title: LEM2 ChIP in IMB-1 RNAi embryo KI1967

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description:
SDQ4051_LEM2_RiIMB1_KI1967_N2_MXEMB
Mixed stage N2 C. elegans embryos

hyb_protocol: DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: Array scanning and raw data extraction were performed according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software v2.5 according to the NimbleScan User's Guide

data_processing:
ChIP-chip_normalization_standard_MA2C_v2. First, all the IP and INPUT log ratio values are read from the pairdata file. Secondly, we build GC bins for INPUT and IP based on the GC counts for every probe sequence, which means that the INPUT or IP values for any probes which have the same GC counts will be put together. After that, for each GC bin, we calculate the mean for IP and INPUT data, and the covariance between this two channels. By default, the robust mean variance method is applied, which generalizes Tukey's theory of bi-weight estimation where the constant C is set to 2.  At last, we adjust the log ratio values for each probe by using the mean and covariance values for their corresponding GC bins, then these values are further normalized by their mean and standard derivation. In a single experiment, median within the sliding window defined by 2x bandwidth parameter is assigned as MA2C score at the center of each probe. In case of replicates, when we calculate the MA2Cscore afterwards, we take the median as the score from all the replicates for all the probes within the sliding window defined by 2x bandwidth parameter.  Processed data are obtained using following parameters: genome version is WS190
Genome_build: WS190
Supplementary_files_format_and_content:  .wig file reports MA2C score.

organism: Caenorhabditis elegans

growth_protocol: Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol: Antibody was incubated with protein A/G beads at 4 oC for at least 1 hr and then washed by extraction buffer. For each reaction, 0.5-2 mg of protein extract was taken and sarkosyl was added to 1% final concentration. Before immunoprecipitation, 10% of extract was taken. The extract was mixed with the antibody-beads complex and incubated overnight at 4C. After washing beads, immune complexes were eluted from beads twice with 150uL elution buffer (1% SDS in TE with 250 mM NaCl) for 15minutes at 65C. Samples were treated with RNase A at room temperature for ~ 1 hr then proteinase K at 55C for ? 1 hr. Samples were transferred to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit.

treatment_protocol: The N2 strain worms were arrested at the L1 larva stage in the liquid S medium for synchronization. Synchronized L1 worms were fed with a bacteria strain HB101, which do not contain induction vectors, at 20oC for 36 hours (L4 stage). L4 worms were harvested, washed and transferred to a new S medium supplemented with a bacteria strain HT115 expressing interfering double-strand RNA from L4440 vector under IPTG (RNAi bacteria). Worms were grown with the RNAi bacteria at 20oC until the gravid stage. Embryos were harvested from the gravid adults by hypochlorite treatment and used in experiments. In parallel, worms were fed with HT115 bacteria bearing L4440 vector without target DNA insertion (empty vector RNAi).

value: IMB-1 RNAi

tag: chip antibody

value: SDQ4051_LEM2 [Novus Biologicals, catalog# 48540002, lot# G3048-198A02, Animal Q4051]

value: input control


title: LEM2 ChIP in NPP-13 RNAi embryo KI1967

status: Public on Aug 15 2016

type: genomic

country: USA

description:
SDQ4051_LEM2_RiNPP13_KI1967_N2_MXEMB
Mixed stage N2 C. elegans embryos

molecule: genomic DNA

label_protocol: DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

tag: strain

tag: treatment

value: NPP-13 RNAi

tag: sample type


title: cultured PBMCs_no YM treatment_rep2

type: RNA

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

country: Spain

institute: Biodonostia Institute

description: cultured human PBMCs stimulated with 0.5% PHA during 72h

hyb_protocol: GeneChip Hybridization, Wash and Stain kit was used for hybridization in a GeneChip Hybridization oven 640 and in a GeneChip Fluidics Station 450 using the protocol FS450_0001, as explained in the protocol provided by Affymetrix.

scan_protocol: Arrays were scanned in a GeneChip 7G scanner and analysed in Affymetrix GeneChip Command Console Scan Control v4.0.0.1567.

data_processing: Quality control, normalization and summarization of the data were performed in Expression Console software build 1.4.0.38 (Affymetrix).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PHA-stimulated PBMCs

label_protocol: Total RNA was labeled using GeneChip® WT PLUS Reagent Kit

growth_protocol: PBMCs were isolated from whole blood and were cultured with RPMI medium supplemented with 5% FBS and antibiotics in a P96 plate (100.000cells/well) for 72h.

extract_protocol: miRNeasy mini kit (Qiagen)

treatment_protocol: To induce PBMC activation,  Phytohemagglutinin (PHA) (ThermoFisher) (0.5%) was used.

tag: tissue

value: PBMCs

tag: gender

value: male


title: BelTatar_54

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress-24 v1.0 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

source_name: Belarusian Lipka Tatars_blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

value: Belarusian Lipka Tatars

tag: region

value: Belarus

value: blood


title: LEM2 ChIP in empty vector RNAi embryo KI2009

description:
SDQ4051_LEM2_RiEV_KI2009_N2_MXEMB
Mixed stage N2 C. elegans embryos

value: empty vector RNAi


title: BelTatar_66


title: Day 0 Control

city: New Delhi

first: Kuldeep

middle: Singh

last: Attri

state: Delhi

address: Sukhdev Vihar

department: Systems Biology

country: India

institute: CSIR-IGIB

description: Poly-A controls were added to input RNA.

hyb_protocol: Labeled fragments were hybridized to Affymetrix WT Mouse ST2.0 gene array for 16hr at 45°C with 60rpm in Affymetrix Hybridization oven 645.

scan_protocol: Hybridized microarrays were washed and stained in Affymetrix fluidic station 450 and scanned in Affymetrix G3000 Gene Array Scanner.

data_processing: Image analysis of microarray chips was carried out by Affymetrix Genechip command console software which uses MAS5 algorithm. Affymetrix Expression Console was used to analyze ,CEL files to generate normalized signal intensities form raw signal intensities using RMA algorithm.

label: Biotin

organism: Mus musculus

source_name: Primary murine cells

label_protocol: 300ng RNA was taken as input RNA and was processed with Ambion WT Expression Kit.cDNAS were fragmented and labeled with Affymetrix terminal labeling kit.

growth_protocol: Murine bone marrow derived macrophage precursors were initially grown in presence of MCSF while post Mtb treatment cells were cultured with MCSF and RANKL growth factors.

extract_protocol: Total RNA from uninfected and Mtb infected cells was isolated by TRIzol RNA isolation method and later purified by RNAeasy column purification.

treatment_protocol: Mtb infections were carried out by infecting primary cells with Mtb at MOI of 1:5 for 4hours.

value: Balb/c

tag: cell type

value: Macrophage-Osteoclast


title: BelTatar_3


title: Col_08_TS

status: Public on Aug 16 2016

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

institute: IDIBELL

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

source_name: Luminal

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: Large Intestine

value: DTS


title: LEM2 ChIP in NPP-13 RNAi embryo KI2009

description:
SDQ4051_LEM2_RiNPP13_KI2009_N2_MXEMB
Mixed stage N2 C. elegans embryos


title: SMC03_LV2

city: Chuncheon

first: Bong-seok

last: Jo

address: Kangwon university street 1

country: South Korea

institute: Kangwon national university

description: Cardiomyocyte, Left ventricle(apex)

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each humanHT-12 expression v.4 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3(Gene Expression Module v3.3.8).

data_processing: Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was normalized by quantile method.

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

extract_protocol: Total RNA was extracted from cells using  the RNeasy mini kit/RNeasy mini spin columns (Qiagen Inc.)

value: Female

tag: age

value: LV(Left ventricle)


title: Col_08_CB

source_name: Center

value: CB


title: HS3ST2-transfected group, replicate 2

city: Singapore

first: George

middle: W

last: Yip

address: 4 Medical Drive, Block MD10

country: Singapore

institute: National University of Singapore

description: Gene expression data from MDA-MB-231 cells transfected withHS3ST2-expression plasmid

hyb_protocol: Fragmented cRNA was hybridised at 45°C for 16 hours to Affymetrix HG U133 Plus 2.0 GeneChips, followed by washing and staining in an Affymetrix FS450 fluidics station.

scan_protocol: GeneChips were scanned using a GCOS 7000 7G scanner.

data_processing: Data were analysed using GeneSpring GX11.0 with RMA normalisation to median signal intensity.

source_name: MDA-MB-231 cells transfected with HS3ST2-expression plasmid

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 3.6 µg of total RNA.

growth_protocol: MDA-MB-231 cells were cultured at 37°C in a humidified atmosphere with 5% carbon dioxide.

extract_protocol: Total RNA extracted using the Qiagen RNeasy Kit.

treatment_protocol: Cells were transfected with HS3ST2 expression plasmid or a control vector.

value: Breast cancer cells

tag: cell line


title: HS3ST2-transfected group, replicate 3


title: SNU03_LV1

description: Cardiomyocyte, Left ventricle

value: Male


title: SNU02_RV_CM

description: Cardiomyocyte, Right vnetricle

hyb_protocol: The whole-genome amplification process requires 200ng of input bisulfite-converted DNA , MA1 and creates a sufficient quantity of DNA (1000X amplification) to be used on a single BeadChip in the infinium methylation assay (Illumina MA2 and MSM). After amplification, the product is fragmented using a proprietary reagent (FMS), precipitated with 2-propanol (plus precipitating reagent; PM1), and resuspended in formamide-containing hybridization buffer (RA1). The DNA samples are denatured at 95°C for 20 min, then placed in a humidified container for a minimum of 16 h at 48°C allowing CpG loci to hybridize to the 50mer capture probes.

