title: GFP1_1578G

city: Boston

first: Margaret

last: Gregor

state: MA

address: 665 Huntington Ave

department: Genetics and Complex Diseases

institute: Harvard School of Public Health

description: gene expression data from adipocytes overexpressing GFP

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol. (Affymetrix GeneChip Manual (rev.1.3))

scan_protocol: The samples were hybridized and scanned according to Affymetrix protocol for Mouse 430A 2.0 chips. (Affymetrix GeneChip Manual (rev.1.3))

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as normalization method. Genome profiling was performed at Harvard Medical School-Partners Healthcare Center for Genetics and Genomics using an Affymetrics platform (Cambridge, MA).

source_name: adipocytes expressing GFP

label_protocol: Affymetrix protocol

growth_protocol: F442A preadipocytes were differentiated according to standard adipogenesis protocol. (see Gregor et al., Cell Reports 2013)

treatment_protocol: Mature (day 6- 8 differentiation) adipocytes were infected with adenovirus expressing sXBP1 or GFP.  After 4-6 days of infection cells were harvested for analysis.

value: F442A cultured adipocyte

tag: cell line

tag: back ground strain

value: Swiss


title: sXBP4_1578T

status: Public on Apr 19 2013

type: RNA

country: USA

description: gene expression data from adipocytes overexpressing spliced XBP1

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: adipocytes expressing spliced XBP1

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

tag: cell type


title: GFP4_1578J


title: 134T_mRNA

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using quantile normalization.
Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system.

organism: Homo sapiens

source_name: Breast tissue

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Ohio State Microarray Core Facility

extract_protocol: RNA was isolated from FFPE tissue using Recover ALL kit (Ambion)

tag: tissue

value: Breast

tag: status

value: primary triple negative cancer

tag: gender

value: Female

tag: age at diagnosis

tag: best stage

tag: grade


title: 27T_mRNA


title: GFP2_1578H


title: GFP3_1578I


title: sXBP2_1578R


title: sXBP3_1578S


title: 132T_mRNA


title: sXBP1_1578Q


title: 130T_mRNA


title: 13T_mRNA


title: 131T_mRNA


title: 129T_mRNA


title: 128T_mRNA


title: 127T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL271 tumor longitudinal sample (CLL271T_longitudinal)

type: genomic

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

hyb_protocol: Affymetrix Hybridization Oven 640 for 16 hrs at 50 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing:
Affymetrix CEL files for each DNA sample were analyzed using Affymetrix's Genotyping Console software for initial quality control, followed by use of the Affymetrix “Birdseed” algorithm to determine final call rates and quality. Call rates for the longitudinal group of samples included in this report were between 95.33% and 99.68%, with a mean and median call rate of 98.67% and 98.92%, respectively.  For normal and enrollment sample call rate information, please refer to GEO accession number GSE30777.  Sample copy number heatmap displays were obtained from CEL files through use of the freely available software dChip adapted to operate in a 64-bit environment.
dChip SNP software (www.dchip.org), build date Feb 25, 2009, compatible with 64-bit OS, analyzed the CEL files.  CEL files were normalized using the invariant set method, followed by model-based expression index calculations, and finally inferred copy number data were generated using the software's median-smoothing algorithm.

molecule: genomic DNA

label_protocol: The DNA was prepared for hybridization to Affymetrix SNP 6.0 arrays according to the manufacturer's recommendations.

extract_protocol: Highly pure, single-positive CD19+ or CD3+ cells (and, in eleven cases, buccal swabs) were digested overnight in 100 mM Tris pH 8.0, 50 mM EDTA, 50 mM NaCl, 0.5% SDS and 100 μg/ml of Proteinase K (Invitrogen) at 560C. DNA was extracted using phenol-chloroform and precipitated using ammonium acetate, ethanol and glycogen.

treatment_protocol: Not applicable

tag: disease state

value: tumor

tag: subject

tag: time reference

value: longitudinal

value: FACS-sorted CD19+ cells


title: primary human: blood; FACS-sorted CD19+ cells CLL253 tumor longitudinal sample (CLL253T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL254 tumor longitudinal sample (CLL254T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL275 tumor longitudinal sample (CLL275T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL269 tumor longitudinal sample (CLL269T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL251 tumor longitudinal sample (CLL251T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL247 tumor longitudinal sample (2 of 2) (CLL247T_long_May2012)


title: 126T_mRNA


title: 124T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL270 tumor longitudinal sample (CLL270T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL259 tumor longitudinal sample (CLL259T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL247 tumor longitudinal sample (1 of 2) (CLL247T_long_Apr2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL248 tumor longitudinal sample (CLL248T_longitudinal)


title: 125T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL249 tumor longitudinal sample (CLL249T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL229 tumor longitudinal sample (CLL229T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL245 tumor longitudinal sample (CLL245T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL242 tumor longitudinal sample (CLL242T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL220 tumor longitudinal sample (1 of 2) (CLL220T_long_Aug2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL237 tumor longitudinal sample (CLL237T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL223 tumor longitudinal sample (1 of 2) (CLL223T_long_Dec2010)


title: 123T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL220 tumor longitudinal sample (2 of 2) (CLL220T_long_Jun2012)


title: 122T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL239 tumor longitudinal sample (CLL239T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL222 tumor longitudinal sample (1 of 2) (CLL222T_long_Jun2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL231 tumor longitudinal sample (CLL231T_longitudinal)


title: 121T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL222 tumor longitudinal sample (2 of 2) (CLL222T_long_Jun2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL216 tumor longitudinal sample (CLL216T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL223 tumor longitudinal sample (2 of 2) (CLL223T_long_Jul2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL241 tumor longitudinal sample (CLL241T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL219 tumor longitudinal sample (CLL219T_long_May2011)


title: 120T_mRNA


title: 12T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL217 tumor longitudinal sample (CLL217T_longitudinal)


title: 119T_mRNA


title: 117T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL212 tumor longitudinal sample (CLL212T_longitudinal)


title: 116T_mRNA


title: 115T_mRNA


title: 114T_mRNA


title: 113T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL213 tumor longitudinal sample (CLL213T_long_Apr2010)


title: 112T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL210 tumor longitudinal sample (CLL210T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL206 tumor longitudinal sample (CLL206T_longitudinal)


title: 111T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL207 tumor longitudinal sample (CLL207T_long_Aug2010_1)


title: primary human: blood; FACS-sorted CD19+ cells CLL205 tumor longitudinal sample (CLL205T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL203 tumor longitudinal sample (CLL203T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL202 tumor longitudinal sample (CLL202T_longitudinal)


title: 110T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL197 tumor longitudinal sample (CLL197T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL209 tumor longitudinal sample (CLL209T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL200 tumor longitudinal sample (CLL200T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL198 tumor longitudinal sample (CLL198T_longitudinal)


title: 11T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL193 tumor longitudinal sample (2 of 2) (CLL193T_long_Jan2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL199 tumor longitudinal sample (CLL199T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL195 tumor longitudinal sample (CLL195T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL193 tumor longitudinal sample (1 of 2) (CLL193T_long_April2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL194 tumor longitudinal sample (2 of 2) (CLL194T_long_Feb2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL187 tumor longitudinal sample (2 of 2) (CLL187T_long_Feb2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL192 tumor longitudinal sample (CLL192T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL196 tumor longitudinal sample (CLL196T_longitudinal)


title: 109T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL194 tumor longitudinal sample (1 of 2) (CLL194T_long_Nov2009)


title: primary human: blood; FACS-sorted CD19+ cells CLL187 tumor longitudinal sample (1 of 2) (CLL187T_long_Feb2010)


title: 101T B5_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL180 tumor longitudinal sample (CLL180T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL186 tumor longitudinal sample (CLL186T_longitudinal)


title: 108T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL176 tumor longitudinal sample (CLL176T_longitudinal)


title: 101T A3_mRNA


title: 100T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL185 tumor longitudinal sample (CLL185T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL189 tumor longitudinal sample (CLL189T_longitudinal)


title: 10T_mRNA


title: 1T_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL184 tumor longitudinal sample (CLL184T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL178 tumor longitudinal sample (CLL178T_longitudinal)


title: 120N_mRNA

value: normal


title: primary human: blood; FACS-sorted CD19+ cells CLL170 tumor longitudinal sample (CLL170T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL167 tumor longitudinal sample (2 of 2) (CLL167T_long_Apr2012)


title: 113N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL168 tumor longitudinal sample (CLL168T_long_Jan2008_2)


title: primary human: blood; FACS-sorted CD19+ cells CLL167 tumor longitudinal sample (1 of 2) (CLL167T_long_Apr2010)


title: 112N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL161 tumor longitudinal sample (CLL161T_longitudinal)


title: 117N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL154 tumor longitudinal sample (CLL154T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL160 tumor longitudinal sample (2 of 2) (CLL160T_long_Feb2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL156 tumor longitudinal sample (2 of 2) (CLL156T_long_Apr2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL156 tumor longitudinal sample (1 of 2) (CLL156T_long_Jan2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL152 tumor longitudinal sample (1 of 2) (CLL152T_long_Jan2010)


title: 111N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL141 tumor longitudinal sample (CLL141T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL152 tumor longitudinal sample (2 of 2) (CLL152T_long_Jul2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL146 tumor longitudinal sample (CLL146T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL155 tumor longitudinal sample (CLL155T_longitudinal)


title: 197N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL143 tumor longitudinal sample (CLL143T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL148 tumor longitudinal sample (CLL148T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL160 tumor longitudinal sample (1 of 2) (CLL160T_long_March2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL137 tumor longitudinal sample (CLL137T_long_4Nov2011)


title: 192N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL139 tumor longitudinal sample (2 of 2) (CLL139T_long_Aug2012)


title: 187N_mRNA


title: 196N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL139 tumor longitudinal sample (1 of 2) (CLL139T_long_Jan2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL134 tumor longitudinal sample (CLL134T_longitudinal)


title: 181N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL140 tumor longitudinal sample (2 of 2) (CLL140T_long_May2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL135 tumor longitudinal sample (1 of 2) (CLL135T_long_Dec2010)


title: 179N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL135 tumor longitudinal sample (2 of 2) (CLL135T_long_May2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL136 tumor longitudinal sample (2 of 2) (CLL136T_long_Nov2011_1)


title: primary human: blood; FACS-sorted CD19+ cells CLL136 tumor longitudinal sample (1 of 2) (CLL136T_long19Oct2009)


title: primary human: blood; FACS-sorted CD19+ cells CLL132 tumor longitudinal sample (2 of 2) (CLL132T_long_Feb2012)


