: Total mRNA was extracted from frozen tissues or sorted Prom1+ and Prom1- cells using PicoPureTM extraction kit (Arcturus).

value: UTERUS

tag: prom1 status

value: POS

tag: strain

value: normal


title: YG69T


title: YG66T

value: F

value: Diffuse


title: YG65T


title: OVCAR3-533533-R7_Selected_Drug_Rep1

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Infinium HD Assay was performed using the BeadArray system according to the manufacturer's instructions (Illumina)

data_processing: Data was extracted using Illumina’s GenomeStudio v2010.3 with Genotyping module 1.8.4 software, with the default Illumina settings and Illumina HumanOmniExpress‐12v1_H manifest cluster file

label: C-Bio and A-DNP

source_name: ovarian cancer cell line

label_protocol: Infinium HD Assay was performed according to the manufacturer's instructions (Illumina)

growth_protocol: Cells were maintained at 37ºC and 5% CO2 in RPMI 1640 containing 10% (v/v) FCS, 50 U.mL-1 penicillin and 50ug.mL-1 streptomycin. 'Selected' cells were cultured in 4uM PHA-533533.

extract_protocol: Total genomic DNA was extracted using a DNeasy Kit (Qiagen, Valencia, CA)

treatment_protocol: Cell pellets were collected from subconfluent cultures, frozen and stored at -80ºC prior to nucleic acid extraction.

tag: cell type

value: Resistant


title: lqz341 Uterus_P1neg_3

description: normal

value: NEG


title: baseline subject 93

description: Sample 185


title: OVCAR3-533533-R6_Selected_Drug_Rep1

scan_protocol: Infinium HD Assay was performed using the BeadArray system according to the manufacturer's instructions (Illumina)