scan_protocol: The Illumina iScan Reader is a two-color (532 nm/658 nm) confocal fluorescent scanner with 0.53-µm pixel resolution. The scanner excites the fluorophors generated during signal amplification/ staining of the allele-specific (one color) extension products on the BeadChips. The image intensities are extracted using Illumina’s iScan Control software.

data_processing: Probe intensity from idat file was processed from RnBeads software using software's instruction. Probes with a detection p-value > 0.01 in all samples and probes for which the beta values had low standard deviations were also excluded. Color bias adjustment and background correction were implemented to eliminate systematic bias using lumi. Then, we performed an adjustment for probe type bias between the Infinium I and Infinium II assays using beta-mixture quantile normalization (BMIQ) on the β-values

label: Cy5 and Cy3

growth_protocol: Frozen cardiac tissue (~200mg) were washed with PBS and minced with sterile scalpels. Incubate with PBS containing 1.0 mg/ml collagenase (type II, Worthington Biochemical B57 Corporation, cat. no. LS004174) for 4 hrs at 37C with gentle agitation.

treatment_protocol: 550ng of input gDNA was used for the bisulfite conversion usingusing the EZ 96-DNA methylation kit (Zymo Research, CA, USA), following the manufacturer’s standard protocol.

value: RV(Right vnetricle)


title: HS3ST2-transfected group, replicate 1


title: AMC09_RV_CM

description: Cardiomyocyte, Right vnetricle


title: SMC08_RV_CM

description: Cardiomyocyte, Right vnetricle


title: AMC05_RV_CM

description: Cardiomyocyte, Right vnetricle


title: SMC08_LV2_CM-1

description: Cardiomyocyte, Left ventricle(apex), replicate


title: SNU05_RV_CM

description: Cardiomyocyte, Right vnetricle


title: SMC04_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: Control vector group, replicate 3

description: Gene expression data from MDA-MB-231 cells transfected with control vector


title: SMC07_RV_CM

description: Cardiomyocyte, Right vnetricle


title: AMC01_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: SNU04_RV_CM

description: Cardiomyocyte, Right vnetricle


title: AMC06_RV_CM

description: Cardiomyocyte, Right vnetricle


title: AMC02_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: SMC01_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: AMC07_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: AMC07_LV2_CF

description: Cardiac Fibroblast, Left ventricle(apex)


title: LEM2 ChIP in empty vector RNAi embryo KI1967

description:
SDQ4051_LEM2_RiEV_KI1967_N2_MXEMB
Mixed stage N2 C. elegans embryos

value: SDQ4051_LEM2 [Novus Biologicals, catalog# 48540002, lot# G3048-198A02, Animal Q4051]

value: input control


title: SNU03_RV_CM

description: Cardiomyocyte, Right vnetricle


title: SMC08_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: Control vector group, replicate 2

source_name: MDA-MB-231 cells transfected with control vector


title: B16-BL6 tumor_ALA+Xray_4

status: Public on Aug 14 2016

city: Tsukuba

first: Junko

last: Takahashi

state: Ibaraki

address: 1-1-1 Umezono

country: Japan

institute: National Institute of Advanced Industrial Science and Technology　(AIST)

description:
ALA Xray 016
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks Xray irradiated after ALA treatment C57BL6J mouse.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60ºC for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent- G4122F Whole Mouse Genome Microarray (44K) for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Hybridized microarray slides washed according to the manufacturer’s instructions were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution.

data_processing: The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 020109_D_F_20090417) to obtain background subtracted and spatially detrended processed signal intensities. The quantile normalization method was used in our microarray analysis.

source_name: B16-BL6 tumor_ALA+Xray

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

extract_protocol: RNA was extracted using the RNeasy mini kit from B16-BL6 melanoma preserved in RNAlater (Qiagen). Isolation was performed according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and its quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: RNAlater conservation at -80ºC

tag: strain background

value: male

value: 8 weeks

value: B16-BL6 mouse melanoma

tag: treated with

value: ALA+Xray


title: Control vector group, replicate 1


title: SNU05_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: B16-BL6 tumor_ALA+Xray_3

description:
ALA Xray 015
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks Xray irradiated after ALA treatment C57BL6J mouse.


title: SMC02_LV2_CF


title: SMC05_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: B16-BL6 tumor_ALA+Xray_1

description:
ALA Xray 013
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks Xray irradiated after ALA treatment C57BL6J mouse.


title: SMC08_LV2_CF


title: SNU03_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: SNU01_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: B16-BL6 tumor_ALA+Xray_2

description:
ALA Xray 014
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks Xray irradiated after ALA treatment C57BL6J mouse.


title: B16-BL6 tumor_Xray_2

description:
ALA Xray 010
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks Xray irradiated C57BL6J mouse.

source_name: B16-BL6 tumor_Xray

value: Xray


title: B16-BL6 tumor_Xray_4

description:
ALA Xray 012
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks Xray irradiated C57BL6J mouse.


title: B16-BL6 tumor_Xray_3

description:
ALA Xray 011
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks Xray irradiated C57BL6J mouse.


title: B16-BL6 tumor_control_3

description:
ALA Xray 003
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks control C57BL6J mouse.

source_name: B16-BL6 tumor_control

value: none (control)


title: B16-BL6 tumor_control_4

description:
ALA Xray 004
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks control C57BL6J mouse.


title: B16-BL6 tumor_ALA control_4

description:
ALA Xray 008
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks ALA treatment C57BL6J mouse.

source_name: B16-BL6 tumor_ALA control

value: 50mg/kg ALA


title: B16-BL6 tumor_ALA control_3

description:
ALA Xray 007
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks ALA treatment C57BL6J mouse.


title: B16-BL6 tumor_ALA control_2

description:
ALA Xray 006
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks ALA treatment C57BL6J mouse.


title: B16-BL6 tumor_control_2

description:
ALA Xray 002
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks control C57BL6J mouse.


title: B16-BL6 tumor_ALA control_1

description:
ALA Xray 005
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks ALA treatment C57BL6J mouse.


title: B16-BL6 tumor_control_1

description:
ALA Xray 001
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks control C57BL6J mouse.


title: B16-BL6 tumor_Xray_1

description:
ALA Xray 009
gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks Xray irradiated C57BL6J mouse.


title: SMC03_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: SNU04_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: SMC02_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: SNU02_LV2_CM

description: Cardiomyocyte, Left ventricle(apex)


title: Control-3

city: Sapporo

first: Norihisa

last: Ichinohe

state: Hokkaido

address: South-1, West-17, Chuo-ku,

department: Department of Tissue Development and Regeneration

institute: Sapporo Medical University School of Medicine

description: Gene expression data of SHPCs with Thy1+ cells tranplantation

hyb_protocol: The procedure of hybridization is followed by GeneChip WT Terminal Labeling and Hybridization User Manual(Affymetrix 702808 Rev.4).

scan_protocol: GeneChip were scaned by GeneChip Scaner 3000(Affymetrix 690036) using GeneChip Operation Software ver1.4(Affymetrix 702387). The procedure of scan is followed by GeneChip Expression Wash, Stain and Scan User Manual(Affymetrix 702731 Rev.3)

data_processing: Data is processed by RMA-Skech algorythm using Expression ConsoleTM Softwere ver.1.2.1（Affymetrix 702387）

organism: Rattus norvegicus

source_name: retrorsine/partial hepatectomy treated rat livers

label_protocol: The procedure of labeling is followed by The Ambion WT Expression Kit For Affymetrix GeneChip Whole Transcript (WT) Expression Arrays Protocol（Ambion 4425209 Rev. C）and  GeneChip WT Terminal Labeling and Hybridization User Manual(Affymetrix 702808 Rev.4)

growth_protocol: female F344 rats were given two intraperitoneal injections of Retrorsine (30 mg/kg body weight; Sigma Chemical Co., St. Louis, MO), two weeks apart 14. Four weeks after the second injection, Partial Hepatectomy was performed. Sorted Thy1+ cells  (DPPIV+ donor cells, 5 × 105 cells) were transplanted into Ret/PH livers (DPPIV− rat) via the spleen

extract_protocol: Total RNAs of recovered tissues were prepared using the RNeasy Mini Kit (Qiagen).

treatment_protocol: 7-µm thick frozen sections were prepared from liver tissues and stained with hematoxylin. Cells forming SHPC clusters were recovered under microscopic observation with assistance from an ultraviolet laser (MMI CellCut; Molecular Machines & Industries, Glattbrugg, Switzerland).

value: liver

value: Hepatosytes beside SHPCs without Thy1+ cells transplantation


title: Thy1-1

value: SHPCs with Thy1+ cells transplantation


title: Thy1-2


title: Thy1-3


title: SHPC-2

description: Gene expression data of SHPCs without Thy1+ cells tranplantation

value: SHPCs without Thy1+ cells transplantation


title: Control-1


title: Peripheral blood B cell #2

status: Public on Aug 13 2016

city: NAGOYA

first: KAZUYUKI

last: SHIMADA

address: 65, Tsurumai-cho, Showa-ku

department: HEMATOLOGY AND ONCOLOGY

institute: NAGOYA UNIVERSITY

description: Gene expression in peripheral blood B-cell

hyb_protocol: For hybridization, 600ng of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/μg cRNA) was fragmented at 60 °C for 30 min in a reaction volume of 25 μL containing 1X Agilent fragmentation buffer and 2X Agilent blocking agent following the manufacturers’ instructions. On completion of the fragmentation reaction, 25 μL of 2X Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray Kit (G4851B) for 17 h at 65 °C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61 × 21 mm, Scan resolution 3 μm, Dye channel set to Green and Green PMT set to 100 %).

data_processing: Signal intensities were normalized to the 75th percentile using GeneSpring version 13.0 (Agilent Technologies), and log2-transformed.

source_name: Healthy Donor #2, PB

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's protocol, and then purified by RNeasy Mini Kit (Qiagen, Venlo, Netherlands).

growth_protocol: The patient derived xenograft IVLBCL models were established from primary patient bone marrow samples.

extract_protocol: Total RNA was extracted from magnetic beads selected CD19 positive cells using TRIzol solution (Life Technologies in Thermo Fisher Scientific, Waltham, MA, USA).

tag: disease

value: Healthy donor

tag: Sex


title: Peripheral blood B cell #1

source_name: Healthy Donor #1, PB


title: SHPC-1


title: IVLBCL #1

description: Gene expression in IVLBCL tumor

source_name: IVLBCL PDX #1, spleen

value: intravascular large B-cell lymphoma (IVLBCL)


title: IVLBCL #4

description: Gene expression in IVLBCL tumor

source_name: IVLBCL PDX #4, spleen

value: Female


title: 129_rentg_4_9094

city: SINGAPORE

first: SUJOY

last: GHOSH

address: 8 COLLEGE ROAD

department: Cardiovascular & Metabolic Diseases

institute: DUKE-NUS Graduate Medical School

description: 129/SvEv, RenTg, Ins2Akita, replicate 4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16hr at 45oC on Affymetric Genechip Mouse Genome 430A 2.0 arrays (mouse 430A_2).