title: 178N_mRNA


title: 177N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL130 tumor longitudinal sample (CLL130T_long_Feb2008_1)


title: 176N_mRNA


title: 175N_mRNA


title: 174N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL126 tumor longitudinal sample (CLL126T_long_July2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL140 tumor longitudinal sample (1 of 2) (CLL140T_long_Mar2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL129 tumor longitudinal sample (CLL129T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL131 tumor longitudinal sample (2 of 2) (CLL131T_long_Feb2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL127 tumor longitudinal sample (CLL127T_longitudinal)


title: 172N_mRNA


title: 170N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL131 tumor longitudinal sample (1 of 2) (CLL131T_long_Mar2010)


title: 167N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL124 tumor longitudinal sample (CLL124T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL120 tumor longitudinal sample (2 of 2) (CLL120T_long_Jul2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL121 tumor longitudinal sample (2 of 2) (CLL121T_long_Jul2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL118 tumor longitudinal sample (2 of 2) (CLL118T_long_Jul2012)


title: 168N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL116 tumor longitudinal sample (CLL116T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL121 tumor longitudinal sample (1 of 2) (CLL121T_long_Jun2009)


title: primary human: blood; FACS-sorted CD19+ cells CLL113 tumor longitudinal sample (CLL113T_longitudinal_2)


title: primary human: blood; FACS-sorted CD19+ cells CLL118 tumor longitudinal sample (1 of 2) (CLL118T_long_Jul2010)


title: 161N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL120 tumor longitudinal sample (1 of 2) (CLL120T_long_Aug2008)


title: 163N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL114 tumor longitudinal sample (CLL114T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLLl11 tumor longitudinal sample (CLLl117T_long_Jul2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL108 tumor longitudinal sample (CLL108T_longitudinal_2)


title: primary human: blood; FACS-sorted CD19+ cells CLL115 tumor longitudinal sample (CLL115T_longitudinal)


title: 160N_mRNA


title: 157N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL109 tumor longitudinal sample (CLL109T_long_Jun2011_2)


title: primary human: blood; FACS-sorted CD19+ cells CLL132 tumor longitudinal sample (1 of 2) (CLL132T_long_Feb2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL110 tumor longitudinal sample (CLL110T_long2_April2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL099 tumor longitudinal sample (CLL099T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL112 tumor longitudinal sample (CLL112T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL097 tumor longitudinal sample (CLL097T_longitudinal)


title: Tumor_99

data_processing: Data were collected as NanoString RCC files and provided as an Excel spreadsheet. Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system. The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using vsn normalization.


title: primary human: blood; FACS-sorted CD19+ cells CLL125 tumor longitudinal sample (CLL125T_longitudinal)


title: 142N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL101 tumor longitudinal sample (CLL101T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL094 tumor longitudinal sample (2 of 2) (CLL094T_long_Jan2008)


title: primary human: blood; FACS-sorted CD19+ cells CLL117 tumor longitudinal sample (CLL117T_long_May2011_2)


title: primary human: blood; FACS-sorted CD19+ cells CLL096 tumor longitudinal sample (1 of 2) (CLL096T_long_Oct2009)


title: 138N_mRNA


title: 140N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL111 tumor longitudinal sample (CLL111T_longitudinal)


title: Tumor_93


title: Tumor_97


title: primary human: blood; FACS-sorted CD19+ cells CLL094 tumor longitudinal sample (1 of 2) (CLL094T_long_8Nov2010)


title: 134N_mRNA


title: 151N_mRNA


title: Tumor_98


title: 131N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL089 tumor longitudinal sample (1 of 2) (CLL089T_long_4Nov2009)


title: Tumor_92


title: Tumor_83


title: Tumor_91


title: Tumor_8


title: primary human: blood; FACS-sorted CD19+ cells CLL089 tumor longitudinal sample (2 of 2) (CLL089T_long_Dec2011)


title: primary human: blood; FACS-sorted CD19+ cells CLL104 tumor longitudinal sample (CLL104T_longitudinal_2)


title: Tumor_79


title: 130N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL096 tumor longitudinal sample (2 of 2) (CLL096T_long_May2012)


title: 128N_mRNA


title: Tumor_73


title: Tumor_72


title: primary human: blood; FACS-sorted CD19+ cells CLL084 tumor longitudinal sample (1 of 3) (CLL084T_long_19May2008)


title: primary human: blood; FACS-sorted CD19+ cells CLL085 tumor longitudinal sample (CLL085T_longitudinal)


title: Tumor_70


title: primary human: blood; FACS-sorted CD19+ cells CLL086 tumor longitudinal sample (CLL086T_longitudinal)


title: 135N_mRNA


title: Tumor_69


title: primary human: blood; FACS-sorted CD19+ cells CLL083 tumor longitudinal sample (CLL083T_longitudinal)


title: 124N_mRNA


title: 126N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL087 tumor longitudinal sample (CLL087T_longitudinal)


title: 132N_mRNA


title: 121N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL084 tumor longitudinal sample (2 of 3) (CLL084T_long_Aug2010)


title: Tumor_67


title: 108N_mRNA


title: Tumor_65


title: TAS10-15-9_mRNA

source_name: Lymph node

value: Lymph Node

value: Metastatic


title: Tumor_64


title: TAS10-15-8_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL081 tumor longitudinal sample (CLL081T_long_Jan2007_2)


title: primary human: blood; FACS-sorted CD19+ cells CLL090 tumor longitudinal sample (CLL090T_longitudinal)


title: Tumor_66


title: Tumor_63


title: primary human: blood; FACS-sorted CD19+ cells CLL084 tumor longitudinal sample (3 of 3) (CLL084T_long_May2012)


title: Tumor_62


title: TAS10-15-6_mRNA


title: Tumor_61


title: TAS10-15-56_mRNA


title: TAS10-15-7_mRNA


title: 127N_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL074 tumor longitudinal sample (CLL074T_long_May2012)


title: primary human: blood; FACS-sorted CD19+ cells CLL072 tumor longitudinal sample (CLL072T_long_12Oct2007)


title: primary human: blood; FACS-sorted CD19+ cells CLL091 tumor longitudinal sample (CLL091T_long_14Dec2009)


title: primary human: blood; FACS-sorted CD19+ cells CLL069 tumor longitudinal sample (CLL069T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL079 tumor longitudinal sample (CLL079T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL078 tumor longitudinal sample (CLL078T_longitudinal)


title: TAS10-15-55_mRNA


title: 125N_mRNA


title: TAS10-15-54_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL075 tumor longitudinal sample (CLL075T_longitudinal)


title: Tumor_60


title: Tumor_6


title: primary human: blood; FACS-sorted CD19+ cells CLL066 tumor longitudinal sample (CLL066T_longitudinal)


title: Tumor_59


title: primary human: blood; FACS-sorted CD19+ cells CLL064 tumor longitudinal sample (CLL064T_longitudinal)


title: TAS10-15-53_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL060 tumor longitudinal sample (CLL060T_longitudinal)


title: Tumor_44


title: primary human: blood; FACS-sorted CD19+ cells CLL056 tumor longitudinal sample (CLL056T_longitudinal)


title: TAS10-15-5_mRNA


title: Tumor_57


title: TAS10-15-52_mRNA


title: TAS10-15-49_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL063 tumor longitudinal sample (CLL063T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL061 tumor longitudinal sample (CLL061T_longitudinal)


title: Tumor_56


title: TAS10-15-48_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL062 tumor longitudinal sample (CLL062T_longitudinal)


title: Tumor_40


title: TAS10-15-51_mRNA


title: Tumor_4


title: Tumor_39


title: Tumor_54


title: TAS10-15-47_mRNA


title: TAS10-15-50_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL049 tumor longitudinal sample (CLL049T_longitudinal)


title: TAS10-15-46_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL058 tumor longitudinal sample (CLL058T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL046 tumor longitudinal sample (CLL046T_long_2Nov2009)


title: primary human: blood; FACS-sorted CD19+ cells CLL055 tumor longitudinal sample (CLL055T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL051 tumor longitudinal sample (CLL051T_longitudinal)


title: Tumor_35


title: Tumor_41


title: Tumor_32


title: TAS10-15-45_mRNA


title: Tumor_31


title: Tumor_30


title: TAS10-15-43_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL048 tumor longitudinal sample (CLL048T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL045 tumor longitudinal sample (CLL045T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL047 tumor longitudinal sample (CLL047T_longitudinal)


title: TAS10-15-44_mRNA


title: TAS10-15-42_mRNA


title: Human Thymus tissue (Dptot)

city: Istanbul

first: ozden

last: hatirnazng

address: IU DETAE Vakıf Gureba C

country: Turkey

institute: Istanbul University

description: Human Whole Genome Gene Expression

hyb_protocol: Following fragmentation, cRNA samples were hybridized for 16 hr at 45C on GeneChip HU-133 Plus.2 Whole Genome Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip scanner 3000

data_processing: Raw microarray data was normalized by the robust multiarray average (RMA) .The data that shows less than 20% expression values and a 2-fold change in either direction from the genes median value is excluded.

