title: Control treatment Fourth Generation Replicate 2

source_name: Whole body tissue

tag: exposure

value: control

tag: generation

value: fourth

tag: life stage

value: Adult (21 day old)


title: Th2_A7601

status: Public on Oct 14 2017

type: RNA

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

country: USA

institute: National Institute of Allergy and Infectious Diseases

description:
Th2 #2
_8924929001_E

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Spleen T-cells

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: Naïve CD4+T cells were isolated from spleen of C57BL/6 mice by MACS separation techniques.

extract_protocol: RNA was isolated with Trizol and Qiagen RNAeasy kit

treatment_protocol: Naive CD4+ T cells were stimulated by bone marrow derived-dendritic cells (BMDC) in the presence of anti-CD3 mAb (0.2 mg/ml) with or without Zymosan-Depleted (pure Dectin-1 ligand; Invivogen, 100 microg/ml). Three days later, these culture supernatants were collected and added into a culture where a new set of naïve CD4+ T cells were stimulated with plate-bound anti-CD3 mAb and soluble anti-CD28 mAb (without BMDCs). The cells were collected at day 5 and proceeded for RNA isolation using Tripure and RNeasy. For other helper T cell induction, navie CD4+ T cells were stimulated by plate bound-anti-CD3 mAb and soluble anti-CD28 mAb in the presence of recombinant-IL-4 (20 ng/ml) and anti-IFN-g mAb (10 mg/ml) for Th2 cells, and recombinant IL-27 (50 ng/ml) for Tr1 cells for 5 days and preceded for RNA isolation.

tag: strain

tag: tissue

value: Spleen

tag: source cell type

value: Naïve CD4+T cells

tag: stimulation

value: plate bound-anti-CD3 mAb and soluble anti-CD28 mAb in the presence of recombinant-IL-4 (20 ng/ml) and anti-IFN-g mAb (10 microg/ml)

tag: cell subtype

value: Th2 T-cell


title: sup_ZD_A7604

description:
Sup-ZD #2
_8924929001_H

value: plate bound-antiCD3 mAb and soluble anti-CD28 mAb in the presence of supernatant of T cell/BMDC coculture (anti-CD3 and Zymosan Depleted)

value: Tr2 T-cell


title: sup_noZD_A7603

description:
Sup-None #2
_8924929001_G

value: plate bound-antiCD3 mAb and soluble anti-CD28 mAb in the presence of supernatant of T cell/BMDC coculture (anti-CD3)

value: T0 T-cell


title: hda19 NaCl stress rep. 1

status: Public on Oct 15 2017

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

hyb_protocol: 600 ng of cRNAs  were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2505B and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package (Ritchie et al., 2015) on R 2.12.1 program.

organism: Arabidopsis thaliana

source_name: hda19 NaCl stress

label_protocol: Fluorescent-labeled (Cy3) cRNAs were prepared from 400 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies)

growth_protocol: Seeds of Arabidopsis thaliana (Venus-UBP1b-overexpressing and Venus control, Col-0 ecotype) were grown on liguid MS medium containing 0.1% pure Agar at 22°C under 16-h-light/8-h-dark for 5 days.

extract_protocol: RNA was extracted from at least three biological replicates with the RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer’s instructions

treatment_protocol: The salt treatment was performed at 5 day after germination in 125 mM NaCl condition. Samples were collected at 2 h after the NaCl treatment.

tag: genotype/variation

value: hda19 mutant

tag: protocol

value: salt stress

tag: ecotype


title: sup_ZD_A7600

description:
Sup-ZD #1
_8924929001_D


title: Tr1_A7598

description:
Tr1 #1
_8924929001_B

value: plate bound-anti-CD3 mAb and soluble anti-CD28 mAb in presence of recombinant IL-27 (50 ng/ml)

value: Tr1 T-cell


title: hda19 non-stress rep. 2

source_name: hda19 non-stress

value: non-stress


title: Th2_A7597

description:
Th2 #1
_8924929001_A


title: hda19 non-stress rep. 1


title: sup_noZD_A7599

description:
Sup-None #1
_8924929001_C


title: Fam_24_9

type: genomic

city: Melbourne

first: Jihoon

middle: Eric

last: Joo

state: Vic

address: 305 Grattan Street

department: Clinical Pathology

country: Australia

institute: University of Melbourne

description: Family 24

hyb_protocol: Illumina's standard protocol using TECAN EVO

scan_protocol: Scanned on Illumina iScan using recommended Illumina scanner setting

data_processing: Raw idat files were imported into R environment and processed using the minfi Bioconductor package. Probes with Detection p-value less than 0.05 were removed.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: whole peripheral blood

extract_protocol:
Genomic DNA extracted from whole blood
Genomic DNA was bisulfite converted using Zymo Gold MethylEasy kit.
Spin columns

tag: status

value: unaffected


title: Fam_24_11

description: Family 24

label_protocol: Illumina's standard protocol using TECAN EVO

value: affected


title: Fam_25_5

description: Family 25


title: Fam_24_1

description: Family 24

source_name: EBV transformed lymphoblastoid


title: Fam_24_4

description: Family 24


title: Fam_24_7

description: Family 24


title: Fam_24_5

description: Family 24


title: Fam_22_17

description: Family 22


title: Fam_24_2

description: Family 24


title: Fam_24_8

description: Family 24


title: Fam_24_6

description: Family 24


title: Fam_25_4

description: Family 25


title: Fam_22_15

description: Family 22


title: Fam_24_12

description: Family 24


title: Fam_22_12

description: Family 22


title: Fam_25_1

description: Family 25


title: Fam_23_1

description: Family 23

source_name: non lymphocyte blood fraction


title: Fam_24_13

description: Family 24


title: Fam_23_5

description: Family 23


title: Fam_22_13

description: Family 22


title: Fam_23_4

description: Family 23


title: Fam_25_2

description: Family 25


title: Fam_22_14

description: Family 22


title: Fam_24_3

description: Family 24


title: Fam_23_3

description: Family 23


title: Fam_25_3

description: Family 25


title: Fam_22_16

description: Family 22


title: Fam_24_10

description: Family 24


title: Fam_23_2

description: Family 23


title: Fam_25_6

description: Family 25


title: Fam_22_7

description: Family 22


title: Fam_22_10

description: Family 22


title: Fam_22_11

description: Family 22


title: Fam_22_9

description: Family 22


title: Fam_22_6

description: Family 22


title: Fam_21_12

description: Family 21


title: Fam_21_10

description: Family 21


title: Fam_22_5

description: Family 22


title: Fam_21_13

description: Family 21


title: Fam_21_15

description: Family 21


title: Fam_21_16

description: Family 21


title: Fam_22_8

description: Family 22


title: Fam_22_2

description: Family 22


title: Fam_22_3

description: Family 22


title: Fam_22_1

description: Family 22


title: Fam_22_4

description: Family 22


title: Fam_21_17

description: Family 21


title: Fam_21_9

description: Family 21


title: Fam_21_11

description: Family 21


title: Fam_21_20

description: Family 21


title: Fam_21_6

description: Family 21


title: Fam_21_19

description: Family 21


title: Fam_21_22

description: Family 21


title: Fam_21_18

description: Family 21


title: Fam_21_7

description: Family 21


title: Fam_21_8

description: Family 21


title: Fam_21_5

description: Family 21


title: Fam_21_14

description: Family 21


title: Fam_21_4

description: Family 21


title: Fam_21_1

description: Family 21

source_name: buffy coat


title: Fam_21_2

description: Family 21


title: Fam_21_3

description: Family 21


title: Fam_21_21

description: Family 21


title: Fam_18_6

description: Family 18

source_name: blood pellet


title: Fam_20_5

description: Family 20


title: Fam_15_5

description: Family 15


title: Fam_15_3

description: Family 15


title: Fam_15_4

description: Family 15


title: Fam_11_6

description: Family 11


title: Fam_11_5

description: Family 11


title: Fam_19_6

description: Family 19


title: Fam_15_6

description: Family 15


title: Fam_15_7

description: Family 15


title: Fam_19_3

description: Family 19


title: Fam_19_7

description: Family 19


title: C15_20h_dex_repC

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: Post fragmentation, hybridization was carried out as described (RD Medh, et al. Genomics 2003. 81(6):543-55

scan_protocol: Gene Array Scanner (Hewlet Packard)

data_processing: By Affymetrix Gene Chip Suites 4.0 and 5.0 (the latter in Gene Spring software version 4.2.1)

source_name: CEM C1-15_20h_dexamethasone

label_protocol: RNA was biotin labeled by use of ENZO Biochem. Trascriptional labeling kit.

growth_protocol: CEM cells were maintained in log growth till the initiation of treatment. Triplicate independent cultures were then placed in tissue culture wells at 2x10E5 cells per ml. growth medium.

extract_protocol: RNA was extracted from concentrated, washed cells by use of Qiagen RNA isolaztion kit.

treatment_protocol: Dex in ethanol was added to 10E-6 M Dex and <1% ethanol final.  Control cultures received ethanol only.