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

data_processing: Background adjusted, quantile normalized gene expression signals were generated by the robust multi-array average method (RMA) using Partek Genomics Suite (v 6.6)

source_name: 129/SvEv, RenTg, Ins2Akita, kidney glomeruli

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix, 2001)

extract_protocol: Total RNA was extracted from mouse glomeruli (isolated from 12 week old male mice) via Qiagen RNeasy Micro Kit

treatment_protocol: Inbred C57BL/6-Ins2C96Y and 129/SvEv-Ins2C96Y mice were crossed with mice bearing a single copy of the ReninTg on the same genetic background, respectively to generate double transgenic mice with type 1 diabetes and hypertension.  At 12 weeks of age, mice were sacrificed for harvesting of glomeruli using Dynabead preparation, mincing, collagenase digestion and sieving.

value: 12 weeks

tag: genotype/variation

value: RenTg, Ins2Akita

value: kidney glomeruli


title: B6_rentg_3_935

description: C57BL/6, RenTg, Ins2Akita, replicate 3

source_name: C57BL/6, RenTg, Ins2Akita, kidney glomeruli

value: male


title: B6_rentg_4_272

description: C57BL/6, RenTg, Ins2Akita, replicate 4


title: B6_rentg_2_270

description: C57BL/6, RenTg, Ins2Akita, replicate 2


title: IVLBCL #3

description: Gene expression in IVLBCL tumor

source_name: IVLBCL PDX #3, spleen

value: Male


title: Peripheral blood B cell #3

source_name: Healthy Donor #3, PB


title: B6_wt_4_269

description: C57BL/6, wild-type, replicate 4

source_name: C57BL/6, wild-type, kidney glomeruli

value: wild-type


title: B6_wt_3_268

description: C57BL/6, wild-type, replicate 3


title: 129_rentg_3_9093

description: 129/SvEv, RenTg, Ins2Akita, replicate 3


title: B6_wt_2_183

description: C57BL/6, wild-type, replicate 2


title: B6_wt_1_9743

description: C57BL/6, wild-type, replicate 1


title: IVLBCL #2

description: Gene expression in IVLBCL tumor

source_name: IVLBCL PDX #2, spleen


title: B6_rentg_1_9965

description: C57BL/6, RenTg, Ins2Akita, replicate 1


title: Lung1, biological rep1

city: shanghai

first: Wu

last: Zhang

address: 197 Rui Jin Er Road

country: China

institute: Shanghai Institute of Hematology

description: Expression data from human osteosarcoma  lung metastases

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US)

source_name: Lung metastasis cells

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)

value: osteosarcoma cells


title: Lung2, biological rep2


title: 129_rentg_2_9980

description: 129/SvEv, RenTg, Ins2Akita, replicate 2


title: Lung3, biological rep3


title: 129_rentg_1_2629

description: 129/SvEv, RenTg, Ins2Akita, replicate 1


title: Bone3, biological rep3

description: Expression data from human osteosarcoma bone primaries

source_name: Bone primary cells


title: IVLBCL #4 liver

hyb_protocol: Test and reference labeled DNA samples were hybridized at 65°C for 40 hours on the 2x400K microarray glass (G4448A, Agilent, Palo Alto, CA) , and washed with Agilent Wash Buffers 1 and 2.

scan_protocol: The slideglass was scanned on an Agilent G2565BA scanner (Agilent, Palo Alto, CA) using a resolution of 3μm per pixel and 100% of the photomultiplicator for both signals.

data_processing: The background biases in the log2 ratio values of the CGH analysis data were adjusted according to standard statistical methods. Specifically, the correlation bias with GC content of the corresponding clone sequence was first removed. Then the probe-specific bias was also removed, where the bias at each probe was estimated by the running mean of the adjacent 10 probed in the both slides.

source_name: IVLBCL PDX #4, liver

label_protocol: DNA was digested with AluI and RsaI restriction enzymes. Sample DNA was labeled with Cy5-dUTP. As reference, mixture of DNA from normal healthy men was labeled with Cy3-dUTP.

extract_protocol: Genomic DNA was extracted from engrafted IVLBCL tumor cells in mouse organs using QIAamp DNA Blood Mini Kit according to the manufacturer's protocol (QIAGEN, Venlo, Netherlands)

tag: mouse's organs with engrafted tumors

source_name: Mixture of DNA from healthy individuals


title: 129_wt_3_9230

description: 129/SvEv, wild-type, replicate 3

source_name: 129/SvEv, wild-type, kidney glomeruli


title: 129_wt_2_9228

description: 129/SvEv, wild-type, replicate 2


title: Peripheral blood B cell #4

source_name: Healthy Donor #4, PB


title: 129_wt_1_2657

description: 129/SvEv, wild-type, replicate 1


title: IVLBCL #3 adrenal gland

source_name: IVLBCL PDX #3, adrenal gland

value: adrenal gland


title: B6*F*Tregs_59

status: Public on Aug 12 2016

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using Illumina BeadArray Reader software

data_processing: Signal values from unambiguous probes were local background corrected and data across arrays were quantile normalized using the lumi package from Bioconductor

source_name: Treg cells; female B6

growth_protocol: mice were maintained on standard chow and water ad libitum

extract_protocol: RNEasy kit was used to extract total RNA from FACS-sorted cells; RNA was converted to cRNA using the Illumina TotalPrep-96 RNA Amplification kit

value: Treg cells

value: female


title: B6*F*Tregs_60


title: B6*F*Tregs_58


title: B6*M*Tregs_57

source_name: Treg cells; male B6


title: B6*M*Tregs_55


title: B6*F*CD4_52

source_name: CD4 T cells; female B6

value: CD4 T cells


title: B6*M*CD4_50

source_name: CD4 T cells; male B6


title: B6*M*CD4_51


title: B6*M*Tregs_56


title: B6*F*CD4_54


title: B6*F*CD4_53


title: IVLBCL #2 spleen

value: spleen


title: B6*M*CD4_49


title: IVLBCL #3 spleen


title: IVLBCL #3 kidney

source_name: IVLBCL PDX #3, kidney

value: kidney


title: IVLBCL #3 BM

source_name: IVLBCL PDX #3, bone marrow

value: bone marrow


title: B6*F*APCs_48

source_name: APCs; female B6

value: APCs


title: B6*M*APCs_44

source_name: APCs; male B6


title: B6*M*APCs_45


title: B6*M*APCs_43


title: B6*F*APCs_46


title: B6*F*Bcells_41

source_name: B cells; female B6

value: B cells


title: B6*F*APCs_47


title: B6*F*Bcells_40


title: SHPC-3

source_name: retrorsine/partial hepatectomy treated rat livers

value: liver

value: SHPCs without Thy1+ cells transplantation


title: B6*F*Bcells_42


title: Control-2

value: Hepatosytes beside SHPCs without Thy1+ cells transplantation


title: IVLBCL #1 spleen

source_name: IVLBCL PDX #1, spleen

value: intravascular large B-cell lymphoma (IVLBCL)