source_name: Human Thymus tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: 2-3 cc bone marrow samples were obtained from childhood T-ALL patients at the time of diagnosis

extract_protocol: Total RNA was isolated with Qiagen Rneasy Plus kit according to the manufacturer's protocol

treatment_protocol: Control thymocyte subsets were sorted by FACS Aria II as described by Weerkamp et al.PNAS 2006

value: DP3poz tot(CD3,CD4,CD8poz)

tag: sample subtype

value: Thymocyte


title: TAS10-15-41_mRNA


title: Tumor_25


title: Tumor_29


title: TAS10-15-40_mRNA


title: Childhood T-ALL (T89)

description: Human Whole Genome Gene Expression

source_name: Human bone marrow at the time of diagnosis

value: Childhood T-cell Acute Lymphoblastic Leukemia

value: patient


title: Tumor_20


title: TAS10-15-4_mRNA


title: Tumor_2


title: TAS10-15-39_mRNA


title: Human Thymus tissue (DN)

description: Human Whole Genome Gene Expression

value: DN(CD4CD8 neg)


title: Childhood T-ALL (T53)

description: Human Whole Genome Gene Expression


title: TAS10-15-38_mRNA


title: Tumor_19


title: Tumor_18


title: Childhood T-ALL (T18)

description: Human Whole Genome Gene Expression


title: TAS10-15-37_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL043 tumor longitudinal sample (CLL043T_longitudinal)


title: TAS10-15-36_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL036 tumor longitudinal sample (CLL036T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL044 tumor longitudinal sample (CLL044T_longitudinal)


title: Childhood T-ALL (T66)

description: Human Whole Genome Gene Expression


title: Tumor_167


title: Human Thymus tissue (DP3negative)

description: Human Whole Genome Gene Expression


title: primary human: blood; FACS-sorted CD19+ cells CLL039 tumor longitudinal sample (CLL039T_longitudinal)


title: Tumor_166


title: TAS10-15-35_mRNA


title: Human Thymus tissue (Total)

description: Human Whole Genome Gene Expression

value: Thymus


title: primary human: blood; FACS-sorted CD19+ cells CLL038 tumor longitudinal sample (CLL038T_longitudinal)


title: Childhood T-ALL (T27)

description: Human Whole Genome Gene Expression


title: primary human: blood; FACS-sorted CD19+ cells CLL035 tumor longitudinal sample (CLL035T_long_one year)


title: primary human: blood; FACS-sorted CD19+ cells CLL040 tumor longitudinal sample (CLL040T_longitudinal)


title: TAS10-15-33_mRNA


title: Tumor_161


title: TAS10-15-34_mRNA


title: Tumor_162


title: primary human: blood; FACS-sorted CD19+ cells CLL033 tumor longitudinal sample (CLL033T_longitudinal)


title: Tumor_159


title: Human Thymus tissue (SP8)

description: Human Whole Genome Gene Expression

value: Single Positive CD8


title: primary human: blood; FACS-sorted CD19+ cells CLL029 tumor longitudinal sample (CLL029T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL027 tumor longitudinal sample (CLL027T_longitudinal)


title: TAS10-15-32_mRNA


title: Childhood T-ALL (T99)

description: Human Whole Genome Gene Expression


title: Childhood T-ALL (T86)

description: Human Whole Genome Gene Expression


title: TAS10-15-31_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL030 tumor longitudinal sample (CLL030T_longitudinal)


title: TAS10-15-30_mRNA


title: Tumor_157


title: Tumor_155


title: Tumor_150


title: primary human: blood; FACS-sorted CD19+ cells CLL041 tumor longitudinal sample (CLL041T_longitudinal)


title: Childhood T-ALL (T98)

description: Human Whole Genome Gene Expression


title: Childhood T-ALL (T37)

description: Human Whole Genome Gene Expression


title: primary human: blood; FACS-sorted CD19+ cells CLL025 tumor longitudinal sample (CLL025T_longitudinal)


title: Childhood T-ALL (T84)

description: Human Whole Genome Gene Expression


title: Tumor_149


title: Childhood T-ALL (T07)

description: Human Whole Genome Gene Expression


title: TAS10-15-27_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL026 tumor longitudinal sample (CLL026T_longitudinal)


title: Tumor_148


title: primary human: blood; FACS-sorted CD19+ cells CLL024 tumor longitudinal sample (CLL024T_longitudinal)


title: TAS10-15-26_mRNA


title: Tumor_147


title: primary human: blood; FACS-sorted CD19+ cells CLL022 tumor longitudinal sample (CLL022T_longitudinal)


title: Human Thymus tissue (ISP)

description: Human Whole Genome Gene Expression

value: ISP(Immature single positive)


title: TAS10-15-25_mRNA


title: TAS10-15-24_mRNA


title: Tumor_160

value: Breast


title: Human Thymus tissue (SP4)

description: Human Whole Genome Gene Expression

value: Single Positive CD4


title: Childhood T-ALL (T70)

description: Human Whole Genome Gene Expression


title: Childhood T-ALL (T112)

description: Human Whole Genome Gene Expression


title: Tumor_140

value: primary triple negative cancer


title: TAS10-15-23_mRNA

value: Female


title: Tumor_138


title: Tumor_136


title: primary human: blood; FACS-sorted CD19+ cells CLL021 tumor longitudinal sample (CLL021T_longitudinal)

value: tumor

value: longitudinal


title: TAS10-15-22_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL012 tumor longitudinal sample (2 of 2) (CLL012T_long_Sept2011)

value: FACS-sorted CD19+ cells


title: primary human: blood; FACS-sorted CD19+ cells CLL012 tumor longitudinal sample (1 of 2) (CLL012T_long_5Oct2009)


title: Childhood T-ALL (T80)

description: Human Whole Genome Gene Expression


title: primary human: blood; FACS-sorted CD19+ cells CLL017 tumor longitudinal sample (CLL017T_longitudinal)


title: Tumor_135


title: TAS10-15-21_mRNA

value: Lymph Node


title: Childhood T-ALL (T77)

description: Human Whole Genome Gene Expression


title: primary human: blood; FACS-sorted CD19+ cells CLL011 tumor longitudinal sample (CLL011T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL013 tumor longitudinal sample (CLL013T_longitudinal)


title: Childhood T-ALL (T43)

description: Human Whole Genome Gene Expression


title: TAS10-15-3_mRNA

value: Metastatic


title: Tumor_134


title: Tumor_129


title: TAS10-15-2_mRNA


title: Childhood T-ALL (T35)

description: Human Whole Genome Gene Expression


title: TAS10-15-20_mRNA


title: Tumor_128


title: TAS10-15-28_mRNA


title: TAS10-15-19_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL020 tumor longitudinal sample (CLL020T_longitudinal)


title: primary human: blood; FACS-sorted CD19+ cells CLL009 tumor longitudinal sample (CLL009T_longitudinal)


title: Childhood T-ALL (T64)

description: Human Whole Genome Gene Expression


title: Childhood T-ALL (T16)

description: Human Whole Genome Gene Expression


title: TAS10-15-18_mRNA


title: Tumor_125


title: TAS10-15-17_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL010 tumor longitudinal sample (CLL010T_longitudinal)


title: Childhood T-ALL (T142)

description: Human Whole Genome Gene Expression


title: TAS10-15-16_mRNA


title: Tumor_120


title: Tumor_124


title: primary human: blood; FACS-sorted CD19+ cells CLL007 tumor longitudinal sample (CLL007T_longitudinal)


title: Childhood T-ALL (T12)

description: Human Whole Genome Gene Expression


title: Childhood T-ALL (T92)

description: Human Whole Genome Gene Expression


title: Childhood T-ALL (T68)

description: Human Whole Genome Gene Expression


title: TAS10-15-15_mRNA


title: Tumor_118


title: primary human: blood; FACS-sorted CD19+ cells CLL006 tumor longitudinal sample (CLL006T_long_Jan2010)


title: primary human: blood; FACS-sorted CD19+ cells CLL004 tumor longitudinal sample (2 of 2) (CLL004T_long_Aug2012)


title: TAS10-15-14_mRNA


title: TAS10-15-13_mRNA


title: Tumor_112


title: Tumor_111


title: primary human: blood; FACS-sorted CD19+ cells CLL008 tumor longitudinal sample (CLL008T_longitudinal)


title: T 4942 +

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

description: Gene expression of tumors

hyb_protocol: 4 µg of Alexa Fluor® 3 labeled target was hybridized on Whole Mouse Genome Microarrays 4x44K (Agilent) according to NuGEN’s Agilent Solution Application Note #1.

scan_protocol: Immediately after washing, slides were scanned with microarray scanner G2565BA (Agilent).

data_processing: Images were analyzed with Feature Extraction software version 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20100123).  Data was normalized with 75 percentile as instructed in Agilent manual. Probes with max normalized intensity of all samples less than 50 are discarded.

label: Alexa Fluor® 3

source_name: Tumor

label_protocol: RNA isolated from flow-sorted normal mouse colons and mouse colon tumors was amplified together with spike-ins (1 µl of a 1:50,000 dilution per reaction, One-Color RNA Spike-In Kit, Agilent Technologies, Santa Clara, CA) using the Ovation Pico WTA System (NuGEN Technologies, Inc., San Carlos, CA). The amplified cDNA was labeled using the BioPrime® Total Genomic Labeling Module (Invitrogen, Life Technologies, Carlsbad, CA).

extract_protocol: Both DNA and RNA were isolated from the flow-sorted cells without delay using the DNA/RNA AllPrep Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Freshly isolated mouse tissue (normal colon or colon tumor) was washed in ice-cold PBS. Cleaned tissue was minced into 15 ml of collagenase solution [RPMI with collagenase D (5 mg/ml; Roche Applied Science, Indianapolis, IN), FBS (5% v/v) and DNase I (1 µg/ml; Sigma, St. Louis, MO)] using two scalpels and incubated on a platform shaker at 37 °C for one hour. During the incubation period, tissue was gently pipetted up and down (without introducing any bubbles) at least 10 times every 15 minutes to release as many cells as possible from the minced tissue pieces. Next, tissue and media mixture was passed over a 70-µm followed by a 40-µm cell strainer (both BD FalconTM, BD Biosciences, San Jose, CA). To minimize cell death and alteration in gene expression, we immediately continued with staining for flow cytometry. After removal of collagenase solution, cells were incubated in Fc blocking solution [PBS with FBS (2% v/v), CD16/CD32 (2% v/v; BD PharmingenTM, BD Biosciences) and donkey serum (5% v/v; Sigma)] on ice for 20 minutes. Fc blocking solution was then removed and cells were stained with Anti-EpCAM rat monoclonal antibody conjugated to allophycocyanin [1:400 dilution in PBS with FBS (2% v/v) to a total volume of 600 µl for normal mouse colons and 400 to 800 µl for mouse colon tumors depending on tumor size; clone G8.8, eBioscience, San Diego, CA] on ice for 30 min. Cells were then washed and resuspended in 0.5 ml to 1.5 ml (depending on pellet size) of PBS with FBS (2% v/v). To exclude dead cells, 7-AAD (BD PharmingenTM, BD Biosciences) was added shortly before starting the sorting process. Lgr5-EGFP high EpCAM high 7-AAD negative cells and Lgr5-EGFP low EpCAM high 7-AAD negative cells were flow-sorted using a FACSAria II system using FACSDiva software version 6.0 (BD Biosciences). After sorting, cells were collected in RPMI with HEPES (50mM) and FBS (50% v/v), and we immediately continued with DNA and RNA isolation. Data was analyzed using both FACSDiva software version 6.0 (BD Biosciences) or FlowJo software version 9.5.2 (Tree Star Inc., Ashland, OR).

