title: Pancreas_E18.5_HNF6-Tg_rep3

first: Laura

last: Crawford

address: 715 PRB 2220 Pierce Ave

department: Diabetes, Endocrinology, & Metab Division

description: No additional description necessary

data_processing: CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis). The

source_name: pooled pancreata, embryonic day 18.5, HNF6 Transgenic

extract_protocol: Pancreata were dissected at e18.5 and postnatal day 1 in ice cold PBS and immediately placed into RNAlater (Ambion).  Total pancreatic RNA was isolated using RNAqueous RNA Isolation Kit (Ambion) according to the manufacturer’s instructions. Agilent’s Bioanalyzer microfluidic assay (Agilent Technologies, Palo Alto CA) was used to assay RNA integrity. Spectrophotometric and fluorometric methods were combined to  quantitate protein and nucleic acids present in the sample, and to ensure quality control of each sample.  RNA samples were bioanalyzed individually and highly pure samples were pooled according to their genotype (3-5 animals per pool) in order to obtain an adequate quantity of RNA.

treatment_protocol: HNF6 expression was driven specifically to pancreatic endocrine cells beginning at embryonic day (e) 11.5 using a 1 kb enhancer from the 5’ pdx1 promoter region.  This transgenic line, termed pdx1PBHnf6, was maintained on an inbred hybrid (B6D2) background.  All mice were kept on a 12 hour light/dark cycle, fed Mouse diet 5015 (LabDiet), and given water ad lib.  For embryonic analyses, the morning of the vaginal plug was considered e0.5.  All mouse studies were performed in accordance with the Vanderbilt Institutional Animal Care and Use Committee guidelines under the supervision of the Division of Animal Care.

tag: Developmental stage

value: embryonic day 18.5

value: pooled pancreata

tag: Genotype

value: HNF6 (hepatic nuclear factor 6) transgenic (overexpression)


title: Pancreas_P1_HNF6-Tg_rep3

status: Public on Mar 01 2008

type: RNA

city: Nashville

state: TN

country: USA

institute: Vanderbilt University

description: No additional description necessary

hyb_protocol: The biotinylated cRNA (15 µg) was fragmented and hybridized to an Affymetrix GeneChip Mouse Genome 430 2.0 Array  containing 45,000 sets of 11 to 25-mer oligomers, representing 39,000 mouse transcripts (34,000 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: pooled pancreata, post-natal day 1, HNF6 Transgenic

label_protocol: Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA).  Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter.  In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.

tag: Strain

value: post-natal day 1

tag: Tissue


title: Pancreas_P1_HNF6-Tg_rep1

description: No additional description necessary

value: post-natal day 1 Tissue:pooled pancreata


title: Pancreas_E18.5_WT_rep3

description: No additional description necessary

source_name: pooled pancreata, embryonic day 18.5, wild type


title: X474

city: Melbourne

first: Prof David

last: Bowtell PhD.

state: VIC

address: Locked Bag 1 A' Beckett St

department: Research Division

country: Australia

institute: PeterMacCallum Cancer Centre

description: Gene expression data from human ovarian carcinoma

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

scan_protocol: GeneChips were scanned using Affymetrix GS300-7G scanner

data_processing: The data were analyzed with Gene Chip Operating Software Version 1.4 using Affymetrix default analysis settings. The CEL files generated was later normalized using the RMA method

organism: Homo sapiens

source_name: Carcinoma of ovary, fallopian tube or peritonem

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

extract_protocol: Trizol extraction and column chromotogrpahy

treatment_protocol: Frozen tissue stored at -80oC taken after surgery

value: Ovary

tag: Type

value: Malignant

tag: Subtype

value: Ser/PapSer

tag: StageCode

value: IIIC


title: Pancreas_E18.5_WT_rep1

description: No additional description necessary

value: wild type


title: X469

value: IC


title: X479

value: IV


title: Pancreas_E18.5_WT_rep2

description: No additional description necessary


title: Pancreas_P1_WT_rep3

description: No additional description necessary

data_processing: CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).  The "Value" column shows this normalized signal intensity value.

source_name: pooled pancreata, post-natal day 1, wild type


title: Pancreas_E18.5_HNF6-Tg_rep1

description: No additional description necessary


title: X450


title: Pancreas_E18.5_HNF6-Tg_rep2

description: No additional description necessary


title: X485


title: Pancreas_P1_WT_rep2

description: No additional description necessary


title: Pancreas_P1_WT_rep1

description: No additional description necessary


title: X484


title: Pancreas_P1_HNF6-Tg_rep2

description: No additional description necessary


title: X488

value: III


title: X498


title: X490

value: Peritoneum


title: X487


title: X459


title: X500


title: X502


title: X496


title: X51016


title: X51005


title: X51062


title: X51080


title: X51053


title: X493


title: X507


title: X51083


title: X51093


title: X49


title: X51171

value: IIIB


title: X516


title: X523


title: X51104

value: IIIA


title: X511


title: X512


title: X533


title: X536


title: X525


title: X550


title: X510


title: X51125


title: X51086


title: X541


title: X558


title: X532


title: X561


title: X570


title: X60020


title: X580


title: X60049

value: Fallopian


title: X60067


title: X60102

value: IIC


title: X563


title: X575


title: X60016


title: X60135

value: Endo


title: X60111


title: X60066


title: X60163


title: X574

value: IA


title: X60169


title: X582


title: X60148


title: X60090


title: X60174


title: X60024


title: X60048


title: X60107

value: IIB


title: X60065


title: X60091


title: X60175


title: X70003


title: X60180


title: X70045


title: X70077


title: X70086


title: X70054


title: X60318


title: X60181


title: X70039


title: X70005


title: X70103


title: X60228


title: X60188


title: X60214


title: X70088


title: X70048


title: X60258


title: X70107


title: X60211


title: X70049


title: X70102


title: X70100


title: X70123


title: X70119


title: X70124


title: X70135


title: X70115

value: NK


title: X70125

value: Ovary


title: X70118

value: Malignant


title: X92004

value: Ser/PapSer


title: X70148


title: X92003

value: IIIC


title: X86058


title: X93031


title: X92071


title: X94019


title: X92065


title: X93006


title: X93075


title: X92074


title: X552


title: X93050


title: X94067


title: X94056


title: X94025


title: X94044


title: X94070


title: X70056

value: LMP


title: X70055


title: X94084


title: X23036


title: X94093


title: X70144


title: X95002


title: X22002


title: X94099


title: X95014


title: X94082


title: X70057


title: X22027

value: IIA


title: X44262

value: IC


title: X23052


title: X60120


title: X23177


title: X51005Epi

value: IV


title: X51174


title: X41170Str

value: Peritoneum


title: X44349Epi


title: X23066


title: X60170


title: X70077Str


title: X32117


title: X60267


title: X70070


title: X41170Epi


title: X44349Str


title: X51068


title: X22058Epi


title: X22058Str


title: X70077Epi


title: X51005Str


title: MO-27aCM-donor1

city: Seattle

first: Lynn

last: Graf

state: WA

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: HS27a conditioned medium: MO-27aCM-donor1

hyb_protocol: standard Affymetrix protocol and reagents

scan_protocol: standard Affymetrix protocol and instruments

data_processing: Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all simples, was also applied.

source_name: CD14+ donor 1, HS27aCM

label_protocol: cRNA was prepared from 2-5 ug total RNA according to Affymetrix protocols using the SuperScriptChoice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).

growth_protocol: Cells were cultured for 2 days in RPMI1640 medium supplemented with 10% FBS/2mM glutamine at 37ºC in 5% CO2. Conditioned medium from the stromal cell lines was collected from 3 million stromal cells grown for 5 days. It was clarified by centrifugation and diluted 1:1 with fresh supplemented RPMI1640 medium as described above just prior to use.

extract_protocol: Total RNA was isolated with Qiagen RNeasy kits according to manufacturer's protocols.

treatment_protocol: Monocytes (CD14+ cells) were isolated with Tuek4 Ab (Dako M0825) and IgG2a+b magnetic beads (Miltenyi) by AutoMacs. They were cultured with CM from each of the 2 stromal cell lines

tag: Gender

value: M, age 28


title: MO-5CM-donor1

description: HS5 conditioned medium: MO-5CM-donor1

source_name: CD14+ donor 1, HS5CM


title: MO-27aCM-donor2

description: HS27a conditioned medium: MO-27aCM-donor2

source_name: CD14+ donor 2, HS27aCM

value: F, age 43


title: MO-5CM-donor2

description: HS5 conditioned medium: MO-5CM-donor2

source_name: CD14+ donor 2, HS5CM


title: Human hypoxia 3 (Affymetrix U133 2.0)

city: Birmingham

first: Grier

last: Page

state: AL

institute: University of Alabama at Birmingham

hyb_protocol: Arrays were hybridized overnight at 45oC, and then washed, stained, and scanned on a GeneChip Scanner 3000 (Affymetrix, Inc., Santa Clara, CA).

data_processing: Gene expression levels were analyzed with GeneChip Operating Software (Affymetrix, Inc., Santa Clara, CA).

label: biotin-labeled cRNA

source_name: HT29 Cell lines

label_protocol: 2ug of total RNA from each sample was used to generate double strand cDNA by linear amplification using oligo dT-T7 primer and reverse transcriptase.  Subsequently, biotin-labeled cRNA was synthesized by in vitro transcription (IVT) using 3’-Amplification Reagents for IVT labeling (Affymetrix, Santa Clara, CA) followed by cRNA fragmentation.

growth_protocol: Cells were cultured in media (HT29: McCoy’s 5a medium supplemented with 7% Fetal Bovine Serum (FBS)) for 5-7 days (media bathing both the apical and basolateral compartments) at 37°C (5% CO2 - 95% air gas mixture).

extract_protocol: Total RNA was purified from HT29 cells using the mirVana™ miRNA Isolation Kit per manufacturer instructions (Ambion, Inc., Austin, TX).

treatment_protocol: In some monolayers, media was removed from the apical side to expose cells to air (A/L or air-liquid interface).

tag: Cells were cultured in media (HT29

tag: Media was not removed from the apical side to expose cells to air (A/L or air-liquid interface)


title: Arabidopsis AtMYB30-ox_6 h_ Xanthomonas inoculated_biological rep1_exp1

status: Public on Feb 29 2008

city: Castanet-Tolosan

first: Dominique

last: ROBY

address: Chemin de Borde Rouge

country: France

institute: CNRS/INRA

description: Gene expression data from Arabidopsis leaves 4 week-old plants from Ws-4, AtMYB30 overexpressor, inoculated with Xcc147 strain, at 108 cfu/ml, 6 h harvest

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45°C on ATH1 Arabidopsis GeneChip. GeneChips were washed and stained in the Affymetrix GenChip Fluidics Station 450

scan_protocol: GeneChips were scanned using the GenChip scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: Biotin

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis plants were grown under controlled conditions as previously described (Lacomme and Roby, 1996, Plant. Mol. Biol., 30, 995-1008)

extract_protocol: Total RNA was extracted as described by Lorrain et al., 2004, Plant cell, 16, 2217-2232

treatment_protocol: Leaves of 4 week-old plants were syringe-infiltrated in totality, with the Xcc147 strain, at 108 cfu/ml, harvested at various times after inoculation, pooled and frozen

tag: Transformation

value: AtMYB30 overexpressor

tag: Age

value: leaves of 4 week-old plants

tag: Bacterial inoculation

value: Xcc147 at 108 cfu/ml

tag: Harvest

value: 6 h post inoculation


title: Human hypoxia 1 (Affymetrix U133 2.0)

scan_protocol: Arrays were hybridized overnight at 45oC, and then washed, stained, and scanned on a GeneChip Scanner 3000 (Affymetrix, Inc., Santa Clara, CA).