title: B6*M*Bcells_37

source_name: B cells; male B6

value: male


title: B6*F*CD8_36

source_name: CD8 T cells; female B6

value: CD8 T cells


title: B6*M*CD8_32

source_name: CD8 T cells; male B6


title: B6*F*CD8_35


title: B6*M*Bcells_39


title: PWD*F*Tregs_30

description: PWD*F*Tregs

source_name: Treg cells; female PWD

value: PWD


title: B6*M*CD8_31


title: PWD*F*Tregs_28

description: PWD*F*Tregs


title: PWD*M*Tregs_27

description: PWD*M*Tregs

source_name: Treg cells; male PWD


title: B6*M*CD8_33


title: PWD*F*Tregs_29

description: PWD*F*Tregs


title: PWD*M*Tregs_26

description: PWD*M*Tregs


title: PWD*F*CD4_23

source_name: CD4 T cells; female PWD


title: B6*F*CD8_34


title: PWD*M*CD4_20

source_name: CD4 T cells; male PWD


title: PWD*F*APCs_18

description: PWD*F*APCs

source_name: APCs; female PWD


title: PWD*M*APCs_15

description: PWD*M*APCs

source_name: APCs; male PWD


title: PWD*F*APCs_17

description: PWD*F*APCs


title: PWD*M*CD4_21


title: PWD*M*Tregs_25

description: PWD*M*Tregs


title: PWD*F*CD4_24


title: PWD*F*APCs_16

description: PWD*F*APCs


title: PWD*M*APCs_13

description: PWD*M*APCs


title: PWD*F*Bcells_11

description: PWD*F*Bcells

source_name: B cells; female PWD


title: PWD*F*Bcells_10

description: PWD*F*Bcells


title: PWD*F*Bcells_12

description: PWD*F*Bcells


title: PWD*M*APCs_14

description: PWD*M*APCs


title: PWD*F*CD4_22


title: PWD*M*CD4_19


title: Bone1, biological rep1

source_name: Bone primary cells

value: osteosarcoma cells


title: B6*M*Bcells_38


title: PWD*M*Bcells_9

description: PWD*M*Bcells

source_name: B cells; male PWD


title: Bone2, biological rep2


title: PWD*F*CD8_5

source_name: CD8 T cells; female PWD


title: Untreated WT labeled with 647 vs Depletion Strain labeled with 555

city: Ithaca

first: John

middle: Daniel

last: Helmann

state: NY

address: 372 Wing Hall, Cornell University

department: Microbiology

institute: Cornell University

hyb_protocol: Equal amounts (100-150 pmol) of labeled cDNA were combined plus hybridization buffer (2X = 50% formamide, 10X SSC, 0.1% SDS). cDNA mix was denatured at 95oC and hybridized 16-18 hours at 42oC to DNA microarray slides which had been prehybridized for at least 30 min at 42oC in 1% bovine serum albumin, 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate (SDS), washed in water and dried. Following hybridization the slides were washed sequentially in: 2X SSC + 0.1% SDS for 5 min at 42oC, 2X SSC + 0.1% SDS for 5 min at room temperature, 2X SSC for 5 min at room temperature, 0.2X SSC for 5 min at room temperature, and finally dipped in water and spun until dry.

scan_protocol: Arrays were scanned using a GenePixTM 4000B array scanner (Axon Instruments, Inc.). Raw data files were produced from the scanned images using the GenePix Pro 4.0 software package (GPR files).

data_processing: Red/green fluorescence intensity values were normalized using the GenePix Pro 4.0 software package such that the ratio of medians of all features was equal to 1

label: Alexa Fluor 555

organism: Bacillus subtilis

source_name: Untreated Depletion strain

label_protocol: Total RNA were then treated with Turbo-DNAse (Thermo Fisher Scientific) to remove any possible DNA contamination, and then reverse transcribed using SuperScript™ Indirect cDNA Labeling System (Thermo Fisher Scientific) into cDNA. cDNA was aliquoted and labelled with either fluorescent dye 555 or dye 647, and hybridized to microarray slides containing 60 nt oligonucleotides for each coding region according to laboratory protocol.

growth_protocol: The wild type and depletion strains were grown separately in liquid LB medium to OD600 ~0.4, and then each diluted 100-fold into two 250 ml flasks each containing fresh 50 ml LB medium. After 1.5 hours of initial growth, one of the two flasks of each strain was supplemented with 50% xylose to a final concentration of 2%, while the other flask was left untreated as control. After another 2.5 hours of growth, cells were collected and total RNA was extracted using phenol-chloroform based method.

extract_protocol: Total RNA was extracted using phenol-chloroform based method. Total RNA was quantified and quality of RNA was tested using Bio-analyzer. RNA quality numbers for all four RNA samples are 10 out of 10.

value: Depletion strain

label: Alexa Fluor 647

source_name: Untreated WT

value: wildtype


title: Xylose treated WT labeled with 555 vs Depletion Strain labeled with 647

source_name: Treated WT

treatment_protocol: The wild type and depletion strains were grown separately in liquid LB medium to OD600 ~0.4, and then each diluted 100-fold into two 250 ml flasks each containing fresh 50 ml LB medium. After 1.5 hours of initial growth, one of the two flasks of each strain was supplemented with 50% xylose to a final concentration of 2%, while the other flask was left untreated as control. After another 2.5 hours of growth, cells were collected and total RNA was extracted using phenol-chloroform based method.

source_name: Treated Depletion strain


title: PWD*F*CD8_6

value: female


title: PWD*M*Bcells_7

description: PWD*M*Bcells


title: PWD*M*CD8_3

source_name: CD8 T cells; male PWD


title: Female Knock Out 4

city: Saint Louis

first: Kooresh

middle: Isaac

last: Shoghi

state: MO

address: 510 South Kingshighway Blvd.

department: Department of Radiology

description: Female Knock out Replicate 4

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spliine normalization with IlluminaGUI in R

source_name: Mice Heart

label_protocol: Biotinylated aRNA were prepared with Message Amp total prep amplifciation kit , Life technoligies

growth_protocol: Wild type and cardiac-specific Erα knockout,  male and female mice of C57BL/6 phenotype were bred and maintained at Washington University School of Medicine animal facility. Mice had free access to regular diet and water.

extract_protocol: RNA was ectracted with Qiagen Total RNA isolation lipid Kit with on-column Dnase 1 treatment in accordance with prescribed protocol provided in the kit. Quality control was performed with Agilient Bioanalyzer

treatment_protocol: No Treatment

value: Female

value: Heart

value: 18 Weeks

value: cardiac-specific estrogen receptor alpha knockout


title: PWD*M*CD8_1


title: PWD*F*CD8_4


title: PWD*M*CD8_2


title: Female Knock Out 2

institute: Washington University School of Medicine

description: Female Knock out Replicate 2


title: Untreated WT labeled with 555 vs Depletion Strain labeled with 647


title: Male Knock Out 4

description: Male Knock out Replicate 4

value: Male


title: CL1-5_Stable-expreesing SPANXA gene_rep2

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from CL1-5 stable-expressing SPANXA

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The expression data were analyzed by GeneSpring GX 13.0 (Silicon Genetics, Redwood City, CA). The Affymetrix CEL files were transformed by GC-RMA algorithm, and each probe set was summarized using the median of the corresponding probes.

source_name: lung cancer cell, CL1-5 stable-expressing SPANXA gene

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

growth_protocol: The human lung cancer cell line, CL1-5, was grown in RPMI-1640 media supplemented with 10% FBS. All cell lines were incubated at 37°C in a humidified 20% O2/5% CO2 environment.

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

treatment_protocol: CL1-5 cells were individually transfected with pEF-V5 vector and SPANXA-V5. The stable-expressing cells were maintained in complete media with 9 mg/ml Blasticidin S.

tag: tumor type

value: lung adenocacinoma

tag: ethnicity

value: Asian

value: 64 years


title: Male Knock Out 3

description: Male Knock out Replicate 3

tag: strain


title: Female Wild Type 4

description: Female Wild type Replicate 4

value: Wild Type


title: Female Knock Out 3

description: Female Knock out Replicate 3


title: Male Knock Out 2

description: Male Knock out Replicate 2


title: Xylose treated WT labeled with 647 vs Depletion Strain labeled with 555


title: Female Wild Type 3

description: Female Wild type Replicate 3


title: CL1-5_Stable-expreesing SPANXA gene_rep3


title: CL1-5_Stable-expreesing SPANXA gene_rep1


title: Female Wild Type 2

description: Female Wild type Replicate 2


title: Male Knock Out 1

description: Male Knock out Replicate 1


title: Female Wild Type 1

description: Female Wild type Replicate 1


title: Female Knock Out 1

description: Female Knock out Replicate 1


title: Male Wild Type 4

description: Male wild type Replicate 4


title: CL1-5_Stable-expressing an empty vector_rep3

description: Gene expression data from CL1-5 stable-expressing an pEF-V5 empty vector

source_name: lung cancer cell, CL1-5 stable-expressing an empty vector


title: CL1-5_Stable-expressing an empty vector_rep2


title: CL1-5_Stable-expressing an empty vector_rep1


title: Male Wild Type 3

description: Male wild type Replicate 3


title: HaCaT_sip53

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

hyb_protocol: Array hybridization was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

scan_protocol: Array scanning was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

data_processing: Microarray Suite software 5.0 (Affymetrix) was used to calculate the average difference (AD) for each gene probe set, which was shown as an intensity value of the gene expression (Ishii et al, Genomics 68:136-143, 2000).

source_name: sip53 transfected HaCaT cells without TGF-beta stimulation

label_protocol: Double-stranded cDNA was synthesized with the SuperScript Choice system (GIBCO) and a T7-(dT) 24 Primer (GE Amersham) from the total RNA. In vitro transcription was performed to produce biotin-labeled cRNA by using a BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to the manufacturer’s instructions (Ishii et al, Genomics 68:136-143, 2000).

growth_protocol: Human immortalized keratinocyte HaCaT cells were maintained in Dulbecco’s modified Eagle’s medium (Sigma) supplemented with 10% (v/v) fetal bovine serum (FBS) (HyClone) and 1% penicillin–streptomycin (Sigma).

extract_protocol: Total RNAs were extracted using RNeasy mini kit (QIAGEN).

treatment_protocol: Cells infected with adenoviral vectors or transfected with siRNAs were stimulated with 5 ng/ml of TGF-beta3 for 24h or left untreated.