title: stimulated subject 93

description: Sample 186


title: lqz340 Uterus_P1pos_3

description: normal


title: YG64T

value: M


title: 176-29404-B

value: no treatment


title: YG63T


title: stimulated subject 92

description: Sample 184

value: male

value: control


title: OVCAR3_Parental_Media_Rep1

value: Parental


title: lqz339 Uterus_P1neg_2

description: normal


title: baseline subject 92

description: Sample 183


title: lqz338 Uterus_P1pos_2

description: normal


title: 179-29401-B


title: 173-29404-D

value: dexamethasone + phytohemagglutinin


title: 174-29404-E

value: vehicle (EtOH) + phytohemagglutinin


title: lqz337 Uterus_P1neg_1

description: normal


title: OVCAR3-533533-R1_Selected_Drug_Rep1


title: lqz334 Uterus_P1pos_1

description: normal


title: 172-28515-D


title: OVCAR3-533533-R3_Selected_Drug_Rep1


title: YG73T


title: YG71T


title: YG61T


title: YG62T


title: 169-28515-E


title: YG60T

value: Mixed


title: 171-28515-B


title: baseline subject 91

description: Sample 181

value: baseline


title: stimulated subject 91

description: Sample 182

value: stimulated

value: case


title: stimulated subject 90

description: Sample 180


title: YG58T


title: OVCAR3-533533-R5_Selected_Drug_Rep1


title: baseline subject 90

description: Sample 179


title: 167-28947-E


title: lqz332 Stomach_P1pos_3

description: normal

source_name: STOMACH

value: STOMACH

value: POS


title: lqz331 Stomach_P1neg_3

description: normal

value: normal


title: lqz330 Stomach_P1pos_2

description: normal


title: lqz326 Stomach_P1pos_1

description: normal


title: 166-28947-D


title: stimulated subject 89

description: Sample 178


title: YG54T

value: Diffuse


title: lqz302 Intestine_P1pos_3

description: normal

source_name: INTESTINE

value: INTESTINE


title: YG55T


title: lqz300 Intestine_P1neg_6

description: normal

value: NEG


title: YG56T

value: M


title: YG53T


title: stimulated subject 88

description: Sample 176


title: baseline subject 89

description: Sample 177


title: lqz298 Stomach_P1neg_2

description: normal


title: YG51T


title: YG52T

value: Intestinal


title: 162-28798-D


title: 164-29310-D


title: 165-29310-E


title: baseline subject 87

description: Sample 173

value: male


title: lqz297 Intestine_P1pos_2

description: normal


title: 160-28798-E


title: lqz294 Intestine_P1neg_5

description: normal


title: 157-28652-D


title: YG50T


title: stimulated subject 87

description: Sample 174

value: control


title: 158-28652-E


title: 156-28355-E


title: stimulated subject 86

description: Sample 172


title: lqz275 tumor

description: tumor

source_name: GASTRIC ADENOCARCINOMA

value: GASTRIC ADENOCARCINOMA

value: tumor N/A

value: tumor


title: baseline subject 88

description: Sample 175


title: YG49T

value: F


title: lqz273 tumor

description: tumor

source_name: B-CELL LYMPHOMA

value: B-CELL LYMPHOMA


title: YG48T


title: YG47T


title: baseline subject 86

description: Sample 171

value: baseline


title: YG46T


title: baseline subject 85

description: Sample 169


title: lqz245 Liver_P1neg_7

description: normal

source_name: LIVER

value: LIVER


title: 155-28355-D

value: dexamethasone + phytohemagglutinin


title: stimulated subject 85

description: Sample 170

value: stimulated


title: YG45T


title: lqz243 Liver_P1neg_6

description: normal

value: normal


title: lqz241 Lung_P1neg_7

description: normal

source_name: LUNG

value: LUNG


title: 154-28355-B

value: no treatment


title: YG44T

value: Mixed


title: baseline subject 84

description: Sample 167


title: 152-28797-D


title: stimulated subject 84

description: Sample 168


title: lqz239 Stomach_P1neg_2

description: normal

value: STOMACH

value: NEG


title: YG42T

value: Diffuse


title: 149-28797-E

value: vehicle (EtOH) + phytohemagglutinin


title: lqz231 Stomach_P1neg_1

description: normal


title: lqz229 Intestine_P1neg_4

description: normal

value: INTESTINE


title: 146-28221-E


title: YG41T

value: M

value: Intestinal


title: stimulated subject 83

description: Sample 166

value: male

value: control


title: 151-28797-B


title: baseline subject 83

description: Sample 165

value: baseline


title: lqz228 Liver_P1pos_4

description: normal

value: LIVER

value: POS


title: YG39T


title: 145-28221-D

value: dexamethasone + phytohemagglutinin


title: stimulated subject 82

description: Sample 164

value: stimulated


title: 177-29401-E


title: baseline subject 82

description: Sample 163


title: stimulated subject 81

description: Sample 162


title: lqz226 Liver_P1pos_3

description: normal

value: normal


title: YG38T

value: F


title: baseline subject 81

description: Sample 161


title: 141-28642-D


title: lqz227 Liver_P1neg_5

description: normal


title: 148-28221-B

value: no treatment


title: YG43T


title: YG36T

value: Mixed


title: YG35T


title: stimulated subject 80

description: Sample 160

value: case


title: 143-28499-D


title: baseline subject 80

description: Sample 159


title: YG40T


title: lqz222 Liver_P1pos_2

description: normal


title: baseline subject 79

description: Sample 158


title: 137-28776-E


title: YG33T

value: other


title: stimulated subject 79

description: Sample 157


title: lqz220 Lung_P1pos_4

description: normal

value: LUNG


title: YG32T

value: Diffuse


title: 135-29439-E

value: vehicle (EtOH) + phytohemagglutinin


title: 139-28642-E


title: lqz219 Lung_P1neg_6

description: normal

value: NEG


title: lqz216 tumor

description: tumor

value: B-CELL LYMPHOMA

value: tumor N/A

value: tumor


title: lqz225 Liver_P1neg_4

description: normal

value: LIVER


title: baseline subject 78

description: Sample 155

value: male

value: baseline


title: 134-29439-D

value: dexamethasone + phytohemagglutinin


title: stimulated subject 78

description: Sample 156

value: stimulated


title: lqz210 tumor

description: tumor

source_name: SQUAMOUS CELL CARCINOMA OF SKIN

value: SQUAMOUS CELL CARCINOMA OF SKIN


title: YG34T

value: M


title: lqz209 tumor

description: tumor

source_name: PROSTATIC ADENOCARCINOMA

value: PROSTATIC ADENOCARCINOMA


title: 130-28598-E


title: YG31T

value: Mixed


title: 132-28598-D


title: 136-28776-D


title: stimulated subject 77

description: Sample 154

value: case


title: YG30T

value: Intestinal


title: baseline subject 77

description: Sample 153


title: lqz246 Liver_P1pos_5

description: normal

value: POS

value: normal


title: lqz207 tumor

description: tumor

source_name: UTERINE ADENOCARCINOMA

value: UTERINE ADENOCARCINOMA


title: lqz202 tumor

description: tumor


title: YG27T

value: F

value: Diffuse


title: YG26T


title: baseline subject 75

description: Sample 150

source_name: whole blood


title: stimulated subject 76

description: Sample 152


title: baseline subject 76

description: Sample 151


title: YG29T


title: 128-28688-E

source_name: PBMCs

value: vehicle (EtOH) + phytohemagglutinin


title: 126-28684-E


title: stimulated subject 75

description: Sample 149


title: YG23T

source_name: primary gastric adenocarcinoma


title: YG24T


title: lqz197 tumor

description: tumor

source_name: HEPATOCELLULAR CARCINOMA

value: HEPATOCELLULAR CARCINOMA

value: tumor N/A

value: tumor


title: lqz174 tumor

description: tumor


title: 123-29443-D

value: dexamethasone + phytohemagglutinin


title: YG21T


title: 127-28688-D


title: baseline subject 74

description: Sample 147

value: male

value: baseline

value: control


title: lqz170 tumor

description: tumor

value: PROSTATIC ADENOCARCINOMA


title: 125-28684-D


title: lqz196 tumor

description: tumor

value: B-CELL LYMPHOMA


title: lqz172 tumor

description: tumor


title: stimulated subject 74

description: Sample 148

value: stimulated


title: 121-29443-E


title: 119-28657-E


title: stimulated subject 73

description: Sample 146


title: YG20T

value: Intestinal


title: lqz171 tumor

description: tumor


title: baseline subject 73

description: Sample 145


title: YG18T


title: stimulated subject 72

description: Sample 144


title: stimulated subject 71

description: Sample 142


title: YG09T

value: M


title: YG15T


title: YG16T


title: 118-28657-D


title: baseline subject 72

description: Sample 143


title: YG19T

value: Mixed


title: lqz168 tumor

description: tumor


title: baseline subject 71

description: Sample 141


title: YG06T


title: lqz167 Prostate_P1pos_3

description: normal

source_name: PROSTATE

value: PROSTATE

value: POS

value: normal


title: lqz160 Prostate_P1neg_4

description: normal

value: NEG


title: 110-28203-E

value: vehicle (EtOH) + phytohemagglutinin


title: 108-28772-E


title: 114-28643-D


title: 112-28643-E


title: lqz166 Prostate_P1neg_5

description: normal


title: 116-28230-D


title: 109-28203-D


title: lqz161 Prostate_P1pos_2

description: normal


title: baseline subject 70

description: Sample 139


title: YG05T


title: stimulated subject 70

description: Sample 140


title: lqz156 Lung_P1neg_5

description: normal

value: LUNG


title: YG04T

value: F

value: Diffuse


title: stimulated subject 69

description: Sample 138

value: male


title: 107-28772-D

value: dexamethasone + phytohemagglutinin


title: stimulated subject 68

description: Sample 136

value: control


title: baseline subject 69

description: Sample 137

value: baseline


title: 101-28686-E


title: lqz159 Intestine_P1pos_1

description: normal

value: INTESTINE


title: YG03T


title: lqz153 Lung_P1pos_1

description: normal


title: stimulated subject 67

description: Sample 134

value: stimulated

value: case


title: 105-28779-D


title: 144-28499-E


title: lqz150 Prostate_P1neg_3

description: normal


title: baseline subject 68

description: Sample 135


title: 117-28230-E


title: 103-28779-E


title: baseline subject 67

description: Sample 133


title: 99-28513-E


title: lqz157 Lung_P1pos_2

description: normal


title: lqz146 Lung_P1neg_3

description: normal


title: stimulated subject 66

description: Sample 132


title: lqz148 Intestine_P1neg_2

description: normal


title: 100-28686-D


title: lqz144 Liver_P1neg_3

description: normal

value: LIVER


title: YG17T

value: M


title: lqz152 Lung_P1neg_4

description: normal


title: baseline subject 64

description: Sample 127


title: lqz138 Lung_P1neg_2

description: normal


title: lqz142 Liver_P1neg_2

description: normal


title: stimulated subject 62

description: Sample 126


title: lqz132 Prostate_P1neg_2

description: normal

value: PROSTATE


title: 98-28513-D


title: lqz136 Intestine_P1neg_1

description: normal


title: stimulated subject 63

description: Sample 125


title: baseline subject 65

description: Sample 129


title: baseline subject 66

description: Sample 131


title: lqz140 Liver_P1neg_1

description: normal


title: 92-28911-E


title: 91-28911-D


title: stimulated subject 65

description: Sample 130


title: baseline subject 63

description: Sample 124


title: baseline subject 62

description: Sample 123


title: lqz134 Lung_P1neg_1

description: normal


title: 87-28949-D


title: 96-28898-D


title: lqz133 Prostate_P1pos_1

description: normal

value: POS


title: 83-28676-E


title: 90-28218-E


title: 85-28949-E


title: 94-28898-E


title: 89-28218-D


title: 82-28676-D


title: stimulated subject 64

description: Sample 128


title: lqz128 tumor

description: tumor

source_name: BRONCHIAL PAPILLARY ADENOMA

value: BRONCHIAL PAPILLARY ADENOMA

value: tumor N/A

value: tumor


title: lqz131 tumor

description: tumor


title: lqz130 tumor

description: tumor

value: HEPATOCELLULAR CARCINOMA


title: 81-28689-E

value: vehicle (EtOH) + phytohemagglutinin


title: stimulated subject 60

description: Sample 120


title: stimulated subject 61

description: Sample 122


title: lqz114 tumor

description: tumor


title: lqz109 Prostate_P1neg_1

description: normal

value: NEG

value: normal


title: baseline subject 61

description: Sample 121

value: male


title: lqz121 tumor

description: tumor


title: lqz107 tumor

description: tumor

value: GASTRIC ADENOCARCINOMA


title: 74-28249-E


title: stimulated subject 59

description: Sample 118


title: lqz104 tumor

description: tumor


title: stimulated subject 58

description: Sample 116


title: 76-28257-E


title: lqz108 tumor

description: tumor


title: baseline subject 59

description: Sample 117

value: baseline


title: 73-28249-D

value: dexamethasone + phytohemagglutinin


title: lqz103 tumor

description: tumor


title: lqz094 tumor

description: tumor


title: 80-28689-D


title: baseline subject 60

description: Sample 119


title: 78-28257-D


title: stimulated subject 57

description: Sample 114

value: stimulated

value: control


title: lqz089 tumor

description: tumor

value: UTERINE ADENOCARCINOMA


title: baseline subject 57

description: Sample 113


title: 71-28923-D


title: baseline subject 58

description: Sample 115

value: case


title: 72-28923-E


title: baseline subject 56

description: Sample 111


title: 69-29328-D


title: stimulated subject 56

description: Sample 112


title: 67-29328-E


title: baseline subject 55

description: Sample 109


title: stimulated subject 55

description: Sample 110


title: lqz086 tumor

description: tumor


title: lqz082 tumor

description: tumor


title: lqz084 tumor

description: tumor


title: 64-29420-D


title: lqz076 tumor

description: tumor


title: baseline subject 53

description: Sample 105


title: lqz072 tumor

description: tumor


title: baseline subject 54

description: Sample 107


title: 60-29306-D


title: 63-29442-E


title: stimulated subject 54

description: Sample 108


title: lqz078 tumor

description: tumor


title: 56-28687-E


title: baseline subject 52

description: Sample 103


title: lqz073 tumor

description: tumor


title: lqz064 tumor

description: tumor


title: 54-28517-E


title: 58-29306-E


title: stimulated subject 52

description: Sample 104


title: stimulated subject 51

description: Sample 102


title: 55-28687-D


title: 62-29442-D


title: lqz074 tumor

description: tumor


title: lqz063 tumor

description: tumor


title: lqz061 tumor

description: tumor


title: 53-28517-D


title: baseline subject 50

description: Sample 99


title: lqz059 tumor

description: tumor


title: baseline subject 49

description: Sample 97


title: 46-28585-D


title: baseline subject 48

description: Sample 95


title: 49-28248-E


title: stimulated subject 48

description: Sample 96


title: stimulated subject 50

description: Sample 100


title: lqz055 tumor

description: tumor


title: 47-28585-E


title: stimulated subject 49

description: Sample 98


title: 44-29510-D


title: lqz056 tumor

description: tumor


title: 42-29399-D


title: 51-28248-D


title: 45-29510-E


title: stimulated subject 47

description: Sample 94


title: lqz053 tumor

description: tumor


title: baseline subject 51

description: Sample 101


title: lqz052 tumor

description: tumor

value: SQUAMOUS CELL CARCINOMA OF SKIN


title: lqz054 tumor

description: tumor


title: lqz049 tumor

description: tumor


title: 38-29441-E


title: 40-29399-E


title: baseline subject 47

description: Sample 93


title: stimulated subject 46

description: Sample 92


title: stimulated subject 45

description: Sample 90


title: baseline subject 45

description: Sample 89


title: 36-28943-E


title: 37-29441-D


title: lqz057 tumor

description: tumor


title: lqz046 tumor

description: tumor


title: lqz041 tumor

description: tumor


title: lqz040 tumor

description: tumor


title: 33-28256-D


title: stimulated subject 44

description: Sample 88


title: baseline subject 44

description: Sample 87


title: stimulated subject 43

description: Sample 86


title: 29-29225-E


title: baseline subject 46

description: Sample 91


title: lqz047 tumor

description: tumor


title: lqz039 tumor

description: tumor


title: lqz038 tumor

description: tumor


title: 31-28256-E


title: 28-29225-D


title: baseline subject 43

description: Sample 85


title: 27-28511-E


title: lqz034 tumor

description: tumor


title: lqz033 tumor

description: tumor


title: 35-28943-D


title: lqz037 tumor

description: tumor


title: 26-28511-D


title: baseline subject 42

description: Sample 83


title: stimulated subject 42

description: Sample 84


title: stimulated subject 41

description: Sample 81


title: lqz079 tumor

description: tumor


title: baseline subject 41

description: Sample 82


title: stimulated subject 53

description: Sample 106


title: stimulated subject 40

description: Sample 80


title: 22-28641-E


title: lqz031 tumor

description: tumor


title: lqz026 tumor

description: tumor


title: stimulated subject 39

description: Sample 78


title: 19-28592-D


title: lqz020 tumor

description: tumor

value: PROSTATIC ADENOCARCINOMA


title: lqz023 tumor

description: tumor


title: 20-28592-E


title: 17-28498-D


title: 24-28641-D


title: lqz068 tumor

description: tumor


title: lqz015 tumor

description: tumor

value: BRONCHIAL PAPILLARY ADENOMA


title: lqz025 tumor

description: tumor

value: tumor N/A


title: baseline subject 39

description: Sample 77


title: 18-28498-E


title: lqz014 tumor

description: tumor

value: tumor


title: baseline subject 40

description: Sample 79


title: 65-29420-E


title: 13-28344-E


title: 11-29516-E


title: baseline subject 38

description: Sample 75


title: lqz012 tumor

description: tumor


title: lqz013 tumor

description: tumor


title: baseline subject 37

description: Sample 73


title: stimulated subject 37

description: Sample 74


title: baseline subject 36

description: Sample 71


title: stimulated subject 36

description: Sample 72


title: lqz009 tumor

description: tumor


title: 10-29516-D


title: 15-28344-D


title: lqz007 tumor

description: tumor


title: 9-29514-E


title: 8-29514-D


title: stimulated subject 38

description: Sample 76


title: baseline subject 35

description: Sample 69


title: stimulated subject 33

description: Sample 66


title: baseline subject 33

description: Sample 65


title: stimulated subject 34

description: Sample 68


title: 4-28354-E


title: baseline subject 34

description: Sample 67


title: 2-29422-E


title: Luc12-2

city: Taipei

first: pei-shan

last: Hou

address: No. 155, Sec. 2, Linong St., Beitou dist.

country: Taiwan

institute: Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming Chiao-Tung University.