value: McCoy’s 5a medium supplemented with 7% Fetal Bovine Serum (FBS)) for 5-7 days (media bathing both the apical and basolateral compartments) at 37°C (5% CO2 - 95% air gas mixture)


title: Human hypoxia 2 (Affymetrix U133 2.0)


title: Human normoxia 3 (Affymetrix U133 2.0)

tag: Media was removed from the apical side to expose cells to air (A/L or air-liquid interface)


title: Arabidopsis AtMYB30-ox_T0 (not inoculated)_biological rep2_exp2

description: Gene expression data from Arabidopsis leaves 4 week-old plants from Ws-4, AtMYB30 overexpressor, not inoculated


title: Arabidopsis AtMYB30-ox_90-105 min_ Xanthomonas inoculated_biological rep2_exp2

description: Gene expression data from Arabidopsis leaves 4 week-old plants from Ws-4, AtMYB30 overexpressor, inoculated with Xcc147 strain, at 108 cfu/ml, pool of 90-105 min harvest

value: 90-105 min post inoculation


title: Arabidopsis wild-type_90-105 min_ Xanthomonas inoculated_biological rep2_exp4

description: Gene expression data from Arabidopsis leaves 4 week-old plants from Ws-4, wild-type, inoculated with Xcc147 strain, at 108 cfu/ml, pool of 90-105 min harvest

value: no


title: Arabidopsis AtMYB30-as_90-105 min_ Xanthomonas inoculated_biological rep1_exp3

description: Gene expression data from Arabidopsis leaves 4 week-old plants from Ws-4, AtMYB30 antisense, inoculated with Xcc147 strain, at 108 cfu/ml, pool of 90-105 min harvest

value: AtMYB30 antisense


title: Arabidopsis AtMYB30-as_90-105 min_ Xanthomonas inoculated_biological rep2_exp4

source_name: Arabidopsis leaves 4 week-old plants from Ws-4, AtMYB30 antisense, inoculated with Xcc147 strain, at 108 cfu/ml, pool of 90-105 min harvest


title: Human normoxia 1 (Affymetrix U133 2.0)


title: Arabidopsis wild-type_90-105 min_ Xanthomonas inoculated_biological rep1_exp3

source_name: Arabidopsis leaves 4 week-old plants from Ws-4, wild-type, inoculated with Xcc147 strain, at 108 cfu/ml, pool of 90-105 min harvest


title: Arabidopsis AtMYB30-ox_2-4 h_ Xanthomonas inoculated_biological rep2_exp2

description: Gene expression data from Arabidopsis leaves 4 week-old plants from Ws-4, AtMYB30 overexpressor, inoculated with Xcc147 strain, at 108 cfu/ml, pool of 2-4 h harvest

value: 2-4 h post inoculation


title: Human normoxia 2 (Affymetrix U133 2.0)


title: Arabidopsis AtMYB30-ox_T0 (not inoculated)_biological rep1_exp1

source_name: Arabidopsis leaves 4 week-old plants from Ws-4, AtMYB30 overexpressor, not inoculated


title: Arabidopsis AtMYB30-ox_90-105 min_ Xanthomonas inoculated_biological rep1_exp1

source_name: Arabidopsis leaves 4 week-old plants from Ws-4, AtMYB30 overexpressor, inoculated with Xcc147 strain, at 108 cfu/ml, pool of 90-105 min harvest


title: Arabidopsis wild-type_2-4 h_ Xanthomonas inoculated_biological rep2_exp2

description: Gene expression data from Arabidopsis leaves 4 week-old plants from Ws-4, wild-type, inoculated with Xcc147 strain, at 108 cfu/ml, pool of 2-4 h harvest


title: Arabidopsis AtMYB30-ox_2-4 h_ Xanthomonas inoculated_biological rep1_exp1

source_name: Arabidopsis leaves 4 week-old plants from Ws-4, AtMYB30 overexpressor, inoculated with Xcc147 strain, at 108 cfu/ml, pool of 2-4 h harvest


title: Arabidopsis wild-type_2-4 h_ Xanthomonas inoculated_biological rep1_exp1

source_name: Arabidopsis leaves 4 week-old plants from Ws-4, wild-type, inoculated with Xcc147 strain, at 108 cfu/ml, pool of 2-4 h harvest


title: Arabidopsis wild-type_6 h_ Xanthomonas inoculated_biological rep1_exp1

description: Gene expression data from Arabidopsis leaves 4 week-old plants from Ws-4, wild-type, inoculated with Xcc147 strain, at 108 cfu/ml, 6 h harvest


title: Arabidopsis wild-type_90-105 min_ Xanthomonas inoculated_biological rep1_exp1


title: Arabidopsis wild-type_T0 (not inoculated)_biological rep2_exp2

description: Gene expression data from Arabidopsis leaves 4 week-old plants from Ws-4, wild-type, not inoculated


title: Arabidopsis wild-type_T0 (not inoculated)_biological rep1_exp1

source_name: Arabidopsis leaves 4 week-old plants from Ws-4, wild-type, not inoculated


title: LNCaP_AndrogenDeprived_12month_1

city: Pittsburgh

first: Beth

middle: R.

last: Pflug

state: PA

address: 5200 Centre Ave

department: Urology

institute: University of Pittsburgh

description: Gene expression data from non-treated LNCaP cells at time point 0.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: LNCaP_AndrogenDeprived_12month_1, LNCaP cells collected at androgen deprivation for 12 months.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2002, Affymetrix).

growth_protocol: LNCaP cells (obtained from ATCC) were cultured in growth media (RPMI plus 10% FBS, 1% P/S) and used as control, untreated cells. Treated cells were initially plated at 2x106 and deprived at approximately 80% confluence.Deprived cells were passaged once following initial deprivation and not split until after month 10, when they were passaged approximately once per 10 days and plated at 1x106 cells in 75cm2 flasks.

extract_protocol: Total RNA was extracted using RNA-Bee as per manufacture's instructions and further cleaned up with Qiagen Rneasy Mini kit following the manufacturer's instructions.

treatment_protocol: Under androgen deprivation treatment for 12 months.

tag: Cultured prostate cancer cells deprived of androgen for 12 months;


title: LNCaP_AndrogenDeprived_11month_1

source_name: LNCaP_AndrogenDeprived_11month_1, LNCaP cells collected at androgen deprivation for 11 months.

treatment_protocol: Under androgen deprivation treatment for 11 months.

tag: Cultured prostate cancer cells deprived of androgen for 11 months;


title: LNCaP_AndrogenDeprived_11month_2

source_name: LNCaP_AndrogenDeprived_11month_2, LNCaP cells collected at androgen deprivation for 11 months.


title: LNCaP_AndrogenDeprived_5month_2

source_name: LNCaP_AndrogenDeprived_5month_2, LNCaP cells collected at androgen deprivation for 5 months.

treatment_protocol: Under androgen deprivation treatment for 5 months.

tag: Cultured prostate cancer cells deprived of androgen for 5 months;


title: LNCaP_Control_12month

source_name: LNCaP_Control_12month, LNCaP cells free of treatment at 12month

growth_protocol: LNCaP cells (obtained from ATCC) were cultured in growth media (RPMI plus 10% FBS, 1% P/S) and used as control, untreated cells. Control cells were passaged approximately once per 10 days and plated at 1x106 cells.

treatment_protocol: Control LNCaP Cells free of treatment.

tag: Cultured prostate cancer cells at 12 months;


title: LNCaP_AndrogenDeprived_12month_2

source_name: LNCaP_AndrogenDeprived_12month_2, LNCaP cells collected at androgen deprivation for 12 months.


title: LNCaP_Control_1month

source_name: LNCaP_Control_1month, LNCaP cells free of treatment at 1month

tag: Cultured prostate cancer cells at one month;


title: LNCaP_Control_CGF

source_name: LNCaP_Control_CGF, LNCaP cells free of treatment from CGF facility

extract_protocol: Total RNA was extracted using Qiagen Rneasy Mini kit following the manufacturer's instructions.

tag: Cultured prostate cancer cells from CGF facility;


title: LCL Unaffected MZ twin pair 4 (CCN4.1)(TP25)

status: Public on Feb 28 2008

city: Brisbane

first: Nicholas

last: Matigian

state: Queensland

address: 170 Kessels Rd, Nathan

institute: National Adult Stem Cell Centre

hyb_protocol: Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.

data_processing: Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared

source_name: Unaffected MZ twin pair 4 (Unaffected patient of MZ twin pair CCN4)

growth_protocol: LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22  LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture.  RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions.  RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value.  All samples had an RIN of 9.9 or 10, which designates very high quality RNA

extract_protocol: LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software

tag: Sample ID

tag: Twin Pair ID

tag: Clinical Status

value: Unaffected

tag: Age of Onset:-N/A

tag: Age at interview & blood sampling

tag: Current Age (2007)

tag: Sex

value: FEMALE

tag: Medication at blood sampling


title: LNCaP_AndrogenDeprived_1month_2

source_name: LNCaP_AndrogenDeprived_1month_2, LNCaP cells collected at androgen deprivation for 1 month.

treatment_protocol: Under androgen deprivation treatment for 1 month.

tag: Cultured prostate cancer cells deprived of androgen for 1 month;


title: LNCaP_Control_5month

source_name: LNCaP_Control_5month, LNCaP cells free of treatment at 5month

tag: Cultured prostate cancer cells at 5 months;


title: LNCaP_Control_Time0

source_name: LNCaP_Control_Time0, LNCaP cells free of treatment at time0.

tag: Cultured prostate cancer cells;


title: LNCaP_AndrogenDeprived_3week_1

source_name: LNCaP_AndrogenDeprived_3week_1, LNCaP cells collected at androgen deprivation for 3 weeks.

treatment_protocol: Under androgen deprivation treatment for 3 weeks.

tag: Cultured prostate cancer cells deprived of androgen for 3 weeks;


title: LNCaP_AndrogenDeprived_5month_1

source_name: LNCaP_AndrogenDeprived_5month_1, LNCaP cells collected at androgen deprivation for 5 months.


title: LNCaP_AndrogenDeprived_3week_2

source_name: LNCaP_AndrogenDeprived_3week_2, LNCaP cells collected at androgen deprivation for 3 weeks.


title: LNCaP_Control_3week

source_name: LNCaP_Control_3week, LNCaP cells free of treatment at 3week.

tag: Cultured prostate cancer cells at 3 weeks;


title: LCL Unaffected MZ twin pair 4 (CCN4.2)(TP26)

scan_protocol: Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.


title: LCL Unaffected MZ twin pair 2 (CCN2.2)(TP18)

source_name: Unaffected MZ twin pair 2 (Unaffected patient of MZ twin pair CCN2)

label_protocol: Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.