tag: cem clone id

value: CEM C1-15

tag: cell type

value: human leukemic cells

tag: time

tag: treatment

value: dexamethasone


title: C15_20h_dex_repA


title: Fam_20_3

description: Family 20


title: Fam_15_1

description: Family 15


title: Fam_19_2

description: Family 19


title: C15_12h_dex_repB

source_name: CEM C1-15_12h_dexamethasone


title: C15_12h_dex_repC


title: Fam_18_2

description: Family 18


title: Fam_19_5

description: Family 19


title: Fam_20_1

description: Family 20


title: Fam_18_4

description: Family 18


title: C15_8h_dex_repC

source_name: CEM C1-15_8h_dexamethasone


title: C15_12h_dex_repA


title: Fam_18_5

description: Family 18


title: Fam_20_2

description: Family 20


title: Fam_20_6

description: Family 20


title: Fam_19_1

description: Family 19


title: Fam_18_3

description: Family 18


title: Fam_19_4

description: Family 19


title: Fam_18_1

description: Family 18


title: C15_8h_dex_repB


title: Fam_17_5

description: Family 17


title: Fam_20_4

description: Family 20


title: Fam_17_6

description: Family 17


title: Fam_15_2

description: Family 15


title: C15_2h_dex_repB

source_name: CEM C1-15_2h_dexamethasone


title: C15_2h_dex_repC


title: Fam_17_2

description: Family 17


title: Fam_17_4

description: Family 17


title: C15_2h_dex_repA


title: Fam_17_3

description: Family 17


title: Fam_17_1

description: Family 17


title: Fam_16_9

description: Family 16


title: C15_20h_con_repC

source_name: CEM C1-15_20h_ethanol

value: ethanol


title: C15_20h_dex_repB


title: C15_20h_con_repA


title: C15_20h_con_repB


title: C15_8h_con_repC

source_name: CEM C1-15_8h_ethanol


title: C15_8h_dex_repA


title: C15_12h_con_repA

source_name: CEM C1-15_12h_ethanol


title: C15_12h_con_repB


title: C15_8h_con_repB


title: C15_8h_con_repA


title: C15_2h_con_repC

source_name: CEM C1-15_2h_ethanol


title: Fam_16_4

description: Family 16


title: Fam_16_7

description: Family 16


title: C15_2h_con_repB


title: Fam_16_8

description: Family 16


title: C6_20h_dex_repC

source_name: CEM C1-6_20h_dexamethasone

value: CEM C1-6


title: Fam_14_13

description: Family 14


title: C15_12h_con_repC


title: C6_12h_dex_repC

source_name: CEM C1-6_12h_dexamethasone


title: C6_20h_dex_repB


title: Fam_14_11

description: Family 14


title: C15_2h_con_repA


title: C6_12h_dex_repB


title: C6_20h_dex_repA


title: C6_12h_dex_repA


title: C6_8h_dex_repC

source_name: CEM C1-6_8h_dexamethasone


title: C6_8h_dex_repB


title: Fam_14_8

description: Family 14


title: Fam_14_12

description: Family 14


title: Fam_14_9

description: Family 14


title: C6_8h_dex_repA


title: C6_2h_dex_repB

source_name: CEM C1-6_2h_dexamethasone


title: C6_2h_dex_repC


title: Fam_14_10

description: Family 14


title: Fam_16_2

description: Family 16


title: Fam_16_5

description: Family 16


title: C6_2h_dex_repA


title: Fam_16_3

description: Family 16


title: Fam_14_5

description: Family 14


title: Fam_14_2

description: Family 14


title: Fam_14_4

description: Family 14


title: C6_20h_con_repC

source_name: CEM C1-6_20h_ethanol


title: Fam_14_1

description: Family 14


title: C6_20h_con_repB


title: Fam_14_3

description: Family 14

source_name: EBV transformed lymphoblastoid


title: Fam_14_7

description: Family 14


title: Fam_16_6

description: Family 16


title: C6_12h_con_repB

source_name: CEM C1-6_12h_ethanol


title: C6_12h_con_repA


title: Fam_13_13

description: Family 13


title: Fam_14_6

description: Family 14


title: Fam_13_11

description: Family 13


title: C6_12h_con_repC


title: Fam_16_1

description: Family 16


title: Fam_13_9

description: Family 13


title: C6_8h_con_repC

source_name: CEM C1-6_8h_ethanol


title: Fam_13_12

description: Family 13

source_name: blood pellet


title: Fam_13_10

description: Family 13


title: C6_8h_con_repB


title: Fam_13_6

description: Family 13


title: C6_20h_con_repA


title: Fam_13_7

description: Family 13


title: C6_2h_con_repB

source_name: CEM C1-6_2h_ethanol


title: Fam_13_8

description: Family 13


title: Fam_13_5

description: Family 13


title: C6_8h_con_repA


title: C14_20h_dex_repC

source_name: CEM C7-14_20h_dexamethasone

value: CEM C7-14


title: C6_2h_con_repA


title: C14_20h_dex_repB


title: C6_2h_con_repC


title: Fam_13_2

description: Family 13


title: C14_12h_dex_repB

source_name: CEM C7-14_12h_dexamethasone


title: C14_20h_dex_repA


title: C14_12h_dex_repA


title: Fam_13_4

description: Family 13


title: Fam_13_3

description: Family 13


title: C14_8h_dex_repB

source_name: CEM C7-14_8h_dexamethasone


title: C14_2h_dex_repC

source_name: CEM C7-14_2h_dexamethasone


title: C14_8h_dex_repC


title: C14_2h_dex_repB


title: Fam_12_5

description: Family 12


title: C14_2h_dex_repA


title: Fam_12_6

description: Family 12


title: C14_20h_con_repC

source_name: CEM C7-14_20h_ethanol


title: C14_20h_con_repB


title: Fam_12_3

description: Family 12


title: Fam_12_1

description: Family 12


title: C14_8h_dex_repA


title: C14_12h_con_repC

source_name: CEM C7-14_12h_ethanol


title: Fam_11_3

description: Family 11


title: Fam_12_2

description: Family 12


title: C14_12h_con_repA


title: Fam_11_4

description: Family 11


title: C14_12h_con_repB


title: C14_20h_con_repA


title: Fam_10_5

description: Family 10


title: Fam_13_1

description: Family 13


title: Fam_11_2

description: Family 11


title: Fam_12_8

description: Family 12


title: Fam_12_7

description: Family 12


title: Fam_10_1

description: Family 10


title: Fam_10_4

description: Family 10


title: Fam_10_3

description: Family 10


title: Fam_10_6

description: Family 10


title: Fam_10_7

description: Family 10


title: C14_2h_con_repC

source_name: CEM C7-14_2h_ethanol


title: C14_2h_con_repB


title: C14_8h_con_repA

source_name: CEM C7-14_8h_ethanol


title: Fam_10_8

description: Family 10


title: C14_8h_con_repC


title: C14_8h_con_repB


title: Fam_10_2

description: Family 10


title: C14_2h_con_repA


title: Fam_11_1

description: Family 11


title: Fam_9_8

description: Family 9


title: Fam_9_6

description: Family 9


title: Fam_9_11

description: Family 9


title: Fam_9_7

description: Family 9


title: C14_12h_dex_repC


title: Fam_9_10

description: Family 9


title: Fam_9_9

description: Family 9


title: Fam_12_4

description: Family 12


title: Fam_8_7

description: Family 8


title: Fam_9_5

description: Family 9


title: Fam_8_1

description: Family 8


title: Fam_8_2

description: Family 8


title: Fam_9_4

description: Family 9


title: Fam_9_3

description: Family 9


title: Fam_9_1

description: Family 9


title: Fam_8_3

description: Family 8


title: Fam_8_4

description: Family 8


title: Fam_8_6

description: Family 8


title: Fam_6_3

description: Family 6


title: Fam_7_2

description: Family 7


title: Fam_7_4

description: Family 7


title: Fam_7_5

description: Family 7


title: Fam_9_2

description: Family 9


title: Fam_7_3

description: Family 7


title: Fam_8_5

description: Family 8


title: Fam_7_1

description: Family 7


title: Fam_4_5

description: Family 4


title: Fam_6_2

description: Family 6


title: Fam_5_4

description: Family 5


title: Fam_4_4

description: Family 4


title: Fam_4_1

description: Family 4


title: Fam_6_1

description: Family 6


title: Fam_5_1

description: Family 5


title: Fam_4_2

description: Family 4


title: Fam_5_2

description: Family 5


title: Fam_3_11

description: Family 3


title: Fam_4_3

description: Family 4


title: Fam_5_3

description: Family 5


title: liver Pfn2-/-, biological replica 1

city: Badalona

first: Mayka

last: Sanchez

address: Ctra Can Ruti, Cami de les Escoles s/n

country: Spain

institute: IMPPC

hyb_protocol: 100ng of total RNA from each sample were processed and hybridized to the microarray, according to the GeneChip WT PLUS Reagent Kit Assay. After hybridization, arrays were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
Data were normalized and summarized using the robust multiarray average (RMA). Statistical analysis was performed using a moderated Student's t test with Linear Models for Microarray Data (LIMMA) and P value adjusted for multiple comparisons with FDR. Data analysis was realized at the Microarray Analysis Service (Hospital del Mar Medical Research Institute, Barcelona).
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

source_name: Pfn2-/-, liver

label_protocol: GeneChip WT PLUS Reagent Kit Assay

growth_protocol: mouse liver dissected from 8-9 months old mice

extract_protocol: After dissection, samples were snap frozen in liquid N2 and subsequently total RNA was extracted using Trizol reagent (Life Technologies) according to the manufacturer's protocol.

treatment_protocol: not applicable

tag: age

value: 9 months

value: liver


title: Fam_3_10

description: Family 3


title: liver wild type, biological replica 3

source_name: wild type, liver

value: wild type

value: 8 months


title: liver wild type, biological replica 2

value: 8.5 months


title: Fam_3_9

description: Family 3


title: liver Pfn2-/-, biological replica 2


title: Marginal Zone B Cells with APRIL plus Rapamycin, replicate 7

city: Barcelona

first: Jordi

last: Sintes

address: Dr Aiguader 88

department: B cell Biology

institute: IMIM

description:
Marginal Zone B Cells with APRIL plus Rapamycin
MZ26

hyb_protocol: After fragmentation, 100 ng of labeled cRNA from each sample was hybridized (to Agilent SurePrint Human v2 GE 8x60K array, ID 039494) in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).  The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 75ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: High Pure RNA Isolation Kit (Roche)

treatment_protocol: Controls: untreated freshly isolated cells.  Treatments: APRIL (500ng/ml) and Rapamycin (10nM) were used to dissect the importance of TACI ligation during mTOR signaling in MZ B cells . Treatments for 3h.

value: spleen

value: Marginal Zone B Cells

value: APRIL plus Rapamycin


title: liver Pfn2-/-, biological replica 3


title: C14_3h_dex_rep3

data_processing: By Affymetrix Gene Chip Suite 5.0 (in Gene Spring software version 4.2.1)

