title: muscle_preTZD_postClamp_IRd_s42

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 42


title: muscle_postTZD_postClamp_IRd+_s40

status: Public on May 17 2010

type: RNA

city: La Jolla

first: Gene

last: Hsiao

state: CA

address: 9500 Gilman Dr

country: USA

institute: UCSD

description: no additional information

hyb_protocol: 15 ug of biotin-tagged cRNA was fragmented following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). 10 ug of fragmented target cRNA was hybridized (45°C with rotation for 16 hr, Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix Human Genome U133 Plus 2.0 array.  The GeneChip® arrays were washed and stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: Data analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as the normalization method

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: skeletal muscle (vastus lateralis)

label_protocol: Biotinylated cRNA were prepared using the Affymetrix GeneChip® IVT Labeling Kit

extract_protocol: Total RNA samples were isolated and processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip® Expression Analysis Technical Manual) using TRIzol Reagent (Invitrogen Corp., Carlsbad, CA)

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 40

tag: tissue

value: muscle

tag: tzd treatment

value: postTZD

tag: clamp status

value: postClamp

tag: insulin resistance

value: IRd (insulin resistant)

tag: response to tzd treatment

value: + (responder)

tag: subject


title: muscle_preTZD_postClamp_IRd_s41

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 41

value: preTZD


title: muscle_preTZD_postClamp_IRd+_s40

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 40


title: adipose_preTZD_IRd_s41

description: no additional information

source_name: adipose tissue (abdominal subcutaneous)

treatment_protocol: pre-TZD, insulin resistant, , subject 41

value: adipose


title: muscle_preTZD_preClamp_IRd_s42

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 42

value: preClamp


title: adipose_postTZD_IRd_s41

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 41


title: muscle_postTZD_postClamp_IRd_s41

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 41


title: muscle_preTZD_preClamp_IRd_s41

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 41


title: muscle_postTZD_preClamp_IRd_s41

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 41


title: adipose_preTZD_IRd+_s40

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, insulin resistant, responder, subject 40


title: muscle_postTZD_postClamp_IRd-_s39

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 39

value: - (non responder)


title: muscle_preTZD_preClamp_IRd-_s39

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 39


title: muscle_postTZD_preClamp_IRd+_s40

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 40


title: muscle_preTZD_postClamp_IRd-_s39

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, non responder, subject 39


title: adipose_preTZD_IRd-_s39

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, non responder, subject 39


title: muscle_preTZD_preClamp_IRd+_s40

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 40


title: adipose_postTZD_IRd+_s40

description: no additional information

treatment_protocol: post-TZD, insulin resistant, responder, subject 40


title: muscle_postTZD_preClamp_IRd-_s39

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 39


title: adipose_preTZD_IRd_s37

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, , subject 37


title: adipose_preTZD_IRd+_s38

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, responder, subject 38


title: adipose_preTZD_IRd-_s36

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, non responder, subject 36


title: adipose_postTZD_IRd+_s38

description: no additional information

treatment_protocol: post-TZD, insulin resistant, responder, subject 38


title: adipose_postTZD_IRd_s37

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 37


title: muscle_postTZD_postClamp_IRd+_s38

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 38


title: muscle_preTZD_preClamp_IRd-_s36

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 36


title: muscle_postTZD_preClamp_IRd+_s38

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 38


title: muscle_preTZD_postClamp_IRd+_s38

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 38


title: muscle_postTZD_preClamp_IRd_s37

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 37


title: muscle_postTZD_postClamp_IRd_s37

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 37


title: adipose_preTZD_IRd+_s35

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, responder, subject 35


title: muscle_preTZD_postClamp_IRd-_s36

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, non responder, subject 36


title: adipose_postTZD_IRd-_s36

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, insulin resistant, non responder, subject 36


title: muscle_preTZD_preClamp_IRd_s37

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 37


title: muscle_preTZD_preClamp_IRd+_s38

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 38


title: NHE1-OX 2wk6

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

hyb_protocol: Hybridizations were carried out by using the Illumina gene expression system according to the manufacturer's instructions.

scan_protocol: Illumina scanner

data_processing: Normalized average intensity of the bead type/target in the group using Cubic spline normalization with BeadStudio 2.3.47.

label: Biotin

organism: Mus musculus

source_name: K-line transgenic sample

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit following the manufacturer's instructions. Input amount: 100ng of total RNA.

extract_protocol: Total RNA was extracted from frozen tissues of using RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

value: heart

tag: strain

value: FVB

tag: gender

value: male

tag: age

value: 14 days


title: muscle_preTZD_postClamp_IRd_s37

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 37


title: adipose_postTZD_IRd+_s35

description: no additional information

treatment_protocol: post-TZD, insulin resistant, responder, subject 35


title: muscle_postTZD_postClamp_IRd+_s35

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 35


title: NHE1-OX 2wn2

source_name: N-line transgenic sample


title: muscle_postTZD_preClamp_IRd-_s36

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 36


title: muscle_preTZD_preClamp_IRd+_s35

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 35


title: NHE1-OX 2wn4


title: muscle_postTZD_postClamp_IRd-_s36

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 36


title: NHE1-OX 2wn3


title: NHE1-OX 2wk5


title: muscle_postTZD_preClamp_IRd+_s35

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 35


title: NHE1-OX 2wc3

source_name: control sample


title: muscle_preTZD_preClamp_IRd_s34

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 34


title: muscle_postTZD_preClamp_IRd_s34

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 34


title: adipose_preTZD_IRd+_s33

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, responder, subject 33


title: adipose_preTZD_IRd_s34

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, , subject 34


title: adipose_postTZD_IRd_s34

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 34


title: muscle_preTZD_postClamp_IRd+_s33

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 33


title: muscle_postTZD_postClamp_IRd_s34

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 34


title: muscle_postTZD_postClamp_IRd+_s33

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 33


title: muscle_preTZD_postClamp_IRd_s34

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 34


title: NHE1-OX 2wc2


title: adipose_postTZD_IRd+_s33

description: no additional information

treatment_protocol: post-TZD, insulin resistant, responder, subject 33


title: adipose_preTZD_IRd-_s32

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, non responder, subject 32


title: NHE1-OX 2wk3


title: muscle_preTZD_preClamp_IRd+_s33

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 33


title: NHE1-OX 2wc1


title: muscle_postTZD_preClamp_IRd+_s33

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 33


title: adipose_postTZD_IRd-_s32

description: no additional information

treatment_protocol: post-TZD, insulin resistant, non responder, subject 32


title: muscle_postTZD_postClamp_IRd-_s32

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 32


title: muscle_preTZD_postClamp_IRd+_s35

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 35


title: adipose_preTZD_IRd_s31

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, insulin resistant, , subject 31


title: muscle_postTZD_preClamp_IRd-_s32

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 32


title: muscle_preTZD_preClamp_IRd-_s32

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 32


title: adipose_postTZD_IRd_s31

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 31


title: muscle_preTZD_postClamp_IRd-_s32

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, non responder, subject 32


title: muscle_postTZD_postClamp_IRd_s31

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 31


title: muscle_preTZD_postClamp_IRd_s31

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 31


title: muscle_postTZD_preClamp_IRd_s31

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 31


title: muscle_preTZD_preClamp_IRd_s31

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 31


title: adipose_postTZD_IRd_s30

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 30


title: adipose_preTZD_IRd_s30

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, , subject 30


title: muscle_postTZD_preClamp_IRd_s30

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 30


title: muscle_postTZD_postClamp_IRd_s30

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 30


title: muscle_preTZD_postClamp_IRd_s30

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 30


title: muscle_preTZD_preClamp_IRd_s30

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 30


title: adipose_postTZD_IRd_s29

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 29


title: adipose_preTZD_IRd_s29

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, , subject 29


title: CHM104

type: genomic

city: Fukuoka

first: Kenshi

last: Hayashi

address: Maidashi 3-1-1, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

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

scan_protocol: The arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CEL files were processed by Affymetrix Genotyping Console 3.0.1. Calls were generated using birdseed-v2 algorithm. Copy number analysis was performed using "Reference Model File Creation and Analysis" mode without with regional GC correction configuration.