tag: strain

value: flow-sorted tumor cells

value: male

tag: age

value: 5.5 months

tag: lrg5 status

value: high


title: T 3326 -

description: Gene expression of tumors

value: 6.5 months

value: low


title: Childhood T-ALL (T11)

description: Human Whole Genome Gene Expression

value: Childhood T-cell Acute Lymphoblastic Leukemia

value: patient


title: T 4942 -

description: Gene expression of tumors


title: Childhood T-ALL (T87)

description: Human Whole Genome Gene Expression


title: Childhood T-ALL (T02)

description: Human Whole Genome Gene Expression


title: T 3326 +

description: Gene expression of tumors


title: Tumor_11

value: Breast


title: TAS10-15-12_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL004 tumor longitudinal sample (1 of 2) (CLL004T_long_Nov2009)


title: Childhood T-ALL (T21)

description: Human Whole Genome Gene Expression


title: TAS10-15-11_mRNA


title: Tumor_108


title: TAS10-15-1_mRNA


title: primary human: blood; FACS-sorted CD19+ cells CLL001 tumor longitudinal sample (CLL001T_longitudinal)


title: Tumor_104


title: Childhood T-ALL (T88)

description: Human Whole Genome Gene Expression


title: Tumor_103


title: primary human: blood; FACS-sorted CD19+ cells CLL002 tumor longitudinal sample (CLL002T_longitudinal)


title: T 4951 +

description: Gene expression of tumors

value: female


title: Childhood T-ALL (T76)

description: Human Whole Genome Gene Expression


title: Childhood T-ALL (T101)

description: Human Whole Genome Gene Expression


title: T 4951 -

description: Gene expression of tumors


title: Childhood T-ALL (T65)

description: Human Whole Genome Gene Expression


title: T 4946 -

description: Gene expression of tumors


title: primary human: blood; FACS-sorted CD19+ cells  (CLL275T)

value: enrollment


title: Tumor_102

value: primary triple negative cancer


title: Tumor_123


title: Tumor_10


title: Tumor_1


title: T 4946 +

description: Gene expression of tumors


title: T 4943 +

description: Gene expression of tumors


title: primary human: blood; FACS-sorted CD19+ cells  (CLL271T)

value: tumor


title: T 4943 -

description: Gene expression of tumors


title: GC B cell_LMP2A_T75

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Total RNA from FACS-sorted GC B cells

hyb_protocol: 10ug of fragmented cRNA was hybridized to HG-U133 Plus 2.0 microarrays

scan_protocol: Affymetrix Standard protocol  Affymetrix Standard protocol

data_processing: Probe level quantile normalisation  and robust multi-array analysis on the raw CEL files were performed using the affy package of the Bioconductor project using default parameters

source_name: Germinal centre (GC) B cells isolated from tonsils via CD10 enrichment, transfected with LMP2A expression vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 25 ug total RNA

growth_protocol: Germinal centre (GC) B cells were isolated from tonsils via CD10 enrichment

extract_protocol: Isolation of total RNA from sorted cells was performed using the RNeasy® Micro Kit from Qiagen (Crawley, UK) according to the manufacturer’s instructions. RNA from transfected and FACS-sorted GC B cells was amplified with Standard ExpressArt® C&E mRNA amplification kit (Amptech).

treatment_protocol: Enriched CD10+ positive cells were transfected and FACS-sorted

tag: patient

value: CD10+ positive, Germinal Centre (GC) B cells

tag: genotype/variation


title: GC B cell_LMP2A_T78

description: Total RNA from FACS-sorted GC B cells


title: T 4939 -

description: Gene expression of tumors


title: primary human: blood; FACS-sorted CD3+ cells  (CLL271N_CD3)

value: normal

value: FACS-sorted CD3+ cells


title: GC B cell_pSG5_T78

description: Total RNA from FACS-sorted GC B cells

source_name: Germinal centre (GC) B cells isolated from tonsils via CD10 enrichment, transfected with empty vector

value: control


title: primary human: blood; FACS-sorted CD19+ cells  (CLL270T)

value: FACS-sorted CD19+ cells


title: Tumor_101


title: T 4939 +

description: Gene expression of tumors

value: flow-sorted tumor cells


title: GC B cell_LMP2A_T73

description: Total RNA from FACS-sorted GC B cells


title: primary human: blood; FACS-sorted CD19+ cells  (CLL269T)


title: primary human: blood; FACS-sorted CD3+ cells  (CLL270N_CD3)


title: GC B cell_pSG5_T75

description: Total RNA from FACS-sorted GC B cells


title: T 4934 -

description: Gene expression of tumors

value: male

value: 7 months


title: GC B cell_pSG5_T73

description: Total RNA from FACS-sorted GC B cells


title: primary human: blood; FACS-sorted CD3+ cells  (CLL275N_CD3)


title: T 4934 +

description: Gene expression of tumors

value: high


title: dentate gyrus subject #8

city: West 168th Street

first: Scott

middle: a

last: Small

institute: Colubmia University

description: gene expression data from entorhinal cortex subject #8

hyb_protocol: HG-U133A microarrays (Affymetrix) were hybridized with fragmented cRNA for 16 h at 45 C with constant rotation (60g)

scan_protocol: Microarrays were washed and stained on a fluidics station, and scanned using a confocal microscope

data_processing: HG-U133A microarrays were analyzed with Affymetrix Microarray Suite v5.0 and GeneSpring v5.0.3 (Silicon Genetics) software, and scaled to a value of 500. Samples with a 3’ntrol genes actin and GAPDH greater than 7 were excluded from analysis. Transcripts whose detection levels had a p-value greater than 0.05 were excluded. Transcripts whose detection levels had a p-value greater than 0.05 were excluded resulting in 6566 transcripts.

source_name: entorhinal cortex subject #8

label_protocol: 10 ug total RNA were used to prepare double-stranded cDNA (Superscript, Invitrogen). The T7-(dT)24 primer for cDNA synthesis contained a T7 RNA polymerase promoter site. In vitro transcription with biotin-labeled ribonucleotides was performed on the cDNA to produce cRNA probes (Bioarray High Yield RNA Transcript Labeling Kit, ENZO Life Sciences).

extract_protocol: Eight brains, free of Alzheimer’ther histopathology, were obtained at autopsy under a protocol approved by the institution’ The dentate gyrus and the entorhinal cortex were identified and sectioned using strict anatomical criteria, following New York Brain Bank procedures. Samples were snap frozen in liquid nitrogen and stored at -80 C.  For each of the 16 brain samples, total RNA was extracted from entorhinal cortex and dentate gyrus with TRIzol (Invitrogen) and purified with RNeasy column (Invitrogen).

tag: individual

value: subject #8

value: entorhinal cortex


title: spheres_rep3

description: Gene expression after confirmation of appropriate LGR5 status

hyb_protocol: Cy3 labeled cRNA was hybridized on Human GE 4x44K v2 Microarrays (Agilent) according to the manufacturer’s protocol version 6.5.

data_processing: Images were analyzed with Feature Extraction software version 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20100123).  Data was normalized with 75 percentile as instructed in Agilent manual.

source_name: SW480 cells, spheres

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 700 ng of total RNA using the Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer’s protocol version 6.5,

growth_protocol: SW480 cells were cultured in Leibovitz's L-15 Medium (Gibco®, Life Technologies, Carlsbad, CA) as recommended by ATCC supplemented with fetal bovine serum (FBS, 10% v/v), L-glutamine (2mM), penicillin (100 U/ml) and streptomycin (100 µg/ml).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) including DNase I treatment (RNase-Free DNase Set, Qiagen, Hilden, Germany). RNA was quantified using a NanoDrop-1000 spectrophotometer (NanoDrop products, Wilmington, DE) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Lentiviral short-hairpin RNA (shRNA) transduction of SW480 cells was done using high-titer lentivirus (Open Biosystems, Thermo Fisher Scientific, Lafayette, CO) according to the manufacturer’s instructions

tag: cell line

value: 50 years


title: entorhinal cortex subject #8

description: gene expression data from dentate gyrus subject #8

source_name: dentate gyrus subject #8

tag: tissue

value: dentate gyrus


title: U251-NC

city: Newhaven

first: Jiangbing

last: zhou

address: 310 Cedar Street, Ste LH 412A

institute: Yale university

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) 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 by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as "Detected" were maintained.

source_name: glioma

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 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.

growth_protocol: U251MG was grown in the DMEM supplemented with 10% FBS (GIBCO)

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer

treatment_protocol: cells were stably transduced with a lentiviral vector containing the mature sequence of miR-218 and control

tag: transduced

value: miR-control


title: U251-miR-218


title: T 4926 -

description: Gene expression of tumors

tag: gender

value: 7.5 months

value: low


title: dentate gyrus subject #7

description: gene expression data from entorhinal cortex subject #7

source_name: entorhinal cortex subject #7

value: subject #7


title: T 4926 +

description: Gene expression of tumors


title: entorhinal cortex subject #7

description: gene expression data from dentate gyrus subject #7

source_name: dentate gyrus subject #7


title: adherent cells_rep3

source_name: SW480 cells, adherent cell fraction


title: spheres_rep2


title: spheres_rep1


title: adherent cells_rep2


title: dentate gyrus subject #6

description: gene expression data from dentate gyrus subject #6

source_name: entorhinal cortex subject #6

value: subject #6


title: N 4977 +

description: Gene expression of normal colon

source_name: Normal colon

value: flow-sorted normal colon cells

value: female

value: 6 months


title: entorhinal cortex subject #6

source_name: dentate gyrus subject #6


title: adherent cells_rep1


title: shLGR5_rep3

source_name: SW480 cells transduced with shRNA against LGR5


title: N 4977 -

description: Gene expression of normal colon


title: N 4978 +

description: Gene expression of normal colon


title: N 4978 -

description: Gene expression of normal colon


title: dentate gyrus subject #5

description: gene expression data from entorhinal cortex subject #5

source_name: entorhinal cortex subject #5

value: subject #5


title: entorhinal cortex subject #5

description: gene expression data from dentate gyrus subject #5

source_name: dentate gyrus subject #5


title: shLGR5_rep2


title: N 4995 +

description: Gene expression of normal colon

value: 4.5 months


title: N 4995 -

description: Gene expression of normal colon


title: shLGR5_rep1

value: male


title: dentate gyrus subject #4

description: gene expression data from entorhinal cortex subject #4

source_name: entorhinal cortex subject #4

value: subject #4


title: primary human: blood; FACS-sorted CD3+ cells  (CLL269N_CD3)

value: normal

value: enrollment

tag: cell type

value: FACS-sorted CD3+ cells


title: entorhinal cortex subject #4

description: gene expression data from dentate gyrus subject #4

source_name: dentate gyrus subject #4


title: control_rep3

source_name: SW480 cells transduced with empty vector control

value: 50 years


title: N 3349 -

description: Gene expression of normal colon

value: 2.5 months


title: dentate gyrus subject #3

description: gene expression data from entorhinal cortex subject #3

source_name: entorhinal cortex subject #3

value: subject #3

value: entorhinal cortex


title: N 3349 +

description: Gene expression of normal colon

value: high


title: N 4960 -

description: Gene expression of normal colon

value: low


title: control_rep2


title: entorhinal cortex subject #3

description: gene expression data from dentate gyrus subject #3

source_name: dentate gyrus subject #3

value: dentate gyrus


title: CD with anemia

city: milan

first: luca

last: elli

address: via f. sforza 35

country: Italy

institute: Fondazione IRCCS Ca' Granda

description: single experimental replicate. Pool of 5 patients

hyb_protocol: Tecan HS4800™ hybridization stations

scan_protocol: Agilent G2565BA Microarray Scanner System ImaGene 9.0 software

data_processing: Before proceeding with data normalization a technical quality assessment was performed based on results from spike in controls,flagging of spots, background intensity levels and signal intensity distribution.