source_name: CEM C7-14_3h_dexamethasone


title: Marginal Zone B Cells with APRIL plus Rapamycin, replicate 6

description:
Marginal Zone B Cells with APRIL plus Rapamycin
MZ25


title: Marginal Zone B Cells with APRIL plus Rapamycin, replicate 2

description:
Marginal Zone B Cells with APRIL plus Rapamycin
MZ21


title: Marginal Zone B Cells with APRIL plus Rapamycin, replicate 5

description:
Marginal Zone B Cells with APRIL plus Rapamycin
MZ24


title: Marginal Zone B Cells with APRIL plus Rapamycin, replicate 3

description:
Marginal Zone B Cells with APRIL plus Rapamycin
MZ22


title: Marginal Zone B Cells with APRIL plus Rapamycin, replicate 1

description:
Marginal Zone B Cells with APRIL plus Rapamycin
MZ20


title: Fam_3_8

description: Family 3


title: Marginal Zone B Cells with APRIL plus Rapamycin, replicate 4

description:
Marginal Zone B Cells with APRIL plus Rapamycin
MZ23


title: Fam_3_4

description: Family 3


title: Fam_3_1

description: Family 3


title: liver wild type, biological replica 1


title: Marginal Zone B Cells with Rapamycin, replicate 5

description:
Marginal Zone B Cells with Rapamycin
MZ19

source_name: Marginal Zone B Cells with Rapamycin

value: Rapamycin


title: C14_3h_dex_rep1


title: C14_3h_dex_rep2


title: Fam_3_6

description: Family 3

source_name: EBV transformed lymphoblastoid


title: Fam_3_3

description: Family 3

value: unaffected


title: Fam_3_7

description: Family 3


title: Fam_2_5

description: Family 2

value: affected


title: C14_3h_con_rep2

source_name: CEM C7-14_3h_ethanol


title: Marginal Zone B Cells with Rapamycin, replicate 3

description:
Marginal Zone B Cells with Rapamycin
MZ17


title: Fam_3_5

description: Family 3


title: Marginal Zone B Cells with Rapamycin, replicate 1

description:
Marginal Zone B Cells with Rapamycin
MZ15


title: Marginal Zone B Cells with Rapamycin, replicate 2

description:
Marginal Zone B Cells with Rapamycin
MZ16


title: C15_3h_dex_rep3

source_name: CEM C1-15_3h_dexamethasone

value: CEM C1-15


title: C14_3h_con_rep3

value: human leukemic cells


title: Marginal Zone B Cells with Rapamycin, replicate 4

description:
Marginal Zone B Cells with Rapamycin
MZ18


title: Marginal Zone B Cells with APRIL, replicate 7

description:
Marginal Zone B Cells with APRIL
MZ14

source_name: Marginal Zone B Cells with APRIL

value: APRIL


title: Fam_1_6

description: Family 1


title: C15_3h_dex_rep1

value: dexamethasone


title: C14_3h_con_rep1

value: ethanol


title: Fam_2_4

description: Family 2

source_name: blood pellet


title: Fam_3_2

description: Family 3


title: Fam_2_3

description: Family 2


title: C15_3h_con_rep3

source_name: CEM C1-15_3h_ethanol


title: Fam_2_2

description: Family 2


title: Fam_2_6

description: Family 2


title: C15_3h_con_rep2


title: Fam_1_4

description: Family 1


title: Marginal Zone B Cells with APRIL, replicate 3

description:
Marginal Zone B Cells with APRIL
MZ10


title: Fam_2_1

description: Family 2


title: Fam_1_3

description: Family 1


title: Marginal Zone B Cells with APRIL, replicate 4

description:
Marginal Zone B Cells with APRIL
MZ11


title: Follicular B cells, replicate 3

description:
Follicular B cells
FO3

source_name: Follicular B cells

value: Follicular B cells

value: control


title: C15_3h_con_rep1


title: Marginal Zone B Cells with APRIL, replicate 1

description:
Marginal Zone B Cells with APRIL
MZ8


title: Follicular B cells, replicate 2

description:
Follicular B cells
FO2


title: Fam_1_1

description: Family 1


title: Marginal Zone B Cells with APRIL, replicate 5

description:
Marginal Zone B Cells with APRIL
MZ12


title: Follicular B cells, replicate 1

description:
Follicular B cells
FO1


title: Marginal Zone B Cells with APRIL, replicate 6

description:
Marginal Zone B Cells with APRIL
MZ13


title: Marginal Zone B Cells, replicate 2

description:
Marginal Zone B Cells
MZ4

source_name: Marginal Zone B Cells


title: Marginal Zone B Cells, replicate 5

description:
Marginal Zone B Cells
MZ5


title: Fam_1_5

description: Family 1


title: Marginal Zone B Cells, replicate 7

description:
Marginal Zone B Cells
MZ2


title: Marginal Zone B Cells, replicate 6

description:
Marginal Zone B Cells
MZ7


title: Marginal Zone B Cells, replicate 3

description:
Marginal Zone B Cells
MZ6


title: Liver Fed high Fruc 1

status: Public on Oct 13 2017

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 38622 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 35967 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Fed with fructose in tap water

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Mice were housed since birth in 12h light/12h dark period and fed a Safe 04 chow diet.

extract_protocol: Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. RNA amounts were determined by NanoDrop®ND-1000 and the RNA quality was assessed using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer.

tag: gender

value: male

tag: genotype

value: wild-type

value: liver


title: Marginal Zone B Cells, replicate 4

description:
Marginal Zone B Cells
MZ3


title: Liver Fasted 6

source_name: Fasted for 24 hours


title: Liver Fasted 1


title: Liver Fed high Glc 6

source_name: Fed with glucose in tap water


title: Fam_1_2

description: Family 1


title: Liver Fed high Fruc 5


title: Liver Fed high Glc 1


title: Liver Fed 1

source_name: Fed with tap water


title: C15_3h_dex_rep2


title: Liver Fed high Fruc 2


title: Marginal Zone B Cells, replicate 1

description:
Marginal Zone B Cells
MZ1


title: Liver Fed 4


title: Liver Fasted 2


title: Liver Fasted 5


title: Liver Fed high Glc 5


title: Liver Fed 3


title: Liver Fed 5


title: Liver Fed high Glc 4


title: Liver Fed high Fruc 4


title: Liver Fed 6


title: Liver Fasted 3


title: Liver Fed high Fruc 3


title: Liver Fed high Fruc 6


title: Liver Fed 2


title: Liver Fed high Glc 2


title: Liver Fasted 4


title: Liver Fed high Glc 3


title: SI024

status: Public on Oct 12 2017

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

hyb_protocol: Cy3-labeled cRNAs (1.65 ug) were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridized for 17 hours at 65°C on 4x44K Whole Human Genome Microarray (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Fluorescence data were analyzed with Feature Extraction Software v.10.5 (Agilent Technologies) an QC Chart tool v.1.3 to obtain background subtracted, spatially detrended Processed Signal intensities and quality control analyses.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: SD_peripheral blood_CLL cells

label_protocol: High quality RNAs were amplified and Cy3-labeled using Low Input Quick Amp Labeling kit (Agilent Technologies, Palo alto, CA, USA). Agilent RNA One-Color Spike-In was added in each sample to provide positive controls for monitoring the microarray workflow from sample amplification and labelling to microarray processing. It contains 10 in vitro synthesized, polyadenylated transcripts derived from the Adenovirus E1A transcriptome that are premixed at various ratios. All cRNA products were purified using RNeasy columns (QIAGEN). Dye incorporation and cRNA yield were checked with InfiniteM200 (Tecan).Samples had to contain at least 6 pmole of cyanine dye/ug of cRNA to be considered suitable for subsequent hybridization.

growth_protocol: Purified CD19+ CLL cells from peripheral blood. To purify CLL, PBMCs were incubated with CD19-specific Microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) and separated by AutoMACS (Miltenyi Biotec), obtaining a purity >99% as assessed by flow-cytometry.

extract_protocol: total RNAs were extracted from purified CD19+ cells using RNeasy Mini kit Plus (QIAGEN, Valencia, CA, USA) following the manufacturer's recommendations.  RNAs were quantified using InfiniteM200 (Tecan)

treatment_protocol: no treatment of cells in vitro

tag: subject status

value: chronic lymphocytic leukemia (CLL) patient

tag: response to lenalidomide

value: stable diseases (SD)

value: Purified CD19+ cells from periferal blood of CLL patient

tag: white blood cell count (wbc)

tag: %neutrophils

tag: %lymphocytes (l)

tag: hemoglobin (hb)

tag: platelets (plt)

tag: rai stage

tag: binet stage

value: C

tag: age at diagnosis

value: F

tag: ighv status

value: unmutated (U)

tag: 17p deletion

value: absent (0)

tag: trisomy 12

tag: 13q deletion

tag: 11q deletion

tag: no. previous therapy

tag: ldh


title: SI016

source_name: PR_peripheral blood_CLL cells

tag: subject status

value: partial responses (PR)

tag: cell type

value: A

tag: gender


title: MO028

tag: response to lenalidomide

tag: white blood cell count (wbc)

tag: %neutrophils

value: M

value: present (1)


title: SVG_cells_zika_48hrs_rep1

city: WInnipeg

first: Sarah

last: Medina

state: Manitoba

address: 1015 Arlington Street

department: One Health

country: Canada

institute: Public Health Agency of Canada

description: Pooled biological triplicate

hyb_protocol: Hybridization and washing was performed according to the Two-Color Microarray-Based Gene Expression Analysis protocol for a 4x44K microarray format (Agilent technologies) following manufacturer's instructions.

scan_protocol: Slides were scanned using the Agilent Microarray Scanner system with surescan technology (v.6.3) following the scan settings for a 4x44K microarray format according to manufacturer's instructions.

data_processing: The .TIFF images were uploaded into Feature Extraction (Agilent technologies, G2567AA FE software, v.11.5), the spots were identified, and the grids constructed using the GE2_1105_Oct12 protocol and the 014850_D_F_20150612 grid file for the whole human genome 4x44K expression arrays which were downloaded from the Agilent technologies website. Background calculations were performed by the Feature Extraction software using spatial and multiplicative detrending and normalization was performed using linear and lowess. The p-value to determine differential expression was 0.01 and the resulting log10 ratios from the feature extraction software were provided as the red (AlexaFlour 647)/green (AlexaFlour 555) channel.  All spots that did not present signal were removed from the results.

label: AlexaFluor 555

label_protocol: Production of aRNA from total RNA was accomplished using the MessageAmpII kit (Life Technologies) following manufacturer's instructions.  Each aRNA was split into two samples (for dye-swapping) and labeled each with AlexaFluor 555 NHS ester, or AlexaFluor 647 NHS ester (Life Technologies).

growth_protocol: SVG cells were maintained in Dulbecco’s modified eagle media, supplemented with 10% fetal bovine serum, 2mM L-glutamine, and penicillin (100 IU/ml)/streptomycin (100μg/ml)

extract_protocol: Total RNA was extracted by using Qiagen RNeasy kit according to manufacturer’s instructions

treatment_protocol: Cells were infected with Zika virus at an MOI= 0.1 and total RNA extracted at 24, 48 and 72 hpi.

value: SVG

tag: infection

tag: time

value: 48 hpi

label: AlexaFluor 647

value: Zika virus


title: FE019

tag: %lymphocytes (l)

tag: hemoglobin (hb)

tag: platelets (plt)

tag: rai stage

tag: binet stage

value: B


title: SI018

tag: age at diagnosis

tag: ighv status

value: munmutated (U)tated (M)

tag: 17p deletion

tag: trisomy 12

tag: 13q deletion


title: SVG_cells_zika_48hrs_rep2

description: Pooled biological triplicate

tag: cell type

value: control


title: SVG_cells_zika_72hrs_rep1

description: Pooled biological triplicate

value: 72 hpi


title: Marginal Zone B Cells with APRIL, replicate 2

description:
Marginal Zone B Cells with APRIL
MZ9

tag: tissue

value: spleen

value: Marginal Zone B Cells

tag: treatment

value: APRIL


title: SVG_cells_zika_24hrs_rep1

description: Pooled biological triplicate

value: 24 hpi


title: SVG_cells_zika_72hrs_rep2

description: Pooled biological triplicate


title: SVG_cells_zika_24hrs_rep2

description: Pooled biological triplicate


title: SI015

tag: subject status

value: chronic lymphocytic leukemia (CLL) patient

tag: response to lenalidomide

value: Purified CD19+ cells from periferal blood of CLL patient

tag: white blood cell count (wbc)

tag: gender

value: unmutated (U)

tag: 11q deletion

tag: no. previous therapy

tag: ldh


title: PC025

source_name: PD_peripheral blood_CLL cells

value: progressive diseases (PD)

tag: %neutrophils

tag: %lymphocytes (l)

tag: hemoglobin (hb)

tag: platelets (plt)

tag: rai stage

value: C

value: absent (0)


title: CT013

value: partial responses (PR)

tag: binet stage

tag: age at diagnosis

value: M

tag: ighv status

tag: 17p deletion

tag: trisomy 12


title: CT014

tag: subject status

tag: cell type

value: F

tag: 13q deletion


title: MO006

tag: response to lenalidomide

tag: white blood cell count (wbc)

value: A

tag: gender

value: present (1)


title: Liver_negcontrol_rep5

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

state: SP

address: Antenor Duarte Vilela, 1331

country: Brazil

institute: Barretos Cancer Hospital

description: Gene expression array of liver in post-natal week 23

hyb_protocol: 1.65 ug of labeled cRNA was hybridized to microarray slides (Whole rat genome-4X44K oligo microarrays-G4112F, Agilent Technologies) at 65°C for 17 hours. Slides were then washed and scanned following Agilent’s recommendations.