molecule: genomic DNA

source_name: complete hydatidiform mole

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from complete hydatidiform mole tissues using the Qiagen DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: complete hydatidiform mole


title: CHM113


title: CHM105


title: CHM118


title: CHM103


title: muscle_postTZD_postClamp_IRd_s29

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 29


title: CHM110


title: CHM114


title: CHM106


title: muscle_preTZD_postClamp_IRd_s29

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 29


title: CHM102


title: CHM115


title: CHM111


title: muscle_preTZD_preClamp_IRd_s29

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 29


title: CHM094


title: CHM095


title: CHM090


title: CHM098


title: CHM116


title: CHM097


title: adipose_postTZD_IRd+_s28

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, insulin resistant, responder, subject 28


title: adipose_preTZD_IRd+_s28

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, responder, subject 28


title: muscle_postTZD_preClamp_IRd_s29

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 29


title: CHM100


title: muscle_postTZD_postClamp_IRd+_s28

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 28


title: CHM088


title: muscle_postTZD_preClamp_IRd+_s28

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 28


title: adipose_preTZD_IRd+_s27

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, responder, subject 27


title: muscle_preTZD_preClamp_IRd+_s28

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 28


title: muscle_postTZD_postClamp_IRd+_s27

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 27


title: CHM117


title: adipose_postTZD_IRd+_s27

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, insulin resistant, responder, subject 27


title: muscle_postTZD_preClamp_IRd+_s27

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 27


title: CHM085


title: CHM083


title: CHM084


title: muscle_preTZD_postClamp_IRd+_s28

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 28


title: muscle_preTZD_postClamp_IRd+_s27

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 27


title: CHM087


title: CHM086


title: adipose_postTZD_IRd-_s26

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, insulin resistant, non responder, subject 26


title: muscle_preTZD_preClamp_IRd+_s27

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 27


title: adipose_preTZD_IRd-_s26

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, insulin resistant, non responder, subject 26


title: CHM081


title: CHM082


title: CHM099


title: muscle_postTZD_postClamp_IRd-_s26

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 26


title: muscle_postTZD_preClamp_IRd-_s26

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 26


title: muscle_preTZD_preClamp_IRd-_s26

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 26


title: muscle_preTZD_postClamp_IRd-_s26

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, post-clamp, insulin resistant, non responder, subject 26


title: adipose_postTZD_IRd_s25

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, insulin resistant, , subject 25


title: CHM078


title: adipose_preTZD_IRd_s25

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, , subject 25


title: muscle_postTZD_postClamp_IRd_s25

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 25


title: CHM093


title: CHM072


title: CHM074


title: CHM101


title: muscle_preTZD_postClamp_IRd_s25

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 25


title: muscle_preTZD_preClamp_IRd_s25

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 25


title: muscle_postTZD_preClamp_IRd_s25

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 25


title: CHM070


title: muscle_postTZD_postClamp_IRd+_s24

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 24


title: CHM075


title: CHM069


title: CHM079


title: adipose_preTZD_IRd+_s24

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, responder, subject 24


title: CHM065


title: adipose_postTZD_IRd+_s24

description: no additional information

treatment_protocol: post-TZD, insulin resistant, responder, subject 24


title: muscle_preTZD_postClamp_IRd+_s24

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 24


title: muscle_postTZD_preClamp_IRd+_s24

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 24


title: CHM064


title: CHM063


title: muscle_preTZD_preClamp_IRd+_s24

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 24


title: CHM080


title: adipose_postTZD_NRd_s23

description: no additional information

treatment_protocol: post-TZD, insulin sensitive, , subject 23

value: NRd (insulin sensitive)


title: CHM062


title: CHM076


title: CHM068


title: CHM060


title: muscle_preTZD_postClamp_NRd_s23

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 23


title: adipose_preTZD_NRd_s23

description: no additional information

treatment_protocol: pre-TZD, insulin sensitive, , subject 23


title: muscle_postTZD_postClamp_NRd_s23

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 23


title: CHM050


title: muscle_postTZD_preClamp_NRd_s23

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 23


title: CHM058


title: CHM055


title: adipose_postTZD_IRd+_s22

description: no additional information

treatment_protocol: post-TZD, insulin resistant, responder, subject 22


title: muscle_preTZD_preClamp_NRd_s23

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 23


title: muscle_postTZD_postClamp_IRd+_s22

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 22


title: muscle_postTZD_preClamp_IRd+_s22

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 22


title: CHM056


title: muscle_preTZD_postClamp_IRd+_s22

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 22


title: CHM067


title: CHM066


title: muscle_preTZD_preClamp_IRd+_s22

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 22


title: adipose_postTZD_IRd+_s21

description: no additional information

treatment_protocol: post-TZD, insulin resistant, responder, subject 21


title: CHM046


title: adipose_preTZD_IRd+_s21

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, responder, subject 21


title: muscle_postTZD_postClamp_IRd+_s21

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 21


title: CHM059


title: adipose_preTZD_IRd+_s22

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, responder, subject 22


title: muscle_postTZD_preClamp_IRd+_s21

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 21


title: CHM039


title: muscle_preTZD_postClamp_IRd+_s21

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 21


title: CHM054


title: CHM073


title: CHM034


title: muscle_preTZD_preClamp_IRd+_s21

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 21


title: CHM057


title: CHM061


title: CHM033


title: CHM040


title: muscle_postTZD_postClamp_NRd_s20

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 20


title: muscle_postTZD_preClamp_NRd_s20

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 20


title: adipose_preTZD_NRd_s20

description: no additional information

treatment_protocol: pre-TZD, insulin sensitive, , subject 20


title: CHM049


title: adipose_postTZD_NRd_s20

description: no additional information

treatment_protocol: post-TZD, insulin sensitive, , subject 20


title: muscle_preTZD_postClamp_NRd_s20

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 20


title: CHM029


title: CHM028


title: CHM030


title: adipose_postTZD_NRd_s19

description: no additional information

treatment_protocol: post-TZD, insulin sensitive, , subject 19


title: CHM043


title: muscle_preTZD_preClamp_NRd_s20

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 20


title: CHM051


title: CHM053


title: CHM047


title: CHM048


title: CHM031


title: muscle_postTZD_postClamp_NRd_s19

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 19


title: muscle_preTZD_preClamp_NRd_s19

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 19


title: muscle_preTZD_postClamp_NRd_s19

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 19


title: CHM038


title: CHM041


title: CHM042


title: muscle_postTZD_preClamp_NRd_s19

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 19


title: adipose_preTZD_NRd_s18

description: no additional information

treatment_protocol: pre-TZD, insulin sensitive, , subject 18


title: adipose_postTZD_NRd_s18

description: no additional information

treatment_protocol: post-TZD, insulin sensitive, , subject 18


title: CHM036


title: muscle_postTZD_postClamp_NRd_s18

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 18


title: muscle_postTZD_preClamp_NRd_s18

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 18


title: muscle_preTZD_postClamp_NRd_s18

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 18


title: CHM026


title: CHM024


title: muscle_preTZD_preClamp_NRd_s18

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 18


title: adipose_postTZD_NRd_s17

description: no additional information

treatment_protocol: post-TZD, insulin sensitive, , subject 17


title: CHM035


title: muscle_postTZD_postClamp_NRd_s17

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 17


title: muscle_postTZD_preClamp_NRd_s17

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 17


title: CHM022


title: CHM032


title: CHM023


title: Tru-cut sample 10000 Normal

city: Biella

first: vijay

middle: kumar

last: singh

state: Biella

address: via Malta 3

country: Italy

institute: Fondazione "Edo ed Elvo Tempia Valenta"

description: Technical replicate in normal orientation of 10000.TC.D

hyb_protocol: Equal amounts (0.75 ug) of labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays representing 41K human unique genes and transcripts (Human Whole Genome Oligo Microarray 1x44K or 4x44K, Agilent Technologies, Palo Alto, CA). All steps were performed following Agilent oligo microarray processing protocol. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the dual-laser microarray scanner Agilent G2505B

data_processing: All data analysis steps were done with statistical computing software “R” and packages from Bioconductor open source software for bioinformatics. In particular, “limma” was used for preprocessing and differential expression analysis. From row feature extraction file, Median foreground and background intensities for each probe were used as expression measure. Before normalization average intensity values were calculated for a probe present in multiple copy. This allows us to have intensity measures from exactly 41k unique probes for the two platforms used in this study (smaller of the 2 raw data files). Then the raw intensities were first background corrected using method “normexp” as provided by a function in the limma package. An offset value of 50 was added to red and green intensities so that log-ratios are shrunk towards zero at lower intensities. In order to set log-ratios average to zero within each array, “loess” normalization was performed by a function provided in the limma package. To have similar log-ratio distributions across all arrays “Aquantile” normalization was performed by a function provided in limma package.

source_name: Human universal reference

label_protocol: RNA isolated from each tissue and from the Human Universal Reference Total RNA (Clontech, Palo Alto, CA) was amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Ambion) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis (in the second round of amplification), cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences, Buckinghamshire UK) able to react with the modified RNA. mRNA quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies). At least 5 ug of mRNA for each sample were labeled and purified with columns.

extract_protocol: Samples were recovered immediately after removal (tru-cut or surgical resection) and put in RNAlater (Ambion Inc, Austin TX) for processing. Tissues were homogenized and total RNA was isolated using TriReagent (Sigma-Aldrich, St. Louis, MO) and RNeasy Mini Kit (Qiagen, Dusseldorf, Germany). TotRNA quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies, Palo Alto, CA) run on the Agilent 2100 bioanalyzer.

treatment_protocol: Each patient received neoadjuvant therapy with Anastrozole (ArimidexTM, Astra Zeneca) 1mg po/die for three months.