source_name: CD with anemia

label_protocol: miRCURY LNA™ microRNA Hi-Power Labeling Kit,Hy3™/Hy5™ (Exiqon, Denmark). The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 6th Gen

extract_protocol: Rneasy Kit Qiagen; RNA quality control with Agilent 2100 bioanalyzer

value: frozen duodenal mucosa biopsy

source_name: reference RNA

tag: reference

value: synthetic RNA


title: N 4960 +

description: Gene expression of normal colon

value: flow-sorted normal colon cells

value: female


title: GFD treated CD

source_name: GFD treated CD


title: N 3350 -

description: Gene expression of normal colon


title: entorhinal cortex subject #2

description: gene expression data from dentate gyrus subject #2

source_name: entorhinal cortex subject #2

value: subject #2


title: classic CD

source_name: classic CD


title: entorhinal cortex subject #1

description: gene expression data from entorhinal cortex subject #1

source_name: dentate gyrus subject #1

value: subject #1


title: N 3350 +

description: Gene expression of normal colon

value: male


title: control_rep1


title: p53_SCC_CATCH-IT_Doxo_replicate_(538379A01)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CATCH-IT profiling of p53 -/- SCC cells after 18 hours of doxorubicin treatment, biological replicate.

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

data_processing: The dye-bias correction of Peng, et al (PMID PMC1913544) was applied to bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 computedby NimbleGen. The supplementary gff and wig files contain the bi-weight mean adjusted log base 2 ratios in MM9 coordinates.

label_protocol: Standard NimbleGen protocol

extract_protocol: CATCH-IT was performed as previously described (PMID: 20508129) with some modifications. Briefly, tissue culture medium was replaced with DMEM media without methionine (Invitrogen Cat# 21013-024) supplemented with 1X glutamine, 0.2 mM L-cystine, 10% FBS, and 1% penicillin-streptomycin, and cells were grown at 37C for starvation fro 30 minutes, followed by 30 minutes incubation at 37C with 4 mM azidohomoalanine (Anaspec Cat# 63669) added to the media. Cells were then harvested, washed with 1X PBS, and resuspended in ice-cold TM2 buffer (10 mM Tris, pH=7.5, 2mM MgCl2). Cells were lysed using 0.2% of NP-40 and nuclei were isolated, followed by digestion of micrococcal nuclease for 10 minutes to produce mostly mononucleosomes. Biotin coupling, chrmatin extraction, streptavidin pulldown, urea wash, and DNA isolation were then performed as previously described.

value: squamous cell carcinoma

source_name: Input


title: N 4961 -

description: Gene expression of normal colon

source_name: Normal colon

value: 4.5 months


title: WT_SCC_CATCH-IT_Acla_2_(559045A01)

description: CATCH-IT profiling of wild-type SCC cells after 24 hours of Aclarubicin treatment at 0.2 micromolar.

value: wild-type


title: WT_SCC_CATCH-IT_Doxo_replicate_(538323A01)

description: CATCH-IT profiling of wild-type SCC cells after 18 hours of doxorubicin treatment, biological replicate.


title: controls

source_name: controls


title: p53_SCC_CATCH-IT_no_Doxo_replicate_(538325A01)

description: CATCH-IT profiling of p53 -/- SCC cells without doxorubicin treatment, biological replicate.


title: NA12234H

status: Public on Apr 18 2013

city: Houston

first: Hui-Qi

last: Qu

state: TX

address: 1200 Herman Pressler

department: Division of Epidemiology, Human Genetics and Environmental Sciences

institute: The University of Texas School of Public Health

description:
HapMap samples
Sample name: CPS227

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Non-normalized_data (ie, Sample_Gene_Profile 0625.txt) was generated by Genome Quebec using Illumina BeadStudio software.
The data were normalised using by robust spline normalization using the Lumi Bioconductor package.
We calculated the polysomal/nonpolysomal mRNA level ratios by normalized data, which is in “logTIfolds38CEUparents.txt” (linked as a supplementary file on the Series record).

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

extract_protocol: From each LCL, 1x108 cells were incubated with 100μg/μl cycloheximide for 5 mins at 37˚C to freeze translational activity and then washed with phosphate buffered saline (PBS) containing 100µg/ml cycloheximide. Cell pellets, collected by centrifugation at 1,000 rpm for 10 min at 4˚C, were lysed with hypotonic polysome lysis buffer [5 mmol/L Tris-HCL (pH 7.5), 2.5 mmol/L MgCl2, 1.5 mmol/L KCL, 100μg/mL cycloheximide , 2 mmol/L dithiothreitol (DTT), 10% Triton X-100, and 10% sodium deoxycholate]. After 2 min of incubation on ice in a prechilled Eppendorf tube, with occasional vortexing, the extracts were centrifuged for 2 mins at 13,000 rpm at 4˚C to remove cellular debris. The supernatant was directly loaded on a 10%–50% linear sucrose gradient [20 mmol/L HEPES-KOH (pH 7.6), 100 mmol/L KCl, 5 mmol/L MgCl2] and then centrifuged in a Beckman SW41 rotor for 120 minutes at 35,000 rpm at 4˚C. After the fractions were collected, RNA from each fraction was extracted using TRIzol (Invitrogen, California) followed by the phenol–chloroform purification. The mRNA concentration of each fraction was quantified by slot-blot hybridization using DIG-labeled oligo-dT to quantify poly-A RNA. Equal amounts of poly-A RNA (5ng/μl) from unfractionated RNA, nonpolysomal RNA (4 fractions before the 80S polysome peak), and polysomal RNA (4 fractions after the polysomal fraction peak) of each individual were evaluated for genome-wide expression profiling on the Illumina HumanRef-8 v3.0 Expression BeadChip.

value: lymphoblastoid cell line

tag: rna fraction

value: Heavy fraction


title: WT_SCC_CATCH-IT_Acla_control_(559054A01)

description: CATCH-IT profiling of wild-type SCC cells without Aclarubicin treatment.


title: N 4961 +

description: Gene expression of normal colon


title: WT_SCC_CATCH-IT_no_Doxo_replicate_(530613A01)

description: CATCH-IT profiling of wild-type SCC cells without doxorubicin treatment, biological replicate.


title: WT_SCC_CATCH-IT_Acla_4_(559205A01)

description: CATCH-IT profiling of wild-type SCC cells after 24 hours of Aclarubicin treatment at 0.4 micromolar.


title: dentate gyrus subject #1

description: gene expression data from dentate gyrus subject #1

source_name: entorhinal cortex subject #1


title: dentate gyrus subject #2

description: gene expression data from entorhinal cortex subject #2

source_name: dentate gyrus subject #2


title: NA12234L

description:
HapMap samples
Sample name: CPS226

value: Lignt fraction


title: p53_SCC_CATCH-IT_no_Doxo_(529584_2)

description: CATCH-IT profiling of p53 -/- SCC cells without doxorubicin treatment.


title: NA12814L

description:
HapMap samples
Sample name: CPS220


title: NA11920L

description:
HapMap samples
Sample name: CPS223


title: NA12814

description:
HapMap samples
Sample name: CPS219

value: Unfractionated RNA


title: NA11920H

description:
HapMap samples
Sample name: CPS224


title: WT_SCC_CATCH-IT_Acla_1_(559206A01)

description: CATCH-IT profiling of wild-type SCC cells after 24 hours of Aclarubicin treatment at 0.1 micromolar.


title: NA12043L

description:
HapMap samples
Sample name: CPS214


title: NA12043H

description:
HapMap samples
Sample name: CPS215


title: NA06994H

description:
HapMap samples
Sample name: CPS218


title: WT_SCC_CATCH-IT_2_(549421)

description: CATCH-IT profiling of wild-type SCC cells, biological replicate.


title: NA06994L

description:
HapMap samples
Sample name: CPS217


title: NA12814H

description:
HapMap samples
Sample name: CPS221


title: NA11920

description:
HapMap samples
Sample name: CPS222


title: NA12043

description:
HapMap samples
Sample name: CPS213


title: NA06994

description:
HapMap samples
Sample name: CPS216


title: WT_SCC_CATCH-IT_1_(559092)

description: CATCH-IT profiling of wild-type SCC cells


title: p53_SCC_CATCH-IT_Doxo_(529556_2)

description: CATCH-IT profiling of p53 -/- SCC cells after 18 hours of doxorubicin treatment.


title: NA11839L

description:
HapMap samples
Sample name: CPS211


title: NA11839H

description:
HapMap samples
Sample name: CPS212


title: NA12234

description:
HapMap samples
Sample name: CPS225


title: WT_SCC_CATCH-IT_Doxo_8h_(538479A01)

description: CATCH-IT profiling of wild-type SCC cells after 8 hours of doxorubicin treatment.

value: wild type


title: NA06993H

description:
HapMap samples
Sample name: CPS209


title: NA12750H

description:
HapMap samples
Sample name: CPS206


title: NA06993

description:
HapMap samples
Sample name: CPS207


title: NA11839

description:
HapMap samples
Sample name: CPS210


title: NA12762H

description:
HapMap samples
Sample name: CPS203


title: NA07034L

description:
HapMap samples
Sample name: CPS199


title: NA12762

description:
HapMap samples
Sample name: CPS201


title: NA07034H

description:
HapMap samples
Sample name: CPS200


title: NA07034

description:
HapMap samples
Sample name: CPS198


title: NA12154L

description:
HapMap samples
Sample name: CPS196


title: NA12156H

description:
HapMap samples
Sample name: CPS194


title: WT_SCC_CATCH-IT_Doxo_4h_(538428A01)

description: CATCH-IT profiling of wild-type SCC cells after 4 hours of doxorubicin treatment.