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

source_name: shLuc, ND12

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

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen Inc).

tag: cell line


title: stimulated subject 35

description: Sample 70


title: 6-28354-D


title: stimulated subject 32

description: Sample 64


title: baseline subject 32

description: Sample 63


title: stimulated subject 31

description: Sample 62


title: LHX12-1

source_name: shLHX2, ND12


title: baseline subject 31

description: Sample 61


title: Luc12-1


title: LHX12-2


title: 16+2

source_name: Dox+ LHX2 in H9, day16


title: 16-1

source_name: Dox- LHX2 in H9, day16


title: 16+1


title: baseline subject 30

description: Sample 60


title: 16-2


title: stimulated subject 29

description: Sample 58


title: 4+2

source_name: Dox+ LHX2 in H9, day4


title: MBD2_3

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a; Affymetrix), and array data were analyzed using MAYDAY 2.12 software. Array data were subjected to robust multiarray average normalization. For determination of differential expression, we calculated fold changes and tested for significance by Significance Analysis of Microarrays (SAM) using 100 permutations with a false discovery rate (Storey) adjusted p<0.05. Data with >1.5 × differential expression (log2 0.5849) were included in the analysis.

source_name: Regulatory T-cells CD4+CD25+

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).

tag: genotype

tag: genetic background

value: Balb/c

value: Regulatory T-cells CD4+CD25+


title: stimulated subject 30

description: Sample 59


title: MBD2_2


title: 4-2

source_name: Dox- LHX2 in H9, day4


title: 4+1


title: 1-29422-D


title: baseline subject 29

description: Sample 57


title: 4-1


title: stimulated subject 28

description: Sample 56


title: MBD2_1


title: baseline subject 28

description: Sample 55


title: Balb/c WT_3

value: WT


title: baseline subject 27

description: Sample 53


title: IVF_control_female_blastocyst_rep1

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

description: IVF control female, blastocyst, replicate1

hyb_protocol: 1.65ug Cy3-labelled RNAs were fragmented at 60°C for 30 minutes and hybridized at 65°C for 17 hours according to manufacture's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images of microarray slides were processed using Feature Extraction software 10.5.1 (Agilent Technologies). All raw data were loaded into Gene Spring GX 12.5 (Agilent Technologies) and transformed by default setting.

source_name: IVF control female, blastocyst

label_protocol: 5.0 ug of amplified RNA was labelled with Cianine-3 (Cy3) dye (GE Healthcare) for 90 minutes at RT. Labelled RNAs were purified with RNeasy MinElute kit (Qiagen) and checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: In vitro fertilized (IVF) or cloned embryos were cultured in potassium modified simplex optimization medium (KSOM) at 37.5 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted with TRIzol (Life Technologies) from epiblasts or extraembryonic regions derived from single embryos and subjected to linear amplification using TargetAmp Two-Round Aminoallyl-aRNA Amplification Kits (Epicentre Biotechnologies).

treatment_protocol: Embryos that reached the blastocyst (E4.0) stage were used to extract total RNA.

value: female

tag: donor cell

value: IVF

value: blastocyst

tag: embryonic day


title: Normal_Colon-CN_223_GB

city: Montpellier Cedex 5

first: Pierre

last: Martineau

address: 208 Rue des Apothicaires

department: IRCM

country: France

institute: Inserm

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with HWS kit.

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

data_processing: Signal intensity for each transcript and detection call (present, absent, or marginal) were determined using MAS 5.0 Software (Affymetrix). Interarray normalization was performed using a set of internal standard genes (normalization set ϩ internal controls) leading to the determination of a scaling factor.

source_name: Tissue samples taken from colorectal cancer patients

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix IVT protocol from 3µg total RNA (3'IVT ExpressTechnical Manual).

extract_protocol: Rneasy kit (Qiagen) for total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Samples were collected before chemotherapy

tag: organism part

value: Normal Colon

tag: patient number

tag: Sex

value: Male

tag: who performance status

tag: tumor location

value: Left colon

tag: differentiation

value: Moderate

tag: pn

tag: pt


title: Primary_Tumor-CT_244_FP

value: Primary Tumor

value: Female

tag: age

value: Transverse colon


title: stimulated subject 26

description: Sample 52

tag: gender

value: male

tag: stimulus

value: stimulated

tag: status

value: control

tag: bmi


title: Normal_Colon-CN_234_YC

value: Caecum


title: Pax6 KO2, E9.5 (1)

city: Saint Louis

middle: Cy

last: Beebe

state: MO

address: 660 S. Euclid Ave.

department: Ophthalmology and Visual Science

institute: Washington University School of Medicine

description:
4147958031_D
Total RNA amplified as cDNA.

hyb_protocol: Performed using standard Illumina protocol on Illumina Mouse6 v1.1 bead arrays by the Genome Technology Access Center (GTAC) at Washington University.

scan_protocol: Standard Illumina protocol for bead arrays.

data_processing:
Background subtraction and cubic spline normalization and differential expression performed using Illumina Genome Studio software.
Value is the mean hybridization intensity for all beads (25-50 per array) containing the indicated oligonucleotide probe.

source_name: Pax6-/- surface ectoderm

label_protocol: The resulting cDNA was biotin labeled using the Illumina biotinylation kit.

growth_protocol: Pregnant mice euthanized and embryos removed at E9.5.

extract_protocol: Total RNA was extracted and purified from the prospective lens tissue obtained from one embryo using a Qiagen RNeasy Microkit (Qiagen# 74004). 15 ng of total RNA was amplified to produce 3–5 μg of cDNA using Nugen WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies Inc, #3300-12).

treatment_protocol: Embryos frozen in OCT and sectioned at 10 microns. Laser microdissection of the lens placode on a Leica LMD-6000 system after slides were dipped in 70% ethanol at 4 °C for 1 min, washed in RNase-free water twice for 30 s, rinsed in 95% ethanol, and stained in Eosin Y. Stained samples were washed in 95% ethanol and dehydrated in 100% ethanol and xylene.

tag: strain/background

value: mixed (FVB; 129)

tag: genotype

tag: tissue

value: surface ectoderm


title: Normal_Colon-CN_227_SS

value: Poor


title: Primary_Tumor-CT_223_GB


title: Liver_Metastasis-HM_223_GB

value: Liver Metastasis


title: Primary_Tumor-CT_227_SS


title: Balb/c WT_2

value: WT

tag: genetic background

value: Balb/c

tag: cell type

value: Regulatory T-cells CD4+CD25+


title: stimulated subject 27

description: Sample 54


title: IVF_control_female_blastocyst_rep3

description: IVF control female, blastocyst, replicate3

value: female

tag: donor cell

value: IVF

value: blastocyst

tag: embryonic day


title: Pax6 KO1, E9.5 (1)

description:
4147958031_F
Total RNA amplified as cDNA.


title: stimulated subject 25

description: Sample 50


title: baseline subject 26

description: Sample 51

value: baseline


title: IVF_control_female_blastocyst_rep2

description: IVF control female, blastocyst, replicate2


title: WT2, E9.5 (1)

description:
4147958031_E
Total RNA amplified as cDNA.

source_name: WT lens placode

value: wild type

value: lens placode


title: Liver_Metastasis-HM_244_FP

tag: organism part

tag: patient number

tag: Sex

value: Female

tag: who performance status

value: Transverse colon

value: Moderate


title: stimulated subject 24

description: Sample 48

source_name: whole blood

value: male

value: stimulated

value: case


title: baseline subject 25

description: Sample 49

value: control


title: Balb/c WT_1


title: Pax6 KO3, E9.5 (1)

description:
4147958031_B
Total RNA amplified as cDNA.

value: mixed (FVB; 129)

value: surface ectoderm


title: IVF_control_male_blastocyst_rep2

description: IVF control male, blastocyst, replicate2

source_name: IVF control male, blastocyst


title: Normal_Colon-CN_222_PEC

value: Normal Colon

value: Male

tag: tumor location

value: Left colon

tag: differentiation

tag: pn

tag: pt


title: mtr10 cells_30-min amino acid starvation_Total RNA, biological rep 1

city: Columbus

first: Hui-Yi

last: Chu

state: OH

department: Molecular Genetics

institute: The Ohio State University

description: Gene expression data of total RNA collected from mtr10-deleted cells in 30-min amino acid starvation condition

hyb_protocol: cRNA were hybridized  on GeneChip Yeast Genome 2.0 Array according to  the manufacturer's instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affy GeneChip Scanner 3000

data_processing: The data were normalized with RMA (affy package in the Bioconductor and R), S. pombe signals were masked

organism: Saccharomyces cerevisiae

source_name: Total RNAs isolated from mtr10 deletion cells starved in amino acid depleted media for 30 min

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol in the microarray center of OSUCCC

growth_protocol: Yeast cells were grown in synthetic defined (SD) media at 30C until the density of cell culture reached to early log phase (OD600~0.35).

extract_protocol: After fractionation, the fractions corresponding to the regions of polyribosome and non-polyribosome were pooled and nucleic acids were precipitated in guanidine-HCl and ethanol. The nucleic acids were pelleted, resuspended in TE buffer, and extracted again with phenol/chloroform method.

treatment_protocol: Cell cultures were split and pelleted by centrifugation. Cell pellets were then resuspended in pre-warmed (30C) SD or SD-aa media and the cultures were returned to shaker for 30 min. Cycloheximide was added to each culture to final concentration 100 µg/ml before cultures were harvested. Cells were washed with 20 ml of cold freshly-prepared lysis buffer (20 mM Tris-HCl with pH 8.0, 140 mM KCl, 1.5 mM MgCl2, 0.5 mM dithiothreitol, 100 µg/ml cycloheximide, 1 mg/ml heparin). Cells were resuspended in lysis buffer with glassbeads and then disrupted by vortexing in the cold room with 10 cycles of 30 seconds burst and 30 seconds ice. RNA concentrations were detemined by A260. 20 OD260 of crude cell lysates were seperated in 10% to 50% sucrose gradients.

value: mtr10 deletion strain

tag: treatment

value: 30-min amino acid starvation

tag: rna subtype

value: Total RNA


title: baseline subject 24

description: Sample 47

tag: gender

tag: stimulus

value: baseline

tag: status

tag: age

tag: bmi


title: IVF_control_male_blastocyst_rep3

description: IVF control male, blastocyst, replicate3

tag: donor cell

value: IVF

tag: tissue

value: blastocyst


title: stimulated subject 23

description: Sample 46


title: mtr10 cells_30-min amino acid starvation_Total RNA, biological rep 2

tag: genotype


title: mtr10 cells_fed_Total RNA, biological rep 2

description: Gene expression data of total RNA collected from mtr10-deleted cells in fed condition

source_name: Total RNAs isolated from mtr10 deletion cells grown in SC media

value: fed


title: stimulated subject 22

description: Sample 44


title: mtr10 cells_fed_Total RNA, biological rep 1


title: IVF_control_male_blastocyst_rep1

description: IVF control male, blastocyst, replicate1

tag: embryonic day


title: Liver_Metastasis-HM_222_PEC

tag: organism part

value: Liver Metastasis

tag: patient number

tag: Sex

value: Moderate


title: msn5 cells_30-min amino acid starvation_Total RNA, biological rep 2

description: Gene expression data of total RNA collected from msn5-deleted cells in 30-min amino acid starvation condition

source_name: Total RNAs isolated from msn5 deletion cells starved in amino acid depleted media for 30 min

value: msn5 deletion strain


title: baseline subject 22

description: Sample 43

value: male


title: Primary_Tumor-CT_213_RG

value: Primary Tumor

value: Female

tag: who performance status

tag: tumor location

tag: differentiation


title: WT1, E9.5 (1)

description:
4147958031_A
Total RNA amplified as cDNA.