tag: age (years)

tag: stage t

tag: pgr (%)

tag: histotype

tag: grading

tag: % response

tag: sample type

value: commercial pool of RNA

source_name: Breast cancer tru-cut sample 10000


title: Tru-cut sample 10000 Dye swap

description: Technical replicate in dye swap orientation of 10000.TC.N


title: muscle_preTZD_preClamp_NRd_s17

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 17


title: CHM019


title: Surgical sample 10000 Dye swap

description: Technical replicate in dye swap orientation of 10000.PO.N

source_name: Breast cancer surgical sample 10000

value: IDC


title: muscle_preTZD_postClamp_NRd_s17

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 17

value: muscle


title: Surgical sample 10000 Normal

description: Technical replicate in normal orientation of 10000.PO.D


title: CHM021


title: adipose_postTZD_NRd_s16

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, insulin sensitive, , subject 16

value: postTZD


title: CHM018


title: Tru-cut sample 09999 Normal

description: Technical replicate in normal orientation of 09999.TC.D

source_name: Breast cancer tru-cut sample 09999


title: muscle_postTZD_preClamp_NRd_s16

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 16


title: muscle_preTZD_postClamp_NRd_s16

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 16

value: postClamp


title: CHM020


title: muscle_postTZD_postClamp_NRd_s16

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 16


title: Surgical sample 09999 Normal

description: Technical replicate in normal orientation of 09999.PO.D

source_name: Breast cancer surgical sample 09999


title: Tru-cut sample 09999 Dye swap

description: Technical replicate in dye swap orientation of 09999.TC.N


title: muscle_preTZD_preClamp_NRd_s16

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 16


title: adipose_postTZD_NRd_s15

description: no additional information

treatment_protocol: post-TZD, insulin sensitive, , subject 15


title: adipose_preTZD_NRd_s15

description: no additional information

treatment_protocol: pre-TZD, insulin sensitive, , subject 15


title: muscle_postTZD_postClamp_NRd_s15

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 15


title: CHM016


title: Surgical sample 09999 Dye swap

description: Technical replicate in dye swap orientation of 09999.PO.N


title: Tru-cut sample 10061 Normal

description: Technical replicate in normal orientation of 10061.TC.D

source_name: Breast cancer tru-cut sample 10061


title: Tru-cut sample 10056 Dye swap

description: Technical replicate in dye swap orientation of 10056.TC.N

source_name: Breast cancer tru-cut sample 10056


title: CHM013


title: muscle_preTZD_postClamp_NRd_s15

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 15


title: Tru-cut sample 10054 Normal

description: Technical replicate in normal orientation of 10054.TC.D

source_name: Breast cancer tru-cut sample 10054


title: CHM014


title: Tru-cut sample 10061 Dye swap

description: Technical replicate in dye swap orientation of 10061.TC.N


title: Tru-cut sample 10054 Dye swap

description: Technical replicate in dye swap orientation of 10054.TC.N


title: adipose_preTZD_NRd_s16

description: no additional information

treatment_protocol: pre-TZD, insulin sensitive, , subject 16


title: Tru-cut sample 10056 Normal

description: Technical replicate in normal orientation of 10056.TC.D


title: Tru-cut sample 10052 Normal

description: Technical replicate in normal orientation of 10052.TC.D

source_name: Breast cancer tru-cut sample 10052


title: Tru-cut sample 10052 Dye swap

description: Technical replicate in dye swap orientation of 10052.TC.N


title: Tru-cut sample 10051 Normal

description: Technical replicate in normal orientation of 10051.TC.D

source_name: Breast cancer tru-cut sample 10051


title: CHM015


title: adipose_postTZD_NRd_s14

description: no additional information

treatment_protocol: post-TZD, insulin sensitive, , subject 14


title: muscle_postTZD_preClamp_NRd_s15

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 15


title: CHM007


title: CHM012


title: muscle_postTZD_postClamp_NRd_s14

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 14


title: adipose_preTZD_NRd_s14

description: no additional information

treatment_protocol: pre-TZD, insulin sensitive, , subject 14


title: CHM011


title: Tru-cut sample 10040 Normal

description: Technical replicate in normal orientation of 10040.TC.D

treatment_protocol: Each patient received neoadjuvant therapy with Anastrozole (ArimidexTM, Astra Zeneca) 1mg po/die for three months.

source_name: Breast cancer tru-cut sample 10040


title: muscle_postTZD_preClamp_NRd_s14

description: no additional information

source_name: skeletal muscle (vastus lateralis)

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 14


title: Tru-cut sample 10051 Dye swap

description: Technical replicate in dye swap orientation of 10051.TC.N


title: Tru-cut sample 10039 Normal

description: Technical replicate in normal orientation of 10039.TC.D

source_name: Breast cancer tru-cut sample 10039


title: muscle_preTZD_postClamp_NRd_s14

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 14


title: muscle_preTZD_preClamp_NRd_s14

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 14


title: adipose_postTZD_IRd-_s13

description: no additional information

source_name: adipose tissue (abdominal subcutaneous)

treatment_protocol: post-TZD, insulin resistant, non responder, subject 13

value: IRd (insulin resistant)


title: CHM006


title: Tru-cut sample 10039 Dye swap

description: Technical replicate in dye swap orientation of 10039.TC.N


title: muscle_postTZD_postClamp_IRd-_s13

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 13


title: CHM008


title: Tru-cut sample 10037 Normal

description: Technical replicate in normal orientation of 10037.TC.D

source_name: Breast cancer tru-cut sample 10037


title: CHM010


title: Tru-cut sample 10037 Dye swap

description: Technical replicate in dye swap orientation of 10037.TC.N


title: muscle_preTZD_preClamp_IRd-_s13

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 13


title: CHM009


title: adipose_postTZD_IRd_s12

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 12


title: muscle_preTZD_preClamp_NRd_s15

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 15


title: muscle_postTZD_preClamp_IRd-_s13

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 13


title: Tru-cut sample 10040 Dye swap

description: Technical replicate in dye swap orientation of 10040.TC.N


title: Tru-cut sample 10036 Normal

description: Technical replicate in normal orientation of 10036.TC.D

source_name: Breast cancer tru-cut sample 10036


title: Tru-cut sample 10028 Dye swap

description: Technical replicate in dye swap orientation of 10028.TC.N

source_name: Breast cancer tru-cut sample 10028


title: CHM003

source_name: complete hydatidiform mole


title: muscle_postTZD_postClamp_IRd_s12

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 12


title: Tru-cut sample 10026 Dye swap

description: Technical replicate in dye swap orientation of 10026.TC.N

source_name: Breast cancer tru-cut sample 10026

source_name: Human universal reference


title: adipose_preTZD_IRd_s12

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, , subject 12


title: Tru-cut sample 10026 Normal

description: Technical replicate in normal orientation of 10026.TC.D


title: Surgical sample 10028 Dye swap

description: Technical replicate in dye swap orientation of 10028.PO.N

source_name: Breast cancer surgical sample 10028


title: adipose_preTZD_IRd-_s13

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, non responder, subject 13


title: muscle_postTZD_preClamp_IRd_s12

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 12


title: Surgical sample 10028 Normal

description: Technical replicate in normal orientation of 10028.PO.D


title: CHM001


title: CHM002


title: muscle_preTZD_preClamp_IRd_s12

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 12


title: CHM005


title: muscle_preTZD_postClamp_IRd-_s13

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, non responder, subject 13


title: Tru-cut sample 10036 Dye swap

description: Technical replicate in dye swap orientation of 10036.TC.N


title: muscle_preTZD_postClamp_IRd_s12

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 12


title: Tru-cut sample 10028 Normal

description: Technical replicate in normal orientation of 10028.TC.D

treatment_protocol: Each patient received neoadjuvant therapy with Anastrozole (ArimidexTM, Astra Zeneca) 1mg po/die for three months.


title: Surgical sample 10026 Normal

description: Technical replicate in normal orientation of 10026.PO.D

source_name: Breast cancer surgical sample 10026


title: adipose_postTZD_IRd-_s11

description: no additional information

treatment_protocol: post-TZD, insulin resistant, non responder, subject 11


title: Tru-cut sample 10018 Normal

description: Technical replicate in normal orientation of 10018.TC.D

source_name: Breast cancer tru-cut sample 10018


title: Surgical sample 10026 Dye swap

description: Technical replicate in dye swap orientation of 10026.PO.N


title: Surgical sample 10018 Normal

description: Technical replicate in normal orientation of 10018.PO.D

source_name: Breast cancer surgical sample 10018

value: ILC


title: Tru-cut sample 10018 Dye swap

description: Technical replicate in dye swap orientation of 10018.TC.N


title: muscle_preTZD_postClamp_IRd-_s11

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, non responder, subject 11

value: preTZD


title: muscle_postTZD_postClamp_IRd-_s11

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 11


title: muscle_postTZD_preClamp_IRd-_s11

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 11


title: adipose_preTZD_IRd-_s11

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, non responder, subject 11

value: adipose


title: Surgical sample 10017 Dye swap

description: Technical replicate in dye swap orientation of 10017.PO.N

source_name: Breast cancer surgical sample 10017


title: Surgical sample 10018 Dye swap

description: Technical replicate in dye swap orientation of 10018.PO.N


title: Tru-cut sample 10017 Normal

description: Technical replicate in normal orientation of 10017.TC.D

source_name: Breast cancer tru-cut sample 10017


title: Tru-cut sample 10017 Dye swap

description: Technical replicate in dye swap orientation of 10017.TC.N


title: muscle_postTZD_preClamp_IRd_s10

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 10

value: preClamp


title: muscle_postTZD_postClamp_IRd_s10

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 10


title: Surgical sample 10017 Normal

description: Technical replicate in normal orientation of 10017.PO.D


title: adipose_preTZD_IRd_s10

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, , subject 10


title: muscle_preTZD_postClamp_IRd_s10

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 10


title: muscle_preTZD_preClamp_IRd-_s11

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 11

value: - (non responder)


title: adipose_postTZD_IRd_s10

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 10


title: Tru-cut sample 10010 Normal

description: Technical replicate in normal orientation of 10010.TC.D

source_name: Breast cancer tru-cut sample 10010


title: adipose_postTZD_IRd_s9

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 9


title: muscle_preTZD_preClamp_IRd_s10

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 10


title: Surgical sample 10010 Normal

description: Technical replicate in normal orientation of 10010.PO.D

source_name: Breast cancer surgical sample 10010


title: adipose_preTZD_IRd_s9

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, , subject 9


title: Surgical sample 10010 Dye swap

description: Technical replicate in dye swap orientation of 10010.PO.N


title: muscle_preTZD_preClamp_IRd_s9

description: no additional information

source_name: skeletal muscle (vastus lateralis)

