title: Control of Proband 13

description: healthy control of proband 13, peripheral whole blood

source_name: whole blood sample from control of proband 13


title: Control of Proband 20

status: Public on Jun 20 2016

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description: healthy control of proband 20, peripheral whole blood

hyb_protocol: For each array, 750 ng of each Cy5- (human universal control) and Cy3-labeled sample cRNA were hybridized using the Agilent in situ hybridization kit. Hybridizations were performed for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent scanner. Images were quantified using Agilent Feature Extraction Software(v 11.0)

data_processing: Agilent Feature Extraction Software (v 11.0) was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Homo sapiens

source_name: whole blood sample from control of proband 20

label_protocol: A total of 500ng RNA was amplified and labeled using the Agilent fluorescent linear amplification kit following the manufacturer’s standard protocol.

extract_protocol: Total RNA extracted using the PAXgene RNA isolation kit in accordance with the manufacturer’s recommendations

tag: tissue

value: whole blood

source_name: Universal Reference RNA (Agilent, catalogue number: 740000)

tag: reference

value: 10 cell lines for human


title: Control of Proband 22

description: healthy control of proband 22, peripheral whole blood

source_name: whole blood sample from control of proband 22


title: Control of Proband 23

description: healthy control of proband 23, peripheral whole blood

source_name: whole blood sample from control of proband 23


title: Control of Proband 27

description: healthy control of proband 27, peripheral whole blood

source_name: whole blood sample from control of proband 27


title: Control of Proband 16

description: healthy control of proband 16, peripheral whole blood

source_name: whole blood sample from control of proband 16


title: Control of Proband 24

description: healthy control of proband 24, peripheral whole blood

source_name: whole blood sample from control of proband 24


title: Control of Proband 31

description: healthy control of proband 31, peripheral whole blood

source_name: whole blood sample from control of proband 31


title: Control of Proband 26

description: healthy control of proband 26, peripheral whole blood

source_name: whole blood sample from control of proband 26


title: Control of Proband 12

description: healthy control of proband 12, peripheral whole blood

source_name: whole blood sample from control of proband 12


title: Control of Proband 9

description: healthy control of proband 9, peripheral whole blood

source_name: whole blood sample from control of proband 9


title: Control of Proband 7

description: healthy control of proband 7, peripheral whole blood

source_name: whole blood sample from control of proband 7


title: Control of Proband 14

description: healthy control of proband 14, peripheral whole blood

source_name: whole blood sample from control of proband 14


title: Control of Proband 15

description: healthy control of proband 15, peripheral whole blood

source_name: whole blood sample from control of proband 15


title: Control of Proband 18

description: healthy control of proband 18, peripheral whole blood

source_name: whole blood sample from control of proband 18


title: Control of Proband 11

description: healthy control of proband 11, peripheral whole blood

source_name: whole blood sample from control of proband 11


title: Control of Proband 10

description: healthy control of proband 10, peripheral whole blood

source_name: whole blood sample from control of proband 10


title: Control of Proband 8

description: healthy control of proband 8, peripheral whole blood

source_name: whole blood sample from control of proband 8


title: Control of Proband 21

description: healthy control of proband 21, peripheral whole blood

source_name: whole blood sample from control of proband 21

source_name: Universal Reference RNA (Agilent, catalogue number: 740000)


title: Control of Proband 19

description: healthy control of proband 19, peripheral whole blood

source_name: whole blood sample from control of proband 19


title: Control of Proband 32

description: healthy control of proband 32, peripheral whole blood

source_name: whole blood sample from control of proband 32


title: Control of Proband 5

description: healthy control of proband 5, peripheral whole blood

source_name: whole blood sample from control of proband 5


title: Control of Proband 4

description: healthy control of proband 4, peripheral whole blood

source_name: whole blood sample from control of proband 4


title: Unaffected twin of Proband 24

description: unaffected twin of proband 24, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 24


title: Control of Proband 1

description: healthy control of proband 1, peripheral whole blood

source_name: whole blood sample from control of proband 1


title: Control of Proband 2

description: healthy control of proband 2, peripheral whole blood

source_name: whole blood sample from control of proband 2


title: Control of Proband 3

description: healthy control of proband 3, peripheral whole blood

source_name: whole blood sample from control of proband 3


title: Unaffected twin of Proband 31

description: unaffected twin of proband 31, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 31


title: Unaffected twin of Proband 30

description: unaffected twin of proband 30, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 30


title: Unaffected twin of Proband 22

description: unaffected twin of proband 22, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 22


title: Unaffected twin of Proband 27

description: unaffected twin of proband 27, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 27


title: Unaffected twin of Proband 33

description: unaffected twin of proband 33, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 33