scan_protocol: The hybridization signals were captured using the GenePix 4000B scanner (Molecular Devices, LLC, Sunnyvale, CA USA).

data_processing: The scanned images were analyzed with Feature Extraction Software v15.5 using the default protocol (GE1-v5_95_Feb07 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Liver, negative control, replicate 5

label_protocol: 150 ng of total RNA was hybridized onto whole rat genome 4x44K oligo microarrays (G4131F, Agilent Technologies, USA) using one color (Cy3) Low input Quick Amp labeling kit (Agilent Technologies, USA), according to manufacturer instructions. Briefly, total RNA plus spike-in controls were reverse transcribed into double stranded cDNA. The primers used for this reaction contained consecutive thymine bases attached to a T7 promoter that paired at the 5’ end of the first strand of cDNAs. Next, the T7 polymerase was added along with nucleotides labeled with fluorescent cyanine-3 (Cy3) dye, which amplified the anti-sense complementary RNAs (cRNA).

extract_protocol: Total RNA was isolated from the frozen liver samples using the RNeasy kit (QIAGEN, USA) according to the manufacturer’s instructions. The extracted RNA was stored at -80°C. RNA was quantified in a spectrophotometer NanoVue (GE Healthcare, UK) and the integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) under standard conditions.

treatment_protocol: Treated only with vehicle.

tag: strain

value: Wistar

tag: Sex

value: Male

tag: tissue

value: Liver

tag: age

value: 23 weeks


title: Liver_DENTAA_rep4

source_name: Liver, DEN/TAA treated animals, replicate 4

treatment_protocol: 6 week-old rats received a single intraperitoneal (i.p.) injection of DEN [200 mg/Kg body weight (b.wt.), in 0.9% saline] (Sigma-Aldrich, USA), and two weeks later, started receiving injections of TAA (200 mg/Kg b.wt., i.p., in 0.9% saline) (Sigma-Aldrich, USA), twice a week in cycles of 3 weeks of treatment, followed by 1 week without treatment, during 23 weeks.


title: Liver_negcontrol_rep4

source_name: Liver, negative control, replicate 4


title: RO003

tag: %neutrophils

tag: %lymphocytes (l)

tag: hemoglobin (hb)

tag: platelets (plt)

tag: 11q deletion

tag: no. previous therapy

tag: ldh


title: SI004

tag: subject status

value: stable diseases (SD)

tag: rai stage

tag: binet stage

value: B

tag: age at diagnosis

tag: ighv status

tag: 17p deletion

tag: trisomy 12


title: FE009

value: chronic lymphocytic leukemia (CLL) patient

tag: response to lenalidomide

tag: cell type

tag: white blood cell count (wbc)

tag: gender


title: Liver_DENTAA_rep1

source_name: Liver, DEN/TAA treated animals, replicate 1

tag: strain

tag: Sex

tag: tissue

tag: age


title: Liver_DENTAA_rep2

source_name: Liver, DEN/TAA treated animals, replicate 2


title: Liver_DENTAA_rep5

source_name: Liver, DEN/TAA treated animals, replicate 5


title: MO001

value: Purified CD19+ cells from periferal blood of CLL patient

tag: %neutrophils

tag: %lymphocytes (l)

tag: hemoglobin (hb)

tag: platelets (plt)

value: munmutated (U)tated (M)

tag: 13q deletion

tag: 11q deletion

tag: no. previous therapy


title: Liver_DENTAA_rep3

source_name: Liver, DEN/TAA treated animals, replicate 3


title: PC005

tag: subject status

tag: rai stage

tag: binet stage

tag: age at diagnosis

tag: ighv status

tag: 17p deletion

tag: ldh


title: Liver_negcontrol_rep3

source_name: Liver, negative control, replicate 3

tag: strain

tag: Sex


title: Liver_negcontrol_rep2

source_name: Liver, negative control, replicate 2

tag: tissue

tag: age


title: Liver_negcontrol_rep1

source_name: Liver, negative control, replicate 1


title: Vehicle treated cultures, day 8, replicate 2

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal. Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters.

data_processing: RMA was applied to cel files using Partek Genomics Suite v6.6

label: Biotin

source_name: Vehicle treated cultures, day 8

label_protocol: All protocols were conducted as described in the Affymetrix WT Plus Reagent Kit Manual and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling

growth_protocol: Embryonic stem cells were derived from Hop+/- and Hopx-/- blastocysts using standard protocols. Briefly, blastocysts were collected at E3.5 and cultured on STO feeder cells in standard ESC media +LIF + 50µM MEK1 inhibitor (Cell Signaling) for 7 days until the blastocyst hatches and forms colony. Individual colonies were subcultured for approximately 1 week when MEK1 inhibitor is removed and cells passaged as a normal ESC line. '

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

treatment_protocol: Cardiac differentiation was adapted from published protocols. Briefly, ESCs were cultured and maintained on a feeder layer of mitotically inactivated MEFs in DMEM with 15% FBS (Fisher Scientific) and ESGRO leukemia inhibitory factor. Differentiation through hanging droplets method was initiated following ESC dissociation and suspension at 5 x 104 cells/ml in DMEM with 10% FBS (Atlanta Biologicals) without LIF in 20µl drops. Two days after droplets formation, EBs were transferred in suspension onto poly-HEMA coated dishes. After another two days, EBs were plated on gelatin coated dishes in cardiac differentiation media [StemPro-34 SF medium (Invitrogen) supplemented with 5 ng/ml VEGF (R&D systems), 10 ng/ml bFGF (R&D systems), 12.5 ng/ml FGF10 (R&D systems), 1mM Ascorbic Acid (Sigma) and 2mM Glutamax (Invitrogen)]. Vehicle or 1ug/ml 4-Hydroxtamoifen (dissolved in ethanol, Sigma-Aldrich) was added at day 5. RNA was isolated from day 8 cultures using Trizol (Life Techonologies) according to manufacturer's instructions.

tag: cell line

value: ESCs

tag: treatment

value: Mock

tag: genotype/variation

value: control

tag: day of collection


title: fat6_d28_uninfected_male

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: mouse 6

hyb_protocol: Whole mouse genome 8x60K microarray hybridizations and washing were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting and 20bit image depth with 3 x 3 micron  pixel resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1. (Agilent) using default parameters (protocol GE1_1105_Oct12) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: uninfected

label_protocol: RNA labeling was performed with the low input Quick Amp Labeling Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: Mtb strain H37Rv was grown in Middlebrook 7H9 broth (BD Biosciences) supplemented with 0.2 % glycerol, 0.05 % Tween 80, and 10 % ADC enrichment (BD Biosciences) until logarithmic growth phase before storage at –80°C. Adipose tissue was separated from skin, minced and digested with type I collagenase (Worthington Chemicals) at 200 U/ml and 3 ml/g in HBSS for 1 h at 37°C under shaking. Samples were centrifuged at 400 g for 10 min, erythrocytes in the pellet were lysed and cells were filtered through 70 μm and 40 μm cell strainers. After a density gradient (Biochrome) separation, the interface was collected .

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol using Glycogen as carrier.

treatment_protocol: Animals were aerosol-infected with 50–200 colony-forming units (CFUs) Mtb, using a Glas-Col inhalation exposure system.

value: Adipose

tag: gender

value: male


title: 4-Hydroxytamoxifen treated cultures, day 8, replicate 1

value: Hdac3 depletion


title: 4-Hydroxytamoxifen treated cultures, day 8, replicate 2


title: Vehicle treated cultures, day 8, replicate 1


title: fat2_d28_uninfected_male

description: mouse 2


title: fat6_d28_Mtb_male

description: mouse 6

source_name: Mtb infected


title: fat1_d28_uninfected_male

description: mouse 1


title: Vehicle treated cultures, day 8, replicate 3


title: 4-Hydroxytamoxifen treated cultures, day 8, replicate 3


title: fat5_d28_uninfected_male

description: mouse 5


title: fat3_d28_uninfected_male

description: mouse 3


title: fat4_d28_Mtb_male

description: mouse 4


title: RO010

tag: response to lenalidomide

value: progressive diseases (PD)

tag: cell type

tag: white blood cell count (wbc)

tag: %neutrophils

tag: %lymphocytes (l)

tag: hemoglobin (hb)

tag: platelets (plt)

value: M

value: unmutated (U)

tag: trisomy 12

value: absent (0)

tag: 13q deletion

tag: 11q deletion

tag: no. previous therapy


title: fat4_d28_uninfected_male

description: mouse 4

tag: tissue


title: fat5_d28_uninfected_female

description: mouse 5

value: female


title: fat6_d28_uninfected_female

description: mouse 6


title: fat3_d28_uninfected_female

description: mouse 3


title: fat2_d28_uninfected_female

description: mouse 2


title: fat6_d28_Mtb_female

description: mouse 6


title: fat5_d28_Mtb_male

description: mouse 5


title: fat1_d28_uninfected_female

description: mouse 1


title: fat5_d28_Mtb_female

description: mouse 5


title: fat2_d28_Mtb_male

description: mouse 2


title: fat4_d28_uninfected_female

description: mouse 4


title: fat1_d28_Mtb_male

description: mouse 1


title: fat3_d28_Mtb_male

description: mouse 3


title: fat4_d28_Mtb_female

description: mouse 4


title: fat3_d28_Mtb_female

description: mouse 3


title: fat3_d14_uninfected_male

description: mouse 3


title: fat2_d14_uninfected_male

description: mouse 2


title: fat4_d14_uninfected_male

description: mouse 4


title: fat5_d14_Mtb_male

description: mouse 5


title: fat1_d28_Mtb_female

description: mouse 1


title: fat3_d14_uninfected_female

description: mouse 3


title: fat1_d14_uninfected_female

description: mouse 1


title: fat4_d14_Mtb_male

description: mouse 4


title: fat5_d14_Mtb_female

description: mouse 5


title: fat6_d14_uninfected_female

description: mouse 6


title: fat5_d14_uninfected_female

description: mouse 5


title: fat2_d14_uninfected_female

description: mouse 2


title: fat1_d14_Mtb_male

description: mouse 1


title: fat2_d28_Mtb_female

description: mouse 2


title: fat4_d14_uninfected_female

description: mouse 4


title: fat1_d14_uninfected_male

description: mouse 1


title: fat6_d14_Mtb_female

description: mouse 6


title: D9 0d1h0m

city: Cambridge

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133_Plus_2 arrays. 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. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Primary Monocytes