title: NA12156L

description:
HapMap samples
Sample name: CPS193


title: NA12154H

description:
HapMap samples
Sample name: CPS197


title: WT_SCC_CATCH-IT_Doxo_0h_(538386A01)

description: CATCH-IT profiling of wild-type SCC cells without doxorubicin treatment.


title: WT_SCC_CATCH-IT_no_Doxo_(529582)


title: NA06993L

description:
HapMap samples
Sample name: CPS208


title: WT_SCC_CATCH-IT_Doxo_1h_(538427A01)

description: CATCH-IT profiling of wild-type SCC cells after 1 hour of doxorubicin treatment.


title: WT_SCC_CATCH-IT_Doxo_24h_(538499A01)

description: CATCH-IT profiling of wild-type SCC cells after 24 hours of doxorubicin treatment.


title: NA12004H

description:
HapMap samples
Sample name: CPS191


title: NA12004

description:
HapMap samples
Sample name: CPS189


title: NA12156

description:
HapMap samples
Sample name: CPS192


title: NA11994H

description:
HapMap samples
Sample name: CPS185


title: NA07056H

description:
HapMap samples
Sample name: CPS188


title: NA07056

description:
HapMap samples
Sample name: CPS186


title: NA12750L

description:
HapMap samples
Sample name: CPS205


title: NA12004L

description:
HapMap samples
Sample name: CPS190


title: WT_SCC_CATCH-IT_Doxo_(529584)

description: CATCH-IT profiling of wild-type SCC cells after 18 hours of doxorubicin treatment.


title: Atm_SCC_CATCH-IT_Doxo_24h_(538428A01_2)

description: CATCH-IT profiling of Atm -/- SCC cells after 24 hours of doxorubicin treatment.

value: Atm -/-


title: NA11931

description:
HapMap samples
Sample name: CPS180


title: NA12812H

description:
HapMap samples
Sample name: CPS179


title: NA11994

description:
HapMap samples
Sample name: CPS183


title: NA12812L

description:
HapMap samples
Sample name: CPS178


title: NA11931H

description:
HapMap samples
Sample name: CPS182


title: NA12892

description:
HapMap samples
Sample name: CPS171


title: NA12892L

description:
HapMap samples
Sample name: CPS172


title: NA07056L

description:
HapMap samples
Sample name: CPS187


title: NA11931L

description:
HapMap samples
Sample name: CPS181


title: NA12812

description:
HapMap samples
Sample name: CPS177


title: NA12815H

description:
HapMap samples
Sample name: CPS176


title: NA12057

description:
HapMap samples
Sample name: CPS168


title: NA11994L

description:
HapMap samples
Sample name: CPS184


title: NA12057H

description:
HapMap samples
Sample name: CPS170


title: NA12815L

description:
HapMap samples
Sample name: CPS175


title: NA12892H

description:
HapMap samples
Sample name: CPS173


title: NA12763L

description:
HapMap samples
Sample name: CPS166


title: NA12750

description:
HapMap samples
Sample name: CPS204


title: NA12763H

description:
HapMap samples
Sample name: CPS167


title: NA12815

description:
HapMap samples
Sample name: CPS174


title: Atm_SCC_CATCH-IT_Doxo_1h_(538323A01_2)

description: CATCH-IT profiling of Atm -/- SCC cells after 1 hour of doxorubicin treatment.


title: Atm_SCC_CATCH-IT_Doxo_8h_(538379A01_2)

description: CATCH-IT profiling of Atm -/- SCC cells after 8 hours of doxorubicin treatment.


title: Atm_SCC_CATCH-IT_Doxo_4h_(538325A01_2)

description: CATCH-IT profiling of Atm -/- SCC cells after 4 hours of doxorubicin treatment.


title: NA12763

description:
HapMap samples
Sample name: CPS165


title: NA12057L

description:
HapMap samples
Sample name: CPS169


title: NA12878L

description:
HapMap samples
Sample name: CPS163


title: NA12248H

description:
HapMap samples
Sample name: CPS161


title: NA12878H

description:
HapMap samples
Sample name: CPS164


title: NA12248L

description:
HapMap samples
Sample name: CPS160


title: NA12878

description:
HapMap samples
Sample name: CPS162


title: NA11995H

description:
HapMap samples
Sample name: CPS158


title: NA12813L

description:
HapMap samples
Sample name: CPS154


title: NA11995L

description:
HapMap samples
Sample name: CPS157


title: NA11995

description:
HapMap samples
Sample name: CPS156


title: NA07055

description:
HapMap samples
Sample name: CPS150


title: NA12751H

description:
HapMap samples
Sample name: CPS149


title: NA12762L

description:
HapMap samples
Sample name: CPS202


title: NA12154

description:
HapMap samples
Sample name: CPS195


title: NA12751

description:
HapMap samples
Sample name: CPS147


title: Atm_SCC_CATCH-IT_Doxo_0h_(530613A01_2)

description: CATCH-IT profiling of Atm -/- SCC cells without doxorubicin treatment.


title: NA07055H

description:
HapMap samples
Sample name: CPS152


title: NA11992H

description:
HapMap samples
Sample name: CPS146


title: NA12813

description:
HapMap samples
Sample name: CPS153


title: NA12813H

description:
HapMap samples
Sample name: CPS155


title: NA12751L

description:
HapMap samples
Sample name: CPS148


title: NA11992L

description:
HapMap samples
Sample name: CPS145


title: NA12146L

description:
HapMap samples
Sample name: CPS142


title: NA12248

description:
HapMap samples
Sample name: CPS159


title: NA12146H

description:
HapMap samples
Sample name: CPS143


title: NA11992

description:
HapMap samples
Sample name: CPS144


title: NA07055L

description:
HapMap samples
Sample name: CPS151


title: NA12146

description:
HapMap samples
Sample name: CPS141


title: NA12873H

description:
HapMap samples
Sample name: CPS140


title: NA12873L

description:
HapMap samples
Sample name: CPS139


title: NA12873

description:
HapMap samples
Sample name: CPS138


title: NA12144H

description:
HapMap samples
Sample name: CPS137


title: NA12144L

description:
HapMap samples
Sample name: CPS136


title: NA12144

description:
HapMap samples
Sample name: CPS135


title: NA11993

description:
HapMap samples
Sample name: CPS132


title: NA12239

description:
HapMap samples
Sample name: CPS129


title: NA11993L

description:
HapMap samples
Sample name: CPS133


title: NA07357L

description:
HapMap samples
Sample name: CPS125


title: NA07357

description:
HapMap samples
Sample name: CPS123


title: NA12239L

description:
HapMap samples
Sample name: CPS130


title: NA12155H

description:
HapMap samples
Sample name: CPS122


title: NA11881H

description:
HapMap samples
Sample name: CPS119


title: NA11918

description:
HapMap samples
Sample name: CPS126


title: NA12264L

description:
HapMap samples
Sample name: CPS112


title: NA07357H

description:
HapMap samples
Sample name: CPS124


title: NA11993H

description:
HapMap samples
Sample name: CPS134


title: NA11881

description:
HapMap samples
Sample name: CPS117


title: NA12239H

description:
HapMap samples
Sample name: CPS131


title: NA12005H

description:
HapMap samples
Sample name: CPS110


title: NA12264

description:
HapMap samples
Sample name: CPS111


title: NA11918H

description:
HapMap samples
Sample name: CPS128


title: NA11881L

description:
HapMap samples
Sample name: CPS118


title: NA12264H

description:
HapMap samples
Sample name: CPS113


title: NA12249L

description:
HapMap samples
Sample name: CPS115


title: NA12155

description:
HapMap samples
Sample name: CPS120


title: NA12249H

description:
HapMap samples
Sample name: CPS116


title: NA11918L

description:
HapMap samples
Sample name: CPS127


title: NA12155L

description:
HapMap samples
Sample name: CPS121


title: NA12005

description:
HapMap samples
Sample name: CPS108


title: NA12249

description:
HapMap samples
Sample name: CPS114


title: NA12005L

description:
HapMap samples
Sample name: CPS109


title: NA11840H

description:
HapMap samples
Sample name: CPS107


title: NA11840L

description:
HapMap samples
Sample name: CPS106


title: NA11831L

description:
HapMap samples
Sample name: CPS103


title: NA11840

description:
HapMap samples
Sample name: CPS105


title: NA11831H

description:
HapMap samples
Sample name: CPS104


title: BL41 ubeh

city: Oslo

first: Nicole

last: Bethge

address: Montebello veien

department: Immunology

country: Norway

institute: Institute for Cancer Research

hyb_protocol: Applied Biosystems manufactures protocol

scan_protocol: Chemoluminescense was measured using the AB1700 Chemoluminescense Analyzer (Applied Biosystems) after incubating the array with alkalic phosphatase-linked digoxygenin antibody.

data_processing: Values represent the normalized expression after running ABarray on R-script.

label: DIG

source_name: cell lines

label_protocol: Standard one-round amplification was performed using the NanoAmp RT-IVT Labeling Kit (Applied Biosystems) according to the manufacturers' protocol. Briefly, cDNA was synthesized from one  g total RNA in an oligo dT primed reaction. Labeled complementary RNA (cRNA) was obtained from double-stranded cDNA in the presence of digoxigenin (DIG)-UTP in an in vitro labeling reaction.

growth_protocol: 72h growth with every 24h adding aza, last 12 h adding TSA

extract_protocol: Trizol

value: B-cell lymphoma cell lines

tag: treatment


title: ROS-50 aza/tsa

value: aza/tsa


title: ROS-50 ubeh


title: NA11831

description:
HapMap samples
Sample name: CPS102


title: HLY-1 aza/tsa


title: BL41 aza/tsa


title: Sudhl4 ubeh


title: Sudhl4 aza/tsa


title: HLY-1 ubeh


title: Ocily10 ubeh


title: Tb927.8.6650_OE_induced_A

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

description:
559558A02_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.8.6650 Over Expression were induced with tetracycline for 48h.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.NimbleGen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.NimbleGen.com.

data_processing: The raw data pair files were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.6.0.0 (Roche NimbleGen, Inc.).

organism: Trypanosoma brucei

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.NimbleGen.com.

growth_protocol: Transgenic PF T. brucei cells harbouring tetracycline-inducible constructs were grown in SDM-79 medium in 27 °C. Cells were seeded at 1.3E+6 cells/ml and harvested after 24h or 48h.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen) and was further purified using RNeasy Mini Kit (Qiagen) as per manufacturers’ intsructions. RNA quality was examined using Agilent 2100 Bioanalyzer.