value: Human immortalized keratinocyte (HaCaT)

tag: adenoviral infection

tag: sirna

value: p53 siRNA (Thermo Scientific stealth select siRNA, HSS110905)

tag: tgfb stimulation

value: no


title: HaCaT_RasN116Y_-

source_name: AdRAS N116Y infected HaCaT cells with TGF-beta stimulation

value: HRAS N116Y


title: HaCaT_LacZ_-

source_name: AdLacZ infected HaCaT cells with TGF-beta stimulation

value: LacZ


title: HaCaT_RasN116Y_TGFB

source_name: AdRAS N116Y infected HaCaT cells without TGF-beta stimulation

value: yes


title: Male Wild Type 1

description: Male wild type Replicate 1

tag: gender

tag: tissue


title: HaCaT_siControl

source_name: siControl transfected HaCaT cells without TGF-beta stimulation

value: control siRNA (Thermo Scientific stealth control siRNA, 12935-112)


title: [murine c-kit bone marrow] [MN1-TEL del DBD] [rep2]

city: London

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

country: United Kingdom

institute: Biomedical Research Centre

description: SAMPLE 3 – Rep2

hyb_protocol: Biotinylated, amplified cRNA targets were prepared by the TargetAmpTM-Nano Labeling kit (epicentre®), from 500 ng of total RNA as starting material and were subsequenctly hybridised to Illumina Mouse WG-6 V.2 BeadChips, and scanned following the manufacturer’s instructions (Illumina).

scan_protocol: scanning was performed following the manufacturer’s instructions (Illumina)

data_processing: The background was subtracted and the data was quantile normalized using Illumina genome studio software version 2010.3. The negative values indicate that the observed signal intensity of the probe is not above background. Quantile normalized average signal intensity values across 3 replicates for each sample are available on Series records [average_normalized.txt].

source_name: murine c-kit bone marrow_retrovirally transduced/transformed

label_protocol: biotin

growth_protocol: retroviral transduction of murine c-kit enriched bone marrow cell with MN1/ MN1-TEL/ MN1-TEL del DBD and according to protocol described in Zeisig et al. 2008, 10 days liquid culture in RPMI + 10% FCS + Penicillin/Streptomycin + IL-3/IL-6 10 ng/µl and SCF 20 ng/µl

extract_protocol: RNA extraction with RNeasy kit following manufacturer´s instructions

treatment_protocol: see growth protocol

tag: cell type

value: murine c-kit bone marrow cells

tag: transduced with

value: MN1-TEL del DBD


title: HaCaT_LacZ_TGFB

source_name: AdLacZ infected HaCaT cells without TGF-beta stimulation

tag: cell line


title: HaCaT_RasG12V_-

source_name: AdRAS G12V infected HaCaT cells with TGF-beta stimulation

value: HRAS G12V


title: HaCaT_RasG12V_TGFB

source_name: AdRAS G12V infected HaCaT cells without TGF-beta stimulation


title: Male Wild Type 2

description: Male wild type Replicate 2

value: Heart

tag: age

value: 18 Weeks


title: [murine c-kit bone marrow] [MN1-TEL] [rep2]

description: SAMPLE 2 – Rep2

tag: strain background


title: [murine c-kit bone marrow] [MN1-TEL del DBD] [rep1]

description: SAMPLE 3 – Rep1


title: MCFDCIS siSNAI2 A

status: Public on Aug 11 2016

city: Dallas

first: Xiaoyu

last: Wang

state: Texas

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

description:
biological replicate 1
9372535073_B

hyb_protocol: Direct Hybridization Assay Protocols in Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide

scan_protocol: illumina HiScan®SQ System User Guide

data_processing: Raw data were generated by GenomeStudioTM Gene Expression Module v1.0 without background subtraction and normalization

source_name: MCFDCIS siSNAI2 A

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit protocol

growth_protocol: Cells were grown in the recomended culture media for 48 h.

extract_protocol: Total RNA was extracted following manufacturer's protocol for Qiagen Rneasy Plus, Cat. No. 74134, Appendix D: Purification of Total RNA containing small RNAs from cells

treatment_protocol: Cells were transfected with control or siRNAs targeting Slug for 72 hours.  Cells were approx 70% confluent at the time of lysis and RNA extraction.

tag: transfection

value: Slug siRNA

value: MCFDCIS


title: [murine c-kit bone marrow] [MN1] [rep1]

description: SAMPLE 1 – Rep1


title: [murine c-kit bone marrow] [MN1] [rep3]

description: SAMPLE 1 – Rep3


title: [murine c-kit bone marrow] [MN1-TEL] [rep3]

description: SAMPLE 2 – Rep3


title: MCFDCIS siSNAI2 B

description:
biological replicate 2
9372535073_J

source_name: MCFDCIS siSNAI2 B


title: MCFDCIS siOTP NT B

description:
biological replicate 2
9372535073_I

source_name: MCFDCIS siOTP NT B

value: Control siRNA


title: [murine c-kit bone marrow] [MN1-TEL del DBD] [rep3]

description: SAMPLE 3 – Rep3


title: HCC1937 dex

city: Lyon

first: Arnaud

last: VIGNERON

address: 28 rue Laennec

country: France

institute: Cancer Research Center of Lyon

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

source_name: HCC1937 cell line

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

growth_protocol: Cells were maintained in DMEM 3mM glucose 0.5 mM glutamine

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

tag: subtype

value: Basal

tag: agent

value: dexamethasone (200nM)


title: MCFDCIS siOTP NT A

description:
biological replicate 1
9372535073_A

source_name: MCFDCIS siOTP NT A


title: [murine c-kit bone marrow] [MN1] [rep2]

description: SAMPLE 1 – Rep2


title: HCC1937 dex +RA

value: dexamethasone (200nM) with retinoic acid (1uM)


title: HCC1937 control

value: untreated


title: OVCA-Tumour-HCC5048T_EXPR

city: Vancouver

first: Kelsie

middle: L

last: Thu

state: British Columbia

address: 675 West 10th Avenue

country: Canada

institute: BC Cancer Research Centre

description:
ovarian carcinoma
HCC5048T

hyb_protocol: As per manufacturer's instructions (Illumina)

data_processing: Background corrected raw data was robust spline normalized using BRB-ArrayTools (developed by Dr Richard Simon and the BRB-ArrayTools Development Team) to generate log2 transformed, normalized expression values; File = UTSW_OVCA_Normalized_Expression_forGEO.txt

source_name: OVCA-Tumour

growth_protocol: Tumour cells were enriched from malignant effusions (OVCA tumour ascites) by two or more cycles of low speed centrifugation plus differential substrate attachment. Cell lines were cultured in ACL4 or RPMI growth media supplemented with 5% FBS.

extract_protocol: Total RNA was extracted from cell pellets using Trizol reagent.

treatment_protocol: No treatments were applied

tag: sample type

value: Tumour

tag: sample source id

value: Female


title: OVCA-CellLine-HCC5018CL_EXPR

description:
ovarian carcinoma
HCC5018CL

scan_protocol: As per manufacturer's instructions (Illumina)

source_name: OVCA-CellLine

value: Cell line


title: OVCA-Tumour-HCC5030T_EXPR

description:
ovarian carcinoma
HCC5030T

label_protocol: As per manufacturer's instructions (Illumina)


title: OVCA-Tumour-HCC5050T_EXPR

description:
ovarian carcinoma
HCC5050T


title: OVCA-CellLine-HCC5050CL_EXPR

description:
ovarian carcinoma
HCC5050CL


title: OVCA-CellLine-HCC5030CL_EXPR

description:
ovarian carcinoma
HCC5030CL


title: OVCA-Tumour-HCC5024T_EXPR

description:
ovarian carcinoma
HCC5024T


title: OVCA-CellLine-HCC5023CL_EXPR

description:
ovarian carcinoma
HCC5023CL


title: OVCA-CellLine-HCC5024CL_EXPR

description:
ovarian carcinoma
HCC5024CL


title: OVCA-Tumour-HCC5023T_EXPR

description:
ovarian carcinoma
HCC5023T


title: OVCA-CellLine-HCC5012CL_EXPR

description:
ovarian carcinoma
HCC5012CL


title: OVCA-CellLine-HCC5036CL_EXPR

description:
ovarian carcinoma
HCC5036CL


title: PWD*M*Bcells_8

description: PWD*M*Bcells

source_name: B cells; male PWD

value: B cells

tag: Sex

value: male

value: PWD


title: [murine c-kit bone marrow] [MN1-TEL] [rep1]

description: SAMPLE 2 – Rep1

value: murine c-kit bone marrow cells


title: OVCA-CellLine-HCC5032CL_EXPR

description:
ovarian carcinoma
HCC5032CL


title: OVCA-CellLine-HCC5048CL_EXPR

description:
ovarian carcinoma
HCC5048CL


title: OVCA-Tumour-HCC5012T_EXPR

description:
ovarian carcinoma
HCC5012T


title: OVCA-Tumour-HCC5036T_EXPR

description:
ovarian carcinoma
HCC5036T


title: Non-demented control 88

city: Shah Alam

first: Ainon

middle: Zahariah

last: Samsudin

state: Selangor

address: Bandar Puncak Alam

country: Malaysia

institute: University Teknologi Mara

description:
Gene expression of non-demented contol subject using human blood
US91203660_252800417088_S01_GE1_107_Sep09_2_2

hyb_protocol: 0.825 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Gene Expression blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2534A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately using cleaning tissue.

scan_protocol: Slides were scanned immediately after washing on the Agilent microarray scanner G2505B (Agilent Technology) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent Technology) using default parameters (protocol available at http://www.chem.agilent.com/library/usermanuals/Public/G4140-90040_Gene Expression_OneColor_6.7.pdf) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral Blood, replicate 1