title: Control of Proband 6

description: healthy control of proband 6, peripheral whole blood

source_name: whole blood sample from control of proband 6


title: Unaffected twin of Proband 19

description: unaffected twin of proband 19, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 19


title: Unaffected twin of Proband 21

description: unaffected twin of proband 21, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 21


title: Unaffected twin of Proband 18

description: unaffected twin of proband 18, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 18

source_name: Universal Reference RNA (Agilent, catalogue number: 740000)


title: Unaffected twin of Proband 16

description: unaffected twin of proband 16, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 16


title: Control of Proband 25

description: healthy control of proband 25, peripheral whole blood

source_name: whole blood sample from control of proband 25


title: Unaffected twin of Proband 32

description: unaffected twin of proband 32, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 32


title: Unaffected twin of Proband 23

description: unaffected twin of proband 23, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 23


title: Unaffected twin of Proband 20

description: unaffected twin of proband 20, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 20


title: Unaffected twin of Proband 26

description: unaffected twin of proband 26, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 26


title: Unaffected twin of Proband 28

description: unaffected twin of proband 28, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 28


title: Unaffected twin of Proband 14

description: unaffected twin of proband 14, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 14


title: Unaffected twin of Proband 17

description: unaffected twin of proband 17, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 17


title: Unaffected twin of Proband 29

description: unaffected twin of proband 29, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 29


title: Primary AML patient 10

status: Public on Jun 21 2016

city: Padova

first: Matteo

last: Zampini

state: PD

address: corso stati uniti 4

country: Italy

institute: Istituto di Ricerca Pediatrica (IRP)  Città della Speranza

description: Gene expression data from pediatric AML patient according to C/EBPδ expression level (gene-level)

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Affymetrix HTA 2.0 microarrays. The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in an Affymetrix Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Affymetrix.

scan_protocol: The Genechips were scanned with an Affymetrix 7G scanner according to manifacturer guidelines.

data_processing: The CEL files generated were analyzed through Affymetrix Expression Console Software (version 1.3) which normalizes array signals using a robust multiarray averaging (RMA) algorithm. Normalized data were analyzed using Transcriptome Analysis Console (TAC) 3.0 Software (Affymetrix). An unpaired t-test was applied to identify differentially expressed transcript genes between sample pairs and probes with P-values less than 0.01 and fold-change >2 were declared significant.

label: biotin

source_name: AML BM

label_protocol: According to the Affymetrix Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

extract_protocol: Total bone marrow RNA was extracted using TRIzol reagent (Invitrogen) according to manufacturer guidelines, quantified using UV spectroscopy (Nanodrop Technologies), and qualitatively assessed using an Agilent2100 Bioanalyzer (Agilent Technologies).

value: Bone Marrow

tag: fab

tag: c/ebpsigma quartile

tag: karyotypic aberration

value: t(8;21) RUNX1/RUNX1T1


title: Unaffected twin of Proband 13

description: unaffected twin of proband 13, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 13


title: Unaffected twin of Proband 15

description: unaffected twin of proband 15, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 15


title: Unaffected twin of Proband 12

description: unaffected twin of proband 12, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 12


title: Unaffected twin of Proband 10

description: unaffected twin of proband 10, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 10


title: Proband 33

description: proband 33 of 33, peripheral whole blood

source_name: whole blood sample from Proband 33


title: Proband 27

description: proband 27 of 33, peripheral whole blood

source_name: whole blood sample from Proband 27

source_name: Universal Reference RNA (Agilent, catalogue number: 740000)


title: Proband 32

description: proband 32 of 33, peripheral whole blood

source_name: whole blood sample from Proband 32


title: Unaffected twin of Proband 6

description: unaffected twin of proband 6, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 6


title: Unaffected twin of Proband 3

description: unaffected twin of proband 3, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 3


title: Proband 30

description: proband 30 of 33, peripheral whole blood

source_name: whole blood sample from Proband 30


title: Primary AML patient 08


title: Unaffected twin of Proband 9

description: unaffected twin of proband 9, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 9


title: Proband 24

description: proband 24 of 33, peripheral whole blood

source_name: whole blood sample from Proband 24


title: Unaffected twin of Proband 4

description: unaffected twin of proband 4, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 4


title: Proband 20

description: proband 20 of 33, peripheral whole blood

source_name: whole blood sample from Proband 20


title: Unaffected twin of Proband 1

description: unaffected twin of proband 1, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 1


title: Unaffected twin of Proband 2

description: unaffected twin of proband 2, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 2


title: Unaffected twin of Proband 11

description: unaffected twin of proband 11, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 11


title: Proband 25

description: proband 25 of 33, peripheral whole blood

source_name: whole blood sample from Proband 25


title: Unaffected twin of Proband 5

description: unaffected twin of proband 5, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 5