treatment_protocol: The cells were treated with 1ug/ml tetracycline to induce RNAi and 100ng/ml tetracycline to induce over-expression, for a duration of 48h (except for Tb927.8.6650 RNAi which was treated for a duration of 24h)

tag: life stage

value: Procyclic Form

value: Tb927.8.6650 over-expression

tag: time point

value: 48h after tet-induction


title: Tb927.8.6650_RNAi_induced_A

description:
559559A04_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.8.6650 RNAi were induced with tetracycline for 24h.

value: 24h after tet-induction


title: Tb927.8.6650_OE_induced_B

description:
559558A05_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.8.6650 Over Expression were induced with tetracycline for 48h.


title: Tb927.8.6650_RNAi_induced_B

description:
559559A12_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.8.6650 RNAi were induced with tetracycline for 24h.


title: Ocily10 aza/tsa


title: Tb927.8.6650_OE_ctrl_A

description:
559559A11_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.8.6650 Over Expression were cultured in parallel with tet-induced cells, and harvested after 48h.

value: 48hr without induction (control)


title: Tb927.8.6650_RNAi_ctrl_A

description:
559559A09_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.8.6650 RNAi were cultured in parallel with tet-induced cells, and harvested after 24h.

value: 24hr without induction (control)


title: Sudhl6 aza/tsa


title: Tb927.8.6650_OE_ctrl_B

description:
559558A12_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.8.6650 Over Expression were cultured in parallel with tet-induced cells, and harvested after 48h.


title: Sudhl6 ubeh


title: Tb927.8.6650_RNAi_ctrl_B

description:
559559A01_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.8.6650 RNAi were cultured in parallel with tet-induced cells, and harvested after 24h.


title: Raji ubeh

value: Raji


title: Raji aza/tsa


title: K422 ubeh


title: Tb927.7.5380_OE_induced_A

description:
559559A02_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.7.5380 Over Expression were induced with tetracycline for 48h.

value: Tb927.7.5380 over-expression


title: Ramos aza/tsa

value: Ramos


title: K422 aza/tsa


title: SC-1 ubeh


title: SC-1 aza/tsa


title: Ramos ubeh


title: Tb927.7.5380_RNAi_induced_B

description:
559558A04_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.7.5380 RNAi were induced with tetracycline for 48h.


title: Ocily3 aza/tsa


title: Tb927.7.5380_OE_ctrl_A

description:
559558A10_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.7.5380 Over Expression were cultured in parallel with tet-induced cells, and harvested after 48h.


title: Tb927.7.5380_OE_induced_B

description:
559559A05_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.7.5380 Over Expression were induced with tetracycline for 48h.


title: Tb927.7.5380_OE_ctrl_B

description:
559558A08_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.7.5380 Over Expression were cultured in parallel with tet-induced cells, and harvested after 48h.


title: Tb927.7.5380_RNAi_ctrl_A

description:
559559A03_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.7.5380 RNAi were cultured in parallel with tet-induced cells, and harvested after 48h.


title: Tb927.7.5380_RNAi_induced_A

description:
559559A08_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.7.5380 RNAi were induced with tetracycline for 48h.


title: Tb927.3.2930_OE_induced

description:
559559A06_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.3.2930 Over Expression were induced with tetracycline for 48h.

value: Tb927.3.2930 over-expression


title: Tb927.7.5380_RNAi_ctrl_B

description:
559559A07_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.7.5380 RNAi were cultured in parallel with tet-induced cells, and harvested after 48h.


title: Tb927.3.2930_RNAi_induced_B

description:
559558A01_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.3.2930 RNAi were induced with tetracycline for 48h.


title: Tb927.3.2930_OE_ctrl

description:
559558A11_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.3.2930 Over Expression were cultured in parallel with tet-induced cells, and harvested after 48h.


title: Tb927.3.2930_RNAi_induced_A

description:
559558A07_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.3.2930 RNAi were induced with tetracycline for 48h.


title: Ocily3 ubeh


title: Tb927.3.2930_RNAi_ctrl_B

description:
559558A03_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.3.2930 RNAi were cultured in parallel with tet-induced cells, and harvested after 48h.


title: Tb927.3.2930_RNAi_ctrl_A

description:
559558A09_532
Stable transgenic procyclic form cells harbouring a construct for Tb927.3.2930 RNAi were cultured in parallel with tet-induced cells, and harvested after 48h.


title: Tdg KD E14, rep1

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

description: Tdg KD E14

hyb_protocol: Hybridization to Affymetrix MoGene-1_0-st-v1 array was carried out by Functional Genomics Core Facility in UNC-CH using standard protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G by Functional Genomics Core Facility in UNC-CH using standard protocol.

data_processing:
Primary analysis was carried out by Functional Genomics Core Facility in UNC-CH using Affymetrix Expression Console software.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: Tdg KD E14

label_protocol: Biotin labeling was carried out by Functional Genomics Core Facility in UNC-CH using GeneChip WT Sense Target Labeling and Control Reagents and standard protocol.

growth_protocol: E14 mESCs are cultured on the 0.1% gelatin coated plates in the DMEM medium (Sigma) supplemented with 100U/ml penicillin/streptomycin, 15% fetal bovine serum (Sigma), 1x nonessential amino acid, 1x sodium pyruvate, 1x GlutaMax, 1x beta-mercaptoethanol (Invitrogen) and 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore).

extract_protocol: Total RNA was extracted from the control and Kdm2b knockdown mESCs using RNeasy mini kit (QIAGEN) following manufacture's instructions.

treatment_protocol: Around 1x10^5 ES cells/well in 24-well plates are infected with lentiviral vectors at 10 MOI. 48 hours after transduction, puromycin (2ug/ml) is added to the medium for selecting transduced cells.

value: embryonic stem

value: Tdg knockdown


title: Tdg KD E14, rep3

description: Tdg KD E14


title: Mild ICP-2

city: Shanghai

first: YouDong

last: Pan

state: Shanghai

address: 320 YueYang Road

department: Shanghai Institutes for Biological Sciences

country: China

institute: Chinese Academy of Sciences

description: Placental Gene-expression Profile

hyb_protocol: 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 4 out of 12 have flags in Detected (“ue”or further data analysis. Differentially expressed genes were identified through volcano plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Placenta from women with mild ICP

label_protocol: 1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The Labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA

growth_protocol: To avoid artifacts from effects of labor, only placental samples obtained from women who had not undergone labor were selected. All samples were collected immediately after Caesarean sections, cut near the center zone of maternal surface villous lobule after deciduas and amnionic membranes were removed, and then rinsed with saline to remove maternal blood.To reduce variations among different individuals, same amount of RNA samples from 5 individuals were pooled for one array.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

value: Female

value: Placenta

tag: disease state

value: mild ICP


title: Severe ICP-1

description: Placental Gene-expression Profile

scan_protocol: scanned with using the Agilent DNA Microarray Scanner (part number G2505B)

source_name: Placenta from women with severe ICP

value: severe ICP


title: Tdg KD E14, rep2

description: Tdg KD E14


title: control E14, rep1

description: control E14

source_name: control E14

value: control


title: Severe ICP-2

description: Placental Gene-expression Profile


title: Healthy-2

description: Placental Gene-expression Profile

source_name: Placenta from healthy pregnant women

value: healthy


title: HOP Phase I rep2

city: Logroño

first: Ramon

last: Gonzalez

address: C. Madre de Dios, 51

department: Instituto de Ciencias de la Vid y del Vino

country: Spain

institute: Consejo Superior de Investigaciones Científicas

description:
HOP 2 MS 10
Competition for 10 generations of the whole genome homozygous yeast deletion collection under Phase I fermentation conditions

hyb_protocol: Reactions hybridized overnight to custom-built TAG4 microarrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450   according to [Pierce SE, Davis RW, Nislow C, Giaever G (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protocols 2: 2958-2974]

scan_protocol: GeneChips were scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix).

data_processing: Data procesing was performed according to [Pierce SE, Davis RW, Nislow C, Giaever G (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protocols 2: 2958-2974]. Perl scripts were downloaded from the supplementary web [Pierce, S.E. et al. A unique and universal molecular barcode array. Nat. Methods 3, 601-603 (2006)]. Data were normalized by quantile. Extracted data are in natural scale, but Ratios used for discussion in the associated manuscript are expressed in log2.

organism: Saccharomyces cerevisiae

source_name: Homozygous collection competition in Phase I fermentation conditions for 10 generations

label_protocol: Amplification of the barcodes (uptags and downtags), with simoultaneous labelling using biotinilated primers was performed according to [Pierce SE, Davis RW, Nislow C, Giaever G (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protocols 2: 2958-2974]

growth_protocol: Bioreactors containing 200 mL of the previously described synthetic must were inoculated to an initial OD600 of 0.2. Cultures were grown in batch mode during about 12 h prior to triggering the continuous cultures. According to the data obtained from batch characterization, dilution rate was set to 0.23 h-1 for competitions mimicking Phase I and to 0.04 h-1 for those mimicking Phase II. Competition experiments using the heterozygous collection were run for 20 generations (corresponding to 60 h for Phase I or 347 h for Phase II) while those performed with the homozygous collection were run for 10 generations (30 h for Phase I or 174 h for Phase II). Yeast cell samples were taken at the onset of the continuous cultures, and after the indicated numbers of generations, in order to compare pool compositions at the beginning and the end of the competition experiments. Additional triplicate competition experiments, using YPD broth (D=0.23 h-1), were performed in order to differentiate deletions unspecifically affecting yeast growth from those specific for Phase I or Phase II fermentation conditions.

extract_protocol: Genomic DNA was extracted bu using the YeaStarTM Genomic DNA Kit (Zymo Research).