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 9


title: muscle_preTZD_preClamp_IRd_s8

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 8


title: adipose_preTZD_IRd_s7

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, insulin resistant, , subject 7


title: muscle_preTZD_postClamp_IRd_s7

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 7


title: muscle_postTZD_preClamp_IRd_s9

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 9


title: muscle_postTZD_postClamp_IRd_s9

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 9


title: Tru-cut sample 10010 Dye swap

description: Technical replicate in dye swap orientation of 10010.TC.N

treatment_protocol: Each patient received neoadjuvant therapy with Anastrozole (ArimidexTM, Astra Zeneca) 1mg po/die for three months.


title: adipose_postTZD_IRd_s8

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 8


title: muscle_postTZD_preClamp_IRd_s8

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 8


title: muscle_preTZD_preClamp_IRd_s7

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 7


title: muscle_postTZD_postClamp_IRd_s8

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 8


title: muscle_postTZD_postClamp_IRd_s7

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 7


title: muscle_postTZD_preClamp_IRd_s7

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 7


title: muscle_preTZD_postClamp_IRd_s9

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 9


title: adipose_preTZD_IRd-_s4

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, non responder, subject 4


title: muscle_postTZD_preClamp_IRd_s5

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 5


title: muscle_postTZD_postClamp_IRd_s5

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 5


title: muscle_preTZD_preClamp_IRd_s5

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 5


title: adipose_postTZD_IRd_s5

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 5


title: adipose_postTZD_IRd-_s6

description: no additional information

treatment_protocol: post-TZD, insulin resistant, non responder, subject 6


title: adipose_postTZD_IRd_s7

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 7


title: adipose_preTZD_IRd_s5

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, , subject 5


title: muscle_preTZD_postClamp_IRd_s8

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 8


title: muscle_preTZD_postClamp_IRd_s5

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 5


title: muscle_postTZD_preClamp_IRd-_s6

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 6


title: muscle_preTZD_preClamp_IRd-_s6

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 6


title: muscle_preTZD_postClamp_IRd-_s4

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, non responder, subject 4


title: adipose_postTZD_IRd-_s4

description: no additional information

treatment_protocol: post-TZD, insulin resistant, non responder, subject 4


title: muscle_postTZD_preClamp_IRd-_s4

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 4


title: Surgical sample 10064 Dye swap

description: Technical replicate in dye swap orientation of 10064.PO.N

source_name: Breast cancer surgical sample 10064

treatment_protocol: Each patient received neoadjuvant therapy with Anastrozole (ArimidexTM, Astra Zeneca) 1mg po/die for three months.


title: muscle_postTZD_postClamp_IRd-_s4

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 4


title: muscle_postTZD_postClamp_IRd-_s3

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 3


title: adipose_postTZD_IRd-_s3

description: CEL file not provided for this Sample.

source_name: adipose tissue (abdominal subcutaneous)

treatment_protocol: post-TZD, insulin resistant, non responder, subject 3


title: Differentiated TS cells

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

description: Gene expression of differentiated mouse trophoblast stem cells

hyb_protocol: For microarray analysis, 100ng of total RNA was amplified and hybridized to the Mouse Gene 1.0 ST array (Affymetrix). This service was performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada

scan_protocol: According to standard Affymetrix protocol. This service was performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada

data_processing: Data was processed using Expression Console from Affymetrics using the PLIER algorithm

source_name: trophoblast stem cells, differentiated

growth_protocol: R1 and E14TG2a (ES cells), A4 and G3 (TS cells) and F3 and F4 (XEN cells) were cultured in the absence of feeder cells according to standard protocols (http://www.sickkids.ca/research/rossant/custom/stemCells.asp). To induce TS cell differentiation, 1 x 10E5 cells were plated on to each well of a 6-well plate in standard TS cell conditions for 24h, rinsed twice with PBS and cultured for six days in unconditioned TS cell media without FGF4 and heparin.

extract_protocol: RNA was processed using the RNeasy Mini Kit (Qiagen) with on-column RNase-free DNase (Qiagen) digestion.

tag: cell line

value: differentiated trophoblast stem cells


title: muscle_preTZD_preClamp_IRd-_s4

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 4

tag: tissue


title: Tru-cut sample 10064 Normal

description: Technical replicate in normal orientation of 10064.TC.D

source_name: Breast cancer tru-cut sample 10064


title: mouse heart_E12.5_WT_rep9

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Samples were hybridized overnight to GeneChips in accordance with Affymetrix protocols.

scan_protocol: Post hybridization washing, staining and fluorescence scanning were performed using Affymetrix instrumentation in accordance with manufacturer recommendations.

data_processing: Scanned GeneChips (CEL files) were processed with Affymetrix GCOS to generate CHP files.

source_name: mouse embryo heart E12.5

label_protocol: Total RNA (10 ng) was converted into biotin-labeled cDNA suitable for hybridization to Affymetrix GeneChips (Affymetrix, Santa Clara, CA) using the WT-Ovation™ Pico amplification kit and the FL-Ovation™ cDNA Biotin V2 kit (NuGen, San Carlos, CA).

growth_protocol: Mice were housed in the MUSC animal facility using institutionally approved protocols.

extract_protocol: Hearts were collected by dissection from wild-type embryos at E12.5. Total RNA was prepared from individual tissue isolates by Trizol extraction and purification with the RNeasy  Mini kit (Qiagen, Valencia, CA).

value: 129P2/OlaHsd backcrossed to C57BL/6 fro 2 generations

tag: stage

value: Heart


title: adipose_preTZD_IRd-_s3

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, insulin resistant, non responder, subject 3

tag: tzd treatment


title: Surgical sample 10064 Normal

description: Technical replicate in normal orientation of 10064.PO.D


title: Surgical sample 10061 Normal

description: Technical replicate in normal orientation of 10061.PO.D

source_name: Breast cancer surgical sample 10061


title: muscle_preTZD_postClamp_IRd-_s3

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, non responder, subject 3

tag: clamp status

tag: insulin resistance


title: Surgical sample 10056 Normal

description: Technical replicate in normal orientation of 10056.PO.D

source_name: Breast cancer surgical sample 10056


title: Surgical sample 10061 Dye swap

description: Technical replicate in dye swap orientation of 10061.PO.N

source_name: Human universal reference


title: muscle_postTZD_preClamp_IRd-_s3

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 3

tag: response to tzd treatment

tag: subject


title: muscle_preTZD_preClamp_IRd-_s3

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 3


title: mouse heart_E12.5_WT_rep8

tag: strain


title: adipose_preTZD_IRd_s2

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, , subject 2


title: Tru-cut sample 10064 Dye swap

description: Technical replicate in dye swap orientation of 10064.TC.N


title: mouse heart_E12.5_WT_rep10


title: adipose_postTZD_IRd_s2

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 2


title: mouse heart_E12.5_WT_rep6


title: adipose_preTZD_IRd-_s6

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, insulin resistant, non responder, subject 6


title: mouse pharyngeal arch_E10.5_WT_rep4

source_name: mouse Second heart field-containing tissue

growth_protocol: Mice were housed in the Medical University of South Carolina animal facility using institutionally approved protocols.

extract_protocol: Pharyngeal arch-containing tissue was collected by dissection from wild-type embryos at E10.5. RNA was prepared from individual tissue isolates by Trizol extraction and purification with the RNeasy  Mini kit (Qiagen, Valencia, CA).

value: 129P2/OlaHsd backcrossed to C57BL/6 for 2 generations

value: Second heart field-containing tissue


title: Surgical sample 10056 Dye swap

description: Technical replicate in dye swap orientation of 10056.PO.N


title: muscle_postTZD_postClamp_IRd_s2

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 2


title: muscle_postTZD_preClamp_IRd_s2

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 2


title: mouse heart_E12.5_WT_rep7


title: muscle_preTZD_postClamp_IRd_s2

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 2


title: Surgical sample 10054 Dye swap

description: Technical replicate in dye swap orientation of 10054.PO.N

source_name: Breast cancer surgical sample 10054


title: Surgical sample 10054 Normal

description: Technical replicate in normal orientation of 10054.PO.D


title: mouse pharyngeal arch_E10.5_WT_rep2


title: mouse pharyngeal arch_E10.5_WT_rep3


title: mouse pharyngeal arch_E10.5_WT_rep5


title: Surgical sample 10052 Normal

description: Technical replicate in normal orientation of 10052.PO.D

source_name: Breast cancer surgical sample 10052


title: Surgical sample 10052 Dye swap

description: Technical replicate in dye swap orientation of 10052.PO.N


title: mouse pharyngeal arch_E10.5_WT_rep1


title: adipose_postTZD_IRd+_s1

description: no additional information

treatment_protocol: post-TZD, insulin resistant, responder, subject 1

value: + (responder)


title: SH6484

city: kamakura

first: yoji

last: ueda

state: Kanagawa

address: 6-10-1 Tebiro

institute: Toray Industries, Inc.

description: no additional information

hyb_protocol: Hybridized for 16 h at 42 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: Hybridized DNA Chip was scanned using FLA-8000 microarray scanner (Fuji Film., Tokyo, Japan).  Array images were analyzed using DNASIS Array (Hitachi Soft, Tokyo, Japan)