value: MALE


title: LCL Unaffected MZ twin pair 3 (CCN3.1)(TP23)

source_name: Unaffected MZ twin pair 3 (Unaffected patient of MZ twin pair CCN3)


title: LCL Unaffected MZ twin pair 5 (CCN5.2)(TP28)

source_name: Unaffected MZ twin pair 5 (Unaffected patient of MZ twin pair CCN5)


title: LNCaP_AndrogenDeprived_1month_1

source_name: LNCaP_AndrogenDeprived_1month_1, LNCaP cells collected at androgen deprivation for 1 month.


title: LCL Unaffected MZ twin pair 2 (CCN2.1)(TP17)


title: Arabidopsis wild-type_90-105 min_ Xanthomonas inoculated_biological rep2_exp2

source_name: Arabidopsis leaves 4 week-old plants from Ws-4, wild-type, inoculated with Xcc147 strain, at 108 cfu/ml, pool of 90-105 min harvest

tag: Genotype

tag: Transformation

tag: Age

tag: Bacterial inoculation

tag: Harvest


title: LCL Unaffected MZ twin pair 1 (CCN1.2R)(TP16)

source_name: Unaffected MZ twin pair 1 Repeat (Unaffected patient of MZ twin pair CCN1)

tag: Sample ID

tag: Twin Pair ID

tag: **Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.2**


title: LCL Unaffected MZ twin pair 1 (CCN1.1R)(TP15)

tag: Clinical Status

tag: Age of Onset:-N/A

tag: Age at interview & blood sampling

tag: **Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.1**


title: LCL Unaffected MZ twin pair 3 (CCN3.2)(TP24)

tag: Current Age (2007)

tag: Sex

tag: Medication at blood sampling


title: Gene expression of mouse ES cells, Eed KO

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2).  PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC1. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8.  PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4.  We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome.

hyb_protocol: 20 micrograms of labeled target RNA was hybridized with Mouse Genome 430 2.0 GeneChip expression arrays (Affymetrix) at 45ﾂｰC for 16 h, as described in the manufacturer's instructions. Washing stages and streptavidin-phycoerythrin staining were conducted using a GeneChip Fluidics Station (Affymetrix).

scan_protocol: The GeneChips were scanned using GeneChip Scanner 3000 (Affymetrix).

data_processing: MAS5 [the standard algorhithm provided by Affymetrix (http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf)]

source_name: Mus musculus embryonic stem cells, Eed KO

label_protocol: cDNA synthesis, cRNA amplification, biotinylation and fragmentation were performed with a One-Cycle Target Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen) and purified with Qiagen RNeasy separation columns (Qiagen).

tag: Embryonic stem cells, Strain; 129/B6 hybrid


title: LCL Unaffected MZ twin pair 1 (CCN1.2)(TP14)

source_name: Unaffected MZ twin pair 1 (Unaffected patient of MZ twin pair CCN1)

tag: **Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.2R**


title: LCL Unaffected MZ twin pair 5 (CCN5.1)(TP27)


title: LCL Unaffected MZ twin pair 1 (CCN1.1)(TP13)

tag: **Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.1R**


title: LCL Concordant for Epilepsy twin pair 4 (CCE4.2)(TP40)

source_name: Concordant for Epilepsy twin pair 4 (Affected patient of MZ twin pair CCE4)

value: Childhood Absence Epilepsy

tag: Age of Onset:-10.5

value: Epilim


title: LCL Concordant for Epilepsy twin pair 4 (CCE4.1)(TP39)

tag: Age of Onset:-11.5

value: Epilim & Lamictal


title: LCL Concordant for Epilepsy twin pair 3 (CCE3.2)(TP36)

source_name: Concordant for Epilepsy twin pair 3 (Affected patient of MZ twin pair CCE3)

tag: Age of Onset:-7


title: Gene expression of mouse ES cells, control of Eed KO

source_name: Mus musculus embryonic stem cells, control of Eed KO


title: LCL Concordant for Epilepsy twin pair 2 (CCE2.2)(TP32)

source_name: Concordant for Epilepsy twin pair 1 (Affected patient of MZ twin pair CCE1)

tag: Age of Onset:-5


title: LCL Concordant for Epilepsy twin pair 2 (CCE2.1)(TP31)

tag: Sample ID

tag: Age of Onset:-4.5


title: LCL Concordant for Epilepsy twin pair 3 (CCE3.1)(TP35)

tag: Twin Pair ID


title: LCL Concordant for Epilepsy twin pair 1 (CCE1.1)(TP21)

tag: Clinical Status

tag: Current Age (2007):25


title: lymph node B cell - Baff-tg - Tg2 - Day3

city: Darlinghurst

first: Sandra

last: Gardam

state: NSW

address: 384 Victoria St

department: Autoimmunity Unit

institute: Garvan Institute of Medical Research

hyb_protocol: 15ug of fragmented RNA was hybridised overnight (16h) at 45C on Affymetrix Mouse Genome 4.30 2.0 Arrays.  Washing and staining performed as per manufacturer's instruction on Affymetrix Fluidics Station 400

scan_protocol: Arrays were scanned using a GeneChip Scanner (Affymetrix).

data_processing: Analysis of data was performed using GeneSpring software (Agilent).  Samples were preprocess with RMA. All samples were normalised on a per gene basis to the median of the control samples run at the same time.

source_name: Lymph node B cell ex vivo purified - Baff-tg - Tg2 - Day3

label_protocol: GeneChip Two Cycle labelling kit (Affymetrix) was used as per manufacturer's instructions

extract_protocol: RNA was extracted using RNeasy Mini Kit from Qiagen as per manufacturer's instructions

tag: Strain

tag: Age

value: 13 weeks

tag: Gender

value: male

tag: Genotype

value: Baff-tg


title: lymph node B cell - Traf3DB/DB - T3KO - Day2

source_name: Lymph node B cell ex vivo purified - Traf3DB/DB - T3KO - Day2

value: 19 weeks


title: LCL Discordant twin pair 5 (DCE5.1)(TP37)

source_name: Discordant twin pair 5 (Affected patient of MZ twin pair DCE5)

value: Juvenile Absence Epilepsy + Febrile Seizures

tag: Age of Onset:-13

tag: Age at interview & blood sampling

tag: Current Age (2007):30

tag: Sex

tag: Medication at blood sampling


title: lymph node B cell - wildtype - control1 - Day3

source_name: Lymph node B cell ex vivo purified - wildtype - control1 - Day3

value: 12 weeks

value: Wildtype


title: lymph node B cell - Traf3DB/DB - T3KO - Day1

source_name: Lymph node B cell ex vivo purified - Traf3DB/DB - T3KO - Day1

value: 26 weeks

value: female


title: lymph node B cell - wildtype - control2 - Day3

source_name: Lymph node B cell ex vivo purified - wildtype - control2 - Day3


title: lymph node B cell - Traf2DB/DB - T2KO - Day1

source_name: Lymph node B cell ex vivo purified - Traf2DB/DB - T2KO - Day1

value: 23 weeks


title: lymph node B cell - wildtype - control3 - Day3

source_name: Lymph node B cell ex vivo purified - wildtype - control3 - Day3

value: 15 weeks


title: lymph node B cell - Traf2DB/DB - T2KO - Day2

source_name: Lymph node B cell ex vivo purified - Traf2DB/DB - T2KO - Day2


title: lymph node B cell - Baff-tg - Tg1 - Day3

source_name: Lymph node B cell ex vivo purified - Baff-tg - Tg1 - Day3


title: lymph node B cell - Traf3lox/lox - control3 - Day2

source_name: Lymph node B cell ex vivo purified - Traf3lox/lox - control3 - Day2


title: LCL Discordant twin pair 4 (DCE4.2)(TP34)

source_name: Discordant twin pair 4 (Affected pateint of MZ twin pair DCE4)

value: Unaffected

tag: Age of Onset:-N/A

tag: Current Age (2007):29


title: LCL Discordant twin pair 5 (DCE5.2)(TP38)

source_name: Discordant twin pair 5 (Unaffected patient of MZ twin pair DCE5)

tag: Age of Onset:- N/A

value: FEMALE


title: lymph node B cell - CD19-cretg - control1 - Day1

source_name: Lymph node B cell ex vivo purified - CD19-cretg - control1 - Day1


title: lymph node B cell - Baff-tg - Tg3 - Day3

source_name: Lymph node B cell ex vivo purified - Baff-tg - Tg3 - Day3


title: lymph node B cell - Traf2lox/lox - control1 - Day1

source_name: Lymph node B cell ex vivo purified - Traf2lox/lox - control1 - Day1

value: 31 weeks


title: LCL Discordant twin pair 3 (DCE3.2)(TP30)

source_name: Discordant twin pair 3 (Unaffected pateint of MZ twin pair DCE3)

tag: Sample ID

tag: Twin Pair ID:DCE3.2

tag: Age at interview & blood sampling:23

tag: Current Age (2007):26

value: MALE


title: LCL Discordant twin pair 4 (DCE4.1)(TP33)

tag: Twin Pair ID:DCE4.1

tag: Clinical Status

value: Childhood Absence Epilepsy

tag: Age of Onset:-7

tag: Age at interview & blood sampling:26

value: Epilim


title: LCL Discordant twin pair 3 (DCE3.1)(TP29)

source_name: Discordant twin pair 3 (Affected pateint of MZ twin pair DCE3)

tag: Twin Pair ID:DCE3.1

tag: Age of Onset:-5


title: LCL Discordant twin pair 2 (DCE2.2)(TP20)

source_name: Discordant twin pair 2 (Unaffected pateint of MZ twin pair DCE2)

tag: Twin Pair ID:DCE2.2

tag: Clinical Status:Unaffected

tag: Age at interview & blood sampling:42

tag: Current Age (2007):45


title: LCL Discordant twin pair 2 (DCE2.1)(TP19)

source_name: Discordant twin pair 2 (Affected pateint of MZ twin pair DCE2)

tag: Twin Pair ID:DCE2.1

tag: Clinical Status:Childhood Absence Epilepsy + Febrile Seizures

tag: Age of Onset:-4

tag: Sex

tag: Medication at blood sampling


title: LCL Discordant twin pair 1 (DCE1.2) (TP12)

source_name: Discordant twin pair 1 (Unsffected pateint of MZ twin pair DCE1)

tag: Sample ID

tag: Twin Pair ID:DCE1.2

tag: Age of Onset:- N/A

tag: Age at interview & blood sampling:39

tag: Current Age (2007):41


title: lymph node B cell - Traf2lox/lox - control1 - Day2

source_name: Lymph node B cell ex vivo purified - Traf2lox/lox - control1 - Day2

tag: Strain

tag: Age

tag: Gender

tag: Genotype


title: lymph node B cell - Traf2lox/lox - control2 - Day2

source_name: Lymph node B cell ex vivo purified - Traf2lox/lox - control2 - Day2


title: CD34AML_UT_6 h_patient_7

status: Public on Feb 27 2008

city: New York

first: Duane

last: Hassane

state: NY

address: 1305 York Avenue, Box 140

institute: Weill Cornell Medical College

description: CD34+ AML Patient 7 Treatment with UT 6 h

hyb_protocol: Affymetrix

scan_protocol: GeneChip Scanner 3000 7G, GCOS

data_processing: MAS 5.0 (BioConductor) Scale 100

source_name: CD34+ Primary Acute Myelogenous Leukemia, 6 h post-treatment with UT

label_protocol: Ovation Biotin RNA Amplification and Labeling System (NuGEN)

extract_protocol: Qiagen RNeasy


title: LCL Discordant twin pair 1 (DCE1.1) (TP11)

source_name: Discordant twin pair 1 (Affected pateint of MZ twin pair DCE1)

tag: Sample ID:TP11

tag: Twin Pair ID:DCE1.1

tag: Clinical Status:Late onset IGE

tag: Age of Onset:-28


title: CD34AML_UT_6 h_patient_8

description: CD34+ AML Patient 8 Treatment with UT 6 h


title: Standard high-fat diet, sample 8843

city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

description: 9-week-old C57Bl/6J-mice were divided into two groups (n=10/group). The control diet was a standard high-fat diet (60% of energy) low in calcium (0.4%). The whey protein diet was a high-calcium (1.8%) high-fat diet with whey protein isolate. After the 21-week treatment, the adipose tissue transcript profiling (2 mice/group) was carried out using Affymetrix Mouse Genome 430 2.0 array.