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

extract_protocol: RNA was prepared using the Ribopure Blood RNA Purification kit (Ambion Technologies, USA) following the manufacturer's recommendations. Then treated with an on-column DNase digestion agent. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from participant was preserved in RNA later immediately

tag: diagnosis

value: Non-demented control

value: whole blood


title: Non-demented control 90

description:
Gene expression of non-demented contol subject using human blood
US91203660_252800417088_S01_GE1_107_Sep09_2_4


title: Non-demented control 89

description:
Gene expression of non-demented contol subject using human blood
US91203660_252800417088_S01_GE1_107_Sep09_2_3

value: female


title: Non-demented control 87

description:
Gene expression of non-demented contol subject using human blood
US91203660_252800417088_S01_GE1_107_Sep09_2_1


title: Non-demented control 86

description:
Gene expression of non-demented contol subject using human blood
US91203660_252800417088_S01_GE1_107_Sep09_1_4


title: Non-demented control 84

description:
Gene expression of non-demented contol subject using human blood
US91203660_252800417088_S01_GE1_107_Sep09_1_2


title: Non-demented control 85

description:
Gene expression of non-demented contol subject using human blood
US91203660_252800417088_S01_GE1_107_Sep09_1_3


title: Non-demented control 83

description:
Gene expression of non-demented contol subject using human blood
US91203660_252800417088_S01_GE1_107_Sep09_1_1


title: Non-demented control 81

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417959_S01_GE1_107_Sep09_2_3


title: Non-demented control 82

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417959_S01_GE1_107_Sep09_2_4


title: Non-demented control 77

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417959_S01_GE1_107_Sep09_1_2


title: Non-demented control 78

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417959_S01_GE1_107_Sep09_1_3


title: Probable AD 90

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417959_S01_GE1_107_Sep09_1_4

value: Probable Alzheimer's Disease


title: Probable AD 88

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417958_S01_GE1_107_Sep09_2_1


title: Probable AD 89

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417958_S01_GE1_107_Sep09_2_4


title: OVCA-Tumour-HCC5022T_EXPR

description:
ovarian carcinoma
HCC5022T


title: Probable AD 86

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417958_S01_GE1_107_Sep09_1_3


title: OVCA-CellLine-HCC5022CL_EXPR

description:
ovarian carcinoma
HCC5022CL


title: Probable AD 87

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417958_S01_GE1_107_Sep09_1_4


title: Non-demented control 79

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417959_S01_GE1_107_Sep09_2_1


title: OVCA-Tumour-HCC5019T_EXPR

description:
ovarian carcinoma
HCC5019T


title: Non-demented control 76

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417959_S01_GE1_107_Sep09_1_1


title: OVCA-CellLine-HCC5019CL_EXPR

description:
ovarian carcinoma
HCC5019CL


title: Non-demented control 80

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417959_S01_GE1_107_Sep09_2_2


title: Non-demented control 75

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417958_S01_GE1_107_Sep09_1_1


title: Probable AD 85

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417958_S01_GE1_107_Sep09_1_2


title: Non-demented control 72

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417957_S01_GE1_107_Sep09_2_2


title: Non-demented control 73

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417957_S01_GE1_107_Sep09_2_3


title: Non-demented control 68

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417957_S01_GE1_107_Sep09_1_1


title: Non-demented control 70

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417957_S01_GE1_107_Sep09_1_4


title: Non-demented control 67

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417938_S01_GE1_107_Sep09_2_3


title: Non-demented control 71

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417957_S01_GE1_107_Sep09_2_1


title: Probable AD 84

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417957_S01_GE1_107_Sep09_1_3


title: Non-demented control 69

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417957_S01_GE1_107_Sep09_1_2


title: Probable AD 82

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417924_S01_GE1_107_Sep09_2_3


title: Non-demented control 66

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417928_S01_GE1_107_Sep09_2_3


title: Non-demented control 65

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417928_S01_GE1_107_Sep09_1_1


title: Probable AD 81

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417924_S01_GE1_107_Sep09_2_2


title: Probable AD 83

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417924_S01_GE1_107_Sep09_2_4


title: Non-demented control 74

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417957_S01_GE1_107_Sep09_2_4


title: Probable AD 80

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417924_S01_GE1_107_Sep09_2_1


title: Probable AD 77

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417924_S01_GE1_107_Sep09_1_1


title: Probable AD 78

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417924_S01_GE1_107_Sep09_1_2


title: Probable AD 76

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417919_S01_GE1_107_Sep09_2_2


title: Non-demented control 64

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417919_S01_GE1_107_Sep09_2_4


title: Non-demented control 63

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417919_S01_GE1_107_Sep09_2_3


title: Non-demented control 62

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417919_S01_GE1_107_Sep09_1_3


title: Probable AD 79

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417924_S01_GE1_107_Sep09_1_4


title: Non-demented control 60

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417919_S01_GE1_107_Sep09_1_1


title: Non-demented control 61

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417919_S01_GE1_107_Sep09_1_2


title: Probable AD 75

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417919_S01_GE1_107_Sep09_2_1


title: Non-demented control 58

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417918_S01_GE1_107_Sep09_2_3


title: Non-demented control 57

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417918_S01_GE1_107_Sep09_2_2


title: Non-demented control 59

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417918_S01_GE1_107_Sep09_2_4


title: Probable AD 74

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417918_S01_GE1_107_Sep09_2_1


title: Probable AD 73

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417918_S01_GE1_107_Sep09_1_4


title: Probable AD 72

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417918_S01_GE1_107_Sep09_1_3


title: Probable AD 71

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417918_S01_GE1_107_Sep09_1_1


title: Probable AD 69

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417526_S01_GE1_107_Sep09_2_2


title: Probable AD 66

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417526_S01_GE1_107_Sep09_1_2


title: Probable AD 68

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417526_S01_GE1_107_Sep09_2_1


title: Probable AD 65

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417526_S01_GE1_107_Sep09_1_1


title: Probable AD 64

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417525_S01_GE1_107_Sep09_2_4


title: Probable AD 62

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417525_S01_GE1_107_Sep09_1_3


title: Probable AD 63

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417525_S01_GE1_107_Sep09_1_4


title: Probable AD 61

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417525_S01_GE1_107_Sep09_1_2


title: Probable AD 60

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417525_S01_GE1_107_Sep09_1_1


title: Probable AD 58

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417521_S01_GE1_107_Sep09_2_3


title: Probable AD 59

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417521_S01_GE1_107_Sep09_2_4


title: Non-demented control 54

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417521_S01_GE1_107_Sep09_2_1


title: Non-demented control 52

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417521_S01_GE1_107_Sep09_1_1


title: Non-demented control 53

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417521_S01_GE1_107_Sep09_1_4


title: Probable AD 57

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417521_S01_GE1_107_Sep09_1_2


title: Probable AD 56

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417520_S01_GE1_107_Sep09_2_4


title: Non-demented control 51

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417520_S01_GE1_107_Sep09_2_3


title: Non-demented control 50

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417520_S01_GE1_107_Sep09_2_1


title: Probable AD 55

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417520_S01_GE1_107_Sep09_2_2


title: Probable AD 54

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417520_S01_GE1_107_Sep09_1_4


title: Non-demented control 49

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417520_S01_GE1_107_Sep09_1_1


title: Probable AD 70

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417526_S01_GE1_107_Sep09_2_4


title: Probable AD 52

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417519_S01_GE1_107_Sep09_2_3


title: Non-demented control 48

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417519_S01_GE1_107_Sep09_2_2


title: Probable AD 51

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417519_S01_GE1_107_Sep09_2_1


title: Probable AD 50

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417519_S01_GE1_107_Sep09_1_4


title: Probable AD 67

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417526_S01_GE1_107_Sep09_1_3


title: Probable AD 49

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417519_S01_GE1_107_Sep09_1_3


title: Probable AD 48

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417519_S01_GE1_107_Sep09_1_2


title: Non-demented control 47

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417384_S01_GE1_107_Sep09_2_4


title: Probable AD 47

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417519_S01_GE1_107_Sep09_1_1


title: Non-demented control 56

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417525_S01_GE1_107_Sep09_2_1


title: Non-demented control 46

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417384_S01_GE1_107_Sep09_2_3


title: Non-demented control 55

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417521_S01_GE1_107_Sep09_2_2


title: Non-demented control 45

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417384_S01_GE1_107_Sep09_2_2


title: Non-demented control 44

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417384_S01_GE1_107_Sep09_2_1


title: Non-demented control 43

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417384_S01_GE1_107_Sep09_1_4


title: Non-demented control 42

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417384_S01_GE1_107_Sep09_1_3


title: Peripheral blood mononuclear cell gDNA [UNK-129C-KW]

city: Boston

first: Michel

last: Massaad

state: MA

address: One Blackfan Circle

department: Mdicine/Immunology

institute: Boston Children's Hospital

description: Hybridized to Genome-Wide Human SNP Array 6.0

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

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

data_processing: We used a custom build, rule based “Variant Explorer” pipeline integrating copy number variation (CNV), family linkage as well as population level homozygosity to aid interpretation of the results. (K.S., publication in process). Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data. analyzed with Birdsuite version 1.4 and PLINK version 1.07

source_name: Blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol:
Blood was extracted from the subjects by venipuncture.
Genomic DNA was extracted from peripheral blood mononuclear cells using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: primary cells

value: Peripheral blood mononuclear cells


title: Peripheral blood mononuclear cell gDNA [UNK-129B-KW]


title: Probable AD 53

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417520_S01_GE1_107_Sep09_1_2


title: Non-demented control 40

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417383_S01_GE1_107_Sep09_2_3


title: Peripheral blood mononuclear cell gDNA [UNK-129E-KW]


title: Non-demented control 41

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417384_S01_GE1_107_Sep09_1_1


title: Non-demented control 39

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417383_S01_GE1_107_Sep09_1_3


title: Probable AD 46

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417382_S01_GE1_107_Sep09_2_4


title: KYSE150-vector control

city: shantou

first: Enmin

last: Li

state: guangdong

address: 22 Xinling Road

institute: Shantou university, medical college

hyb_protocol: After fragmentation of these amplified RNA (aRNA), sample was hybridized to the Affymetrix PrimeViewTM Human Gene Expression Array for 16-18 h at 45°C.