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Saccharomyces cerevisiae

source_name: genome reconstructed strain

label_protocol: Yeast genomic DNA (10 µg, purified on a Qiagen column) was digested with 0.15 U of deoxyribonuclease I (DNase I) [Gibco-BRL polymerase chain reaction (PCR) grade] in 1× One-Phor-All buffer (Pharmacia) containing 1.5 mM CoCl2 for 5 min at 37°C.  After heat inactivation of the DNase I, digested DNA were purified by ethanol precipitation.  Labeling reactions were performed with purified digested DNA using a BioPrime labeling kit (Invitrogen) according to the manufacturer's directions in a 50-μL volume with a modified dNTP pool: 120 mmol/L each of dATP, dGTP, dTTP; 60 mmol/L dTTP; and 60 mmol/L of either Cy3-dUTP for the experimental sample or Cy5-dUTP for the wild type reference (PerkinElmer Life and Analytical Sciences, Waltham, MA; Woodbridge, ON, Canada). Labeled DNA was subsequently purified using a Microcon YM-30 filter (Millipore, Billerica, MA)

growth_protocol: YPDA medium consists of 1% yeast extract, 2% peptone, 2% glucose, and 0.04% adenine (Sigma-Aldrich, St. Louis, MO, USA) and SD medium consists of 2% glucose and 0.67% Difco™ yeast nitrogen base without amino acids (YNB; BD Biosciences, San Jose, CA, USA), supplemented as needed with amino acids and nucleic acid bases to cover auxotrophic requirements.

extract_protocol: RNA samples were collected from Colon26 cells in primary tumours and their liver metastases using TRI reagent (SIGMA).

tag: genome/variation

value: genome reconstructed

source_name: wild type strain

value: wild type


title: muscle_postTZD_postClamp_IRd+_s1

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 1

value: muscle


title: Surgical sample 10051 Normal

description: Technical replicate in normal orientation of 10051.PO.D

treatment_protocol: Each patient received neoadjuvant therapy with Anastrozole (ArimidexTM, Astra Zeneca) 1mg po/die for three months.

tag: age (years)

value: commercial pool of RNA

source_name: Breast cancer surgical sample 10051


title: muscle_preTZD_preClamp_IRd_s2

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 2


title: muscle_postTZD_preClamp_IRd+_s1

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 1

value: postTZD


title: Surgical sample 10051 Dye swap

description: Technical replicate in dye swap orientation of 10051.PO.N

tag: stage t


title: P19_differentiation_12day_repA

description: P19CL6 cells, DMSO differentiation 12 days

data_processing: P19CL6 sample microarray data were normalized using the ArrayQuest webtool (Argraves et al., 2005) to implement the Bioconductor (Gentleman et al., 2004) build of GCRMA (Wu et al., 2003).

label_protocol: Total RNA (2 micrograms) was converted into biotin-labeled cRNA using  the SuperScript II cDNA synthesis kit (Invitrogen, Carlsbad, CA) and the Enzo HighYield in vitro transcription amplification kit (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: P19CL6  cells are maintained in undifferentiated state through frequent (q 48 hr) passage in alpha-MEM plus 10% ES cell grade FBS and P/S at 1:20.

extract_protocol: RNA was prepared from cultures by Trizol extraction and purification with the RNeasy  Mini kit (Qiagen, Valencia, CA).

treatment_protocol: P19CL6  cells are differentiated by plating at a density of 3.7 x 10E5 cells/10cm dish in differentiation medium containing alpha-MEM, 10% FBS, P/S and 1% DMSO, followed by new differentiation medium every 48 hours.


title: P19_differentiation_10day_repA

description: P19CL6 cells, DMSO differentiation 10 days


title: P19_differentiation_10day_repB

source_name: P19CL6 cells, DMSO differentiation 10 days


title: P19_differentiation_12day_repC

source_name: P19CL6 cells, DMSO differentiation 12 days


title: muscle_preTZD_postClamp_IRd+_s1

description: no additional information

source_name: skeletal muscle (vastus lateralis)

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 1

value: postClamp

value: IRd (insulin resistant)


title: P19_differentiation_8day_repB

description: P19CL6 cells, DMSO differentiation 8 days


title: P19_differentiation_8day_repA

source_name: P19CL6 cells, DMSO differentiation 8 days


title: P19_differentiation_6day_repC

description: P19CL6 cells, DMSO differentiation 6 days


title: muscle_preTZD_preClamp_IRd+_s1

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 1

value: preTZD


title: P19_differentiation_10day_repC


title: P19_differentiation_4day_repC

description: P19CL6 cells, DMSO differentiation 4 days


title: P19_differentiation_4day_repB

source_name: P19CL6 cells, DMSO differentiation 4 days


title: P19_growth_repA

description: P19CL6 cells, normal growth

source_name: P19CL6 cells, normal growth


title: P19_differentiation_6day_repB

source_name: P19CL6 cells, DMSO differentiation 6 days


title: P19_differentiation_4day_repA


title: P19_growth_repC

description: P19CL6 cells, normal growth


title: P19_differentiation_8day_repC


title: P19_growth_repB

description: P19CL6 cells, normal growth


title: JUSO 4 hr Interferon-alpha-2a 1461896077_G

status: Public on May 16 2010

city: Bern

first: Fredy

last: Siegrist

address: Freiburgstrasse 15

department: Department of Nephrology

country: Switzerland

institute: University Hospital Bern

hyb_protocol: Labeled, unfragmented cRNA (500 ng) of each cell line was hybridized to commercial microarrays using the manufacturer’s protocol (Sentrix HumanRef-8 Expression BeadChips; Illumina, Inc., San Diego, CA).

scan_protocol: Data were collected using a confocal scanner (Illumina beadstation).

data_processing: Data analysis was performed using Illumina Genomestudio (www.illumina.com) and R/Bioconductor software. The data was normalized using the package limma and the functions lumiT and lumiN(method='quantile).

label_protocol: TotalRNA was biotin-labeled using a commercial kit and the protocol supplied (Agilent Technologies, Basel, Switzerland).

growth_protocol: Cell lines were cultured at 37°C in a 5% CO2 atmosphere in RPMI 1640 medium (GIBCO Life Sciences, Paisley, U.K.) supplemented with 10% fetal bovine serum (FBS), L-glutamine (2 mM), sodium pyruvate (1 mM), nonessential amino acids, antibiotics, and 10 mM HEPES buffer.

extract_protocol: Total RNA was extracted with TRI reagent (Molecular Research Center, Inc., Cincinnati, OH).

treatment_protocol: The cell lines were grown without (control) or with 100 U/ml human IFN- 2A (Roferon, F. Hoffmann-La Roche Ltd., Basel, Switzerland) for 4 or 24 h.

tag: incubation time

tag: treatment

tag: treatment dose u/ml

tag: ifna responder

tag: tgfb responder

tag: ifna and tgfb responder

tag: culture vessel

value: 6-well plate

tag: timepoint 4h treatment

value: same end point

tag: ivt on extraction day

value: TRUE

tag: sentrix barcode

tag: sample section

value: G

value: JUSO


title: JUSO 24 hr Interferon-alpha-2a 1461896068_B

value: B

tag: cell line


title: JUSO 24 hr Interferon-alpha-2a 1461896072_D

value: D


title: PANC1 24 hr Interferon-alpha-2a 1461896054_H

value: H


title: JUSO 24 hr control medium 1461896077_A

value: control medium

value: A


title: JUSO 24 hr control medium 1461896054_G


title: PANC1 24 hr Interferon-alpha-2a 1461896068_A


title: PANC1 4 hr Interferon-alpha-2a 1461896066_E

value: E


title: JUSO 24 hr Interferon-alpha-2a 1461896080_B


title: JUSO 4 hr Interferon-alpha-2a 1461896068_E


title: JUSO 24 hr control medium 1461896072_G


title: JUSO 4 hr Interferon-alpha-2a 1461896066_A


title: PANC1 24 hr Interferon-alpha-2a 1461896077_E


title: PANC1 4 hr Interferon-alpha-2a 1461896066_H


title: PANC1 24 hr control medium 1461896080_A


title: HCT116 24 hr Interferon-alpha-2a 1461896066_F

value: T25 flask

value: not same day

value: F


title: adipose_preTZD_IRd+_s1

description: CEL file not provided for this Sample.

source_name: adipose tissue (abdominal subcutaneous)

treatment_protocol: pre-TZD, insulin resistant, responder, subject 1

tag: tissue

value: adipose

tag: tzd treatment

tag: insulin resistance

tag: response to tzd treatment

value: + (responder)

tag: subject


title: HCT116 24 hr control medium 1461896080_G

tag: incubation time


title: Calu6 24 hr Interferon-alpha-2a 1461896062_E

description: Tissue_unknown (probably lung)

tag: treatment


title: HCT116 24 hr control medium 1461896072_A

tag: treatment dose u/ml


title: HCT116 24 hr control medium 1461896067_E

tag: ifna responder


title: HCT116 24 hr Interferon-alpha-2a 1461896062_G

tag: tgfb responder


title: HCT116 4 hr Interferon-alpha-2a 1461896077_H

tag: ifna and tgfb responder


title: HCT116 4 hr Interferon-alpha-2a 1461896068_F

tag: culture vessel


title: Calu6 24 hr Interferon-alpha-2a 1461896065_D

description: Tissue_unknown (probably lung)

tag: timepoint 4h treatment


title: Calu6 24 hr Interferon-alpha-2a 1461896063_E

description: Tissue_unknown (probably lung)

tag: ivt on extraction day


title: PANC1 24 hr control medium 1461896077_C

tag: sentrix barcode

value: C


title: HCT116 24 hr Interferon-alpha-2a 1461896072_F

tag: sample section


title: Calu6 4 hr Interferon-alpha-2a 1461896080_D

description: Tissue_unknown (probably lung)

value: 6-well plate

tag: cell line


title: PANC1 4 hr Interferon-alpha-2a 1461896068_D

value: same end point


title: H3K4me2_rep3_13587002

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

description: Sample labeling, hybridization and array scanning were performed by NimbleGen Systems Inc. according to standard procedures.