hyb_protocol: according the standard protocol

scan_protocol: according the standard protocol

data_processing: The data was pre-processed with the robust multichip algorithm (RMA), normalized per chip to the median, and analyzed with Genespring 7.2. (Agilent, USA).

source_name: standard high-fat diet, sample 8843

label_protocol: according the standard protocol

extract_protocol: Total RNA from the epididymal fat pads of two control mice, and two high-calcium whey protein fed mice were collected with Trizol (Gibco), purified with RNeasy Mini Kit (Qiagen) and measured with 260 and 280 nm.


title: CD34AML_PTL_6 h_patient_5

description: CD34+ AML Patient 5 Treatment with PTL 6 h

source_name: CD34+ Primary Acute Myelogenous Leukemia, 6 h post-treatment with PTL


title: CD34AML_UT_6 h_patient_4

description: CD34+ AML Patient 4 Treatment with UT 6 h


title: CD34AML_PTL_6 h_patient_8

description: CD34+ AML Patient 8 Treatment with PTL 6 h


title: CD34AML_UT_6 h_patient_6

description: CD34+ AML Patient 6 Treatment with UT 6 h


title: High-calcium diet, rep2

source_name: dietary calcium and dairy proteins, sample 8815

tag: 9-week-old C57Bl/6J-mice were divided into two groups (n=10/group). The control diet was a standard high-fat diet (60% of energy) low in calcium (0.4%). The whey protein diet was a high-calcium (1.8%) high-fat diet with whey protein isolate. After the 21-week treatment, the adipose tissue transcript profiling (2 mice/group) was carried out using Affymetrix Mouse Genome 430 2.0 array.


title: Dietary calcium and dairy proteins, sample 8850

source_name: dietary calcium and dairy proteins, sample 8850


title: CD34AML_UT_6 h_patient_3

description: CD34+ AML Patient 3 Treatment with UT 6 h


title: CD34AML_PTL_6 h_patient_13

description: CD34+ AML Patient 13 Treatment with PTL 6 h


title: CD34AML_UT_6 h_patient_13

description: CD34+ AML Patient 13 Treatment with UT 6 h


title: CD34AML_PTL_6 h_patient_3

description: CD34+ AML Patient 3 Treatment with PTL 6 h


title: CD34AML_UT_6 h_patient_5

description: CD34+ AML Patient 5 Treatment with UT 6 h


title: CD34AML_PTL_6 h_patient_7

description: CD34+ AML Patient 7 Treatment with PTL 6 h


title: High-calcium diet, rep1

source_name: High-calcium diet, rep1


title: CD34AML_PTL_6 h_patient_6

description: CD34+ AML Patient 6 Treatment with PTL 6 h


title: CD34AML_PTL_6 h_patient_4

description: CD34+ AML Patient 4 Treatment with PTL 6 h


title: CD34AML_PTL_6 h_patient_2

description: CD34+ AML Patient 2 Treatment with PTL 6 h


title: CD34AML_UT_6 h_patient_2

description: CD34+ AML Patient 2 Treatment with UT 6 h


title: CD34AML_UT_6 h_patient_12

description: CD34+ AML Patient 12 Treatment with UT 6 h


title: CD34AML_UT_6 h_patient_11

description: CD34+ AML Patient 11 Treatment with UT 6 h


title: CD34AML_PTL_6 h_patient_12

description: CD34+ AML Patient 12 Treatment with PTL 6 h


title: CD34AML_PTL_6 h_patient_11

description: CD34+ AML Patient 11 Treatment with PTL 6 h


title: CD34AML_PTL_6 h_patient_10

description: CD34+ AML Patient 10 Treatment with PTL 6 h


title: CD34AML_PTL_6 h_patient_1

description: CD34+ AML Patient 1 Treatment with PTL 6 h


title: Mll-AF9 HSC-replicate 3

status: Public on Feb 25 2008

city: Minneapolis

first: Ashish

last: Kumar

state: MN

address: 425 East River Road

institute: University of Minnesota

description: no additional information

hyb_protocol: As per Affymetrix protocols

scan_protocol: As per Affymetrix protocols

data_processing: Expression values were obtained using RMA and normalized by the LOESS method

source_name: sorted HSCs

label_protocol: Labeling was carried out using the 2 cycle labeling reaction protocol (Affymetrix)

growth_protocol: Samples were FACS sorted from whole bone marrow cells

extract_protocol: Total RNA was extracted using the pico-pure RNA extraction kit (Arcturus)

treatment_protocol: Cells were collected directly in RNA extraction buffer

tag: Mll-AF9 knock-in, C57/BL6, 6-8 weeks old


title: CD34AML_UT_6 h_patient_10

description: CD34+ AML Patient 10 Treatment with UT 6 h


title: Mll-AF9 CMP-replicate 3, second run

description: All of the CMP samples, except one, were processed twice (ie, first run and second run) and thus have 2 CEL files; 1 CEL file per Sample.

source_name: sorted CMPs


title: Mll-AF9 CMP-replicate 2, second run


title: Mll-AF9 CLP-replicate 1

description: no additional information


title: Mll-AF9 HSC-replicate 1

description: no additional information


title: Mll-AF9 CLP-replicate 4

description: no additional information


title: Mll-AF9 CMP-replicate 2, first run


title: Mll-AF9 HSC-replicate 2

description: no additional information


title: CD34AML_UT_6 h_patient_1

description: CD34+ AML Patient 1 Treatment with UT 6 h


title: Mll-AF9 CLP-replicate 3

description: no additional information


title: Mll-AF9 HSC-replicate 4

description: no additional information


title: Mll-AF9 CLP-replicate 6

description: no additional information


title: Mll-AF9 CLP-replicate 7

description: no additional information


title: F9 Embryonal Carcinoma cell line Replicate 3

first: Lisa

last: Dailey

address: 550 1st Avenue

department: Microbiology

institute: NYU School of Medicine

hyb_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

data_processing: GCOS version 1.4, default parameters

growth_protocol: maintained at on 0.2% gelatinized tissue culture plates in DMEM supplemented with 10% fetal calf serum. RNA was extracted from cells at approximately 80% confluence.

extract_protocol: Trizol according to the manufacturer's recommendations

tag: Embryonal Carcinoma cell line


title: Mll-AF9 CLP-replicate 5

description: no additional information


title: Mll-AF9 CMP-replicate 4, first run


title: Mll-AF9 CLP-replicate 2

description: no additional information


title: F9 Embryonal Carcinoma cell line Replicate 2

scan_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array


title: Mll-AF9 CMP-replicate 3, first run


title: Mll-AF9 GMP-replicate 3

description: no additional information

source_name: sorted GMPs


title: Mll-AF9 HSC-replicate 5

description: no additional information


title: Mll-AF9 CMP-replicate 1, second run


title: Mll-AF9 CMP-replicate 1, first run


title: F9 Embryonal Carcinoma cell line Replicate 1

label_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array


title: Mll-AF9 GMP-replicate 4

description: no additional information


title: Mll-AF9 CMP-replicate 4, second run


title: Mll-AF9 GMP-replicate 2

description: no additional information


title: Wild type HSC-replicate 5

description: no additional information

tag: Wild type C57/BL6 6-8 weeks old


title: Wild type HSC-replicate 4

description: no additional information


title: Wild type HSC-replicate 1

description: no additional information


title: Wild type CLP-replicate 4

description: no additional information

source_name: sorted CLPs


title: Wild type CLP-replicate 8

description: no additional information


title: Wild type HSC-replicate 2

description: no additional information


title: Wild type CLP-replicate 3

description: no additional information


title: Wild type CLP-replicate 7

description: no additional information


title: Wild type GMP-replicate 4

description: no additional information


title: Wild type CLP-replicate 6

description: no additional information


title: Wild type CMP-replicate 3, second run


title: Wild type CMP-replicate 2, second run


title: Wild type CMP-replicate 2, first run


title: Wild type CLP-replicate 2

description: no additional information


title: Wild type CMP-replicate 1, second run


title: Wild type CMP-replicate 3, first run


title: Wild type CMP-replicate 5


title: Wild type CMP-replicate 4, second run


title: Wild type GMP-replicate 1

description: no additional information


title: Wild type GMP-replicate 2

description: no additional information


title: Wild type HSC-replicate 3

description: no additional information


title: Wild type CMP-replicate 1, first run


title: Wild type CMP-replicate 4, first run


title: Wild type CLP-replicate 5

description: no additional information


title: Wild type GMP-replicate 3

description: no additional information


title: Wild type CLP-replicate 1

description: no additional information


title: Wild type GMP-replicate 5

description: no additional information


title: HEK293 siStarPap 5

city: Madison

first: Christy

last: Barlow

state: WI

address: 1300 University Ave

institute: University of Wisconsin

hyb_protocol: Hybridization cocktail prepared for each sample protocols and 10 ug of cRNA applied to HC U133 2.0 GeneChip for hybridization at 45C for 16 h.  All protocols and procedures followed by AFX Expression Analysis Manual

scan_protocol: AFX Fluidics450 Station scanned accroding to all AFX protocols and procedures defined for the AFX HG_u133 2.0 GeneChip

data_processing: The measurement of changes in expression were analyzed using empirical Bayes methodology Ebarrays.  Posterior probablilities of differential expression were calculated assuming the log normal Normal expression model.

source_name: siRNA

label_protocol: Ambion MessageAmp II Biotin Enhanced kit

growth_protocol: 10% DMEM

extract_protocol: Qiagen Rneasy mini RNA extraction kit with on-column Dnase treatment

treatment_protocol: Calcium phosphate transfection of siRNA

tag: HEK293 cells


title: HEK293 siPIPKIa 4


title: HEK293 siStarPap 6


title: HEK293 siPIPKIa 6


title: HEK293 siPIPKIa 5


title: HEK293 siControl 6


title: pediatric T-ALL patient #122

status: Public on Feb 23 2008

city: Utrecht

first: Jules

last: Meijerink

address: Uppsalalaan 8

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

description: pediatric T-ALL patient #122

hyb_protocol: Hybridization of Humane Genome U133 plus2.0 oligonucleotide microarrays (Affymetrix, Santa-Clara, USA) and washing steps were performed according to the manufacturers’ protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip scanner 3000

data_processing: Probeset intensities were extracted from CEL-files using GeneChip Operating Software (GCOS), version 1.4.0.036 (Affymetrix).  Probe intensities were normalized using the variance stabilization procedure (Bioconductor package VSN) in the statistical data analysis environment R, version 2.2.0. Differentially expressed genes between T-ALL subgroups were calculated using a Wilcoxon statistical test, and corrected for multiple testing error according to the false discovery rate procedure as developed by Hochberg and Benjaminin using the Bioconductor package Multtest.