scan_protocol: Following hybridization, the microarrays were washed and stained with Streptavidin Phycoerythrin on the Affymetrix Fluidics Station 450. Microarrays were scanned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using default analysis settings and global scaling as normalization method by Partek® Genomics Suite 6.6. Values presented are log2 RMA signal intensity..

source_name: KYSE150-vector control

label_protocol: After having passed RNA measurement on the Nanodrop ND-1000 and denaturing gel electrophoresis, a total of 500 ng RNA was used for a single round of amplification and simultaneously labeled with biotincongugated nucleotide.

growth_protocol: KYSE150 cells were cultured in RPMI-1640 medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum. All cells were maintained at 37°C in ahumidified 5% CO2 atmosphere.

extract_protocol: Total RNA are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step.

treatment_protocol: Chemically modified Stealth siRNAs (Hs_SMYD3_7 FlexiTubesiRNA: 5′-AGTATCTCTTTGCTCAATCAA-3′; Hs_SMYD3_11 FlexiTubesiRNA: 5′-CAAGTATGGAAGGAAGTTCAA-3′) were purchased from QIAGEN. SMYD3-specific small hairpin RNA lentiviruses (SMYD3 shRNA1, SMYD3 shRNA2 and control shRNA) were purchased from GenePharma of China. The shRNA sequences were similar to siRNAs and were ligated into the pGLV3/H1/GFP/+Puro Vector. Two SMYD3 lentivirus shRNAs were mixed and used to simultaneously infect KYSE150 and SHEEC cells, following the manufacturer’s instructions, when cells reached 30-40% confluence. Seventy-two hours later, cells were passaged or harvested for further analysis.

value: esophageal squamous carcinoma cell (ESCC)


title: Peripheral blood mononuclear cell gDNA [UNK-129-KW]


title: KYSE150-SMYD3 knockdown

source_name: KYSE150-SMYD3 knockdown


title: Peripheral blood mononuclear cell gDNA [UNK-129F-KW]


title: Probable AD 45

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417382_S01_GE1_107_Sep09_2_3


title: Peripheral blood mononuclear cell gDNA [UNK-129A-KW]


title: Peripheral blood mononuclear cell gDNA [UNK-129M-KW]


title: Non-demented control 38

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417382_S01_GE1_107_Sep09_2_2


title: Non-demented control 37

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417382_S01_GE1_107_Sep09_1_4


title: Non-demented control 36

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417382_S01_GE1_107_Sep09_1_2


title: Peripheral blood mononuclear cell gDNA [UNK-129D-KW]


title: Probable AD 44

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417382_S01_GE1_107_Sep09_1_3


title: Probable AD 43

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417382_S01_GE1_107_Sep09_1_1


title: Probable AD 41

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417090_S01_GE1_107_Sep09_2_3


title: Non-demented control 35

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417090_S01_GE1_107_Sep09_1_4


title: Non-demented control 34

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417090_S01_GE1_107_Sep09_1_3


title: Probable AD 38

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417089_S01_GE1_107_Sep09_2_3


title: Probable AD 37

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417089_S01_GE1_107_Sep09_2_2


title: Non-demented control 33

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417090_S01_GE1_107_Sep09_1_2


title: Non-demented control 32

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417090_S01_GE1_107_Sep09_1_1


title: Non-demented control 31

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417089_S01_GE1_107_Sep09_1_4


title: Probable AD 42

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417090_S01_GE1_107_Sep09_2_4


title: Non-demented control 30

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417089_S01_GE1_107_Sep09_1_3


title: Probable AD 40

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417090_S01_GE1_107_Sep09_2_2


title: Probable AD 39

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417090_S01_GE1_107_Sep09_2_1


title: Probable AD 36

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417024_S01_GE1_107_Sep09_2_4


title: Non-demented control 28

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417089_S01_GE1_107_Sep09_1_1


title: Probable AD 35

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417024_S01_GE1_107_Sep09_2_3


title: Probable AD 34

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417024_S01_GE1_107_Sep09_2_1


title: Non-demented control 29

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417089_S01_GE1_107_Sep09_1_2


title: Probable AD 33

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417024_S01_GE1_107_Sep09_1_3


title: Probable AD 32

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417024_S01_GE1_107_Sep09_1_2


title: Probable AD 31

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417024_S01_GE1_107_Sep09_1_1


title: Probable AD 30

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417022_S01_GE1_107_Sep09_2_4


title: Non-demented control 27

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417022_S01_GE1_107_Sep09_2_3


title: Non-demented control 26

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417022_S01_GE1_107_Sep09_2_2


title: Probable AD 29

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417022_S01_GE1_107_Sep09_1_4


title: OVCA-CellLine-HCC5030CL_SNP6

scan_protocol: The Arrays werewashed and scanned according to manufacturer instructions (Affymetrix)

data_processing:
CHP files were created from CEL file intensities using the Affymetrix Genotyping Console using the BIRDSEED V2 algorithm with default settings.  CEL files were imported into Partek Genomics Suite Software with correction for fragment length, GC content, probe sequence. The corrected probe intensities were then quantile normalized. Copy number profiles were generated using Partek's Paired Copy Number Analysis workflow using patient matched constitutional DNA (ie. BloodLine) as a baseline for defining somatic alterations in each OVCA sample (tumour/cell line/xenograft). The Genomic Segmentation algorithm was applied with SNR=0.3, a 30 marker minimum segment size, and p-values < 10-7 for defining copy number alterations (CNAs).
SNP array normalized probe data = UTSWovca_SNP_Feb2015_AllCopyNumber_transpose.txt

growth_protocol: Tumour cells were enriched from malignant effusions (OVCA tumour ascites) by two or more cycles of low speed centrifugation plus differential substrate attachment. Cell lines were cultured in ACL4 or RPMI growth media supplemented with 5% FBS. Xenografts were generated by injecting purified tumour cells intraperitoneally into athymic nude mice.

extract_protocol: Genomic DNA was extracted from cell pellets using the Qiagen DNeasy Blood and Tissue kit

value: cell line

value: ovarian carcinoma


title: OVCA-CellLine-HCC5032CL_SNP6


title: OVCA-CellLine-HCC5024CL_SNP6


title: OVCA-Tumour-HCC5030T_SNP6


title: OVCA-CellLine-HCC5012CL_SNP6


title: OVCA-BloodLine-HCC5024BL_SNP6

source_name: OVCA-BloodLine

value: blood line

value: lymphoblast


title: Probable AD 28

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417022_S01_GE1_107_Sep09_1_3


title: OVCA-CellLine-HCC5023CL_SNP6


title: OVCA-CellLine-HCC5050CL_SNP6


title: Probable AD 27

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417022_S01_GE1_107_Sep09_1_2


title: OVCA-Tumour-HCC5032T_SNP6

value: Tumour


title: OVCA-CellLine-HCC5018CL_SNP6

value: Female


title: OVCA-BloodLine-HCC5050BL_SNP6


title: OVCA-Tumour-HCC5023T_SNP6


title: OVCA-CellLine-HCC5048CL_SNP6


title: OVCA-Tumour-HCC5050T_SNP6


title: OVCA-BloodLine-HCC5032BL_SNP6


title: Probable AD 26

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417022_S01_GE1_107_Sep09_1_1


title: OVCA-Tumour-HCC5018T_SNP6


title: OVCA-BloodLine-HCC5030BL_SNP6


title: OVCA-Tumour-HCC5024T_SNP6


title: OVCA-BloodLine-HCC5023BL_SNP6


title: Non-demented control 24

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417021_S01_GE1_107_Sep09_2_3


title: OVCA-BloodLine-HCC5018BL_SNP6


title: OVCA-BloodLine-HCC5048BL_SNP6


title: OVCA-Tumour-HCC5036T_SNP6


title: Non-demented control 25

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417021_S01_GE1_107_Sep09_2_4


title: Non-demented control 23

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417021_S01_GE1_107_Sep09_2_2


title: OVCA-Tumour-HCC5012T_SNP6


title: OVCA-BloodLine-HCC5012BL_SNP6


title: Non-demented control 22

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417021_S01_GE1_107_Sep09_2_1


title: OVCA-CellLine-HCC5036CL_SNP6


title: Non-demented control 21

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417021_S01_GE1_107_Sep09_1_4


title: OVCA-Tumour-HCC5048T_SNP6


title: Non-demented control 20

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417021_S01_GE1_107_Sep09_1_3


title: Non-demented control 18

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417021_S01_GE1_107_Sep09_1_1


title: Non-demented control 19

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417021_S01_GE1_107_Sep09_1_2


title: Non-demented control 17

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417014_S01_GE1_107_Sep09_2_4


title: Probable AD 25

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417014_S01_GE1_107_Sep09_2_3


title: OVCA-BloodLine-HCC5036BL_SNP6


title: Non-demented control 16

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417014_S01_GE1_107_Sep09_2_2


title: Probable AD 24

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417014_S01_GE1_107_Sep09_1_4


title: Probable AD 23

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417013_S01_GE1_107_Sep09_2_4


title: Probable AD 22

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417013_S01_GE1_107_Sep09_2_3


title: Probable AD 21

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417013_S01_GE1_107_Sep09_1_4


title: OVCA-BloodLine-HCC5022BL_SNP6


title: Probable AD 20

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417013_S01_GE1_107_Sep09_1_3


title: OVCA-CellLine-HCC5022CL_SNP6


title: Probable AD 19

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417013_S01_GE1_107_Sep09_1_2


title: Probable AD 18

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417012_S01_GE1_107_Sep09_2_4


title: Probable AD 16

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417012_S01_GE1_107_Sep09_1_4


title: Probable AD 17

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417012_S01_GE1_107_Sep09_2_3


title: Probable AD 15

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417012_S01_GE1_107_Sep09_1_2


title: OVCA-Tumour-HCC5022T_SNP6


title: Sort-purified (CD8/Thy1.1)  TCR SV40-I CD8 T cells from pre-malignant (liver) lesions 32-34d post tumor initiation rep4

city: New York

first: Andrea

last: Schietinger

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: D32-34 TCR SV40-I_4

scan_protocol: BeadChips were scanned on an Illumina BeadArray Reader

data_processing: Signal intensities were quantile normalized using the Bioconductor package lumi (v.2.14.1).