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

growth_protocol: Leukopaks from healthy donors (discarded byproducts of blood component donation, Massachusetts General Hospital, Boston) were incubated with RosetteSep Monocyte Enrichment Cocktail (Stem Cell Technologies) and purified according to the manufacturer.  The isolated monocytes were then re-suspended for culture in RPMI + 0.5% FBS (Thermo Fisher), pretreated with 1 µM inhibitor compounds or DMSO (Sigma) for 30 minutes and then stimulated with 0.5 ug/ml R848 (Invivogen) for 0, 15, 30 minutes (phosphoprotein) or 1  hour.


title: fat5_d14_uninfected_male

description: mouse 5


title: D4 0d1h0m


title: fat2_d14_Mtb_male

description: mouse 2


title: fat4_d14_Mtb_female

description: mouse 4


title: fat2_d14_Mtb_female

description: mouse 2


title: fat3_d14_Mtb_female

description: mouse 3


title: fat1_d14_Mtb_female

description: mouse 1


title: fat6_d14_uninfected_male

description: mouse 6


title: fat3_d14_Mtb_male

description: mouse 3


title: D5 0d1h0m


title: D1 0d1h0m


title: B6 0d1h0m


title: D8 0d1h0m


title: B3 0d1h0m


title: B9 0d1h0m


title: BrdU incorporation rad53K227A mutant 200mM HU 60 minutes from G1 release_input

status: Public on Oct 11 2017

city: Pavia

first: Giordano

last: Liberi

address: Via Abbiategrasso 209

institute: Istituto di Genetica Molecolare IGM-CNR

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
The rMAT library package from R statistical language is used for peak calling
samples were normalized using MAT (Model based analysis of Tilling arrays) algrothim
The parameters used for peak calling are  dMax=300, dMerge=300 , nProbesMin=8
Threshold of rMAT Score =1.5
bed file and bedgraph file are generated with custom made function.
SacCer1 genome build (Oct 2003)
bed file (enriched peak interval file) and bedgraph file (Intensity values for genomic position)

organism: Saccharomyces cerevisiae

source_name: rad53K227A INPUT BrdU 60 min 200 mM HU

label_protocol:
Whole genome amplificatio ki protocol (Sigma-Aldrich WGA1-50RXN)
library is replicated using a linear, isothermal amplification in the initial stages, followed by a limited round of geometric (PCR) amplifications

growth_protocol: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) and released in YP+2% glucose with 200 mM hydroxyurea (HU) and 200ug/ml BrdU.

extract_protocol: ssDNA-BrdU-IP on chip profiles were determined as described (Viggiani et al., 2010)

treatment_protocol: cells were released in HU with 200 ug/ml of BrdU and fixed with 0.1% Sodium Azide on ice for 30 minutes

tag: strain

value: MATa, ade2-1 trp1-1 leu2-3 112 his3-11,15 ura3 can1-100 GAL PSI+RAD5+ ura3::URA3/GPD-TK(7x), rad53K227A-KanMX7

tag: antibody


title: B4 0d1h0m

tag: treatment


title: D3 0d1h0m


title: A3 0d1h0m

value: DMSO


title: D6 0d1h0m


title: B7 0d1h0m


title: B8 0d1h0m


title: A5 0d1h0m


title: BrdU incorporation rad53K227A mutant 200mM HU 60 minutes from G1 release

source_name: rad53K227A IP BrdU 60 min 200 mM HU

tag: genotype/variation

value: MATa, ade2-1 trp1-1 leu2-3 112 his3-11,15 ura3 can1-100 GAL PSI+RAD5+ ura3::URA3/GPD-TK(7x), rad53K227A-KanMX6

value: anti-BrdU MI-11-3 (MBL)


title: B1 0d1h0m


title: A4 0d1h0m


title: B5 0d1h0m


title: A2 0d1h0m


title: A1 0d1h0m


title: A7 0d1h0m


title: OsbZIP48 knock-down showing lethal phenotype, Biological replicate 2

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: Gene expression data of OsbZIP48-KD  10-day-old Pusa Basmati-1 light grown seedling

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 h at 450C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300.

data_processing: First-order analysis was performed using Affymetrix Gene Chip Operating (GCOS) software 1.2.1. Normalization of data and differential expression analysis was done using Expression Console 1.4.1.46 (Affymetrix).

organism: Oryza sativa Indica Group

source_name: 10-day-old seedling

label_protocol: Biotinylated aRNA were prepared according to the revised 3' IVT Affymetrix protocol from 500ng total RNA.

growth_protocol: Seeds of each line were surface sterilized with 70% ethanol followed by 0.1 % HgCl2 with repeated rinses with Mili-Q water, and were allowed to imbibe in water for 16 h. The seedlings were grown in light for ten days on half MS basal medium at 28±1oC.

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

tag: cultivar

value: Pusa Basmati 1

value: Whole seedling

tag: age

value: 10 days old

tag: transgene

value: OsbZIP48 knock-down


title: ATDC5 Day 15 rep 2

city: Stanford

first: Nidhi

last: Bhutani

state: California

address: 300 Pasteur Drive, R164 Edwards Bldg

department: Orthopaedic Surgery

institute: Stanford University

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing:
Data were processed using dChip software. Background correction was applied and normalization to the median array intensity was performed, gene level expression were summarized from the corrected intensities.
probe group file: MoGene-1_0-st-v1.r3.cdf
meta-probeset file: MoGene-1_0-st-v1.na32.mm9.transcript.csv

source_name: ATDC5 Day 15

label_protocol: Ambion WT Expression kit  was used to generate ssDNA performed using Afymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: ATDC5 chondroprogenitor cells were maintained in DMEM/F12, 5% fetal bovine serum, 2mM L-Glutamine, 1x Antibiotic-Antimycotic (all Fisher Scientific) and 12.5μg/mL ascorbic acid (Eastman) in an undifferentiated state (day 0). To differentiate the cells into chondrocytes, the basal media was supplemented with 1x Insulin-Transferrin-Selenite (Invitrogen) for 15 days (day 15).

extract_protocol: QIAGEN RNeasy.

treatment_protocol: Growth in chondrogenic media in the presence of Insulin-Transferrin-Selenite  for 15 days.

tag: cell type

value: ATDC5 chondroprogenitor

tag: Stage

value: after 15 days of differentiation in chondrogenic media


title: ATDC5 Day 0 rep 2

source_name: ATDC5 Day 0

value: prior to differentiation


title: B2 0d1h0m


title: BrdU incorporation wild type 200mM HU 60 minutes from G1 release_input

source_name: WT BrdU INPUT 60 min 200 mM HU

value: MATa, ade2-1 trp1-1 leu2-3 112 his3-11,15 ura3 can1-100 GAL PSI+RAD5+ ura3::URA3/GPD-TK(7x)


title: OsbZIP48 knock-down showing lethal phenotype, Biological replicate 1


title: BrdU incorporation sen1 mutant 200mM HU 60 minutes from G1 release

source_name: sen1 BrdU IP 60 min 200 mM HU

value: MATa, ade2-1 trp1-1 leu2-3 112 his3-11,15 ura3 can1-100 GAL PSI+RAD5+ ura3::URA3/GPD-TK(7x), KanMX6-pGAL1-URL-3HA-SEN1


title: ATDC5 Day 15 rep 1


title: A9 0d1h0m


title: BrdU incorporation wild type 200mM HU 60 minutes from G1 release

source_name: WT BrdU IP 60 min 200 mM HU


title: A6 0d1h0m


title: BrdU incorporation sen1 mutant 200mM HU 60 minutes from G1 release_input

source_name: sen1 BrdU INPUT 60 min 200 mM HU

value: MATa, ade2-1 trp1-1 leu2-3 112 his3-11,15 ura3 can1-100 GAL PSI+RAD5+ ura3::URA3/GPD-TK(7x), KanMX6-pGAL1-URL-3HA-SEN2


title: OsbZIP48 knock-down showing similar phenotype as wild type, Biological replicate 2


title: ATDC5 Day 0 rep 1


title: OsbZIP48 knock-down showing similar phenotype as wild type, Biological replicate 1


title: pANDA vector control, Biological replicate 1

description: Gene expression data of panda 10-day-old Pusa Basmati-1 light  grown seedling

value: vector control


title: OsbZIP48 over-expression 10-day-old seedling, Biological replicate 1

description: Gene expression data of OsbZIP48-OE 10-day-old Pusa Basmati-1 light grown seedling

value: OsbZIP48 over-expression


title: OsbZIP48 over-expression 10-day-old seedling, Biological replicate 2


title: B4NU vector control, Biological replicate 2

description: Gene expression data of b4nu 10-day-old Pusa Basmati-1 light grown seedling


title: pANDA vector control, Biological replicate 2


title: wt4

status: Public on Oct 10 2017

city: Warsaw

first: Tomasz

last: Wilanowski

state: Mazowieckie

address: 3 Pasteur Street

department: Department of Cell Biology

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

description: Gene expression data from kidney of Grhl1wt and Grhl1 ko mice

hyb_protocol: Labeled, fragmented cDNA (Affymetrix GeneChip® WT Terminal Labeling and Controls Kit, ) was hybridized to Mouse Gene 2.0 arrays for 16 hours at 45°C (at 60 rpm) (Affymetrix GeneChip® Hybridization, Wash, and Stain Kit).  Arrays were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed using R/Bioconductor statistical environment. Intensities of microarrays were log2-transformed and normalized by RMA method.

source_name: kidney of mouse aged about 6 months

label_protocol: Mouse RNA samples (500ng) were processed and labeled for array hybridization using the Ambion WT Expression kit.

extract_protocol: Ron’s FastTRI Extraction Reagent was performed according to the manufacturer's instructions.

value: Kidney

tag: grhl1 gene status

value: Wild-type


title: ko10

value: Grh1 KO


title: ko15


title: wt5


title: CD5- NK1.1+ γδ

city: Fukuoka

first: Yasunobu

last: Yoshikai

address: 3-1-1 Maidashi Higashi-ku

department: Division of Host Defense

institute: Medical Institute of Bioregulation, Kyushu University

description: SAMPLE 2

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Gene 2.0 ST array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Power Tool version 1.15.0 software, and obtained normalized intensity values.