data_processing: Raw fluorescence values were used to calculate log2 of precipitated/input ratios for each probe.

source_name: H3K4me2 IP human sperm

extract_protocol: Chromatin immuno precipitation (ChIP) using H3K4me2 (Upstate #07030) was performed on 2x10e7 spermatozoa obtained from 9 donors using a standard ChIP protocol with several modifications  Input and precipitated DNA were amplified according to the WGA2 protocol (Sigma).

tag: IP DNA from purified sperm samples from 9 normospermic donors

source_name: H3K4me2 input human sperm

tag: Input DNA from purified sperm samples from 9 normospermic donors


title: Calu6 4 hr Interferon-alpha-2a 1461896065_F

description: Tissue_unknown (probably lung)

value: TRUE


title: H3K27me3_rep1_13591402

hyb_protocol: Sample labeling, hybridization and array scanning were performed by NimbleGen Systems Inc. according to standard procedures.

source_name: H3K27me3 IP human sperm

extract_protocol: Chromatin immuno precipitation (ChIP) using H3K27me3 (Upstate #07449) was performed on 2x10e7 spermatozoa obtained from 9 donors using a standard ChIP protocol with several modifications  Input and precipitated DNA were amplified according to the WGA2 protocol (Sigma).

source_name: H3K27me3 input human sperm


title: MIAPACA 4 hr Interferon-alpha-2a 1461896080_F

value: FALSE

value: MIAPACA


title: MIAPACA 24 hr Interferon-alpha-2a 1461896064_F


title: H3K4me2_rep1_13156002

scan_protocol: Sample labeling, hybridization and array scanning were performed by NimbleGen Systems Inc. according to standard procedures.

extract_protocol: Chromatin immuno precipitation (ChIP) using H3K4me2 (Upstate #07030) was performed on 2x107 spermatozoa obtained from 9 donors using a standard ChIP protocol with several modifications  Input and precipitated DNA were amplified according to the WGA2 protocol (Sigma).


title: MIAPACA 24 hr control medium 1461896077_B

value: B


title: PANC1 24 hr control medium 1461896066_C


title: Calu6 24 hr control medium 1461896078_B

description: Tissue_unknown (probably lung)


title: MIAPACA 4 hr Interferon-alpha-2a 1461896062_F


title: MIAPACA 24 hr control medium 1461896065_B


title: MIAPACA 24 hr Interferon-alpha-2a 1461896072_C


title: Calu6 24 hr control medium 1461896072_H

description: Tissue_unknown (probably lung)


title: MIAPACA 4 hr Interferon-alpha-2a 1461896067_H


title: HCT116 4 hr Interferon-alpha-2a 1461896080_C


title: A549 24 hr Interferon-alpha-2a 1461896078_E


title: Calu6 24 hr control medium 1461896063_B

description: Tissue_unknown (probably lung)


title: A549 24 hr Interferon-alpha-2a 1461896067_F


title: MIAPACA 24 hr Interferon-alpha-2a 1461896078_D

value: D


title: A549 4 hr Interferon-alpha-2a 1461896066_B


title: H3K27me3_rep3_14735802

label_protocol: Sample labeling, hybridization and array scanning were performed by NimbleGen Systems Inc. according to standard procedures.


title: A549 4 hr Interferon-alpha-2a 1461896067_G

value: G


title: A549 24 hr Interferon-alpha-2a 1461896064_A


title: Calu6 4 hr Interferon-alpha-2a 1461896064_B

description: Tissue_unknown (probably lung)


title: A549 4 hr Interferon-alpha-2a 1461896078_G


title: H3K27me3_rep2_13160902


title: CHM005

hyb_protocol: DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip arrays were scanned using the BeadArray Reader (Illumina).

data_processing: The scanned data files were processed by BeadStudio (Illumina). BeadStudio was also used to calculate the Log R ratio and B allele frequency using a cluster file (Human1M-Duov3_B.egt) supplied by Illumina.

label: Alexa555 and Alexa647

source_name: complete hydatidiform mole

label_protocol: As per manufacturer (Illumina)

tag: tissue

value: complete hydatidiform mole


title: CHM006


title: LS174-T 24 hr Interferon-alpha-2a 1461896068_C

value: same start point


title: AsPC1 24 hr Interferon-alpha-2a 1461896080_H

value: H


title: A549 24 hr control medium 1461896063_H

value: control medium

value: T25 flask


title: AsPC1 24 hr Interferon-alpha-2a 1461896066_D


title: AsPC1 24 hr Interferon-alpha-2a 1461896077_F

value: F


title: A549 24 hr control medium 1461896062_C


title: LS174-T 24 hr control medium 1461896064_H


title: AsPC1 4 hr Interferon-alpha-2a 1461896062_H


title: LS174-T 24 hr Interferon-alpha-2a 1461896067_B


title: AsPC1 4 hr Interferon-alpha-2a 1461896068_G


title: H3K4me2_rep2_13694302

extract_protocol: Chromatin immuno precipitation (ChIP) using H3K4me2 (Upstate #07030)  was performed on 2x107 spermatozoa obtained from 9 donors using a standard ChIP protocol with several modifications  Input and precipitated DNA were amplified according to the WGA2 protocol (Sigma).


title: AsPC1 24 hr control medium 1461896078_C


title: A549 24 hr control medium 1461896065_G


title: LS174-T 4 hr Interferon-alpha-2a 1461896065_H


title: AsPC1 24 hr control medium 1461896063_G


title: LS174-T 24 hr control medium 1461896063_C


title: AsPC1 4 hr Interferon-alpha-2a 1461896064_C


title: AsPC1 24 hr control medium 1461896062_B


title: LS174-T 4 hr Interferon-alpha-2a 1461896063_F


title: LS174-T 24 hr Interferon-alpha-2a 1461896077_D


title: LS174-T 24 hr control medium 1461896080_E

value: E


title: LS174-T 4 hr Interferon-alpha-2a 1461896072_B


title: CHM003


title: CHM002


title: D10 24 hr Interferon-alpha-2a 1461896078_F

value: not same day


title: D10 24 hr Interferon-alpha-2a 1461896064_G


title: D10 24 hr Interferon-alpha-2a 1461896062_A

value: A


title: D10 4 hr Interferon-alpha-2a 1461896065_E


title: CHM001


title: D10 4 hr Interferon-alpha-2a 1461896064_D


title: D10 24 hr control medium 1461896078_H


title: D10 24 hr control medium 1461896067_A


title: ME15 4 hr Interferon-alpha-2a 1461896067_C

value: C


title: ME15 24 hr Interferon-alpha-2a 1461896063_D


title: ME15 24 hr Interferon-alpha-2a 1461896064_E


title: D10 24 hr control medium 1461896065_C


title: ME15 24 hr control medium 1461896078_A


title: D10 4 hr Interferon-alpha-2a 1461896063_A


title: ME15 4 hr Interferon-alpha-2a 1461896068_H


title: NOMID normal 2

status: Public on May 15 2010

city: Bethesda

first: Madson

middle: Q

last: Almeida

state: MD

address: 10 Center Drive, MSC 1103

department: Section on Genetics and Endocrinology / NICHD

institute: NIH

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Normalization was performed for each Illumina sample/array as previously described (Cheadle et al. J Mol Diagn, 5:73-81).

source_name: cartilage

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.

tag: age

value: child

value: cartilage


title: ME15 24 hr Interferon-alpha-2a 1461896072_E

value: FALSE


title: NOMID normal 1

description: replicate 1


title: NOMID bone tumor 3

description: replicate 3

source_name: bone tumor

value: bone tumor


title: ME15 4 hr Interferon-alpha-2a 1461896062_D


title: ME15 24 hr control medium 1461896066_G


title: MIAPACA 24 hr control medium 1461896067_D

value: MIAPACA


title: NOMID normal 3

description: replicate 3


title: S. mutans UA159 1% sucrose biofilm 34h replicate 1

city: Rochester

first: Marlise

middle: I

last: Klein

state: NY

address: 601 Elmwood Ave.

department: Dentistry - Center for Oral Biology

institute: University of Rochester

hyb_protocol: The slides were hybridized to a mixture containing equal amounts of test and reference cDNA for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems). Hybridized slides were washed and scanned using a GenePix scanner (Axon Instruments).

scan_protocol: Hybridized slides were washed and scanned using a GenePix scanner (Axon Instruments, Inc., Union City, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website. Single-channel images of the slides were loaded into Spotfinder and overlaid. A spot grid was created according to PFGRC specifications and manually adjusted to fit all spots. The Microarray Data Analysis System (MIDAS) software was used to normalize the spot intensity data using LOWESS and standard deviation regularization with default setting. MIDAS also utilized In-Slide Replicate Analysis to average the intensities of the spots that were replicated on the microarray slide. Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P value of 0.001.

organism: Streptococcus mutans UA159

source_name: S. mutans UA159 biofilm RNA

label_protocol: Once RNA was purified as described above, cDNA was generated from 2ug RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Invitrogen, Gaithersburg, MD) to increase cDNA yields. Purified cDNAs were coupled to Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: Biofilm preparation. Hydroxyapatite discs (2.93 cm2) were coated with amylase-active sterile clarified human saliva (sHA). Biofilms of S. mutans UA159 were formed on sHA discs placed in a vertical position in batch cultures at 37oC in 5% CO2. The biofilms were grown in buffered tryptone yeast-extract broth, pH 7.0, containing specific concentrations of sucrose and/or starch (soluble starch – 80% amylopectin and 20% amylose; Sigma Chemical Company, St Louis, MO). The concentrations of 0.5% sucrose (suc), 0.5% sucrose + 1% starch (st) and 1% sucrose were used.