tag: strain/background

value: mixed (FVB; 129)

value: wild type

value: lens placode


title: Cumulus_clone_injection_blastocyst_rep3

description: cumulus clone, nuclear injection, blastocyst, replicate3

value: female

value: cumulus cell


title: baseline subject 23

description: Sample 45

value: control


title: Cumulus_clone_injection_blastocyst_rep2

description: cumulus clone, nuclear injection, blastocyst, replicate2


title: Normal_Colon-CN_213_RG

value: Normal Colon

value: Left colon

tag: pn

tag: pt


title: WT3, E9.5 (1)

description:
4147958031_C
Total RNA amplified as cDNA.


title: Cumulus_clone_injection_blastocyst_rep4

description: cumulus clone, nuclear injection, blastocyst, replicate4

tag: gender


title: Liver_Metastasis-HM_213_RG


title: Cumulus_clone_injection_blastocyst_rep1

description: cumulus clone, nuclear injection, blastocyst, replicate1


title: Primary_Tumor-CT_222_PEC

value: Male


title: Cumulus_clone_fusion_blastocyst_rep4

description: cumulus clone, cell fusion, blastocyst, replicate4

source_name: cumulus clone, cell fusion, blastocyst

value: blastocyst


title: baseline subject 21

description: Sample 41

tag: stimulus

value: baseline

tag: status

value: case


title: stimulated subject 20

description: Sample 40

value: stimulated

tag: age

tag: bmi


title: Primary_Tumor-CT_196_TD

value: Well


title: msn5 cells_fed_Total RNA, biological rep 2

description: Gene expression data of total RNA collected from msn5-deleted cells in fed condition

source_name: Total RNAs isolated from msn5 deletion cells grown in SC media

value: msn5 deletion strain

tag: treatment

value: fed

tag: rna subtype

value: Total RNA


title: msn5 cells_fed_Total RNA, biological rep 1

tag: genotype


title: Normal_Colon-CN_196_TD

tag: organism part

value: Female


title: stimulated subject 21

description: Sample 42

value: male


title: msn5 cells_30-min amino acid starvation_Total RNA, biological rep 1

value: 30-min amino acid starvation


title: baseline subject 20

description: Sample 39


title: Primary_Tumor-CT_189_JR

value: Primary Tumor

tag: patient number


title: wild-type cells_30-min amino acid starvation_Total RNA, biological rep 2

description: Gene expression data of total RNA collected from wild-type cells in 30-min amino acid starvation condition

source_name: Total RNAs isolated from wild-type cells starved in amino acid depleted media for 30 min

value: wild-type (BY4742)


title: Cumulus_clone_fusion_blastocyst_rep3

description: cumulus clone, cell fusion, blastocyst, replicate3

value: female

tag: donor cell

value: cumulus cell

tag: tissue

tag: embryonic day


title: IVF_control_male_extraembryonic_E6.5_rep3

description: E6.5 IVF control, male, extraembryonic, replicate3

source_name: E6.5 IVF control, male, extraembryonic

treatment_protocol: Embryos that reached the 2-cell stage were transferred into the oviducts of ICR recipient mice at day 1 of pseudopregnancy (the day a copulatory plug was observed after mating with a vasectomized male mouse). On day 7 of pregnancy, corresponding to E6.5, the implanted embryos were recovered carefully from the uteri and isolated from decidua using fine forceps and a needle under a dissecting microscope. After incubation in PBS with 0.25% pancreatin and 0.05% trypsin for 10 minutes at 4 °C, embryos were transferred to DMEM containing 10% FBS and then the visceral endoderm layer was detached from epiblast or extraembryonic ectoderm by being gently aspirated through a mouth pipette several times. Thereafter, the epiblast was separated from the extraembryonic ectoderm using a fine tungsten needle. Isolated epiblasts or extraembryonic regions (extraembryonic ectoderm and ectoplacental cone) were subjected to microarray gene analyses.

value: IVF

value: extraembryonic


title: baseline subject 19

description: Sample 37


title: Liver_Metastasis-HM_196_TD

value: Liver Metastasis

tag: Sex

tag: who performance status

tag: tumor location

value: Left colon

tag: differentiation


title: wild-type cells_30-min amino acid starvation_Total RNA, biological rep 1


title: stimulated subject 18

description: Sample 36

tag: gender

value: control


title: Liver_Metastasis-HM_179_AB

value: Male

value: Rectum


title: stimulated subject 19

description: Sample 38

tag: stimulus

value: stimulated

value: case


title: Normal_Colon-CN_189_JR

value: Normal Colon

value: Well

tag: pn

tag: pt


title: IVF_control_male_extraembryonic_E6.5_rep1

description: E6.5 IVF control, male, extraembryonic, replicate1

value: male


title: wild-type cells_fed_Total RNA, biological rep 2

description: Gene expression data of total RNA collected from wild-type cells in fed condition

source_name: Total RNAs isolated from wild-type cells grown in SC media

value: fed

value: Total RNA


title: Cumulus_clone_fusion_blastocyst_rep1

description: cumulus clone, cell fusion, blastocyst, replicate1

value: blastocyst


title: Cumulus_clone_fusion_blastocyst_rep2

description: cumulus clone, cell fusion, blastocyst, replicate2

value: female


title: Normal_Colon-CN_149_JGI

tag: age


title: baseline subject 18

description: Sample 35

value: baseline

tag: status

tag: bmi


title: stimulated subject 17

description: Sample 34


title: IVF_control_female_extraembryonic_E6.5_rep2

description: E6.5 IVF control, female, extraembryonic, replicate2

value: IVF


title: baseline subject 17

description: Sample 33


title: Liver_Metastasis-HM_149_JGI


title: Primary_Tumor-CT_130_YL

value: Primary Tumor

value: Female

value: Poor


title: IVF_control_male_extraembryonic_E6.5_rep2

description: E6.5 IVF control, male, extraembryonic, replicate2

value: extraembryonic


title: Primary_Tumor-CT_149_JGI

value: Male

value: Left colon


title: mtr10 cells_30-min amino acid starvation_non-polysome associated RNA, biological rep 1

description: Gene expression data of non-polysome associated mRNA collected from mtr10-deleted cells in 30-min amino acid starvation condition

source_name: Non-polysome-associated RNAs isolated from mtr10 deleteion cells starved in amino acid depleted media for 30 min

tag: genotype

value: mtr10 deletion strain

tag: treatment

value: 30-min amino acid starvation

tag: rna subtype

value: non-polysome bound mRNA


title: mtr10 cells_30-min amino acid starvation_non-polysome associated RNA, biological rep 2


title: stimulated subject 16

description: Sample 32

value: stimulated

value: case


title: baseline subject 16

description: Sample 31

value: male


title: Normal_Colon-CN_119_PM

tag: organism part

value: Normal Colon

tag: patient number


title: mtr10 cells_fed_non-polysome associated RNA, biological rep 2

description: Gene expression data of non-polysome associated mRNA collected from mtr10-deleted cells in fed condition

source_name: Non-polysome-associated RNAs isolated from mtr10 deleteion cells grown in SC media

value: fed


title: mtr10 cells_30-min amino acid starvation_polysome associated RNA, biological rep 1

description: Gene expression data of polysome associated mRNA collected from mtr10-deleted cells in 30-min amino acid starvation condition

source_name: Polysome-associated RNAs isolated from mtr10 deleteion cells starved in amino acid depleted media for 30 min

value: Polysome bound mRNA


title: IVF_control_female_extraembryonic_E6.5_rep3

description: E6.5 IVF control, female, extraembryonic, replicate3

value: female

tag: donor cell

tag: tissue

tag: embryonic day


title: mtr10 cells_30-min amino acid starvation_polysome associated RNA, biological rep 2


title: IVF_control_male_embryonic_E6.5_rep3

description: E6.5 IVF control, male, embryonic, replicate3

source_name: E6.5 IVF control, male, embryonic

value: IVF

value: embryonic


title: baseline subject 15

description: Sample 29

value: baseline

value: control


title: mtr10 cells_fed_non-polysome associated RNA, biological rep 1


title: mtr10 cells_fed_polysome associated RNA, biological rep 2

description: Gene expression data of polysome associated mRNA collected from mtr10-deleted cells in fed condition

source_name: Polysome-associated RNAs isolated from mtr10 deleteion cells grown in SC media


title: Primary_Tumor-CT_115_CB

source_name: Tissue samples taken from colorectal cancer patients

value: Primary Tumor

tag: Sex

value: Female

tag: who performance status

tag: tumor location

value: Right colon

value: Moderate


title: IVF_control_female_embryonic_E6.5_rep3

description: E6.5 IVF control, female, embryonic, replicate3

source_name: E6.5 IVF control, female, embryonic

tag: gender


title: IVF_control_male_embryonic_E6.5_rep1

description: E6.5 IVF control, male, embryonic, replicate1


title: stimulated subject 14

description: Sample 28

source_name: whole blood

tag: stimulus


title: Primary_Tumor-CT_119_PM

value: Left colon

tag: pn

tag: pt


title: baseline subject 14

description: Sample 27

tag: status

tag: age


title: Normal_Colon-CN_115_CB

tag: differentiation


title: Liver_Metastasis-HM_115_CB

value: Liver Metastasis


title: IVF_control_female_embryonic_E6.5_rep1

description: E6.5 IVF control, female, embryonic, replicate1


title: IVF_control_female_embryonic_E6.5_rep2

description: E6.5 IVF control, female, embryonic, replicate2


title: mtr10 cells_fed_polysome associated RNA, biological rep 1

tag: genotype

value: mtr10 deletion strain

tag: treatment


title: stimulated subject 15

description: Sample 30

value: stimulated

tag: bmi


title: IVF_control_female_extraembryonic_E6.5_rep1

description: E6.5 IVF control, female, extraembryonic, replicate1

value: extraembryonic


title: stimulated subject 13

description: Sample 26

value: male

value: case


title: Fibroblast_clone_extraembryonic_E6.5_rep2

description: E6.5 tailtip fibroblast clone, extraembryonic, replicate2

value: tail tip fibroblast cell


title: Liver_Metastasis-HM_109_JC

tag: organism part

tag: patient number

value: Male

value: Rectum

value: Well


title: wild-type cells_fed_Total RNA, biological rep 1

description: Gene expression data of total RNA collected from wild-type cells in fed condition

value: wild-type (BY4742)

value: fed

tag: rna subtype

value: Total RNA


title: msn5 cells_30-min amino acid starvation_non-polysome associated RNA, biological rep 1

description: Gene expression data of non-polysome associated mRNA collected from msn5-deleted cells in 30-min amino acid starvation condition

source_name: Non-polysome-associated RNAs isolated from msn5 deleteion cells starved in amino acid depleted media for 30 min

value: msn5 deletion strain

value: 30-min amino acid starvation

value: non-polysome bound mRNA


title: Liver_Metastasis-HM_089_NC

value: Female

value: Transverse colon

value: Moderate


title: stimulated subject 12

description: Sample 24

value: stimulated

value: control


title: msn5 cells_30-min amino acid starvation_non-polysome associated RNA, biological rep 2