source_name: CD5- NK1.1+ γδ T cells in the liver of 3-week-old WT mice

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Single-cell suspensions were isolated from liver of 3-week-old WT mice. After cells were staind with mAbs, CD5+ NK1.1- γδ T cells and CD5- NK1.1+ γδ T cells were sorted using a FACSAria (BD Bioscience)

tag: strain background

value: WT

value: liver

tag: sorted cell population

value: Bcl11b-independent DN2a-γδ T cells (CD5- NK1.1+ γδ T cells)


title: ko12


title: ko8


title: TR WT 3N

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

description: Run-on labelling for WT PY4997

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. macroarrays were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 3 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, macroarrays were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the macroarrays were either checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) until quantification.

data_processing: Raw data was pre-processed in Excel 2007 and comes from image quantization and local background subtracted. Only data above 10% regard to local background was considered. Each GRO replicate were corrected by normalization with gDNA hybridization for corresponding macroarray used. Processed data is the average that results from Median Absolute Desviation normalization of each gDNA corrected replicate using ArrayStat software. For TR the average processed value for each gene was corrected by percentage of uridines present in each probe-coding strand as described in García-Martinez 2004.

source_name: Wild type cells grown in YPD to exponential phase.

label_protocol: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, the cells were washed and then were permeabilized with 20 mL of 0.5% sarkosyl. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

growth_protocol: Experiments were initiated from exponential cultures growing in YPD

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automatic device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

value: PY4997 wild type


title: ko14


title: TR WT 4N

description: Run-on labelling for WT PY4996

value: PY4996 wild type


title: wt7


title: wt1


title: ko11


title: B4NU vector control, Biological replicate 1

value: Pusa Basmati 1

value: Whole seedling

value: 10 days old


title: ko9


title: wt2


title: HT_shDNMT1_2

city: Kubang Kerian

first: Kah Keng

last: Wong

state: Kelantan

address: School of Medical Sciences, Health Campus

department: Department of Immunology

country: Malaysia

institute: Universiti Sains Malaysia

hyb_protocol: Fragmentation and hybridization were performed using the Gene expression hybridization kit (Agilent), according to the manufacturer's instruction. Briefly, 600ng of Cy3 labeled, linearly amplified cRNA was fragmented at 60°C for 30 minutes followed by hybridization at 65°C for 17 hours in a hybridization oven equipped with rotisserie rotated at 10 x g. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: After the washing step, the dried microarray slides were scanned immediately using Agilent DNA Microarray Scanner (G2539A).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent)

source_name: HT transduced with DNMT1 shRNA

label_protocol: Total RNA (200ng) extracted from HT or RL cells transduced with different shRNA (non-silencing control or shRNA targeting DNMT1) were amplified and labeled using Low Input Quick Amp labeling kit, one color (Agilent) according to the manufacturer's instruction, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: HT and RL cells were grown separately in RPMI-1640 medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin, 100µg/ml streptomycin

extract_protocol: Total RNA was extracted from cells using the GeneJET RNA Purification kit (Thermo Scientific).

treatment_protocol: Cells were transduced with lentivirus vectors expressing shRNA non-silencing control or shRNA targeting DNMT1

tag: cell line

value: HT

value: GCB-DLBCL cells


title: wt3


title: TR cln3Δ

description: Run-on labelling for cln3Δ mutant

source_name: Wild type cells in YPD with KCl 0.6M

value: cln3Δ mutant


title: ko13


title: wt6


title: HT_Non-silencing control_2

source_name: HT transduced with non-silencing shRNA control


title: HT_Non-silencing control_1


title: CellLine_SW948

city: Candiolo

first: Ludovic

last: Barault

state: Torino

address: IRCC Candiolo

department: Department of Oncology

institute: University of Torino

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

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

data_processing:
R Bioconductor - Minfi  [Matrix.processed.txt] Average beta values and detection p-values. Available on the Series record. Obtained through preprocessIllumina function (using background correction and control normalization).  [Matrix.Signal.Intensities.txt] Red and Green signal intensities. Available on the Series record.
Average beta values and detection p-values. Available on the Series record. Obtained through preprocessIllumina function (using background correction and control normalization).
Red and Green signal intensities. Available on the Series record.

label: Cy3, Cy5

source_name: Colorectal Cancer Cell line

label_protocol: Standard Illumina labelling protocol

growth_protocol: All cells were maintained in the media recommanded by supplier.

extract_protocol: Wizard SV Genomic DNA Purification System (Promega)

treatment_protocol: All cells were maintained in absence of drug

value: Colorectal Cancer Cell line

tag: supplier

value: ATCC


title: CellLine_T84


title: HT_shDNMT1_1


title: CellLine_NCIH630

value: KCLB


title: TR whi5Δ

description: Run-on labelling for whi5Δ mutant

value: whi5Δ mutant


title: CellLine_LS123


title: CellLine_LS513


title: CellLine_KM12


title: CellLine_HT55

value: ECACC


title: TR WT 2N

description: Run-on labelling for WT PY4993

value: PY4993 wild type


title: CellLine_Gp5D


title: CellLine_VACO6

data_processing:
R Bioconductor - Minfi  [Matrix.processed.txt] Average beta values and detection p-values. Available on the Series record. Obtained through preprocessIllumina function (using background correction and control normalization).  [Matrix.Signal.Intensities.txt] Red and Green signal intensities. Available on the Series record.
Average beta values and detection p-values (normalized.txt available on the Series record). Obtained through preprocessIllumina function (using background correction and control normalization).
Methylated and Unmethylated signal obtained through getMeth and getUnmeth function after preprocessRaw. Available on the Series record.

value: Prof. Markovitz


title: CellLine_WiDR

value: WiDR

value: Prof. Bernards


title: CellLine_VACO5


title: CellLine_VACO432

value: Prof. Bert Vogelstein


title: CellLine_V411


title: CellLine_V457


title: CellLine_V481


title: CellLine_SW837


title: CellLine_SW620


title: CellLine_V703


title: CellLine_SW48


title: CellLine_SW1116


title: CellLine_SW480


title: CellLine_SW1463


title: CellLine_SW403


title: CellLine_SNUC5


title: CellLine_SNUC4


title: CellLine_SW1417


title: CellLine_SNU977


title: CellLine_SNUC1


title: CellLine_SNU81


title: CellLine_SNU769B


title: CellLine_SNU61


title: CellLine_SW1222

value: Dr Herlyn


title: CellLine_SNU479


title: CellLine_SNU503


title: CellLine_SNU283


title: CellLine_SNU407


title: CellLine_SNU175


title: CellLine_SNU254


title: CellLine_SNU1746


title: CellLine_SNUC2B


title: CellLine_SNU1460


title: CellLine_SNU1684


title: CellLine_SNU1181


title: CellLine_SNUC2A


title: CellLine_SNU1033


title: CellLine_SNU1411


title: CellLine_SNU1040


title: CellLine_SNU1047


title: CellLine_SNU1406


title: CellLine_SNU1544


title: CellLine_SKCO1


title: CD45+CD33+CD19-CD3- cells from engrafted AML blasts treated with vehicle, replicate 1

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

description: Gene expression data from sorted CD45+CD33+CD19-CD3- AML blasts treated with vehicle

hyb_protocol: In accordance with manufacturer's protocols

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

data_processing: Data was normalized using MAS5 algorithm and baseline transformation to the median of all samples using GeneSpring 7.0 software.

source_name: Purified cells from engrafted AML blasts

treatment_protocol: AML-transplanted mice were treated IP daily for 10 days with 100 mg CWP/kg body weight starting 2 weeks after transplantation. Vehicle control-treated transplanted mice were injected as described above with 100 mL saline solution/kg body weight. Engrafted AML-blasts were sorted based on CD45/CD33 expression and absence of CD19/CD3 prior to total RNA extraction.

value: bone marrow

value: sorted CD45+CD33+CD19-CD3- AML blasts

value: vehicle


title: CellLine_RKO

value: RKO


title: CellLine_RW7213

value: Diego Arango


title: CD45+CD33+CD19-CD3- cells from engrafted AML blasts treated with CWP, replicate 1

description: Gene expression data from sorted CD45+CD33+CD19-CD3- AML blasts treated with CWP

label_protocol: In accordance with manufacturer's protocols

value: CWP


title: CD45+CD33+CD19-CD3- cells from engrafted AML blasts treated with CWP, replicate 2


title: CellLine_RCM1

value: Colorectal Cancer Cell line

value: HSRRB


title: CD45+CD33+CD19-CD3- cells from engrafted AML blasts treated with vehicle, replicate 2


title: CD5+ NK1.1- γδ

description: SAMPLE 1

source_name: CD5+ NK1.1- γδ T cells in the liver of 3-week-old WT mice

value: WT

value: liver

value: Bcl11b-dependent γδ T cell subset (CD5+ NK1.1- γδ T cells)


title: CellLine_OXCO3

value: Prof. Cerundolo


title: CellLine_OXCO1


title: CellLine_OXCO2


title: CellLine_OUMS23

value: JCRB


title: CellLine_SNU1235

value: KCLB


title: CellLine_NCIH508

value: ATCC


title: CellLine_NCIH498


title: CellLine_NCIH716


title: CellLine_MIP101

value: Prof. Jessup


title: CellLine_MDST8

value: ECACC


title: CellLine_LS180


title: CellLine_LS1034


title: CellLine_LIM2550

value: CBA


title: CellLine_LIM2551


title: CellLine_NCIH684


title: CellLine_NCIH747


title: CellLine_LIM2412

value: Dr. Walker


title: CellLine_LIM2405


title: WT_com72h Replicate 2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: WT_com72h Replicate 2

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: SIRT WT ES cells grown in complete medium for 72 hours