extract_protocol: The biofilms were removed from HA disc in sufficient volume of RNALater, according to manufacture instructions, and stored at 4oC, overnight. Next day, the biofilm samples were washed with cold 1X PBS and sonicated at 7 watts for 30 sec (2 sonication-washings). The supernatant was discarded and biofilm pellets were homogenized and RNA extracted by repeated acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at –20°C overnight. RNA pellets were resuspended in 50 μL nuclease-free H2O, and treated with DNase I to remove contaminant genomic DNA. Two types of commercially available DNase I treatments were used: (i) on-column DNase I (Qiagen RNeasy Mini Kit, Qiagen Sciences, Germantown, MD, USA) and (ii) protein-engineered DNase I in solution (Turbo DNase, Ambion). An aliquot of the extracted RNA was treated first using Qiagen’s RNeasy on-column DNase I (Q, 2.7 U DNase I/10 μg RNA) and then with Ambion’s Turbo DNase I (T, 2 U Turbo DNase I/10 μg RNA), followed by Qiagen RNeasy MinElute (for DNase I removal) according to the manufacturer’s protocols with the exception of Qiagen’s on-column DNase I. The RNeasy on-column DNase I protocol was modified by adding a washing step with 350 μl of RLT buffer containing 36% ethanol prior to column washing with RW1 buffer (RLT and RW1 buffers are proprietary solutions of Qiagen Sciences). RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA).The quality of the purified RNA was examined by an Agilent 2100 electrophoresis bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to verify RNA integrity.

tag: biofilm age

value: 34 hours

tag: growth condition

value: 1% sucrose

source_name: wild-type mid-log RNA

growth_protocol: Cells were grown in Brain-Heart medium to OD600 of 0.5 in a 5% CO2 incubator at 37°C.

tag: growth phase

value: mid-log


title: S. mutans UA159 1% sucrose biofilm 34h replicate 3


title: S. mutans UA159 1% sucrose biofilm 34h replicate 4


title: S. mutans UA159 1% sucrose biofilm 34h replicate 2


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 34h replicate 3

value: 0.5% sucrose + 1% starch


title: Rat sublingual gland

city: Niigata-city, Chuo-ku

first: Tomoko

last: Nashida

address: 1-8 Hamaura-cho

department: Life Dentistry at Niigata

institute: The Nippon Dental University

description: Gene expression in normal rat sublingual gland

hyb_protocol: Cyanine 3-labeled cRNA targets were hybridized to Whole Rat Genome Oligo Microarray at 65°C for 17 h following the procedures recommended by the manufacturer (Agilent Technologies). After hybridization, the microarray slide was washed and dried according to the protocol provided by the manufacturer.

scan_protocol: The microarray slide was scanned on an Agilent DNA microarray scanner (Agilent Technologies). The scan resolution was 5 micrometer.

data_processing: The data were analyzed using GeneSpring softwere (Agilent Tech.).

organism: Rattus norvegicus

source_name: sublingual gland

label_protocol: Synthesis of cDNA and the following synthesis of the fluorescent-labeled cRNA were performed from 500 ng of total RNA obtained from the three salivary glands using the Quick Amp Labeling Kit (Agilent Tech).

growth_protocol: Male Wistar rats (8-week-old) were purchased from S.L.C Corp. Japan (Hamamatsu, Japan) and housed in an environmentally controlled room (12 h light-dark cycle, 23 ± 3°C and 50 ± 20% relative humidity). The animals had ad libitum access to certified rodent chow (Oriental Yeast, Tokyo, Japan) and water, and were acclimatized under these conditions for two week before experimentation.

extract_protocol: Parotid, submandibular, and sublingual glands were isolated, cut to approximately 30 mg, washed with PBS, and soaked in 0.5 ml RNAlatter (Ambion Inc., Austin, TX, USA).  Total RNA was prepared using an RNeasy Plus Mini Kit (Qiagen, Chatsworth, CA, USA) according to the manufacturer’s instructions.

tag: strain

value: Wistar

tag: gender

value: male

value: 10 weeks

value: sublingual gland


title: Rat submandibular gland

description: Gene expression in normal rat submandibular gland

source_name: submandibular gland

value: submandibular gland


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 34h replicate 2


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 34h replicate 4


title: S. mutans UA159 0.5% sucrose biofilm 34h replicate 2

value: 0.5% sucrose


title: LSK cells from heterozygous JAK2V617F mouse rep4

city: Cambridge

first: Fatima

last: Al-Shahrour

state: MA

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

description: Gene expression data from LSK cells from Jak2V617F mouse

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix GCS 3000 7G scanner using Affymetrix standard protocol

data_processing: Signal normalization was performed by RMA method. RMA expression measure was computed using Bioconductor Affy package in R language (Bioconductor 2.5; R version 2.11.0).

source_name: Lineagelow Sca1+cKit high Cells

label_protocol: NuGen Ovation Biotin labeling system

growth_protocol: LKS cells were isolated from JAK2V617F or WT mice using high-speed multiparameter flow cytometry.

extract_protocol: RNA was extracted using Qiagen RNeasy Micro Kit according to manufacturers instruction. The RNA was amplified using a linear amplification protocol (Nugen Ovation V2 amplification system)

treatment_protocol: The cells were treated with RLT lysis buffer (Qiagen) containing beta-mercaptoethanol to stabilize RNA.

tag: cell type

value: Lineagelow Sca1+cKit high Cells

tag: genotype/variation

value: mutant JAK2V617F (heterozygous)


title: S. mutans UA159 0.5% sucrose biofilm 34h replicate 3


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 34h replicate 1


title: Rat parotid gland

description: Gene expression in normal rat parotid gland

source_name: parotid gland

value: parotid gland


title: S. mutans UA159 0.5% sucrose biofilm 34h replicate 4


title: ME15 24 hr control medium 1461896065_A

tag: incubation time

tag: treatment

value: control medium

tag: treatment dose u/ml

tag: ifna responder

tag: tgfb responder

tag: ifna and tgfb responder

tag: culture vessel

value: T25 flask

value: not same day

value: A


title: LSK cells from wild type mouse rep3

description: Gene expression data from LSK wild type mouse

value: Wild type


title: NOMID bone tumor 2

description: replicate 2

value: child

value: bone tumor


title: NOMID bone tumor 1

description: replicate 1


title: S. mutans UA159 1% sucrose biofilm 30h replicate 4

value: 30 hours

value: 1% sucrose

value: mid-log


title: LSK cells from wild type mouse rep4


title: S. mutans UA159 1% sucrose biofilm 30h replicate 3


title: S. mutans UA159 1% sucrose biofilm 30h replicate 2


title: LSK cells from heterozygous JAK2V617F mouse rep2


title: S. mutans UA159 1% sucrose biofilm 30h replicate 1


title: S. mutans UA159 0.5% sucrose biofilm 34h replicate 1

value: 34 hours


title: LSK cells from heterozygous JAK2V617F mouse rep3


title: LSK cells from wild type mouse rep2


title: LSK cells from heterozygous JAK2V617F mouse rep1


title: LSK cells from wild type mouse rep1


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 30h replicate 4

value: 0.5% sucrose + 1% starch


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 30h replicate 1


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 30h replicate 3


title: S. mutans UA159 0.5% sucrose biofilm 30h replicate 4


title: S. mutans UA159 0.5% sucrose biofilm 30h replicate 2


title: S. mutans UA159 1% sucrose biofilm 24h replicate 4

value: 24 hours


title: S. mutans UA159 0.5% sucrose biofilm 30h replicate 3

value: 0.5% sucrose


title: S. mutans UA159 1% sucrose biofilm 24h replicate 2


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 24h replicate 1


title: Media+DMSO+LPS rep 3

city: Ames

first: Diane

last: Birt

state: IA

address: 215 Mackay Iowa State University

department: Food Science and Human Nutrition

institute: Iowa State University

description: Gene expression data from macrophages treated with DMSO vehicle control and LPS

hyb_protocol: After fragmentation, 15 ug of labeled cRNA were hybridized for 16 hr at 45°C on GeneChip mouse expression set 430 assay (Affymatrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed using a Genechip Scanner 3000 7G (Affymatrix).

data_processing: The data were analyzed in R/Bioconductor 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: RAW264.7 mouse macrophage treated with DMSO and LPS

label_protocol: RNA was labeled using the one-cycle target labeling and control reagent package according to manufacturer's protocol (Affymatrix)

growth_protocol: RAW 264.7 mouse macrophages were grown in high-glucose Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum, 1.5g/L sodium bicarbonate and 100IU/mL penicillin/streptomycin at 37°C under 5% CO2. Cells were passaged or plated for treatment upon reaching 80% confluency.

extract_protocol: Cells were washed twice with phosphate buffered saline on ice and collected. Trizol (Invitrogen) method was used to extract RNA followed by purification using an Rneasy kit (QIagen)

treatment_protocol: The cells were treated with solvent control (0.1% DMSO in media), H. perforatum sub-fraction at 10 ug/mL, or 4-component-system composed of 0,07 uM amentoflavone, 0.08 uM quercetin, 0.2 uM chlorogenic acid, and 0.03 uM pseudohypericin, with or without 10 ug/mL LPS induction for 8 h. Treatments were applied in dark followed by a 30 min exposure to ambient light before plates were moved back to the incubator.