title: Normal_Colon-CN_089_NC

value: Normal Colon


title: msn5 cells_30-min amino acid starvation_polysome associated RNA, biological rep 2

description: Gene expression data of polysome associated mRNA collected from msn5-deleted cells in 30-min amino acid starvation condition

source_name: Polysome-associated RNAs isolated from msn5 deleteion cells starved in amino acid depleted media for 30 min

value: Polysome bound mRNA


title: baseline subject 12

description: Sample 23

value: male

value: baseline


title: Fibroblast_clone_extraembryonic_E6.5_rep1

description: E6.5 tailtip fibroblast clone, extraembryonic, replicate1

value: female

tag: donor cell

value: tail tip fibroblast cell

tag: tissue

value: extraembryonic

tag: embryonic day


title: Fibroblast_clone_embryonic_E6.5_rep3

description: E6.5 tailtip fibroblast clone, embryonic, replicate3

value: embryonic


title: Primary_Tumor-CT_094_AM

value: Primary Tumor

tag: Sex

value: Male

tag: who performance status

tag: tumor location

value: Rectum-sigmoid junction

value: Poor


title: msn5 cells_30-min amino acid starvation_polysome associated RNA, biological rep 1

value: msn5 deletion strain

value: 30-min amino acid starvation


title: stimulated subject 11

description: Sample 22

tag: gender

tag: stimulus


title: baseline subject 11

description: Sample 21

tag: status


title: msn5 cells_fed_non-polysome associated RNA, biological rep 2

description: Gene expression data of non-polysome associated mRNA collected from msn5-deleted cells in fed condition

source_name: Non-polysome-associated RNAs isolated from msn5 deleteion cells grown in SC media

value: fed

value: non-polysome bound mRNA


title: IVF_control_male_embryonic_E6.5_rep2

description: E6.5 IVF control, male, embryonic, replicate2

value: IVF


title: msn5 cells_fed_non-polysome associated RNA, biological rep 1


title: Primary_Tumor-CT_073_PD

tag: age

value: Left colon

value: Well

tag: pn

tag: pt


title: Fibroblast_clone_embryonic_E6.5_rep1

description: E6.5 tailtip fibroblast clone, embryonic, replicate1


title: Sertoli_clone_extraembryonic_E6.5_rep4

description: E6.5 neonatal Sertoli clone, extraembryonic, replicate4

value: male

value: neonatal Sertoli cell


title: msn5 cells_fed_polysome associated RNA, biological rep 2

description: Gene expression data of polysome associated mRNA collected from msn5-deleted cells in fed condition

source_name: Polysome-associated RNAs isolated from msn5 deleteion cells grown in SC media

tag: genotype

tag: treatment

value: Polysome bound mRNA


title: baseline subject 13

description: Sample 25

value: baseline

value: case

tag: bmi


title: stimulated subject 10

description: Sample 20

value: stimulated

value: control


title: Liver_Metastasis-HM_073_PD

tag: organism part

value: Liver Metastasis

tag: patient number

value: Male

tag: differentiation


title: baseline subject 10

description: Sample 19


title: Sertoli_clone_extraembryonic_E6.5_rep3

description: E6.5 neonatal Sertoli clone, extraembryonic, replicate3

tag: donor cell

tag: tissue

value: extraembryonic


title: msn5 cells_fed_polysome associated RNA, biological rep 1

value: msn5 deletion strain

tag: rna subtype


title: Fibroblast_clone_embryonic_E6.5_rep2

description: E6.5 tailtip fibroblast clone, embryonic, replicate2

value: female

value: tail tip fibroblast cell

value: embryonic

tag: embryonic day


title: Liver_Metastasis-HM_094_AM

tag: Sex

tag: who performance status

tag: tumor location

value: Rectum-sigmoid junction

value: Poor


title: Sertoli_clone_extraembryonic_E6.5_rep2

description: E6.5 neonatal Sertoli clone, extraembryonic, replicate2

tag: gender


title: wild-type cells_30-min amino acid starvation_non-polysome associated RNA, biological rep 1

description: Gene expression data of non-polysome associated mRNA collected from wild-type cells in 30-min amino acid starvation condition

source_name: Non-polysome-associated RNAs isolated from wild-type cells starved in amino acid depleted media for 30 min

value: wild-type (BY4742)

value: 30-min amino acid starvation

value: non-polysome bound mRNA


title: wild-type cells_30-min amino acid starvation_non-polysome associated RNA, biological rep 2


title: stimulated subject 9

description: Sample 18

value: male

tag: stimulus

tag: status

tag: age


title: Normal_Colon-CN_061_CM

value: Normal Colon

value: Left colon

value: Moderate

tag: pn

tag: pt


title: Sertoli_clone_extraembryonic_E6.5_rep1

description: E6.5 neonatal Sertoli clone, extraembryonic, replicate1

value: neonatal Sertoli cell


title: Normal_Colon-CN_073_PD

value: Well


title: baseline subject 9

description: Sample 17

value: baseline

value: control

tag: bmi


title: Sertoli_clone_embryonic_E6.5_rep3

description: E6.5 neonatal Sertoli clone, embryonic, replicate3

source_name: E6.5 neonatal Sertoli clone, embryonic


title: Normal_Colon-CN_059_MT

tag: organism part

value: Male


title: baseline subject 8

description: Sample 15


title: Primary_Tumor-CT_059_MT

value: Primary Tumor

tag: patient number


title: Cumulus_clone_extraembryonic_E6.5_rep3

description: E6.5 cumulus clone, extraembryonic, replicate3

source_name: E6.5 cumulus clone, extraembryonic

value: female

value: cumulus cell

value: extraembryonic


title: Primary_Tumor-CT_061_CM

tag: differentiation


title: Sertoli_clone_embryonic_E6.5_rep2

description: E6.5 neonatal Sertoli clone, embryonic, replicate2

tag: donor cell

value: embryonic


title: wild-type cells_fed_non-polysome associated RNA, biological rep 2

description: Gene expression data of non-polysome associated mRNA collected from wild-type cells in fed condition

source_name: Non-polysome-associated RNAs isolated from wild-type cells grown in SC media

tag: genotype

value: wild-type (BY4742)

tag: treatment

value: fed


title: Primary_Tumor-CT_056_MC


title: stimulated subject 8

description: Sample 16

value: stimulated


title: stimulated subject 6

description: Sample 12

value: male


title: stimulated subject 7

description: Sample 14


title: wild-type cells_30-min amino acid starvation_polysome associated RNA, biological rep 2

description: Gene expression data of polysome associated mRNA collected from wild-type cells in 30-min amino acid starvation condition

source_name: Polysome-associated RNAs isolated from wild-type cells starved in amino acid depleted media for 30 min

value: 30-min amino acid starvation

tag: rna subtype

value: Polysome bound mRNA


title: wild-type cells_30-min amino acid starvation_polysome associated RNA, biological rep 1


title: Liver_Metastasis-HM_050_NC1B

value: Liver Metastasis

tag: Sex

value: Rectum


title: baseline subject 6

description: Sample 11


title: Liver_Metastasis-HM_059_MT

tag: who performance status

value: Left colon

value: Well


title: Cumulus_clone_extraembryonic_E6.5_rep2

description: E6.5 cumulus clone, extraembryonic, replicate2

tag: tissue

tag: embryonic day


title: Primary_Tumor-CT_045_JC

tag: tumor location


title: Cumulus_clone_embryonic_E6.5_rep3

description: E6.5 cumulus clone, embryonic, replicate3

source_name: E6.5 cumulus clone, embryonic

tag: gender


title: Sertoli_clone_embryonic_E6.5_rep1

description: E6.5 neonatal Sertoli clone, embryonic, replicate1

value: neonatal Sertoli cell


title: stimulated subject 5

description: Sample 10

tag: stimulus

tag: status

value: case

tag: age


title: baseline subject 7

description: Sample 13

value: baseline

value: control

tag: bmi


title: Cumulus_clone_extraembryonic_E6.5_rep1

description: E6.5 cumulus clone, extraembryonic, replicate1

value: female

value: cumulus cell


title: wild-type cells_fed_non-polysome associated RNA, biological rep 1

value: non-polysome bound mRNA


title: wild-type cells_fed_polysome associated RNA, biological rep 2

description: Gene expression data of polysome associated mRNA collected from wild-type cells in fed condition

source_name: Polysome-associated RNAs isolated from wild-type cells grown in SC media

value: wild-type (BY4742)


title: baseline subject 5

description: Sample 9


title: Cumulus_clone_embryonic_E6.5_rep1

description: E6.5 cumulus clone, embryonic, replicate1

value: embryonic


title: Liver_Metastasis-HM_056_MC

tag: organism part

value: Male

value: Moderate

tag: pn

tag: pt


title: Cumulus_clone_embryonic_E6.5_rep2

description: E6.5 cumulus clone, embryonic, replicate2

tag: donor cell


title: wild-type cells_fed_polysome associated RNA, biological rep 1

tag: genotype

value: fed


title: yeast with Rnase H overexpression vector, biological rep2

city: Vancouver

first: Yujia Alina

last: Chan

state: British Columbia

address: 2185 East Mall

country: Canada

institute: University of British Columbia

description: Gene expression data from Saccharomyces cerevisiae overexpressing Rnase H

hyb_protocol: 4 ug of fragmented cRNA was hybridized to a GeneChIP Yeast Genome 2.0 using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: Arrays were scanned by the Gene Chip Scanner 3000 7G.

data_processing: The data were analyzed using Expression Console™ Software (Affymetrix) with the MAS5.0 statistical algorithm. All arrays were scaled to a median target intensity of 500.

source_name: yeast cells, p425-GPD-Rnase H1

label_protocol: biotinated cRNA was prepared using a Message Apm III RNA Amplification Kit (A&B Applied Biosystems) from 150 ng of total RNA with 8 h of IVT incubation

growth_protocol: Strains were grown in SC-Leucine at 30°C.

extract_protocol: Total RNA was isolated from 1 unit of A600 mid-log phase cells using a RiboPure Yeast kit (A&B Applied Biosystems).

treatment_protocol: Strains either harbored the RNase H1 over-expression plasmid (p425-GPD-RNase H1) or control plasmid (p425-GPD).

tag: strain

value: MATa ura3∆0 leu2∆0 his3∆1 met15∆0, p425-GPD-RNase H1-LEU2


title: yeast with Rnase H overexpression vector, biological rep1


title: aCD4+CyA_150d_3

city: Bergisch Gladbach

first: Bernhard

last: Gerstmayer

state: NRW

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec

hyb_protocol: The fluorescently labeled samples were hybridized overnight to custom PIQOR TM Microarrays Rat Antisense using theGeneTAC hybridisation station Genomics Solutions.