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Grown in high-glucose DMEM medium containing 10% ES cell FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 10 μM 2-mercaptoethanol, and 500 units/ml leukocyte inhibitory factor, with 200 uM methionine (com) or 6 uM methionine (6met)

extract_protocol: Qiagen RNA easy mini kit with on-column DNAseI treatment

value: ES cell

tag: genotype

value: wildtype

tag: medium

value: complete

tag: timepoint


title: WT_com72h Replicate 1

description: WT_com72h Replicate 1


title: WT_com6h Replicate 1

description: WT_com6h Replicate 1

source_name: SIRT WT ES cells grown in complete medium for 6 hours


title: WT_com6h Replicate 3

description: WT_com6h Replicate 3


title: WT_com6h Replicate 2

description: WT_com6h Replicate 2


title: WT_com24h Replicate 3

description: WT_com24h Replicate 3

source_name: SIRT WT ES cells grown in complete medium for 24 hours


title: CellLine_LS411N


title: WT_6met72h Replicate 1

description: WT_6met72h Replicate 1

source_name: SIRT WT ES cells grown in methionine-restricted medium for 72 hours

value: methionine-restricted


title: WT_com24h Replicate 1

description: WT_com24h Replicate 1


title: CellLine_LIM2099

value: Colorectal Cancer Cell line


title: WT_com24h Replicate 2

description: WT_com24h Replicate 2


title: WT_6met72h Replicate 2

description: WT_6met72h Replicate 2


title: CellLine_LS174T


title: CellLine_LoVo

value: LoVo


title: CellLine_LIM1899


title: WT_com72h Replicate 3

description: WT_com72h Replicate 3


title: WT_6met6h Replicate 2

description: WT_6met6h Replicate 2

source_name: SIRT WT ES cells grown in methionine-restricted medium for 6 hours


title: CellLine_LIM2537


title: WT_6met6h Replicate 3

description: WT_6met6h Replicate 3


title: CellLine_KM20


title: CellLine_KM12SM


title: CellLine_KM12C


title: WT_6met6h Replicate 1

description: WT_6met6h Replicate 1


title: CellLine_HUTU80


title: CellLine_LIM1215

value: Dr. Whitehead


title: CellLine_HT29


title: WT_6met72h Replicate 3

description: WT_6met72h Replicate 3


title: CellLine_HT115


title: CellLine_HROC87

value: Dr. Linnebacher


title: CellLine_HROC69


title: CellLine_HROC80


title: CellLine_HROC39


title: CellLine_HROC46


title: CellLine_HROC32


title: CellLine_HROC24


title: CellLine_HDC9

value: DKFZ


title: CellLine_HROC18


title: CellLine_HRA16


title: WT_6met24h Replicate 3

description: WT_6met24h Replicate 3

source_name: SIRT WT ES cells grown in methionine-restricted medium for 24 hours


title: WT_6met24h Replicate 1

description: WT_6met24h Replicate 1


title: WT_6met24h Replicate 2

description: WT_6met24h Replicate 2


title: KO_com6h Replicate 2

description: KO_com6h Replicate 2

source_name: SIRT knockout ES cells grown in complete medium for 6 hours

value: SIRT KO


title: KO_com6h Replicate 1

description: KO_com6h Replicate 1


title: KO_com72h Replicate 1

description: KO_com72h Replicate 1

source_name: SIRT knockout ES cells grown in complete medium for 72 hours


title: KO_com24h Replicate 2

description: KO_com24h Replicate 2

source_name: SIRT knockout ES cells grown in complete medium for 24 hours


title: KO_com24h Replicate 1

description: KO_com24h Replicate 1


title: KO_6met72h Replicate 2

description: KO_6met72h Replicate 2

source_name: SIRT knockout ES cells grown in methionine-restricted medium for 72 hours


title: CellLine_HDC82


title: KO_com72h Replicate 3

description: KO_com72h Replicate 3


title: KO_com72h Replicate 2

description: KO_com72h Replicate 2


title: KO_com6h Replicate 3

description: KO_com6h Replicate 3


title: KO_6met72h Replicate 3

description: KO_6met72h Replicate 3


title: CellLine_HDC8


title: KO_com24h Replicate 3

description: KO_com24h Replicate 3


title: CellLine_HDC143


title: KO_6met6h Replicate 2

description: KO_6met6h Replicate 2

source_name: SIRT knockout ES cells grown in methionine-restricted medium for 6 hours


title: CellLine_HDC54


title: CellLine_HDC142


title: CellLine_HCT8


title: CellLine_HCT15


title: CellLine_HDC135


title: CellLine_HDC114


title: CellLine_HCC2998


title: KO_6met24h Replicate 3

description: KO_6met24h Replicate 3

source_name: SIRT knockout ES cells grown in methionine-restricted medium for 24 hours


title: KO_6met72h Replicate 1

description: KO_6met72h Replicate 1


title: KO_6met6h Replicate 3

description: KO_6met6h Replicate 3


title: KO_6met24h Replicate 2

description: KO_6met24h Replicate 2


title: CellLine_HCA46


title: KO_6met6h Replicate 1

description: KO_6met6h Replicate 1


title: CellLine_GEO

value: GEO

value: Prof. Tortora


title: CellLine_FET

value: FET

value: IFOM


title: CellLine_DiFi

value: DiFi

value: Dr. Baselga


title: CellLine_HCA24

value: ECACC


title: CellLine_CX1

value: CLS


title: CellLine_DLD1

value: ATCC


title: CellLine_COLO94H


title: CellLine_COLO60H


title: CellLine_COLO320HSR


title: CellLine_COLO205


title: CellLine_HCT116


title: CellLine_COGA8

value: Prof. Huber


title: CellLine_COLO201


title: CellLine_GP2d


title: CellLine_COLO678

value: DSMZ


title: CellLine_COGA5

value: Colorectal Cancer Cell line


title: CellLine_COGA3


title: CellLine_COGA5L


title: CellLine_COGA2


title: KO_6met24h Replicate 1

description: KO_6met24h Replicate 1

value: ES cell

value: methionine-restricted


title: CellLine_COGA1


title: CellLine_COLO320DM


title: CellLine_COCM1

value: JCRB


title: CellLine_COGA12


title: CellLine_Co115

value: Dr. Hamelin


title: CellLine_CL14


title: CellLine_CL40


title: CellLine_CL11


title: CellLine_CL34


title: CellLine_CACO2


title: CellLine_CCK81


title: CellLine_CaR1


title: CellLine_C99


title: Class I X Knot rep2

city: Atlanta

first: Ravi

last: Das

state: Georgia

address: 145 Piedmont Ave SE, Georgia State University,  GA

department: Neuroscience

institute: Georgia State University

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Drosophila Melanogaster Genome Oligo Microarrays 4 x 44K (table 3) using Agilent’s recommended hybridization chamber and oven.Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies)

data_processing: The Agilent Feature Extraction Software (FES, v.10.5.1.1) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. GeneSpring (Agilent) was used to normalize and analyze raw dataset. The raw data was quantile normalized, and the values were thresholded to 1.

organism: Drosophila melanogaster

source_name: Class I X Knot da neuron-Larval L3 Stage

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Drosophila stocks were kept at 25°C and raised on standard cornmeal-molasses-agar diet, and crosses were performed at 29°C

extract_protocol: The isolation and purification of  Class I, Class I X Cut  and Class I X Knot da neurons was performed as previously described (Iyer et al., 2009). Briefly, 40-50 age-matched third instar larvae expressing mCD8::GFP under the control of the GAL4221,UAS-Cut;Gal4221 or UAS-Knot;Gal4221 driver were collected and washed several times in ddH20. The larvae were rinsed in RNAse away followed by ddH20 and finally dissected. The tissue was then dissociated using a combination of enzymatic and mechanical perturbations to yield single cell suspensions which were filtered using a 30µm membrane. The filtrate was incubated with magnetic beads coupled with rat anti-CD8 antibody (Invitrogen) for 60 minutes. Finally the Class I,Class I X Cut and Class I X Knot neurons attached to the magnetic beads were separated using a powerful magnetic field. The cells were washed 5 times, before lysing them in SuperAmp™ (Miltenyi Biotec) RNA lysis buffer followed by storage of the RNA at -80˚C.

treatment_protocol: Age-matched third larvae were used without any treatment.

value: Oregon-R

tag: developemental stage

value: Larval L3

value: dendritic arborization (da) neurons


title: CellLine_C84


title: Class I X Knot rep1


title: Class I control rep3

source_name: Class I da neuron-Larval L3 Stage


title: Class I control rep2


title: CellLine_C75

source_name: Colorectal Cancer Cell line


title: CellLine_C80


title: Class I X Knot rep3


title: CellLine_C32


title: AML patient bone marrow stroma cells #13_1

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm using Partek Genomics Suite 6.6 software.

source_name: AML patient bone marrow stroma

growth_protocol: aMEM supplemented with 20% FBS + 2 mM L-glutamine

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

tag: subject status

value: acute myeloid leukemia (AML) patient

tag: tissue

value: bone marrow

value: mesenchymal stem cells (MSCs)


title: Class I X Cut rep 1

source_name: Class I X Cut da neuron-Larval L3 Stage

tag: genotype/variation


title: AML patient bone marrow stroma cells #12_2


title: AML patient bone marrow stroma cells #11_2


title: Normal patient bone marrow stroma cells #3_2

source_name: Normal patient bone marrow stroma

value: normal; healthy


title: Class I control rep1


title: Class I X Cut rep 2


title: AML patient bone marrow stroma cells #13_2


title: CellLine_C146

value: Lindy Durrant


title: AML patient bone marrow stroma cells #11_1


title: AML patient bone marrow stroma cells #12_1


title: CellLine_C170


title: CellLine_C10

value: ECACC


title: CellLine_C125PM


title: Class I X Cut rep 3


title: Normal patient bone marrow stroma cells #2_2


title: CellLine_C106


title: Normal patient bone marrow stroma cells #2_1


title: CellLine_HCA7


title: Normal patient bone marrow stroma cells #3_1


title: OM_Subject 68

status: Public on Oct 08 2017

city: Washington

first: Matthew

middle: David

last: Barberio

state: District of Columbia

address: 111 Michigan Avenue

department: Exercise and Nutrition Sciences

institute: George Washington University

description: Gene Expression data from visceral adipose tissue

hyb_protocol: Following fragmentation, 15ug of cRNA was hybridized at 45C for 16 hours on GeneChip Human Genome U1333 Plus 2.0 Array. GeneChips were washed and stained in Affymetrix Fluidics Station 450 (Fluids Protocol FS450_0001)

scan_protocol: After washing and staining, GeneChips were scanned on the Affymetrix GeneChip Scanner 3000 (GSC3000)

data_processing: Data was analyzed in Expression Console software. Signal intensity was determined with Probe Logarithmic Intensity Error (PLIER) Estimation. Resulting CHP files were analyzed in Partek Genomics Suite and raw intensity values were Log Transformed for statisitcal analysis.

source_name: Visceral Adipose Tissue

label_protocol: Biotinylated cRNA was prepared from 100-300 ng total RNA according to standard Affymetrix Protocol (Manual Target Preparation for Gene Chip 3' Expression Arrays)

extract_protocol: Qiagen Rneasy Lipid Tissue Mini Kit. RNA extraction was performed according to manufactuere instructions.