tag: cell line

value: Media + DMSO + LPS


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 24h replicate 4


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 24h replicate 2


title: S. mutans UA159 1% sucrose biofilm 24h replicate 1


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 24h replicate 3


title: Fraction rep 3

description: Gene expression data from macrophages treated with H.perforatum fraction

source_name: RAW264.7 mouse macrophage treated with fraction

value: Fraction


title: Fraction+LPS rep 3

description: Gene expression data from macrophages treated with H.perforatum fraction and LPS

source_name: RAW264.7 mouse macrophage treated with fraction and LPS

value: Fraction + LPS


title: 4CS rep 3

description: Gene expression data from macrophages treated with the four component system

source_name: RAW264.7 mouse macrophage treated with 4CS

value: 4CS (0.07 uM amentoflavone, 0.08 uM quercetin, 0.2 uM chlorogenic acid, and 0.03 uM pseudohypericin)


title: S. mutans UA159 0.5% sucrose biofilm 24h replicate 2


title: S. mutans UA159 0.5% sucrose biofilm 24h replicate 3


title: S. mutans UA159 0.5% sucrose biofilm 24h replicate 4


title: Media+DMSO rep 3

description: Gene expression data from macrophages treated with DMSO vehicle control

source_name: RAW264.7 mouse macrophage treated with DMSO

value: Media + DMSO


title: 4CS+LPS rep 3

description: Gene expression data from macrophages treated with the four component system and LPS

source_name: RAW264.7 mouse macrophage treated with 4CS and LPS

value: 4CS (0.07 uM amentoflavone, 0.08 uM quercetin, 0.2 uM chlorogenic acid, and 0.03 uM pseudohypericin) + LPS


title: S. mutans UA159 0.5% sucrose biofilm 24h replicate 1


title: 4CS+LPS rep 2


title: Media+DMSO+LPS rep 2


title: 4CS rep 2


title: S. mutans UA159 1% sucrose biofilm 21h replicate 4

value: 21 hours


title: Fraction+LPS rep 2


title: S. mutans UA159 1% sucrose biofilm 21h replicate 3


title: S. mutans UA159 1% sucrose biofilm 21h replicate 2


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 21h replicate 2


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 21h replicate 3


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 21h replicate 4


title: S. mutans UA159 1% sucrose biofilm 21h replicate 1


title: S. mutans UA159 0.5% sucrose biofilm 21h replicate 4


title: S. mutans UA159 0.5% sucrose biofilm 21h replicate 2


title: S. mutans UA159 0.5% sucrose biofilm 21h replicate 1


title: Fraction rep 2


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 21h replicate 1


title: S. mutans UA159 0.5% sucrose biofilm 21h replicate 3


title: Media+DMSO rep 2


title: Fraction rep 1


title: Media+DMSO rep 1


title: Media+DMSO+LPS rep 1


title: 4CS+LPS rep 1


title: Fraction+LPS rep 1


title: 4CS rep 1


title: Liver_Tob1KO_24hr_rep2

city: Boston

first: Hasan

middle: Huseyin

last: Otu

address: 4 Blackfan Circle Rm. 238

department: Medicine

institute: Harvard Medical School

description: Gene expression data from Tob1 null mouse liver at 24hr. After 2/3 hepatoctamy

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: CEL files were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM) mismatch (MM) difference model.

source_name: Liver, Tob1 null, 24hr after 2/3 hepatectomy

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

growth_protocol: Tob1 null mice on a C57BL/6 background were a generous gift from Dr. Indrani Bagchi (University of Ilinois at Urbana-Champaign).  These mice are derived from a line produced and maintained by Dr. Tadashi Yamamoto. Animals were maintained in a pathogenfree facility administered by Harvard Medical School in accordance with the institutional guidelines of Harvard Medical School and Beth Israel Deaconess Medical Center.

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

treatment_protocol: All surgeries were performed according to the National Institutes of Health guidelines for the humane treatment of laboratory animals and with approval of the Harvard Institutional Animal Care and Use Committee. Mice mice were anesthetized with 60mg/kg ketamine (Hospira) and 7mg/kg xylazine (Phoenix Pharmaceuticals), and positioned supine. A transverse incision was made inferior to the xiphoid process, which was excised. The median and left lateral lobes of the liver were eviscerated and ligated. At tissue recovery, mice were anesthetized and weighed. Livers were excised, rinsed, blotted and weighed. Sections were snap frozen in liquid nitrogen, fixed in 10% neutral buffered formalin or preserved in RNAlater (Qiagen). Mortality was less than 5% and not associated with a particular genoptype.

value: male

value: 7-10 weeks

tag: tissue

value: Liver

value: Tob1 null


title: Liver_Tob1KO_24hr_rep1

tag: age


title: N2 vs ok165 (rep3)

city: Salt Lake City

first: Bargavi

last: Thyagarajan

state: UT

address: Huntsman Cancer Institute, 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

hyb_protocol: Agilent Two-color GE Hyb/Wash Protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing: Images from the microarray scanner were processed in Agilent Feature Extraction software version 8.5.1.1. Lowess normalized log base 10 ratios were produced, and were converted to log base 2.

organism: Caenorhabditis elegans

source_name: L4 larval stage WT whole worms

label_protocol: Agilent Two-Color LRILAK Labeling Protocol

growth_protocol: Standard C. elegans growth protocols on plates were followed. Adult worms were treated with hypochlorite to obtain synchronized progeny. L4 stage larvae were used for RNA extraction and gene expression profiling

extract_protocol: Trizol extraction and phenol/chloroform extraction were performed to obtain total RNA from worm samples. Rneasy kit (Qiagen) was used to clean-up the RNA sample and to perform Dnase treatment.

treatment_protocol: Standard C. elegans growth protocols were used. The worms were grown on plates with OP50 bacteria at 20C

value: N2 (wild type)

tag: developmental stage

value: L4 larval stage

source_name: L4 larval stage ets-4(ok165) mutant whole worms


title: N2 vs uz1 (rep3)

source_name: L4 larval stage ets-4(uz1) mutant whole worms


title: Experiment 2, Blastomere pair H, Cell 2

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

description:
Experiment 2, blastomere pair H, cell 2.
Exp2H2

hyb_protocol: Purified cRNA (1 µg) was fragmented to uniform size and applied to Agilent 4x44K Whole Mouse Genome microarrays (Design ID 14868, Agilent Technologies, Santa Clara, CA) in hybridization buffer. All fragmented samples were visualized on the Agilent Bioanalyzer to verify complete fragmentation to ~0.1 kb size before the sample was applied to the array. Arrays were hybridized at 65° C for 17 h on a rotating incubator and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA). To compare individual expression values across arrays, raw intensity data from each gene probe was normalized to the 75th percentile intensity of probes above background on each array and further scaled assuming maximum correlation for all genes within and across pairs.

source_name: blastomere cell

label_protocol: Labeled cRNA was prepared from each RNA sample. Briefly, the Poly(A)+ RNA population within total RNA was amplified  by using Arcturus RiboAmp HS reagents (Molecular Devices, Sunnyvale, CA)  as described by others (Somers, Smith et al. 2006; Jones, Cram et al. 2008). After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed with T7 RNA polymerase.  The resulting cRNA was again assayed by spectrophotometry and on the Agilent Bioanalyzer.

growth_protocol: Embryos were derived from CF-1 females by natural breeding. CF-1 stud males were introduced to the female mice at 17.00 h, and females selected for retrieval of 2-cell stage embryos between 10.00 and 11.00 h the day following observation of the copulatory plug, i.e. ~36 h post coitus, pc.  Oviducts were flushed in CZB-Hepes buffer (Chatot, Ziomek et al. 1989) lacking glucose (mCZB-Hepes) to collect embryos. Micromanipulation of embryos was performed under an inverted microscope (Nikon, DIAPHOT-300) equipped with a standard micromanipulation system (Leitz, Model M).  Two-cell stage embryos were transferred to 2 µl microdrops of Ca+, Mg+ free PBS supplemented with 0.1% polyvinyl alcohol (PBS-PVA), which were covered with mineral oil.  An embryo was secured by using a holding pipette and a slit made in the ZP close to the side of one blastomere by means of a sharp glass needle.  The blunt tip of a glass rod was then used to put pressure on the ZP-enclosed embryo, thereby allowing the blastomere closest to the slit to be squeezed out, generally without apparent damage.  The second blastomere was recovered in a similar manner.

extract_protocol: Total RNA was isolated by using the RNAqueous-Micro® Technology (AM1931; Applied BioSystems), as described by the manufacturer. The procedure employs an initial extraction in guanidinium thiocyanate solution, dilution in ethanol solution, and purification on an RNA-binding glass fiber filter. The concentrated RNA was eluted from the column and assessed for quantity and quality on an Agilent Bioanalyzer with the RNA6000 Pico Lab Chip (Agilent Technologies).

value: 2-cell embryos ~36h post coitus

value: blastomere cell


title: Liver_normal_24hr_rep1

description: Gene expression data from normal mouse liver at 24hr. After 2/3 hepatoctamy

source_name: Liver, normal, 24hr after 2/3 hepatectomy

value: Wild Type


title: Experiment 2, Blastomere pair G, Cell 2

description:
Experiment 2, blastomere pair G, cell 2.
Exp2G2


title: N2 vs uz1 (rep2)


title: Liver_normal_24hr_rep2