tag: yeast collection

value: Whole genome homozygous deletion collection

tag: phase or medium

value: Phase I

tag: number of generations


title: Healthy-1

description: Placental Gene-expression Profile

source_name: Placentas from healthy pregnant women


title: HOP Phase II rep1

description:
HOP 1 10g F2
Competition for 10 generations of the whole genome homozygous yeast deletion collection under Phase II fermentation conditions

source_name: Homozygous collection competition in Phase II fermentation conditions for 10 generations

value: Pase II


title: HOP Phase I rep3

description:
HOP 3 MS 10
Competition for 10 generations of the whole genome homozygous yeast deletion collection under Phase I fermentation conditions


title: HOP Phase II rep2

description:
HOP 2 10g F2
Competition for 10 generations of the whole genome homozygous yeast deletion collection under Phase II fermentation conditions


title: HOP YPD rep3

description:
HOP 3 YPD 10
Competition for 10 generations of the whole genome homozygous yeast deletion collection in YPD

source_name: Homozygous collection competition in YPD for 10 generations

value: YPD


title: B cell 5. donor

scan_protocol: Genechip scanner 3000

data_processing: Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

label: Biotin

source_name: buffy coat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

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

value: whole blood


title: B cell 4. donor

hyb_protocol: according to the standard Affymetrix protocol


title: HOP Phase I rep1

description:
HOP 1 MS 10
Competition for 10 generations of the whole genome homozygous yeast deletion collection under Phase I fermentation conditions


title: Mild ICP-1

description: Placental Gene-expression Profile


title: HOP Phase II rep3

description:
HOP 3 10g F2
Competition for 10 generations of the whole genome homozygous yeast deletion collection under Phase II fermentation conditions


title: control E14, rep2

description: control E14


title: control E14, rep3

description: control E14


title: B cell 3. donor


title: HOP YPD rep2

description:
HOP 2 YPD 10
Competition for 10 generations of the whole genome homozygous yeast deletion collection in YPD


title: B cell 2. donor


title: Series 2 Day 5 Dawn

first: Justin

last: Ashworth

address: 401 Terry Ave N

institute: Institute for Systems Biology

description:
Paired dye-flipped arrays.
252985410004_201101211359_S01_GE2_107_Sep09_1_4.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410004_201101211359_S01_GE2_107_Sep09_1_3.txt: Cy5-labeled sample and Cy3-labeled reference.

hyb_protocol: Array slides were hybridized with equal amounts of oppositely labeled sample and internal reference RNA according to standard Agilent array hybridization protocols.

scan_protocol: Arrays slides were scanned using an Agilent two-color microarray slide scanner.

data_processing:
Two-color expression data were processed using the limma package in R for Agilent two-color microarray data. This included background correction (normexp method), within-array normalization (loess method), and between-array normalization (Aquantile method). Expression ratios were calculated relative to the mean within-experiment expression level for each probe in order to remove batch effects between experiments.
Two sets of value columns are included in the value Matrix (see supplemental 'value_Matrix' file). The first set of values (also used in the VALUE column of below sample tables) contain the normalized log2 ratios for each gene within each growth series (labels: X400/800.Day#.Dk/Lt). The second set of values are log2 ratios for merged, paired samples from each growth series, as derived from the first of values (labels: Day#.Lt/Dk). The first set of values was used for statistical analysis. The second set of (derived) values is provided for the purposes of simplicity, illustration and reference. Separating these two sets of expression values are boolean (TRUE/FALSE) columns indicating the significance of association for each gene with four experimental conditions (as indicated by characteristics in the metadata) by two-factor ANOVA with a permuted p-value cutoff of 0.01.

organism: Thalassiosira pseudonana CCMP1335

source_name: Filtered cells 2 Day 5 Dawn

label_protocol: Transcribed mRNA was amplified and labeled using the Agilent Quick-Amp Labeling Kit (two-color).

growth_protocol: Axenic cultures of Thalassiosira pseudonana CCMP1335 (Provasoli-Guillard National Center for Culture of Marine Phytoplankton) were grown in ESAW medium modified with lower levels of nitrate (80 µM), silicic acid (110 µM) and phosphate (20 µM) and grown in bioreactors. Prior to the experiment, the diatoms were acclimated to constant 20°C temperature and ambient CO2 under a 12hr:12hr dark:light diurnal cycle at 125 µmol photons m-2 s-1 of photosynthetically active radiation (PAR) provided by fluorescent lamps. Cultures were considered acclimated when the growth rates of three consecutive growth curves were significantly equal to each other. Chemicals were purchased from Sigma–Aldrich (St. Louis, MO). During the experiments the bioreactors were equilibrated at ambient (400 ppm) or elevated (800 ppm) CO2 by bubbling of mixed gasses (2L/min) and stirring (50 rpm) in a 10L glass bioreactor system (BioFlow). CO2-scrubbed ambient air and pure CO2 gas were mixed and regulated using two mass-flow controller/monitors (G265, Qubit Systems, Inc., Kingston, Canada) and solenoid controller.

extract_protocol: Total RNA was extracted using the mirVANA kit from Invitrogen (total RNA extraction protocol).

treatment_protocol: Cells (approx. 3x10^7) were harvested by filtration (30-200mL) and flash-frozen.

tag: condition

value: Dawn

tag: growth phase

value: Stationary

tag: co2 gas input

source_name: common internal reference sample

value: common internal reference sample


title: B cell 1. donor


title: Series 2 Day 3 Dawn

description:
Paired dye-flipped arrays.
252985410003_201101211307_S01_GE2_107_Sep09_1_4.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410003_201101211307_S01_GE2_107_Sep09_1_3.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells 2 Day 3 Dawn

value: Exponential


title: Series 2 Day 4 Dawn

description:
Paired dye-flipped arrays.
252985410003_201101211307_S01_GE2_107_Sep09_1_2.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410003_201101211307_S01_GE2_107_Sep09_1_1.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells 2 Day 4 Dawn


title: Series 2 Day 3 Dusk

description:
One array for this sample.
252985410002_201101211253_S01_GE2_107_Sep09_1_3.txt: Cy3-labeled sample and Cy5-labeled common reference.

source_name: Filtered cells 2 Day 3 Dusk

value: Dusk


title: Pool for sample 26

description:
HOP 1 t=0 F2
Control for competition 26

source_name: Initial pool for competition 26

value: Preculture


title: HOP YPD rep1

description:
HOP 1 YPD 10
Competition for 10 generations of the whole genome homozygous yeast deletion collection in YPD


title: siHIRA 2

city: Glasgow

first: Peter

middle: D.

last: Adams

address: Switchback Rd, Bearsden

institute: University of Glasgow, Beatson Institute for Cancer Research

description: Gene expression data from HeLA cells and siHIRA knockdown

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133Plus2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

molecule: polyA RNA

source_name: HeLA tissue

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

growth_protocol: HeLa cells were nucleofacted with respective siRNAs and RNA was isolated after 72 hours

extract_protocol: RNA was extracted using RNA easy mini kit Cat:74104

treatment_protocol: No treatment other then nucleofaction

value: HeLa

tag: transfection

value: HIRA siRNA


title: Pool for sample 28

description:
HOP 3 t=0 F2
Control for competition 28

source_name: Initial pool for competition 28


title: Series 2 Day 4 Dusk

description:
Paired dye-flipped arrays.
252985410004_201101211359_S01_GE2_107_Sep09_1_2.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410004_201101211359_S01_GE2_107_Sep09_1_1.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells 2 Day 4 Dusk


title: siHIRA 4


title: siHIRA 3


title: Series 2 Day 2 Dawn

description:
One array for this sample.
252985410002_201101211253_S01_GE2_107_Sep09_1_4.txt: Cy3-labeled sample and Cy5-labeled common reference.

source_name: Filtered cells 2 Day 2 Dawn


title: Pool for sample 27

description:
HOP 2 t=0 F2
Control for competition 27

source_name: Initial pool for competition 27


title: Series 2 Day 2 Dusk

description:
Paired dye-flipped arrays.
252985410002_201101211253_S01_GE2_107_Sep09_1_2.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410002_201101211253_S01_GE2_107_Sep09_1_1.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells 2 Day 2 Dusk


title: NTG 3

description: Gene expression data from HeLA cells and NTG control

value: Dharmacon control siRNA


title: HIP Phase II rep2

description:
HIP 3 20g F2
Competition for 20 generations of the whole genome heterozygous yeast deletion collection under Phase II fermentation conditions

source_name: Heterozygous collection competition in Phase II fermentation conditions for 20 generations

value: Whole genome heterozygous deletion collection


title: HIP Phase II rep1

description:
HIP 2 20g F2
Competition for 20 generations of the whole genome heterozygous yeast deletion collection under Phase II fermentation conditions


title: NTG 2


title: Series 2 Day 1 Dusk

description:
Paired dye-flipped arrays.
252985410001_201101191050_S01_GE2_107_Sep09_1_3.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410001_201101191050_S01_GE2_107_Sep09_1_1.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells 2 Day 1 Dusk


title: Pool for samples 21, 22, 24 and 25

description:
HOP 2-3 Precultivo t=0
Control for competitions 21, 22, 24 and 25

source_name: Initial pool for competitions 21, 22, 24 and 25


title: HIP Phase II rep3

description:
HIP 4 20g F2
Competition for 20 generations of the whole genome heterozygous yeast deletion collection under Phase II fermentation conditions


title: Pool for samples 20 and 23

description:
HOP 1 Precultivo t=0
Control for competitions 20 and 23

source_name: Initial pool for competitions 20 and 23


title: HIP Phase I rep3

description:
HIP MS 20
Competition for 20 generations of the whole genome heterozygous yeast deletion collection under Phase I fermentation conditions

source_name: Heterozygous collection competition in Phase I fermentation conditions for 20 generations


title: siHIRA 1


title: NTG 4


title: HIP Phase I rep2

description:
HIP 4 MS 20
Competition for 20 generations of the whole genome heterozygous yeast deletion collection under Phase I fermentation conditions


title: NTG 1


title: Series 2 Day 1 Dawn

description:
Paired dye-flipped arrays.
252985410001_201101191050_S01_GE2_107_Sep09_1_4.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410001_201101191050_S01_GE2_107_Sep09_1_2.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells 2 Day 1 Dawn


title: Series 1 Day 5 Dusk

description:
Paired dye-flipped arrays.
252985410007_201108021125_S01_GE2_107_Sep09_1_3.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410009_201108021057_S01_GE2_107_Sep09_1_1.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells Day 5 Dusk

source_name: common internal reference sample


title: Series 1 Day 5 Dawn

description:
Paired dye-flipped arrays.
252985410007_201108021125_S01_GE2_107_Sep09_1_4.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410009_201108021057_S01_GE2_107_Sep09_1_2.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells Day 5 Dawn


title: HIP Phase I rep1

description:
HIP 3 MS 20
Competition for 20 generations of the whole genome heterozygous yeast deletion collection under Phase I fermentation conditions


title: Series 1 Day 3 Dawn

description:
Paired dye-flipped arrays.
252985410006_201108021030_S01_GE2_107_Sep09_1_4.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410008_201108021111_S01_GE2_107_Sep09_1_2.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells Day 3 Dawn


title: Series 1 Day 1 Dusk

description:
Paired dye-flipped arrays.
252985410005_201108021044_S01_GE2_107_Sep09_1_3.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410007_201108021125_S01_GE2_107_Sep09_1_1.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells Day 1 Dusk