value: Visceral Adipose Tissue

tag: gender

value: Female

tag: bmi

tag: ethnicity

value: Hispanic

tag: height (cm)

tag: weight (kg)


title: OM_Subject 59

tag: age


title: OM_Subject 61

value: Black


title: OM_Subject 56


title: Normal patient bone marrow stroma cells #1_2

tag: cell type


title: OM_Subject 45


title: OM_Subject 48


title: OM_Subject 72


title: OM_Subject 41

value: White


title: OM_Subject 51


title: OM_Subject 43


title: Normal patient bone marrow stroma cells #1_1


title: OM_Subject 34


title: OM_Subject 32


title: OM_Subject 38


title: OM_Subject 31


title: genomic data from OS 222

city: New York City

first: Shengyang

last: Wu

state: NY

address: 560 First Avenue

department: Radiation Oncology

institute: New York University School of Medicine

hyb_protocol: GenomeStudio software

scan_protocol: GenomeStudio software

data_processing: GenomeStudio software

label: Cy5 and Cy3

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

growth_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

extract_protocol: all samples were decalcified, and DNA was extracted, bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

treatment_protocol: Standard Illumina Protocol

tag: Sex

value: female

value: bone

tag: diagnosis

value: Osteosarcoma


title: OM_Subject 30


title: CellLine_C70

tag: cell line

value: Colorectal Cancer Cell line

tag: supplier


title: OM_Subject 29


title: OM_Subject 28


title: genomic data from OS 227

value: male


title: genomic data from OS 221


title: OM_Subject 25


title: genomic data from OS 223


title: genomic data from OS 214


title: genomic data from OS 210


title: genomic data from LYSATE SS9

source_name: LYSATE SS9

value: Synovial sarcoma


title: genomic data from LYSATE SS7

source_name: LYSATE SS7


title: genomic data from LYSATE SS30

source_name: LYSATE SS30


title: genomic data from LYSATE SS26

source_name: LYSATE SS26


title: genomic data from LYSATE SS29

source_name: LYSATE SS29


title: genomic data from LYSATE SS27

source_name: LYSATE SS27


title: genomic data from OS 207


title: genomic data from OS 218


title: genomic data from LYSATE OS11

source_name: LYSATE OS11


title: genomic data from OS 208


title: genomic data from LYSATE SS28

source_name: LYSATE SS28


title: genomic data from LYSATE OS12

source_name: LYSATE OS12


title: genomic data from LYSATE EWS9

source_name: LYSATE EWS9

value: Ewing’s sarcoma


title: genomic data from LYSATE OS4

source_name: LYSATE OS4


title: genomic data from LYSATE OS3

source_name: LYSATE OS3


title: genomic data from LYSATE EWS6

source_name: LYSATE EWS6


title: OM-Subject 13


title: OM_Subject 22


title: OM_Subject 15


title: genomic data from LYSATE SS17

source_name: LYSATE SS17


title: genomic data from LYSATE EWS5

source_name: LYSATE EWS5


title: OM_Subject 11


title: OM_Subject 24


title: OM_Subject 19


title: OM_Subject 12


title: genomic data from LYSATE ChOS3

source_name: LYSATE ChOS3


title: OM_Subject 8

source_name: Visceral Adipose Tissue


title: OM_Subject 9


title: genomic data from LYSATE EWS16

source_name: LYSATE EWS16


title: OM_Subject 2


title: genomic data from LYSATE2ndOS1

source_name: LYSATE 2ndOS1


title: OM_Subject 4


title: OM_Subject 1


title: genomic data from LYSATE EWS23

source_name: LYSATE EWS23


title: genomic data from LYSATE EWS15

source_name: LYSATE EWS15


title: genomic data from HSRC-003


title: genomic data from LYSATE EWS18

source_name: LYSATE EWS18


title: genomic data from HSRC-001-A


title: genomic data from HSRC-004-A


title: genomic data from HSRC-007


title: genomic data from LYSATE EWS27

source_name: LYSATE EWS27


title: OM_Subject 31

description: genomic DNA from Visceral Adipose Tissue

hyb_protocol: Bisulphite convereted DNA (EZ DNA Methylatiion Gold Kit - Zymo research) was amplfied, fragmented, and hybridized to Infinium HumanMethylation 450k BeadChips according the stadard Illumina protocol (Infiium HD Assay)

scan_protocol: BeadChips were scanned on an Illumina HiScan Scanner according to Illumina standard settings.

data_processing: Files were processed in GenomeStudio Software

label: biotin and 2,4-dinitrophenol

source_name: Genomic DNA from Visceral Adipose Tissue

label_protocol: Stadnard Protocol.

extract_protocol: Qiagen DNeasy blood and Tissue Kit. Genomic DNA was extracted according to manufactuer protocol.


title: OM_Subject 32


title: OM_Subject 38


title: OM_Subject 30


title: OM_Subject 43


title: OM_Subject 41


title: OM_Subject 59


title: OM_Subject 56


title: RSi16

status: Public on Oct 07 2017

city: Minneapolis

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Agilent Rhesus (8x60K) oligonucleotide microarrays  were used. Dry slides were scanned on an Agilent Technologies Scanner G2505C US93503719 using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 10.7.3.1) and the GE1-v5_95_Feb07 extraction protocol.

organism: Macaca mulatta

source_name: RNA, liver necropsy

growth_protocol: 31 Indian-orgin Rhesus Macaques were used. 11 adults (4 uninfected, 5 SIV-infected, 2 SIV-infected + cART treatment) and 20 infants (7 uninfected, 9 SIV-infected, 4 SIV-infected + cART treatment).

extract_protocol: Total RNA was isolated from frozen liver powder obtained from necropsies using the NucleoSpin RNA isolation kit (Macherey-Nagel)

treatment_protocol: Microarray analysis was performed on post-necropsy liver samples on 31 animals. (11 adults and 20 infants). Of the adults 4 were uninfected, 5 SIV-infected, and 2 SIV-infected + cART treatment). Of the infants, 7 were uninfected, 9 SIV-infected, and 4 SIV-infected + cART treatment.

tag: animal#

value: liver

tag: batch

tag: treatment

value: SIV+ cART infant

tag: treatment 1

tag: treatment 2

tag: treatment 3


title: RPi16

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

tag: tissue


title: Z09064

value: SIV+ adult

value: SIV


title: Z09086


title: AM10043

value: Uninfected adult

value: Uninfected


title: OM_Subject 45

tag: gender

value: Female

tag: bmi


title: OM_Subject 22

tag: ethnicity

value: Hispanic

tag: height (cm)


title: A15387


title: OM_Subject 34

value: Black

tag: age

tag: weight (kg)


title: OM_Subject 24

value: White


title: RHi16


title: A15188

value: Uninfected infant


title: A15187

value: SIV+ infant


title: OM_Subject 01


title: RUH16


title: OM_Subject 25


title: A15186


title: A15185


title: OM_Subject 11


title: Z09068


title: A15180


title: OM_Subject 12


title: OM_Subject 19


title: genomic data from HSRC-002-A

tag: Sex

value: bone


title: A15066


title: Z09096


title: A15067


title: A15068


title: OM_Subject 09


title: A14206


title: A14204


title: A14225


title: A14205


title: A14203


title: A14113


title: A14112


title: A13274

value: SIV+ cART adult


title: A14114


title: A14049


title: A14115


title: OM_Subject 28


title: OM_Subject 04


title: A13273


title: A15065


title: Monocyte sample 239

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: University of California, Los Angeles

description:
sample 239
9967453004_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using log2-quantile normalization with the lumi package in R

source_name: Human peripheral monocytes

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

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

treatment_protocol: Blood was drawn into three 8 mL Cell Preparation Tubes (CPT) containing sodium citrate. Peripheral blood mononuclear cells (PBMCs) were then isolated through centrifugation within 6 hours of collection. PBMCs were washed with phosphate buffered saline, and then monocytes were isolated through Rosette separation (RosetteSep®; Stem Cell Technologies) according to the manufacturer instructions.

tag: arbitrary subject id

tag: timepoint

tag: hiv status

value: male

tag: gnf

tag: hand severity

tag: race

value: white

tag: smoke

tag: alcohol

tag: education

tag: stripe

value: C

tag: arrayid


title: Monocyte sample 241

description:
sample 241
9967453004_E

tag: bmi

value: E


title: Monocyte sample 245

description:
sample 245
9967453004_I

value: black

value: I


title: Monocyte sample 244

description:
sample 244
9967453004_H

value: H


title: Monocyte sample 237

description:
sample 237
9967453004_A

value: A


title: Monocyte sample 233

description:
sample 233
9967453003_I

value: hisp


title: Monocyte sample 247

description:
sample 247
9967453004_K

value: K


title: Monocyte sample 243

description:
sample 243
9967453004_G

value: G


title: Monocyte sample 246

description:
sample 246
9967453004_J

value: J


title: Monocyte sample 235

description:
sample 235
9967453003_K


title: Monocyte sample 248

description:
sample 248
9967453004_L

value: L


title: Monocyte sample 231

description:
sample 231
9967453003_G


title: Monocyte sample 229

description:
sample 229
9967453003_E


title: Monocyte sample 225

description:
sample 225
9967453003_A


title: Monocyte sample 242

description:
sample 242
9967453004_F

value: F


title: Monocyte sample 240

description:
sample 240
9967453004_D

value: D


title: Monocyte sample 227

description:
sample 227
9967453003_C


title: Monocyte sample 223

description:
sample 223
9967453002_K


title: Monocyte sample 238

description:
sample 238
9967453004_B

value: B


title: Monocyte sample 236

description:
sample 236
9967453003_L


title: Monocyte sample 232

description:
sample 232
9967453003_H


title: Monocyte sample 234

description:
sample 234
9967453003_J


title: Monocyte sample 228

description:
sample 228
9967453003_D


title: Monocyte sample 222

description:
sample 222
9967453002_J


title: Monocyte sample 224

description:
sample 224
9967453002_L


title: Monocyte sample 226

description:
sample 226
9967453003_B


title: Monocyte sample 230

description:
sample 230
9967453003_F


title: Monocyte sample 221

description:
sample 221
9967453002_I


title: Monocyte sample 220

description:
sample 220
9967453002_H


title: Monocyte sample 216

description:
sample 216
9967453002_D


title: Monocyte sample 218

description:
sample 218
9967453002_F


title: Monocyte sample 213

description:
sample 213
9967453002_A


title: Monocyte sample 215

description:
sample 215
9967453002_C


title: Monocyte sample 212

description:
sample 212
9967453001_L


title: Monocyte sample 214

description:
sample 214
9967453002_B


title: Monocyte sample 217

description:
sample 217
9967453002_E


title: Monocyte sample 210

description:
sample 210
9967453001_J


title: Monocyte sample 208

description:
sample 208
9967453001_H


title: Monocyte sample 205

description:
sample 205
9967453001_E


title: Monocyte sample 209

description:
sample 209
9967453001_I


title: Monocyte sample 202

description:
sample 202
9967453001_B


title: Monocyte sample 207

description:
sample 207
9967453001_G


title: Monocyte sample 211

description:
sample 211
9967453001_K


title: Monocyte sample 193

description:
sample 193
9965581144_E


title: Monocyte sample 197

description:
sample 197
9965581144_I


title: Monocyte sample 198

description:
sample 198
9965581144_J


title: Monocyte sample 206

description:
sample 206
9967453001_F


title: Monocyte sample 200

description:
sample 200
9965581144_L


title: Monocyte sample 195

description:
sample 195
9965581144_G


title: Monocyte sample 201

description:
sample 201
9967453001_A


title: Monocyte sample 199

description:
sample 199
9965581144_K


title: Monocyte sample 219

description:
sample 219
9967453002_G