source_name: pediatric T-ALL patient #122, unknown

label_protocol: Copy-DNA and ccRNA syntheses from total RNA, hybridization of Humane Genome U133 plus2.0 oligonucleotide microarrays (Affymetrix, Santa-Clara, USA) and washing steps were performed according to the manufacturers’ protocol.

extract_protocol: Genomic DNA and total cellular RNA were isolated using Trizol (Invitrogen) according to the manufacturers’ protocol, with minor modifications. An additional phenol-chloroform extraction was performed and the RNA was precipitated with isopropanol along with 1 mL (20 mg/mL) glycogen (Roche, Almere, The Netherlands). After precipitation, RNA pellets were dissolved in 20 mL RNAse-free TE-buffer (10 mM Tris-HCl, 1 mM EDTA, pH=8.0). The RNA concentration was quantified spectrophotometrically. Integrity of total RNA was checked using the Agilent 2100 Bio-analyzer (Agilent, Santa-Clara, USA).

treatment_protocol: Leukemic cells were isolated and enriched from these samples. Within 24 hours after sampling, mononuclear cells were isolated by density gradient centrifugation using Lymphoprep (density 1.077 g/mL; Nycomed Pharma, Oslo, Norway), and centrifuged at 480g for 15 minutes at room temperature. The collected mononuclear cells were washed twice and kept in culture medium consisting of RPMI 1640 medium (Dutch modification without L-glutamine; Gibco BRL, Life Technologies, Breda, The Netherlands), 20% fetal calf serum (FCS; Integro, Zaandam, The Netherlands), 2 mM L-glutamine (Gibco BRL, Life Technologies) 5 µg/mL insulin, 5 µg/mL transferrin, 5 ng/mL sodium selenite (ITS media supplement; Sigma, St Louis, MO), 100 IU/mL penicillin, 100 µg/mL streptomycin, 0.125 µg/mL fungizone (Gibco BRL, Life Technologies), and 0.2 mg/mL gentamycin (Gibco BRL, Life Technologies). Contaminating nonleukemic cells were removed by immunomagnetic beads. as described by Kaspers et al (1994). All resulting samples contained 90% leukemic cells, as determined morphologically by May-Grünwald-Giemsa-stained cytospins (Merck, Darmstadt, Germany). Viably frozen T-ALL cells were used for DNA and RNA extraction, and a minimum of 5 million leukemic cells were lysed in Trizol reagent (Invitrogen, Life Technologies, Breda, The Netherlands) and stored at -80°C.