source_name: mouse splenocytes

label_protocol: Illumina TotalPrep RNA Amplification Kit (Applied Biosystems)

extract_protocol: After FACS-sorting , T-cells were washed twice with cold PBS and cell pellets were frozen and stored at -80C until all samples were collected. RNA was isolated using Qiagen RNeasy Plus Mini and Micro Kit per the manufacturer’s instructions and the yield was determined on a Qubit® 2.0 Fluorometer (Life Technologies, Grand Island, NY). Samples were subsequently analyzed for RNA integrity using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA). RNA that was determined to be of high quality (RINe ≥ 6.5) was amplified using the Ovation® PicoSL WTA System V2 (NuGEN Technologies, Inc., San Carlos, CA), biotin labeled using the Encore® BiotinIL Module (NuGEN Technologies, Inc., San Carlos, CA), and subsequently processed on a MouseRef-8 v2.0 Expression BeadChip (Illumina, Inc., San Diego, CA).

treatment_protocol: D32-34 TCR SV40-I: Naive TCR SV40-I CD8 T cells (Thy1.1) were adoptively transferred into  ASTxCreERT2 mice; 1-2  days later mice were treated with tamoxifen; 34 days post tamoxifen treatment, donor T cells were isolated from pre-malignant lesions from livers of ASTxCreERT2 and flow sorted using the antibodies CD8 and Thy1.1.

value: TCR SV40-I transgenic CD8 T cells

tag: cell subtype

value: Sort-purified (CD8/Thy1.1)  TCR SV40-I CD8 T cells isolated from pre-malignant (liver) lesions 32-34 days post tumor initiation


title: Sort-purified (CD8/Thy1.1)  TCR SV40-I CD8 T cells from pre-malignant (liver) lesions 32-34d post tumor initiation rep2

description: D32-34 TCR SV40-I_2

treatment_protocol: D32-34 TCR SV40-I: Naive TCR SV40-I CD8 T cells (Thy1.1) were adoptively transferred into  ASTxCreERT2 mice; 1-2  days later mice were treated with tamoxifen; 33 days post tamoxifen treatment, donor T cells were isolated from pre-malignant lesions from livers of ASTxCreERT2 and flow sorted using the antibodies CD8 and Thy1.1.


title: Probable AD 14

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800417012_S01_GE1_107_Sep09_1_1


title: Sort-purified (CD8/Thy1.1)  TCR SV40-I CD8 T cells from pre-malignant (liver) lesions 32-34d post tumor initiation rep3

description: D32-34 TCR SV40-I_3


title: Sort-purified (CD8/Thy1.1)  TCR SV40-I CD8 T cells from pre-malignant (liver) lesions 32-34d post tumor initiation rep1

description: D32-34 TCR SV40-I_1

treatment_protocol: D32-34 TCR SV40-I: Naive TCR SV40-I CD8 T cells (Thy1.1) were adoptively transferred into  ASTxCreERT2 mice; 1-2  days later mice were treated with tamoxifen; 32 days post tamoxifen treatment, donor T cells were isolated from pre-malignant lesions from livers of ASTxCreERT2 and flow sorted using the antibodies CD8 and Thy1.1.


title: Non-demented control 14

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416967_S01_GE1_107_Sep09_2_4

value: male


title: OVCA-CellLine-HCC5019CL_SNP6


title: Non-demented control 13

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416967_S01_GE1_107_Sep09_2_3


title: Sort-purified (CD8/Thy1.1)  TCR SV40-I CD8 T cells from pre-malignant (liver) lesions 8-12d post tumor initiation rep3

description: D8-12 TCR SV40-I_3

treatment_protocol: D8-12 TCR SV40-I: Naive TCR SV40-I CD8 T cells (Thy1.1) were adoptively transferred into  ASTxCreERT2 mice; 1-2  days later mice were treated with tamoxifen; 9  days post tamoxifen treatment, donor T cells were isolated from pre-malignant lesions from livers of ASTxCreERT2 mice and flow sorted using the antibodies CD8 and Thy1.1.

value: Sort-purified (CD8/Thy1.1)  TCR SV40-I CD8 T cells isolated from pre-malignant (liver) lesions 8-12 days post tumor initiation


title: OVCA-Xenograft-HCC5048X_SNP6

description: HCC5048X (this sample is identified as TX-OV-132x in the work of Reynolds et al.)

source_name: OVCA-Xenograft

value: Xenograft


title: Non-demented control 11

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416967_S01_GE1_107_Sep09_2_1

value: Non-demented control


title: Sort-purified (CD8/Thy1.1)  TCR SV40-I CD8 T cells from pre-malignant (liver) lesions 8-12d post tumor initiation rep1

description: D8-12 TCR SV40-I_1

treatment_protocol: D8-12 TCR SV40-I: Naive TCR SV40-I CD8 T cells (Thy1.1) were adoptively transferred into  ASTxCreERT2 mice; 1-2  days later mice were treated with tamoxifen; 8  days post tamoxifen treatment, donor T cells were isolated from pre-malignant lesions from livers of ASTxCreERT2 mice and flow sorted using the antibodies CD8 and Thy1.1.


title: OVCA-Xenograft-HCC5012X_SNP6

description: HCC5012X (this sample is identified as TX-OV-143x in the work of Reynolds et al.)


title: OVCA-Tumour-HCC5019T_SNP6


title: OVCA-BloodLine-HCC5019BL_SNP6


title: Probable AD 13

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416967_S01_GE1_107_Sep09_1_4

value: whole blood


title: Probable AD 12

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416967_S01_GE1_107_Sep09_1_2

value: female


title: Non-demented control 12

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800416967_S01_GE1_107_Sep09_2_2


title: Probable AD 11

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416966_S01_GE1_107_Sep09_2_3

value: Probable Alzheimer's Disease


title: Sort-purified (CD8/Thy1.1) effector TCR SV40-I CD8 T cells replicate#1

description: Effector 1

treatment_protocol: Effector TCR SV40-I CD8 T cells: Naive TCR SV40-I CD8 T cells (Thy1.1) were adoptively transferred into B6 (Thy1.2) wild-type mice; one day later mice were immunized with a listeria strain expressing the SV40-I epitope; one week post listeria infection, donor T cells were isolated from spleens of infected mice and flow sorted using the antibodies CD8 and Thy1.1 (= Effector CD8 T cells).


title: OVCA-CellLine-HCC5044CL_SNP6


title: Sort-purified (CD8/Thy1.1) effector TCR SV40-I CD8 T cells replicate#2

description: Effector 2

treatment_protocol: Effector TCR SV40-I CD8 T cells: Naive TCR SV40-I CD8 T cells (Thy1.1) were adoptively transferred into  B6 (Thy1.2) wild-type mice; one day later mice were immunized with a listeria strain expressing the SV40-I epitope; one week post listeria infection, donor T cells were isolated from spleens of infected mice and flow sorted using the antibodies CD8 and Thy1.1 (= Effector CD8 T cells).


title: OVCA-Xenograft-HCC5023X_SNP6

description: HCC5023X (this sample is identified as TX-OV-075x in the work of Reynolds et al.)


title: Sort-purified (CD8/Thy1.1)  TCR SV40-I CD8 T cells from pre-malignant (liver) lesions 8-12d post tumor initiation rep2

description: D8-12 TCR SV40-I_2

treatment_protocol: D8-12 TCR SV40-I: Naive TCR SV40-I CD8 T cells (Thy1.1) were adoptively transferred into  ASTxCreERT2 mice; 1-2  days later mice were treated with tamoxifen; 12  days post tamoxifen treatment, donor T cells were isolated from pre-malignant lesions from livers of ASTxCreERT2 mice and flow sorted using the antibodies CD8 and Thy1.1.


title: OVCA-CellLine-HCC5075CL_SNP6


title: OVCA-BloodLine-HCC5044BL_SNP6


title: OVCA-BloodLine-HCC5076BL_SNP6


title: OVCA-Tumour-HCC5076T_SNP6


title: OVCA-Tumour-HCC5075T_SNP6


title: Probable AD 10

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416966_S01_GE1_107_Sep09_2_2


title: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#3

description: Naïve 3

treatment_protocol: Naïve (CD44 low) CD8 T cells were isolated from spleens of transgenic TCR SV40-I (Thy1.1) transgenic mice (transgenic mice expressing CD8 T cells specific for epitope I of the SV40 large T antigen) and sorted by flow cytometric analysis for CD8+/CD44low.


title: OVCA-CellLine-HCC5076CL_SNP6


title: OVCA-CellLine-HCC5020CL_SNP6


title: Non-demented control 15

description:
Gene expression of non-demented contol subject using human blood
US81403231_252800417012_S01_GE1_107_Sep09_1_3


title: Probable AD 9

description:
Gene expression of Alzheimer's disease patient using human blood
US81403231_252800416966_S01_GE1_107_Sep09_1_4


title: Sort-purified (CD8/Thy1.1) effector TCR SV40-I CD8 T cells replicate#3

description: Effector 3


title: OVCA-BloodLine-HCC5075BL_SNP6


title: OVCA-Tumour-HCC5006T_SNP6


title: OVCA-BloodLine-HCC5079BL_SNP6