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

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

organism: Rattus norvegicus

source_name: kidney allografts

label_protocol: 1 µg of each total RNA sample was used for the T7-based amplification procedure, 1 µg of the resulting aRNA  was labeled by reverse transcription with either Cy3-dCTPs or Cy5-dCTPs as described elsewhere PMID: 8800675

growth_protocol: Orthotopic kidney transplantation was performed in bilaterally nephrectomized recipients using standard method Lee S. An improved technique of renal transplantation in the rat. Surgery 1967;615:771-773..

extract_protocol: Total RNA was isolated using the Strataprep-Total-RNA-Miniprep-KitTM Stratagene, Heidelberg, Germany

treatment_protocol: To generate the control samples recipients were left untreated and kidney grafts removed on day 3. For the different immunosuppressive regimens the recipient rats  were treated with the anti-CD4 mAb RIB5/2 at different dosages   intraperitoneally on days -1 until +3 with or without CsA subcutaneously on days 0 to 9. CsA Sandimmun® was purchased from Novartis Pharma GmbH, Nürnberg, Germany.

tag: cells

value: control pool

tag: stimuation

value: day 3, untreated

tag: molecule

value: total RNA pool from 3 different samples

tag: stimulation

value: day 150, 10mg/kg RIB5/2 / 10mg/kg CyA

value: total RNA from kidney allografts


title: stimulated subject 4

description: Sample 8

value: male

value: stimulated

value: case


title: baseline subject 4

description: Sample 7

value: baseline


title: aCD4+CyA_150d_1


title: aCD4+CyA_150d_2


title: Normal_Colon-CN_026_SA

value: Normal Colon

tag: patient number

tag: Sex

tag: who performance status

value: Left colon


title: aCD4+CyA_25d_3

value: day 25, 10mg/kg RIB5/2 / 10mg/kg CyA


title: wild type yeast with empty vector, biological rep1

description: Gene expression data from wild type Saccharomyces cerevisiae

source_name: yeast cells, p425-GPD

value: MATa ura3∆0 leu2∆0 his3∆1 met15∆0, p425-GPD-LEU2


title: Primary_Tumor-CT_022_JB

source_name: Tissue samples taken from colorectal cancer patients

value: Primary Tumor

value: Female

tag: tumor location

tag: differentiation

value: Well


title: stimulated subject 2

description: Sample 4

tag: gender

tag: stimulus

tag: status

tag: age


title: wild type yeast with empty vector, biological rep2


title: Normal_Colon-CN_022_JB

tag: organism part

tag: pn

tag: pt


title: Liver_Metastasis-HM_044_MB

value: Liver Metastasis


title: baseline subject 3

description: Sample 5

tag: bmi


title: baseline subject 2

description: Sample 3


title: aCD4+CyA_25d_2

tag: cells

value: control pool


title: Primary_Tumor-CT_044_MB


title: Normal_Colon-CN_044_MB


title: stimulated subject 1

description: Sample 2


title: aCD4+CyA_25d_1

tag: stimuation

value: day 3, untreated


title: aCD4+CyA_3d_3

tag: molecule

value: total RNA pool from 3 different samples

value: day 3, 10mg/kg RIB5/2 / 10mg/kg CyA


title: Liver_Metastasis-HM_005_JME

value: Male

value: Moderate


title: stimulated subject 3

description: Sample 6

value: male

value: stimulated


title: Liver_Metastasis-HM_016_MV


title: aCD4+CyA_3d_2

tag: stimulation

value: total RNA from kidney allografts


title: baseline subject 1

description: Sample 1

value: baseline

value: case


title: aCD4+CyA_3d_1


title: aCD4_150d_2

value: day 150, 20mg/kg RIB5/2


title: aCD4_150d_1


title: Normal_Colon-CN_016_MV

value: Normal Colon

tag: patient number

value: Left colon


title: WT6w repl1 vs TG6w repl3

city: Miami

first: John

middle: R.

last: Bethea

state: FL

address: 1095 NW 14th Terrace

department: The Miami Project to Cure Paralysis

institute: University of Miami

description:
314d
Biological replicate 1 of WT mice 6 weeks after injury vs Biological replicate 3 of TG mice 6 weeks after injury

hyb_protocol: Targets and 2x GEx Hybridization Buffer HI-RPM were mixed and and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Hybridization was for 17 hours at 65 degree C, at 10 rpm

scan_protocol: Microarrays were scanned using Molecular Device scanner 4000B at the resolution 5 micron.

data_processing: GenePix Pro 6.0 was used for feature extraction. R package limma was used for lowess and quantile normalization, for contrasts calculating and for determining of the differentially expressed transcripts.

label_protocol: RNA was amplified and labeled using Amino Allyl MesAmp II aRNA Amplification kit (Ambion) according to the manufacturer instructions

growth_protocol: Adult (3-4 months), female GFAP-IκBα-dn(IκBα-dn) transgenic mice were generated and characterized in our laboratory (Brambilla, Bracchi-Ricard et al. 2005). All animals, IκBα-dn and wild type (WT) littermates (LM), were kept as a colony in a virus/antigen-free environment at the University of Miami Miller School of Medicine, Miami, FL, USA. IκBα-dn mice were obtained by breeding heterozygous IκBα-dn males with WT females. Mice were housed under diurnal lightning conditions and allowed free access to food and water.

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

treatment_protocol: Surgeries were performed at the Animal and Surgical Core Facility of the Miami Project to Cure Paralysis according to protocols approved by the Institutional Animal Care and Use Committee of the University of Miami. Contusion injury was induced with the Electromagnetic Spinal Cord Injury Device (developed at the Ohio State University) adapted to the mouse (Jakeman, Guan et al. 2000; Brambilla, Bracchi-Ricard et al. 2005).

tag: strain background

tag: genotype/variation

value: wild type

value: adult (3-4 months)

value: female

tag: time after injury

value: 6 weeks

value: transgenic (GFAP-IκBα-dn)


title: TG3w repl1 vs WT3w repl1

description:
314a
Biological replicate 1 of TG mice 3 weeks after injury vs Biological replicate 1 of WT mice 3 weeks after injury

value: 3 weeks


title: TG3d repl3 vs WT3d repl3

description:
313a
Biological replicate 3 of TG mice 3 days after injury vs Biological replicate 3 of WT mice 3 days after injury

value: 3 days


title: Treatment Gamma tocotrienol-biological replicate 2

city: Rome

first: Guido

last: Leoni

address: Via Pontina

department: Bioinformatics

country: Italy

institute: IRBM

description: Gene expression data from HeLa cells treated with gamma tocotrienol

hyb_protocol: The labeled cRNA was hybridized to the NuGO Affymetrix Human Genechip NuGO_Hs1a520180 (custom designed by the European Nutrigenomics Organisation NuGO, consisting of 23,941

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

data_processing: Three biological replicates were generated for each experimental condition. Microarrays statistical analysis was performed using oneChannelGUI R package, Raw signal intensities were normalized using GCRMA method as background correction

label_protocol: 2μg of high quality total RNA was used with the Affymetrix Eukaryotic One-Cycle Target Labeling and Control reagents to generate biotin-labeled antisense cRNA

growth_protocol: HeLa cells were obtained from the American Tissue Culture Collection (Manassas, VA, USA). Cells were grown in DMEM medium (Euroclone) supplemented with 10% Foetal Bovine Serum (FBS, Sigma-Aldrich), Pen/Strep (Euroclone), 2mM glutamine (Euroclone) and non-essential aminoacid (Sigma Aldrich). Before any experimental session, cells were synchronized in G1/G0 by starvation in serum-free medium for two days. Once synchronized, 300.000 cells were seeded onto multi well plates or phenol red DMEM according to experimental planning, where appropriate, incubated with ICI 182.780  (10-5 M in ethanol) for 30 minute

extract_protocol: Protocol of DNA extraction was adapted from Gooch and Yee (Gooch, 1999)with some modification described in Comitato et al., 2010

treatment_protocol: Purified T3s  were added to the culture medium for the indicated period of time. Final TRF concentration in culture media was set at 10 or 20 µg/ml, to standardize the present study with our previous reports. Control cells were treated with the same volumes of DMSO and/or ethanol vehicle alone.

tag: treatment

value: Gamma tocotrienol

tag: cell line

value: HeLa


title: aCD4_25d_3

value: control pool

value: day 3, untreated

value: total RNA pool from 3 different samples

value: day 25, 20mg/kg RIB5/2


title: Treatment Gamma tocotrienol-biological replicate 3


title: TG6w repl1 vs WT6w repl3

description:
314b
Biological replicate 1 of TG mice 6 weeks after injury vs Biological replicate 3 of WT mice 6 weeks after injury

tag: gender


title: Primary_Tumor-CT_016_MV

value: Primary Tumor

tag: Sex

value: Female

tag: who performance status

tag: tumor location

tag: differentiation

value: Well


title: Treatment Gamma tocotrienol-biological replicate 1


title: WT3d repl2 vs TG3d repl1

description:
313b
Biological replicate 2 of WT mice 3 days after injury vs Biological replicate 1 of TG mice 3 days after injury

tag: age


title: TG3w repl3 vs WT3w repl2

description:
313c
Biological replicate 3 of TG mice 3 weeks after injury vs Biological replicate 2 of WT mice 3 weeks after injury


title: TG naïve repl1 vs WT naïve repl3

description:
312c
Biological replicate 1 of TG naive mice vs Biological replicate 3 of WT naïve mice

value: naïve


title: WT naïve repl1 vs TG naïve repl3

description:
312a
Biological replicate 1 of WT naive mice vs Biological replicate 3 of TG naïve mice

value: wild type


title: WT6w repl2 vs TG6w repl2

description:
314c
Biological replicate 2 of WT mice 6 weeks after injury vs Biological replicate 2 of TG mice 6 weeks after injury

value: adult (3-4 months)


title: TG naïve repl2 vs WT naïve repl2

description:
312b
Biological replicate 2 of TG naive mice vs Biological replicate 2 of WT naïve mice

value: female


title: Treatment Delta tocotrienol-biological replicate 1

description: Gene expression data from HeLa cells treated with delta tocotrienol

value: Delta tocotrienol


title: Treatment Delta tocotrienol-biological replicate 2


title: aCD4_25d_2

value: total RNA from kidney allografts


title: TG6w repl2 vs TG3d repl3

description:
277d
Biological replicate 2 of TG mice 6 weeks after injury vs Biological replicate 3 of TG mice 3 days after injury

value: transgenic (GFAP-IκBα-dn)

value: 6 weeks


title: Treatment Alpha tocotrienol-biological replicate 3

description: Gene expression data from HeLa cells treated with alpha tocotrienol

value: Alpha tocotrienol


title: aCD4_25d_1


title: aCD4_3d_3

value: day 3, 20mg/kg RIB5/2


title: aCD4_3d_2

value: control pool


title: Liver_Metastasis-HM_003_JCP

tag: organism part

value: Liver Metastasis

value: Male

value: Rectum-sigmoid junction

tag: pn

tag: pt


title: Treatment Alpha tocotrienol-biological replicate 2

value: HeLa


title: primary rat islets, untreated, biological rep5

city: Durham

first: Heather

middle: L.