tag: pediatric T-ALL patient #122, unknown


title: HEK293 siControl 5


title: pediatric T-ALL patient #120

description: pediatric T-ALL patient #120

source_name: pediatric T-ALL patient #120, unknown

tag: pediatric T-ALL patient #120, unknown


title: pediatric T-ALL patient #140

description: pediatric T-ALL patient #140

source_name: pediatric T-ALL patient #140, unknown

tag: pediatric T-ALL patient #140, unknown


title: pediatric T-ALL patient #128

description: pediatric T-ALL patient #128

source_name: pediatric T-ALL patient #128, unknown

tag: pediatric T-ALL patient #128, unknown


title: pediatric T-ALL patient #124

description: pediatric T-ALL patient #124

source_name: pediatric T-ALL patient #124, HOXA

tag: pediatric T-ALL patient #124, HOXA


title: HEK293 siStarPap 4


title: pediatric T-ALL patient #126

description: pediatric T-ALL patient #126

source_name: pediatric T-ALL patient #126, unknown

tag: pediatric T-ALL patient #126, unknown


title: pediatric T-ALL patient #133

description: pediatric T-ALL patient #133

source_name: pediatric T-ALL patient #133, unknown

tag: pediatric T-ALL patient #133, unknown


title: pediatric T-ALL patient #132

description: pediatric T-ALL patient #132

source_name: pediatric T-ALL patient #132, unknown

tag: pediatric T-ALL patient #132, unknown


title: pediatric T-ALL patient #129

description: pediatric T-ALL patient #129

source_name: pediatric T-ALL patient #129, unknown

tag: pediatric T-ALL patient #129, unknown


title: HEK293 siControl 4


title: pediatric T-ALL patient #125

description: pediatric T-ALL patient #125

source_name: pediatric T-ALL patient #125, unknown

tag: pediatric T-ALL patient #125, unknown


title: pediatric T-ALL patient #135

description: pediatric T-ALL patient #135

source_name: pediatric T-ALL patient #135, unknown

tag: pediatric T-ALL patient #135, unknown


title: pediatric T-ALL patient #130

description: pediatric T-ALL patient #130

source_name: pediatric T-ALL patient #130, unknown

tag: pediatric T-ALL patient #130, unknown


title: pediatric T-ALL patient #136

description: pediatric T-ALL patient #136

source_name: pediatric T-ALL patient #136, unknown

tag: pediatric T-ALL patient #136, unknown


title: pediatric T-ALL patient #121

description: pediatric T-ALL patient #121

source_name: pediatric T-ALL patient #121, unknown

tag: pediatric T-ALL patient #121, unknown


title: pediatric T-ALL patient #123

description: pediatric T-ALL patient #123

source_name: pediatric T-ALL patient #123, unknown

tag: pediatric T-ALL patient #123, unknown


title: pediatric T-ALL patient #131

description: pediatric T-ALL patient #131

source_name: pediatric T-ALL patient #131, unknown

tag: pediatric T-ALL patient #131, unknown


title: pediatric T-ALL patient #137

description: pediatric T-ALL patient #137

source_name: pediatric T-ALL patient #137, unknown

tag: pediatric T-ALL patient #137, unknown


title: pediatric T-ALL patient #109

description: pediatric T-ALL patient #109

source_name: pediatric T-ALL patient #109, LMO2

tag: pediatric T-ALL patient #109, LMO2


title: Mll-AF9 GMP-replicate 1

description: no additional information

source_name: sorted GMPs

tag: Mll-AF9 knock-in, C57/BL6, 6-8 weeks old


title: pediatric T-ALL patient #101

description: pediatric T-ALL patient #101

source_name: pediatric T-ALL patient #101, HOXA

tag: pediatric T-ALL patient #101, HOXA


title: pediatric T-ALL patient #107

description: pediatric T-ALL patient #107

source_name: pediatric T-ALL patient #107, LMO2

tag: pediatric T-ALL patient #107, LMO2


title: pediatric T-ALL patient #127

description: pediatric T-ALL patient #127

source_name: pediatric T-ALL patient #127, unknown

tag: pediatric T-ALL patient #127, unknown


title: pediatric T-ALL patient #95

description: pediatric T-ALL patient #95

source_name: pediatric T-ALL patient #95, HOX11L2

tag: pediatric T-ALL patient #95, HOX11L2


title: pediatric T-ALL patient #103

description: pediatric T-ALL patient #103

source_name: pediatric T-ALL patient #103, LMO2

tag: pediatric T-ALL patient #103, LMO2


title: pediatric T-ALL patient #98

description: pediatric T-ALL patient #98

source_name: pediatric T-ALL patient #98, HOX11

tag: pediatric T-ALL patient #98, HOX11


title: pediatric T-ALL patient #100

description: pediatric T-ALL patient #100

source_name: pediatric T-ALL patient #100, HOXA

tag: pediatric T-ALL patient #100, HOXA


title: pediatric T-ALL patient #106

description: pediatric T-ALL patient #106

source_name: pediatric T-ALL patient #106, LMO2

tag: pediatric T-ALL patient #106, LMO2


title: pediatric T-ALL patient #104

description: pediatric T-ALL patient #104

source_name: pediatric T-ALL patient #104, LMO2

tag: pediatric T-ALL patient #104, LMO2


title: pediatric T-ALL patient #99

description: pediatric T-ALL patient #99

source_name: pediatric T-ALL patient #99, HOX11

tag: pediatric T-ALL patient #99, HOX11


title: pediatric T-ALL patient #94

description: pediatric T-ALL patient #94

source_name: pediatric T-ALL patient #94, HOX11L2

tag: pediatric T-ALL patient #94, HOX11L2


title: pediatric T-ALL patient #96

description: pediatric T-ALL patient #96

source_name: pediatric T-ALL patient #96, HOX11L2

tag: pediatric T-ALL patient #96, HOX11L2


title: pediatric T-ALL patient #105

description: pediatric T-ALL patient #105

source_name: pediatric T-ALL patient #105, LMO2

tag: pediatric T-ALL patient #105, LMO2


title: pediatric T-ALL patient #87

description: pediatric T-ALL patient #87

source_name: pediatric T-ALL patient #87, HOX11L2

tag: pediatric T-ALL patient #87, HOX11L2


title: pediatric T-ALL patient #102

description: pediatric T-ALL patient #102

source_name: pediatric T-ALL patient #102, unknown

tag: pediatric T-ALL patient #102, unknown


title: pediatric T-ALL patient #92

description: pediatric T-ALL patient #92

source_name: pediatric T-ALL patient #92, HOX11L2

tag: pediatric T-ALL patient #92, HOX11L2


title: pediatric T-ALL patient #97

description: pediatric T-ALL patient #97

source_name: pediatric T-ALL patient #97, HOX11L2

tag: pediatric T-ALL patient #97, HOX11L2


title: pediatric T-ALL patient #86

description: pediatric T-ALL patient #86

source_name: pediatric T-ALL patient #86, HOX11L2

tag: pediatric T-ALL patient #86, HOX11L2


title: pediatric T-ALL patient #84

description: pediatric T-ALL patient #84

source_name: pediatric T-ALL patient #84, TAL1

tag: pediatric T-ALL patient #84, TAL1


title: pediatric T-ALL patient #81

description: pediatric T-ALL patient #81

source_name: pediatric T-ALL patient #81, TAL1

tag: pediatric T-ALL patient #81, TAL1


title: pediatric T-ALL patient #90

description: pediatric T-ALL patient #90

source_name: pediatric T-ALL patient #90, HOX11L2

tag: pediatric T-ALL patient #90, HOX11L2


title: pediatric T-ALL patient #89

description: pediatric T-ALL patient #89

source_name: pediatric T-ALL patient #89, HOX11L2

tag: pediatric T-ALL patient #89, HOX11L2


title: pediatric T-ALL patient #91

description: pediatric T-ALL patient #91

source_name: pediatric T-ALL patient #91, HOX11L2

tag: pediatric T-ALL patient #91, HOX11L2


title: pediatric T-ALL patient #83

description: pediatric T-ALL patient #83

source_name: pediatric T-ALL patient #83, TAL1

tag: pediatric T-ALL patient #83, TAL1


title: pediatric T-ALL patient #82

description: pediatric T-ALL patient #82

source_name: pediatric T-ALL patient #82, TAL1

tag: pediatric T-ALL patient #82, TAL1


title: pediatric T-ALL patient #88

description: pediatric T-ALL patient #88

source_name: pediatric T-ALL patient #88, HOX11L2

tag: pediatric T-ALL patient #88, HOX11L2


title: pediatric T-ALL patient #93

description: pediatric T-ALL patient #93

source_name: pediatric T-ALL patient #93, HOX11L2

tag: pediatric T-ALL patient #93, HOX11L2


title: pediatric T-ALL patient #63

description: pediatric T-ALL patient #63

source_name: pediatric T-ALL patient #63, unknown

tag: pediatric T-ALL patient #63, unknown


title: pediatric T-ALL patient #79

description: pediatric T-ALL patient #79

source_name: pediatric T-ALL patient #79, TAL1

tag: pediatric T-ALL patient #79, TAL1


title: pediatric T-ALL patient #80

description: pediatric T-ALL patient #80

source_name: pediatric T-ALL patient #80, TAL1

tag: pediatric T-ALL patient #80, TAL1


title: pediatric T-ALL patient #70

description: pediatric T-ALL patient #70

source_name: pediatric T-ALL patient #70, unknown

tag: pediatric T-ALL patient #70, unknown


title: pediatric T-ALL patient #77

description: pediatric T-ALL patient #77

source_name: pediatric T-ALL patient #77, TAL1

tag: pediatric T-ALL patient #77, TAL1


title: pediatric T-ALL patient #45

description: pediatric T-ALL patient #45

source_name: pediatric T-ALL patient #45, LMO2

tag: pediatric T-ALL patient #45, LMO2


title: pediatric T-ALL patient #78

description: pediatric T-ALL patient #78

source_name: pediatric T-ALL patient #78, TAL1

tag: pediatric T-ALL patient #78, TAL1


title: ES

city: kyoto

first: jiyoung

last: lee

address: 53 Kawahara-cho, Shogoin, Sakyo

department: Molecular Genetics

institute: kyoto university

description: ES

hyb_protocol: RNA samples were hybridized to a Mouse Genome 430 2.0 Microarray (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

scan_protocol: Gene Chips were scanned with a GeneChip Scanner (Affymetrix).

data_processing: The data were analyzed using GeneChip Software v1.4 (Affymetrix).

source_name: Mouse embryonic stem cell (ES, R1 cell line)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: GS cells were cultured in GS cell medium, which was based on StemPro-34 with modifications (Biol Reprod 2003; 69: 612-619). ES and mGS cells were cultured in a standard ES cell culture medium.

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


title: pediatric T-ALL patient #49

description: pediatric T-ALL patient #49

source_name: pediatric T-ALL patient #49, unknown

tag: pediatric T-ALL patient #49, unknown


title: pediatric T-ALL patient #61

description: pediatric T-ALL patient #61

source_name: pediatric T-ALL patient #61, unknown

tag: pediatric T-ALL patient #61, unknown


title: pediatric T-ALL patient #46

description: pediatric T-ALL patient #46

source_name: pediatric T-ALL patient #46, LMO2

tag: pediatric T-ALL patient #46, LMO2


title: pediatric T-ALL patient #53

description: pediatric T-ALL patient #53

source_name: pediatric T-ALL patient #53, unknown

tag: pediatric T-ALL patient #53, unknown


title: pediatric T-ALL patient #64

description: pediatric T-ALL patient #64

source_name: pediatric T-ALL patient #64, unknown

tag: pediatric T-ALL patient #64, unknown


title: pediatric T-ALL patient #40

description: pediatric T-ALL patient #40

source_name: pediatric T-ALL patient #40, TAL1

tag: pediatric T-ALL patient #40, TAL1


title: mGS

description: mGS

source_name: Mouse multipotent germline stem cell (mGS)


title: ICR Trp53KO

description: ICR Trp53KO

source_name: Trp53 KO mouse germline stem cell (GS)

tag: Trp53 KO mouse germline stem cell (GS)


title: pediatric T-ALL patient #76

description: pediatric T-ALL patient #76

source_name: pediatric T-ALL patient #76, TAL1

tag: pediatric T-ALL patient #76, TAL1


title: pediatric T-ALL patient #47

description: pediatric T-ALL patient #47

source_name: pediatric T-ALL patient #47, unknown

tag: pediatric T-ALL patient #47, unknown


title: pediatric T-ALL patient #36

description: pediatric T-ALL patient #36

source_name: pediatric T-ALL patient #36, HOX11

tag: pediatric T-ALL patient #36, HOX11


title: pediatric T-ALL patient #38

description: pediatric T-ALL patient #38

source_name: pediatric T-ALL patient #38, TAL1

tag: pediatric T-ALL patient #38, TAL1


title: GS

description: GS

source_name: Mouse germline stem cell (GS)

tag: Mouse germline stem cell (GS)


title: pediatric T-ALL patient #32

description: pediatric T-ALL patient #32

source_name: pediatric T-ALL patient #32, HOX11L2

tag: pediatric T-ALL patient #32, HOX11L2


title: pediatric T-ALL patient #35

description: pediatric T-ALL patient #35

source_name: pediatric T-ALL patient #35, HOX11L2

tag: pediatric T-ALL patient #35, HOX11L2


title: pediatric T-ALL patient #39

description: pediatric T-ALL patient #39

source_name: pediatric T-ALL patient #39, HOX11

tag: pediatric T-ALL patient #39, HOX11


title: pediatric T-ALL patient #34

description: pediatric T-ALL patient #34

source_name: pediatric T-ALL patient #34, TAL1

tag: pediatric T-ALL patient #34, TAL1


title: pediatric T-ALL patient #74

description: pediatric T-ALL patient #74

source_name: pediatric T-ALL patient #74, TAL1

tag: pediatric T-ALL patient #74, TAL1


title: pediatric T-ALL patient #43

description: pediatric T-ALL patient #43

source_name: pediatric T-ALL patient #43, LMO2

tag: pediatric T-ALL patient #43, LMO2


title: pediatric T-ALL patient #73

description: pediatric T-ALL patient #73

source_name: pediatric T-ALL patient #73, TAL1

tag: pediatric T-ALL patient #73, TAL1


title: pediatric T-ALL patient #29

description: pediatric T-ALL patient #29

source_name: pediatric T-ALL patient #29, HOX11L2

tag: pediatric T-ALL patient #29, HOX11L2


title: pediatric T-ALL patient #22

description: pediatric T-ALL patient #22

source_name: pediatric T-ALL patient #22, TAL1

tag: pediatric T-ALL patient #22, TAL1


title: pediatric T-ALL patient #21

description: pediatric T-ALL patient #21

source_name: pediatric T-ALL patient #21, TAL1

tag: pediatric T-ALL patient #21, TAL1


title: pediatric T-ALL patient #85

description: pediatric T-ALL patient #85

source_name: pediatric T-ALL patient #85, TAL1

tag: pediatric T-ALL patient #85, TAL1


title: pediatric T-ALL patient #19

description: pediatric T-ALL patient #19

source_name: pediatric T-ALL patient #19, HOX11L2

tag: pediatric T-ALL patient #19, HOX11L2


title: pediatric T-ALL patient #9

description: pediatric T-ALL patient #9

source_name: pediatric T-ALL patient #9, HOX11

tag: pediatric T-ALL patient #9, HOX11


title: pediatric T-ALL patient #14

description: pediatric T-ALL patient #14

source_name: pediatric T-ALL patient #14, TAL1

tag: pediatric T-ALL patient #14, TAL1


title: pediatric T-ALL patient #27

description: pediatric T-ALL patient #27

source_name: pediatric T-ALL patient #27, HOXA

tag: pediatric T-ALL patient #27, HOXA


title: pediatric T-ALL patient #12

description: pediatric T-ALL patient #12

source_name: pediatric T-ALL patient #12, HOX11L2

tag: pediatric T-ALL patient #12, HOX11L2


title: pediatric T-ALL patient #75

description: pediatric T-ALL patient #75

source_name: pediatric T-ALL patient #75, TAL1

tag: pediatric T-ALL patient #75, TAL1


title: pediatric T-ALL patient #24

description: pediatric T-ALL patient #24

source_name: pediatric T-ALL patient #24, HOXA

tag: pediatric T-ALL patient #24, HOXA


title: pediatric T-ALL patient #31

description: pediatric T-ALL patient #31

source_name: pediatric T-ALL patient #31, TAL1

tag: pediatric T-ALL patient #31, TAL1


title: pediatric T-ALL patient #10

description: pediatric T-ALL patient #10

source_name: pediatric T-ALL patient #10, HOX11L2

tag: pediatric T-ALL patient #10, HOX11L2


title: pediatric T-ALL patient #23

description: pediatric T-ALL patient #23

source_name: pediatric T-ALL patient #23, HOX11L2

tag: pediatric T-ALL patient #23, HOX11L2


title: pediatric T-ALL patient #30

description: pediatric T-ALL patient #30

source_name: pediatric T-ALL patient #30, TAL1

tag: pediatric T-ALL patient #30, TAL1


title: pediatric T-ALL patient #13

description: pediatric T-ALL patient #13

source_name: pediatric T-ALL patient #13, HOX11

tag: pediatric T-ALL patient #13, HOX11


title: pediatric T-ALL patient #8

description: pediatric T-ALL patient #8

source_name: pediatric T-ALL patient #8, TAL1

tag: pediatric T-ALL patient #8, TAL1


title: pediatric T-ALL patient #5

description: pediatric T-ALL patient #5

source_name: pediatric T-ALL patient #5, HOX11L2

tag: pediatric T-ALL patient #5, HOX11L2


title: HS5+MO-donor3

status: Public on Feb 22 2008

data_processing: Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all samples, was also applied.

source_name: HS5, +CD14 donor 3

growth_protocol: All cells were cultured for 2 days in RPMI1640 medium supplemented with 10% FBS/0.4 mg/ml glutamine at 37ºC in 5% CO2.

treatment_protocol: Stromal cells were cultured with and without monocytes (CD14+ cells isolated with Tuek4 Ab and IgG2a+b magnetic beads with AutoMacs).

tag: Gender

value: M, age:24


title: HS27a+MO-donor3

source_name: HS27a, +CD14 donor 3


title: HS27a-rep1

source_name: HS27a, no CD14


title: pediatric T-ALL patient #6

description: pediatric T-ALL patient #6

source_name: pediatric T-ALL patient #6, HOX11L2

tag: pediatric T-ALL patient #6, HOX11L2


title: pediatric T-ALL patient #11

description: pediatric T-ALL patient #11

source_name: pediatric T-ALL patient #11, TAL1

tag: pediatric T-ALL patient #11, TAL1


title: HS27a-rep2


title: HS5-rep2

source_name: HS5, no CD14


title: HS27a+MO-donor4

source_name: HS27a, +CD14 donor 4

value: M, age:31


title: pediatric T-ALL patient #1

description: pediatric T-ALL patient #1

source_name: pediatric T-ALL patient #1, TAL1

tag: pediatric T-ALL patient #1, TAL1


title: HS5+MO-donor4

source_name: HS5, +CD14 donor 4


title: pediatric T-ALL patient #7

description: pediatric T-ALL patient #7

source_name: pediatric T-ALL patient #7, HOX11L2

tag: pediatric T-ALL patient #7, HOX11L2


title: HS5-rep1


title: Recent-onset T1D_sample6

city: Milwaukee

first: Martin

last: Hessner

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from unstimulated Tregs from a recent-onset T1D subject

hyb_protocol: Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix, 900432) and cRNA was synthesized, labeled, fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA).