last: Hayes

state: NC

address: 4321 Medical Park Dr., Ste. 200

department: Sarah W. Stedman Nutrition and Metabolism Center

institute: Duke University

hyb_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® Rat Genome 230 2.0 Arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols (Affymetrix, Santa Clara,CA).

scan_protocol: Targets were scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix protocols (Affymetrix, Santa Clara,CA).

data_processing: RMA using ExpressionFileCreator of GenePattern, Broad Institute.  Data was quantile normalized and background corrected.

source_name: primary rat islets, untreated

label_protocol: Biotin labeling was performed using the Encore Biotin Module (Nugen, San Carlos, CA).

growth_protocol: After isolation, rat islets were cultured in RPMI medium containing 10% FBS and 8 mM glucose.

extract_protocol: Total RNA was isolated using Qiagen microRNA kits. Total RNA was assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, Santa Clara, CA) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE).

treatment_protocol: Rat islets were left untreated or treated with adenoviruses expressising either βgal or Pdx-1 at an approximate concentration of 2x109 particles/ml medium for 18 h and then cultured in virus-free medium until the islets were collected 48 h after addition of adenovirus. Five replicates for each condition were used.

value: male

tag: strain

value: Wistar

value: 8 weeks

tag: tissue

value: pancreatic islet


title: TG naïve repl2 vs TG3w repl1

description:
277c
Biological replicate 2 of TG naive mice vs Biological replicate 1 of TG mice 3 weeks after injury

value: adult (3-4 months)

value: naïve

value: 3 weeks


title: primary rat islets, Pdx-1 treated, biological rep5

source_name: primary rat islets, Pdx-1 treated


title: primary rat islets, βgal treated, biological rep5

source_name: primary rat islets, βgal treated


title: Treatment Alpha tocotrienol-biological replicate 1


title: primary rat islets, Pdx-1 treated, biological rep4


title: primary rat islets, βgal treated, biological rep4


title: aCD4_3d_1

tag: cells

tag: stimuation

value: day 3, untreated

tag: molecule

value: total RNA pool from 3 different samples

tag: stimulation

value: total RNA from kidney allografts


title: primary rat islets, untreated, biological rep4


title: primary rat islets, Pdx-1 treated, biological rep3


title: Control-biological replicate 3

description: Geneexpression data from HeLa cells untreated

source_name: Control-biological replicate 3

tag: treatment

value: Control


title: TG6w repl3 vs TG3w repl3

description:
277a
Biological replicate 3 of TG mice 6 weeks after injury vs Biological replicate 3 of TG mice 3 weeks after injury

tag: strain background

tag: genotype/variation

value: transgenic (GFAP-IκBα-dn)

value: female

tag: time after injury

value: 6 weeks


title: Control-biological replicate 2

source_name: Control-biological replicate 2

tag: cell line


title: TG naïve repl3 vs TG6w repl1

description:
277b
Biological replicate 3 of TG naive mice vs Biological replicate 1 of TG mice 6 weeks after injury

tag: gender


title: primary rat islets, βgal treated, biological rep3


title: primary rat islets, untreated, biological rep3


title: TG3w repl2 vs TG3d repl2

description:
333d
Biological replicate 2 of TG mice 3 weeks after injury vs Biological replicate 2 of TG mice 3 days after injury

value: 3 days


title: TG3d repl1 vs TG naïve repl1

description:
333c
Biological replicate 1 of TG mice 3 days after injury vs Biological replicate 1 of TG naïve mice


title: Control-biological replicate 1

source_name: Control-biological replicate 1


title: primary rat islets, Pdx-1 treated, biological rep2


title: WT naïve repl2 vs WT3w repl1

description:
333a
Biological replicate 2 of WT naive mice vs Biological replicate 1 of WT mice 3 weeks after injury

value: wild type


title: WT naïve repl3 vs WT6w repl1

description:
139d
Biological replicate 3 of WT naive mice vs Biological replicate 1 of WT mice 6 weeks after injury


title: WT3d repl3 vs WT6w repl2

description:
333b
Biological replicate 3 of WT mice 3 days after injury vs Biological replicate 2 of WT mice 6 weeks after injury


title: primary rat islets, Pdx-1 treated, biological rep1


title: primary rat islets, βgal treated, biological rep2


title: WT3d repl1 vs WT naïve repl1

description:
139a
Biological replicate 1 of WT mice 3 days after injury vs Biological replicate 1 of WT naïve mice


title: primary rat islets, untreated, biological rep2


title: primary rat islets, untreated, biological rep1


title: WT6w repl3 vs WT3d repl3

description:
139c
Biological replicate 3 of WT mice 6 weeks after injury vs Biological replicate 3 of WT mice 3 weeks after injury


title: WT3w repl2 vs WT3d repl2

description:
139b
Biological replicate 2 of WT mice 3 weeks after injury vs Biological replicate 2 of WT mice 3 days after injury


title: primary rat islets, βgal treated, biological rep1


title: CGH_ESCC_169

city: beppu

first: sawada

last: genta

address: tsurumihara

institute: kyushu university

hyb_protocol: Hybridization of genomic DNA onto the Agilent-014693 Human Genome Microarray Kit 244K (Agilent Technologies) was performed according to Agilent's Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol.

scan_protocol: Arrays were analyzed using the Agilent DNA microarray scanner according to Agilent's user manual.

data_processing: The raw signal intensities were measured and transformed into log ratio to reference DNA with 'Feature Extraction' software (version 9.1) from Agilent Technologies. The log ratio was thereafter used as the signal intensity of each probe.

source_name: esophageal squamous cell carcinoma

label_protocol: Labeling was performed according to the manufacturer's instructions.

extract_protocol: Total DNA was extracted from tumor tissue with QIAamp DNA Micro Kit (Qiagen) according to the manufacturer's protocols.

treatment_protocol: Laser micro-dissection.

tag: disease status

value: esophageal squamous cell carcinoma (ESCC)

value: ESCC tumor

tag: his type

value: moderate

tag: depth

tag: lymph node metastasis

value: positive

source_name: reference DNA

tag: sample type

value: reference


title: CGH_ESCC_164

value: male

tag: age


title: Aged-Biological rep 1

city: Boulder

first: Bradley

middle: B

last: Olwin

state: CO

address: 347 UCB

department: MCD-Biology

institute: University of Colorado

description:
Aged-1
Gene expression data from satellite cells

hyb_protocol: Labeled cRNA (5 μg) was fragmented and hybridized to Affymetrix 430 v.2 mouse microarrays at the University of Colorado Core facilities.

scan_protocol: GeneChips were scanned on a GeneChip Scanner 3000 (Affymetrix) and intensity data recovered in GCOS (Affymetrix).

data_processing: CEL files from two biological pools at each timepoint were imported directly into GeneSpring 12.5 (Agilent).

source_name: Syn-4 isolated satellite cells from hindlimb muscle, aged

label_protocol: Biotin-labeled antisense RNA was generated with IVT Labeling Kit (Affymetrix).

growth_protocol: SCs were isolated as primary cells directly from young and aged C57BL/6 mice.

extract_protocol: RNA was isolated followed by two rounds of linear T7-based amplification (RiboAmp HA kit, Arcturus).

treatment_protocol: SCs from 6-8 young or old mice were isolated, pooled, and FACS sorted for Syndecan-4 expression.

tag: strain/background

tag: developmental stage

value: aged adult

tag: tissue

value: hindlimb muscle

tag: cell type

value: syndecan-4-isolated satellite cells


title: CGH_ESCC_149


title: Aged-Biological rep 2

description:
Aged-2
Gene expression data from satellite cells


title: BT112, Combo treated, biological rep 2

city: Boston

first: Rosalind

middle: A

last: Segal

state: MA

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

hyb_protocol: Arrays were washed and stained on Fluidics stations 450 using Affymetrix hybe/wash/stain (cat # 900720).

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

data_processing: Data was processed by the DFCI microarray facility http://chip.dfci.harvard.edu. Biological duplicate samples were tested; arrays were visualized and analyzed. MAS5 data provided.

source_name: GBM LDE225 1 uM +BKM120 100 nM 5 days

label_protocol: Affymetrix 3 IVT Express protocol  (cat # 702646). Labeled with Biotin

growth_protocol: Human GBM tumor initiating cells (hBT70 and hBT112) were grown in NS-A stem cell media with EGF (20ng/ml), bFGF (20ng/ml), 0.2% Heparin (1ul/ml).

extract_protocol: Cells were collected and lysed in Buffer RLT  and RNA was isolated with Rneasy Plus Mini Kit.  Reverse transcription was performed with a high capacity cDNA reverse transcription kit.

treatment_protocol: hBT112 and hBT70 were treated with vehicle, LDE 225, BKM120 or a combination of both LDE225 and BKM120 for 5 days.

tag: tumor

value: LDE225 1 uM and BKM 120 100 nM for 5 days


title: HS5 replicate 3

city: Aurora

first: Manoj

last: Pillai

address: Building 500 - 13001 E. 17th Place, Campus Box C290, Room E1354

hyb_protocol: C3 labelled cRNA was hybridized to custom miRNA micro-array using manufacturer ( Dharmacon/ Thermofisher Scientific) in-house protocols

scan_protocol: Slides were scanned immediately after washing by manufacturer's in house custom protocols

data_processing: Relative Intensity data for 6 samples was subjected to statistical filtering, keeping miRNA probes with P-value <= 0.05 in at least 2 of the 6 experiments. This resulted in 426 miRNA probes passing statistical filters. The remaining data was inter-array scaled and transformed to log(2).

source_name: Bone Marrow Stroma

label_protocol: Cy3 labelled cRNA was prepared from 0.1 ug RNA using Thermofisher's protocols

growth_protocol: HS27a and HS5 were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin

extract_protocol: Total RNA was extracted from logarithmically growing cells using Trizol reagent ( Invitrogen, Carlsbad, CA) using manufacturer's protocols

treatment_protocol: No treatment was performed. Whole cells were used. Comparisons were made between the two cell lines.