scan_protocol: After hybridization arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on a GeneChip® Scanner 3000.

data_processing: Bayesian Hierarchical Analysis (using the BGX: R package) was used to find differentially expressed genes across 12 T1D and 15 controls. Details are in the supplementary notes to the accompanying paper.  For SAM analysis, we used RMA normalised intensity values as input. For analysis of 10 T1D and 10 Controls, we used adaptive MCMC methods and probe affinity effects.

source_name: Un-stimulated CD4+CD25+high regulatory T cells from PBMCs

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were collected using vacutainers with ACD solution B of trisodium citrate and isolated using Ficoll-Hypaque density centrifugation according to the recommended protocol (Amersham Pharmacia, Uppsala, Sweden).

extract_protocol: Total RNA was extracted from T cells using TRIzol Reagent (Invitrogen) according to the recommended protocol. The GeneChip® Human Genome U133 Plus 2.0 array was selected for this study which interrogates more than 47,000 probe sets, representing roughly 39,000 unique UniGenes.

treatment_protocol: The PBMCs were counted and stained with a cocktail of fluorochrome-conjugated monoclonal antibodies in PBS (APC-aCD4 (clone RPA-T4), APC-Cy7-aCD25 (clone M-A251), FITC-aCD14 (clone M5E2), FITC-aCD32 (clone FL18.26), FITC-aCD116 (cloneM5D12), PE-Cy7-aCD8 (clone RPA-T8) all from BD Pharmingen, San Diego, CA) and sorted on a FACSAria (BD Biosciences, San Diego, CA). Cells were first gated on the live lymphocyte population, eliminating dead cells and debris. Two additional gates were set up to eliminate non-CD4 T cells (FITC-stained cells and CD8-PE-Cy7 stained cells). CD4+ T cells were further gated as CD4+25- and CD4+CD25+high using the Fluorochrome Minus One (FMO) method, which allows for a more precise definition of cells having fluorescence above the background level. The 1% of cells expressing the highest level of CD25 were collected and defined as CD4+25+high T cells, known to be enriched for Tregs.

tag: HLA risk

value: High

tag: Height

tag: Weight

tag: BMI

tag: Age

value: 10.16 years

value: Female

tag: Race

value: White

tag: Glucose

value: 188 mg/dl


title: Recent-onset T1D_sample11

value: Medium

value: 13.03 years

value: 81 mg/dl


title: Recent-onset T1D_sample10

value: Low

value: 11.45 years

value: 247 mg/dl


title: Recent-onset T1D_sample9

value: 12.2 years

value: 83 mg/dl


title: Mouse Salmonella Study - Infected

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

hyb_protocol: Standard Affymetrix hybridization and staining protocol

scan_protocol: Affymetrix 3000 scanner

data_processing: GCOS

source_name: Mouse intestine

label_protocol: Affymetrix One-Cycle labeling protocol

extract_protocol: Trizol extraction protocol

tag: Salmonella infected


title: Recent-onset T1D_sample1

value: 70 kg

value: 24.4 years

value: Male

value: 288 mg/dl


title: Recent-onset T1D_sample3

value: 18.16 years

value: Other

value: 114 mg/dl


title: npGEC cells infected with Kx2, biological rep3

city: Saint Louis

first: Marios

last: Giannakis

state: MO

address: 4444 Forest Park Blvd.

department: Developmental Biology

institute: Washington University in Saint Louis

description: Gene expression data from mouse non-progenitor gastric epithelial cells, infected with H. pylori isolate Kx2 (cancer-associated)

hyb_protocol: Following fragmentation, 25 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GS300

molecule: polyA RNA

source_name: Mouse non-progenitor gastric epithelial cells, infected with H. pylori isolate Kx2 (cancer-associated)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA.

growth_protocol: Cells were grown to 70% confluence in RPMI 1640 medium supplemented with 10% FBS at 37C

extract_protocol: Qiagen RNeasy mini-prep kit.

treatment_protocol: After 24h of infection, medium and non-attached bacteria were washed off and the mouse cells harvested by trypsinization (5mins at 37C). Following neutralization with ice-cold medium, and a PBS wash, cells were flash frozen in liquid nitrogen

tag: Cells grown in T75 cell culture flasks


title: npGEC cells infected with Kx1, biological rep2

description: Gene expression data from mouse non-progenitor gastric epithelial cells, infected with H. pylori isolate Kx1 (ChAG-associated)

source_name: Mouse non-progenitor gastric epithelial cells, infected with H. pylori isolate Kx1 (ChAG-associated)


title: npGEC cells infected with Kx2, biological rep1


title: npGEC cells uninfected, biological rep3

description: Gene expression data from uninfected mouse non-progenitor gastric epithelial cells

source_name: Mouse non-progenitor gastric epithelial cells, uninfected


title: Recent-onset T1D_sample8

value: 9.27 years

value: White

value: 245 mg/dl


title: Healthy control_sample12

description: Gene expression data from unstimulated Tregs from a healthy control

value: 76 kg

value: 16.82 years

value: 75 mg/dl


title: Recent-onset T1D_sample4

value: High

value: 8.02 years

value: Female

value: 328 mg/dl


title: Healthy control_sample15

value: Low

value: 52 kg

value: 27.24 years

value: 79 mg/dl


title: Recent-onset T1D_sample7

value: Medium

value: 11.22 years

value: 230 mg/dl


title: Recent-onset T1D_sample5

value: 26 kg

value: 7.21 years

value: 180 mg/dl


title: npGEC cells infected with Kx2, biological rep2


title: npGEC cells infected with Kx1, biological rep3


title: Healthy control_sample13

value: 32.78 years

value: Male

value: White

value: 114 mg/dl


title: Recent-onset T1D_sample2

value: High

value: 13.88 years

value: 196 mg/dl


title: npGEC cells infected with Kx1, biological rep1


title: Mouse Salmonella Study - Control

tag: Uninfected, healthy


title: Healthy control_sample14

value: Low

value: 22.84 years

value: Female

value: 88 mg/dl


title: npGEC cells uninfected, biological rep2


title: Healthy control_sample11

value: 57.67 years

value: 78 mg/dl


title: mGEP cells infected with Kx2, biological rep3

description: Gene expression data from mouse gastric epithelial progenitor cells, infected with H. pylori isolate Kx2 (cancer-associated)

source_name: Mouse gastric epithelial progenitor cells, infected with H. pylori isolate Kx2 (cancer-associated)


title: npGEC cells uninfected, biological rep1


title: Healthy control_sample8

value: 30.94 years

value: 93 mg/dl


title: pediatric T-ALL patient #25

description: pediatric T-ALL patient #25

source_name: pediatric T-ALL patient #25, HOX11

tag: pediatric T-ALL patient #25, HOX11


title: mGEP cells infected with Kx2, biological rep2


title: Healthy control_sample10

value: 57.96 years

value: 83 mg/dl


title: mGEP cells infected with Kx2, biological rep1


title: mGEP cells infected with Kx1, biological rep3

description: Gene expression data from mouse gastric epithelial progenitor cells infected with H. pylori isolate Kx1 (ChAG-associated)

source_name: Mouse gastric epithelial progenitor cells, infected with H. pylori isolate Kx1 (ChAG-associated)


title: Healthy control_sample6

value: 24.43 years

value: 95 mg/dl


title: mGEP cells infected with Kx1, biological rep1


title: Healthy control_sample3

value: 9.9 years

value: Male

value: White

value: 94 mg/dl


title: Healthy control_sample4

value: High

value: 59 kg

value: 40.56 years

value: 74 mg/dl


title: Healthy control_sample7

value: Low

value: 25.25 years

value: Female

value: 80 mg/dl


title: Healthy control_sample5

value: Medium

value: 65 kg

value: 33.7 years

value: Asian

value: 85 mg/dl


title: Healthy control_sample1

value: 13.4 years

value: 101 mg/dl


title: mGEP cells uninfected, biological rep1

description: Gene expression data from uninfected mouse gastric epithelial progenitor cells

source_name: Mouse gastric epithelial progenitor cells, uninfected


title: mGEP cells infected with Kx1, biological rep2


title: Healthy control_sample9

value: 57.76 years

value: Male

value: White

value: 104 mg/dl


title: mGEP cells uninfected, biological rep2


title: prCAD mutant retina replicate 2

status: Public on Feb 21 2008

city: Baltimore

first: Amir

last: Rattner

state: MD

address: 725 North Wolfe St., PCTB Room 805

department: Molecular Biology and Genetics

institute: Johns Hopkins University

description:
prCAD mutant retina replicate 2
contact Amir Rattner (arattne1<at>jhmi.edu) for details

hyb_protocol: Affymetrix protocol Johns Hopkins Microarray Core Facility http://www.microarray.jhmi.edu/

data_processing: RMA (bioconductor)

source_name: prCAD mutant retina

extract_protocol: Total RNA from retinas was extracted with Trizol (Invitrogen, Carlsbad, CA) and the RNeasy Mini kit (Qiagen, Valencia, CA).

tag: prCAD mutant retina, 129 background, about 4 weeks old


title: mGEP cells uninfected, biological rep3


title: wild type retina control replicate 2

description:
wild type retina control replicate 2
contact Amir Rattner (arattne1<at>jhmi.edu) for details

scan_protocol: Affymetrix protocol Johns Hopkins Microarray Core Facility http://www.microarray.jhmi.edu/

source_name: wild type 129 mouse retina

tag: wild type 129 mouse retina, about 4 weeks old


title: wild type retina control replicate 1

description:
wild type retina control replicate 1
contact Amir Rattner (arattne1<at>jhmi.edu) for details

label_protocol:
Affymetrix protocol
Johns Hopkins Microarray Core Facility
http://www.microarray.jhmi.edu/


title: Healthy control_sample2

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

value: 14.9 years

tag: Gender

value: 86 mg/dl


title: wild type retina control replicate 3

description:
wild type retina control replicate 3
contact Amir Rattner (arattne1<at>jhmi.edu) for details


title: prCAD mutant retina replicate 3

description:
prCAD mutant retina replicate 3
contact Amir Rattner (arattne1<at>jhmi.edu) for details


title: Gene expression of mouse ES cells, Gata6 overexpression at day 1

description: The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2)1-5.  PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC13-7. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8.  PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog9. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4.  We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome.

hyb_protocol: 20 micrograms of labeled target RNA was hybridized with Mouse Genome 430 2.0 GeneChip expression arrays (Affymetrix) at 45°C for 16 h, as described in the manufacturer's instructions. Washing stages and streptavidin-phycoerythrin staining were conducted using a GeneChip Fluidics Station (Affymetrix).

source_name: Mus musculus embryonic stem cells, Gata6 overexpression day 1

tag: Embryonic stem cells, Strain; 129/B6 hybrid


title: Gene expression of mouse ES cells, Pou5f1 conditional KO at day 2

description: The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2).  PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC1. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8.  PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4.  We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome.