value: Stromal Cell line HS5


title: HS5 replicate 2


title: BT112, LDE225 treated, biological rep 2

source_name: GBM LDE225 1 uM, 5days

tag: treatment

value: LDE225 at 1 uM for 5 days


title: BT112, BKM120 treated, biological rep 2

source_name: GBM BKM120 100nM, 5days

value: BKM 120 100 nM for 5 days


title: Young-Biological rep 1

description:
Young-1
Gene expression data from satellite cells

source_name: Syn-4 isolated satellite cells from hindlimb muscle, young

value: young adult


title: BT112, Combo treated, biological rep 1


title: CGH_ESCC_161


title: BT112, BKM120 treated, biological rep 1


title: HS5 replicate 1


title: Young-Biological rep 2

description:
Young-2
Gene expression data from satellite cells


title: CGH_ESCC_156

value: well

value: negative


title: CGH_ESCC_151


title: HS27A replicate 3

value: Stromal Cell line HS27A


title: BT112, DMSO treated, biological rep 1

source_name: GBM control 5days

value: DMSO


title: BT112, DMSO treated, biological rep 2

source_name: GBM control 5 days


title: HS27A replicate 2


title: CGH_ESCC_146

value: esophageal squamous cell carcinoma (ESCC)

value: ESCC tumor

value: poor


title: Wild_type_strep_bacterial_exposure_6hrs_rep3

city: Notre Dame

first: Erliang

last: Zeng

state: IN

address: 384 Fitzpatrick Hall

institute: University of Notre Dame

description: SAMPLE 27

hyb_protocol: One μg of cDNA was labeled with Cy3-random nonamers (Roche NimbleGen) for microarray hybridization.

scan_protocol: After extensive washing, the arrays were dried and then scanned using a NimbleGen MS 200 Microarray Scanner.

data_processing: Array data was extracted and analyzed using NimbleSan software v2.5 (Roche NimbleGen, Inc.). The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5.

organism: Streptococcus pyogenes

label_protocol: Double-stranded cDNA was synthesized from 10 μg of total RNA using random hexamer primers with the SuperScript cDNA synthesis kit (Invitrogen).

extract_protocol: Total RNA extraction and purification from the bacterial pellets were performed using the RNeasy isolation kit per manufacturer's instructions (Qiagen). RNA sample integrity was confirmed on an Agilent Bioanalyzer (Agilent Technologies) and RNA concentration was measured with a NanoDrop analyzer.

treatment_protocol: For SLS exposure conditions, bacterial pellets containing GAS ∆SagA mutants were incubated with 1. supernatants containing wtSLS; 2. supernatants containing SLS S39A isoform; or 3. sterile TH media with 10mg/ml of BSA. The bacteria pellets were quickly resuspended after which the bacterial pellets were recollected for RNA isolation.  A total of three exposure timepoints were used: 0h (immediately after exposure to SLS-containing supernatants) 3h post-exposure, and 6h post-exposure. The pellets were frozen at -80C until used for RNA extraction.

tag: strain

value: Group A Streptococcus (GAS)

value: ∆SagA mutant

tag: incubated with

value: supernatants containing wild type streptolysin S (SLS) for 6 hrs

value: Bacterial pellets


title: CGH_ESCC_136

value: female

value: moderate

value: reference


title: CGH_ESCC_137

value: male

value: positive


title: CGH_ESCC_139


title: Wild_type_strep_bacterial_exposure_6hrs_rep1

description: SAMPLE 25

tag: genotype/variation


title: HS27A replicate 1

tag: cell line


title: A2B2 mRNA

city: Cambridge

first: Carl

middle: G

last: de Boer

address: 415 Main St

institute: The Broad Institute

description: polyA+ RNA

hyb_protocol: We performed the microarray hybridization as described elsewhere (ZHANG et al. 2004).

scan_protocol: We scanned the slides using an Agilent scanner.

data_processing:
We quantified the data from the array images using ImaGene.
Agilent feature extraction files: the raw data read from the Agilent image files using ImaGene.
The GFF files include features of the region tageted for tiling array analysis in gff format (https://genome.ucsc.edu/FAQ/FAQformat.html#format3).  These include the locations of genomic features (ORFs, transcripts) as well as the locations of the inserts, and the KanMX selectable marker.
microarray_normalized_log+.wig and microarray_normalized_log-.wig include the tiling array data across each of the four inserts in wig format (https://genome.ucsc.edu/goldenPath/help/wiggle.html) for the top and bottom DNA strands, respectively.  This data are provided on a log scale and were normalized as follows:
First, we normalized the data using spacial detrending of the microarray slide. Next, we normalized the tiling array data using a background model (HUBER et al. 2006) which relates, for each probe (k), the signal intensity (yk) to the background signal (Bk) plus the amount of nucleic acid in the sample (xk) times the proportionality factor (ak), or yk=Bk+xk*ak. Here, we want to determine the amount of nucleic acid in the sample (xk). We modified this normalization protocol to take advantage of the fact that the target sequences of many probes were absent from some samples (e.g. the A1B1probe target sequences are absent from the A2B2 strain). Here, we estimated separate mRNA and gDNA background signals (Bk) for each probe by taking the median signal intensity of the probe in strains lacking the target DNA sequences. We estimated the proportionality factor for each probe (ak), corresponding to how probe intensity changes with the amount of nucleic acid, by comparing the background-normalized gDNA signal at each probe to the actual amount of gDNA present in the sample, where the target DNA was present in the sample. We estimated the amount of mRNA at each probe using this model, and scaled the amounts to the median intensity across the kanMX gene to make mRNA levels comparable across constructs. All files reference the sequences contained within the accompanying ".seq" files.
Note: the coordinates in these files do not correspond to genomic coordinates as the construct was integrated into the genome (thereby altering the length of the chromosome).  However, positions  1..5001 in these files corresponds to positions 42000..47000 of chromosome 4 in the yeast genome (May, 2008 genome version) and positions 12341..20888 correspond to positions 47800..56347 of chromosome 4.

source_name: Cells grown in YPD

label_protocol: We labelled RNA and DNA samples with G-coupled Cy3 and Cy5 dyes, respectively (Createch).

growth_protocol: We grew these four yeast strains in YPD to an OD of ~1.0.

extract_protocol: We collected mRNA using the hot acid phenol method. We treated the total RNA with DNase I, purified it using an RNeasy mini kit (Qiagen) and, isolated the mRNA using a NucleoTrap mRNA mini kit (Clontech). We isolated genomic DNA (gDNA) separately using a YeaStar Genomic DNA kit (Zymo Research).

tag: integrated sequence


title: A2B1 mRNA

description: polyA+ RNA


title: Wild_type_strep_bacterial_exposure_3hrs_rep3

description: SAMPLE 24

value: supernatants containing wild type streptolysin S (SLS) for 3 hrs


title: Wild_type_strep_bacterial_exposure_6hrs_rep2

description: SAMPLE 26


title: BT70, Combo treated, biological rep 2

value: LDE225 1 uM and BKM 120 100 nM for 5 days


title: BT112, LDE225 treated, biological rep 1

value: LDE225 at 1 uM for 5 days


title: Wild_type_strep_bacterial_exposure_3hrs_rep2

description: SAMPLE 23


title: CGH_ESCC_141

tag: disease status

tag: gender

value: well


title: BT70, Combo treated, biological rep 1


title: CGH_ESCC_135

tag: his type

tag: depth


title: A1B1 mRNA

description: polyA+ RNA


title: BT70, BKM120 treated, biological rep 2

value: BKM 120 100 nM for 5 days


title: Wild_type_strep_bacterial_exposure_3hrs_rep1

description: SAMPLE 22

tag: sample type


title: BT70, BKM120 treated, biological rep 1


title: A2B2 gDNA


title: A2B1 gDNA


title: CGH_ESCC_132

value: esophageal squamous cell carcinoma (ESCC)

tag: age

tag: lymph node metastasis

value: negative


title: CGH_ESCC_131

value: ESCC tumor


title: A1B1 gDNA


title: CGH_ESCC_126


title: CGH_ESCC_129


title: CGH_ESCC_127


title: A1B2 mRNA

description: polyA+ RNA


title: Wild_type_strep_bacterial_exposure_0hrs_rep2

description: SAMPLE 20

value: Group A Streptococcus (GAS)

value: supernatants containing wild type streptolysin S (SLS) for 0 hr


title: BT70, LDE225 treated, biological rep 2


title: BT70, LDE225 treated, biological rep 1


title: Wild_type_strep_bacterial_exposure_0hrs_rep3

description: SAMPLE 21

value: ∆SagA mutant


title: A1B2 gDNA


title: Wild_type_strep_bacterial_exposure_0hrs_rep1

description: SAMPLE 19

value: Bacterial pellets


title: E400H_3 with array type rice from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

description:
oryza sativa (nipponbare)  - dev.stage (boyes et al. plant cell 2001): mature seed
One of the key questions for future agriculture will be to save agronomical relevant biodiversity. To do so, it is important to select the best crop cultivars that will germinate efficiently (good seed vigor) and for a long period of time (good seed longevity). Surprisingly, while mankind rely heavily on cereals, very few studies have identified genes positively related to cereal seed vigor and longevity. To close this scientific gap, we aimed to identify genes positively involved in rice seed vigor and longevity. We thus used a “controlled deterioration treatment (Tesnier et al., 2002) to mimic natural seed ageing. Seeds are first equilibrated at 25°C and 85% relative hygrometry during three days. Then, during 15 days, three different batch of seeds are either (i) kept at 25°C and 85% RH (control seeds), (ii) placed at 40°C and 85% RH (loss of seed vigor) or (iii) placed at 45°C and 85% RH (loss of germination capacity). Finally, seeds are equilibrated at 25°C and 32% RH during three days. Using this CDT treatment, we obtained rice seeds with contrasted seed vigor or germination capacity. We extracted the total RNA from the embryos and we analysed their transcriptome using the Affymetrix Rice Genome Array.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Oryza sativa

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: embryonic axis - Controlled deterioration treatment: • 3 days at 85% relative hygrometry and 25°C • 14 days at 85% relative hygrometry and 40°C • 3 days at 32% relative hygrometry and 25°C

treatment_protocol: Name:40°C - growth conditions - temperature,temperature:time 14day .

value: seed

tag: cultivar

value: nipponbare


title: CGH_ESCC_122

tag: tissue

value: reference


title: BT70, DMSO treated, biological rep 2

value: DMSO


title: TH_control_exposure_6hrs_rep3

description: SAMPLE 18

value: 10mg/ml of BSA for 6 hrs


title: TH_control_exposure_6hrs_rep2

description: SAMPLE 17


title: TH_control_exposure_6hrs_rep1

description: SAMPLE 16


title: E400H_1 with array type rice from Affymetrix


title: CGH_ESCC_130

value: male

value: poor

value: positive


title: TH_control_exposure_3hrs_rep3

description: SAMPLE 15

value: 10mg/ml of BSA for 3 hrs


title: E40_4H_3 with array type rice from Affymetrix


title: TH_control_exposure_3hrs_rep1

description: SAMPLE 13


title: CGH_ESCC_120

value: well


title: E400H_2 with array type rice from Affymetrix


title: BT70, DMSO treated, biological rep 1


title: CGH_ESCC_121

value: esophageal squamous cell carcinoma (ESCC)

value: female


title: TH_control_exposure_3hrs_rep2

description: SAMPLE 14


title: CGH_ESCC_119

value: ESCC tumor

value: moderate


title: TH_control_exposure_0hrs_rep3

description: SAMPLE 12

value: Group A Streptococcus (GAS)

value: 10mg/ml of BSA for 0 hr