source_name: Mus musculus embryonic stem cells, conditional Oct3/4 KO (day 2)


title: prCAD mutant retina replicate 1

description:
prCAD mutant retina replicate 1
contact Amir Rattner (arattne1<at>jhmi.edu) for details


title: Gene expression of mouse ES cell, Gata6 overexpression at day 2

source_name: Mus musculus embryonic stem cells, Gata6 overexpression day 2


title: Gene expression of mouse ES cells, control of Gata6 overexpression experiments

source_name: Mus musculus embryonic stem cells, Gata6 overexpression day 0


title: BAF250 knock-out ES cells, wild type

city: Berkeley

first: Ping

last: Hu

address: Hearst & Oxford

department: MCB

institute: University of California, Berkeley

description: Gene expression data from wild type ES cells.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mouse total RNA from wild type mouse ES cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: ES cells are cultured in gelatin wells with feeder free ES cell medium: 1 x GMEM medium supplemented with 2 mM glutamine, 1 mM sodium pyruvate,1 x nonessential amino acids,10% (v/v) fetal bovine serum,a 1:1000 dilution of beta-mercaptoethanol stock solution, and 500-1000 units per ml of leukocyte inhibitory factor.

tag: knock-out ES cell lines are derived in vitro from wild type E14g ES cell line.


title: Gene expression of mouse ES cell, constitutive Ring1B KO

source_name: Mus musculus embryonic stem cells, constitutive Ring1B KO


title: Gene expression of mouse ES cell, control of Ring1A/B double KO

source_name: Mus musculus embryonic stem cells, wild-type


title: BAF250 knock-out ES cells, het

description: Gene expression data from BAF250 knock-out heterozygous ES cells compared wild type ES cells.

source_name: mouse total RNA of het, BAF250 knock-out heterozygous ES cells


title: Gene expression of mouse ES cells, conditional Pou5f1 KO at day 0

source_name: Mus musculus embryonic stem cells, conditional Oct3/4 KO (day 0)


title: BAF250 knock-out ES cells, ko1

description: Gene expression data from BAF250 knock-out homozygouse ES cells compared to wild type ES cells.

source_name: mouse total RNA of ko1, BAF250 knock-out homozygous ES cells


title: Gene expression of mouse ES cells, conditional Pou5f1 KO at day 1

source_name: Mus musculus embryonic stem cells, conditional Oct3/4 KO (day 1)


title: Gene expression of mouse ES cells, Ring1A/B double KO

source_name: Mus musculus embryonic stem cells, conditional Ring1A/B-dKO (day 4)


title: BAF250 knock-out ES cells, ko2

description: Gene expression data from BAF250 knock-out homozygous ES cells compared to wild type ES cells.

source_name: mouse total RNA of ko2, BAF250 knock-out homozygous ES cells


title: Chondrogenic progenitor cells from OA male 1

city: Göttingen

first: Nicolai

last: Miosge

address: Robert-Koch-Str. 40

department: Prothetik, Oral biology and Tissue regeneration

country: Germany

institute: University Göttingen

description: standard Affymetrix protocol

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS5 signal

source_name: human late-stage OA repair tissue

label_protocol: standard Affymetrix protocol

extract_protocol: Qiagen protocol

tag: migratory cells only found in diseased OA tissue with stem cell characteristics


title: Chondrogenic progenitor cells from OA female 3

description: standard Affymetrix protocol


title: Chondrogenic progenitor cells from OA female 2

description: standard Affymetrix protocol


title: Gene expression of mouse ES cells, control of constitutive Ring1B KO


title: Healthy chondrocytes 1

description: standard Affymetrix protocol

source_name: healthy chondrocytes

tag: healthy chondrocytes


title: Chondrogenic progenitor cells from OA male 2

description: standard Affymetrix protocol


title: Chondrogenic progenitor cells from OA male 3

description: standard Affymetrix protocol


title: Healthy chondroctyes 2

description: standard Affymetrix protocol


title: Chondrogenic progenitor cells from OA female 1

description: standard Affymetrix protocol


title: wild type biol. rep. 2

status: Public on Feb 20 2008

city: Tel Aviv

first: yael

last: Galon-Wolfenson

address: tel aviv university

department: Plant Sciences

country: Israel

institute: Tel Aviv University

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Statistical analysis was performed using the Partek® Genomics Suite™ software (http://www.partek.com/partekgs), with default parameters. Microarray-data of the 3-week-old WT, camta3-1 and camta3-2 was pre-processed by the Robust Multiarray Average (RMA) algorithm (Irizarry et al., 2003). Expression values were log2 transformed and genes showing expression values under 5 in all the arrays were filtered out.

source_name: wild type

label_protocol: 10 μg of RNA was subjected to reverse transcription to synthesize cDNA probes using standard Affymetrix procedures

extract_protocol: Two biological replicates were taken for 3–week-old camta3-1 mutant (HF5 and HF9), camta3-2 mutant (HF6 and HF10) and wild type-WT (HF7 and HF8). Total RNA was extracted using RNeasy mini kit (Qiagene).

tag: wild type


title: T36 BAL Urethane Treated

city: Denver

first: Robert

middle: S

last: Stearman

state: CO

address: 4200 E Ninth Ave

department: Medicine/Pulmonary

institute: UCHSC

description: Gene expression data from normal mouse lung tissue

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip MOE430 2.0 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method arbitrarily set to 500

source_name: A/J mouse (Jackson Labs) bronchoalveolar lavage cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 to 5 microg total RNA

tag: Age matched Control, no treatment


title: T34 BAL Urethane Treated


title: T31 BAL Urethane Treated


title: T9 BAL Urethane Treated


title: wild type biol. rep. 1


title: T32 BAL Urethane Treated


title: T7 BAL Urethane Treated


title: T33 BAL Urethane Treated


title: camta3-1 biol. rep. 1

source_name: camta3 mutant-1

tag: camta3 mutant-1


title: T35 BAL Urethane Treated


title: camta3-2 biol. rep. 2

source_name: camta3 mutant-2

tag: camta3 mutant-2


title: T8 BAL Urethane Treated


title: camta3-1 biol. rep. 2


title: C37 BAL Normal Control


title: C36 BAL Normal Control


title: C35 BAL Normal Control


title: T5 BAL Urethane Treated


title: T3 BAL Urethane Treated


title: camta3-2 biol. rep. 1


title: C33 BAL Normal Control


title: C14 BAL Normal Control


title: HIV+ Individual HIV-2a

status: Public on Feb 19 2008

first: Ahmad

last: Sedaghat

address: 733 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

description:
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.

hyb_protocol: 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).

data_processing: Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

source_name: HIV+ Individual HIV-2a

label_protocol: The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).

growth_protocol: RNA was isolated from fresh cells.

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).

treatment_protocol:
CD4+ T cells were positively selected to >98% purity from freshly
isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).

tag: CD4+ T-cells from HIV+ donor


title: HIV+ Individual HIV-3a

source_name: HIV+ Individual HIV-3a


title: HIV+ Individual HIV-1a

source_name: HIV+ Individual HIV-1a


title: HIV+ Individual HIV-11a

source_name: HIV+ Individual HIV-11a


title: HIV+ Individual HIV-6a

source_name: HIV+ Individual HIV-6a


title: HIV+ Individual HIV-4a

source_name: HIV+ Individual HIV-4a


title: C6_C13 BAL Normal Control


title: HIV+ Individual HIV-5a

source_name: HIV+ Individual HIV-5a


title: HIV+ Individual HIV-10a

source_name: HIV+ Individual HIV-10a


title: HIV+ Individual HIV-8a

source_name: HIV+ Individual HIV-8a


title: Normal Control C-8a

source_name: Normal Control C-8a

tag: CD4+ T-cells from normal HIV- donor


title: Normal Control C-7a

source_name: Normal Control C-7a


title: Normal Control C-6a

source_name: Normal Control C-6a


title: Normal Control C-1a

source_name: Normal Control


title: Normal Control C-2a

source_name: Normal Control C-2a


title: Normal Control C-10a

source_name: Normal Control C-10a


title: HIV+ Individual HIV-9a

source_name: HIV+ Individual HIV-9a


title: Normal Control C-5a

source_name: Normal Control C-5a


title: Normal Control C-3a

source_name: Control C-3a


title: Sez-4 cell line starved of IL-2 and activated with IL-2 biological rep3

city: Philadelphia

first: Mariusz

last: Wasik

address: 3620 Hamilton Walk

department: Pathology

institute: University of Pennsylvania

description: Gene expression profiling of Sez-4 cell line

hyb_protocol: according to the manufacturer’s instructions as found in GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 2

data_processing: CEL files and MAS5.0 values with global scaling set to 150 were exported from Affymetrix GCOS (v1.4) software

label_protocol: 3ug of input total RNA were amplified and labeled using the Affymetrix 1-cycle kit

growth_protocol: Sez-4 cell line was cultured at 37°C and 5% CO2 in the presence of 200U of IL-2 in standard RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 1% penicillin/streptomycin/fungizone mixture and 2mM L-glutamine.

extract_protocol: total RNA was isolated using a TRIZOL and Qiagen Rneasy protocols

treatment_protocol: Sez-4 cell line was starved of IL-2 for 16h, washed twice and placed into 6-well plates in 10ml RPMI (10% FBS) for 2h followed by pre-treating for 30’ with pan-Jak inhibitor (300 nM), Jak3 inhibitor (300 nM), or drig solvent and cultured with IL-2 (200U) or medium alone for 4 h.

tag: Sez-4 T-cell line was derived from leukemic (Sezary) cells of a patient with a cutaneous T-cell lymphoma


title: Sez-4 cell line starved of IL-2 and activated with IL-2 biological rep1

scan_protocol: according to the manufacturer’s instructions as found in GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 2


title: Sez-4 cell line starved of IL-2, pre-treated with Jak3 inhibitor and activated with IL-2 biological rep3


title: Sez-4 cell line starved of IL-2, pre-treated with pan-Jak inhibitor and activated with IL-2 biological rep2


title: Sez-4 cell line starved of IL-2, pre-treated with Jak3 inhibitor and activated with IL-2 biological rep1


title: Sez-4 cell line starved of IL-2, pre-treated with pan-Jak inhibitor and activated with IL-2 biological rep1


title: Sez-4 cell line starved of IL-2 biological rep2

source_name: Sez-4 cell line starved of IL-2


title: HIV+ Individual HIV-7a

source_name: HIV+ Individual HIV-7a


title: Sez-4 cell line starved of IL-2 and activated with IL-2 biological rep2


title: Sez-4 cell line starved of IL-2 biological rep3


title: Sez-4 cell line starved of IL-2, pre-treated with Jak3 inhibitor and activated with IL-2 biological rep2


title: Sez-4 cells starved of IL-2 and activated with IL-21 biological rep3

source_name: Sez-4 cell line starved of IL-2 and activated with IL-21 biological rep3

treatment_protocol: Sez-4 cell line was starved of IL2 for 16h, washed twice and placed into 6-well plates in 10ml RPMI (10% FBS) for 2 h followed by addition of IL-2 (200U), IL-15 (20ng/mL), or IL-21 (100 ng/ml) or medium alone for 4 h.


title: Sez-4 cell line starved of IL-2 biological rep1


title: Sez-4 cells starved of IL-2 biological rep3

source_name: Sez-4 cell line starved of IL-2 biological rep3


title: Sez-4 cells starved of IL-2 and activated with IL-2 biological rep2

source_name: Sez-4 cell line starved of IL-2 and activated with IL-2 biological rep2


title: Sez-4 cells starved of IL-2 biological rep2

source_name: Sez-4 cell line starved of IL-2 biological rep2


title: Sez-4 cells starved of IL-2 biological rep1

source_name: Sez-4 cell line starved of IL-2 biological rep1