title: Proband 22

description: proband 22 of 33, peripheral whole blood

source_name: whole blood sample from Proband 22


title: Proband 26

description: proband 26 of 33, peripheral whole blood

source_name: whole blood sample from Proband 26


title: Proband 17

description: proband 17 of 33, peripheral whole blood

source_name: whole blood sample from Proband 17


title: Proband 23

description: proband 23 of 33, peripheral whole blood

source_name: whole blood sample from Proband 23

source_name: Universal Reference RNA (Agilent, catalogue number: 740000)


title: Unaffected twin of Proband 8

description: unaffected twin of proband 8, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 8


title: Proband 29

description: proband 29 of 33, peripheral whole blood

source_name: whole blood sample from Proband 29


title: Proband 21

description: proband 21 of 33, peripheral whole blood

source_name: whole blood sample from Proband 21


title: Proband 31

description: proband 31 of 33, peripheral whole blood

source_name: whole blood sample from Proband 31


title: Proband 28

description: proband 28 of 33, peripheral whole blood

source_name: whole blood sample from Proband 28


title: Proband 18

description: proband 18 of 33, peripheral whole blood

source_name: whole blood sample from Proband 18


title: Unaffected twin of Proband 7

description: unaffected twin of proband 7, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 7


title: Proband 6

description: proband 6 of 33, peripheral whole blood

source_name: whole blood sample from Proband 6


title: Proband 5

description: proband 5 of 33, peripheral whole blood

source_name: whole blood sample from Proband 5


title: Proband 8

description: proband 8 of 33, peripheral whole blood

source_name: whole blood sample from Proband 8


title: Proband 11

description: proband 11 of 33, peripheral whole blood

source_name: whole blood sample from Proband 11


title: RAS_RG_partial clear gut_-18hr_rep2

city: Edmonton

first: Kirst

last: King-Jones

state: Alberta

address: 11455 saskatchewan driver

department: Biological Sciences

country: Canada

institute: University of Alberta

description: This sample is of RasV12 ring gland of 8hours PPF. It is the second of three wild-type biological replicates used in this experiment.

hyb_protocol: Hybridization was performed by the Alberta Transplant Applied Genomics Centre, AB, Canada, following the standard protocol.

scan_protocol: Scanning was performed by the Alberta Transplant Applied  Genomics Centre, AB, Canada, following the standard operating protocol.

data_processing: The raw data (.pair file) was analyzed with Arraystar 4.0 (based on RMA: Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249). Background correction was carried out with the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.).

organism: Drosophila melanogaster

source_name: Drosophila melanogaster phm22_RasV12 ring gland 8hr PPF

label_protocol: Nucleic acid labeling was carried out by authors, following the standard operating protocol provided by Roche one-colour DNA labeling kit (Cat. No. 05223555001).

growth_protocol: Drosophila larvae were reared in the dark on yeast paste at 25°C. (Ou et al., PLoS Biology, 2011)

extract_protocol: Total RNA was extracted using TRIzol and the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen). RNA quality and concentration was determined by analysis with a NanoDrop-1000 spectrophotometer and an Agilent 2100 bioanalyzer at the Molecular Biology Service Unit (University of Alberta, Edmonton, Canada).

treatment_protocol: Genotypes: Samples 1-24: w1118. Samples 25-30: phantom-Gal4/w1118 (control cross). Samples 31-36: phantom-Gal4/RasV12 (constitutively active form of Ras. Samples 37-42: phantom-Gal4/Torso-RNAi.

tag: genotype

value: RasV12 overexpression

tag: phenotype

value: developmental acceleration

tag: accession

value: Ring gland, late third instar


title: Proband 14

description: proband 14 of 33, peripheral whole blood

source_name: whole blood sample from Proband 14


title: Proband 9

description: proband 9 of 33, peripheral whole blood

source_name: whole blood sample from Proband 9


title: RAS_RG_partial clear gut_-18hr_rep3

description: This sample is of RasV12 ring gland of 8hours PPF. It is the last of three wild-type biological replicates used in this experiment.


title: Proband 12

description: proband 12 of 33, peripheral whole blood

source_name: whole blood sample from Proband 12


title: Proband 15

description: proband 15 of 33, peripheral whole blood

source_name: whole blood sample from Proband 15


title: Proband 7

description: proband 7 of 33, peripheral whole blood

source_name: whole blood sample from Proband 7

source_name: Universal Reference RNA (Agilent, catalogue number: 740000)


title: Proband 13

description: proband 13 of 33, peripheral whole blood

source_name: whole blood sample from Proband 13


title: Proband 10

description: proband 10 of 33, peripheral whole blood

source_name: whole blood sample from Proband 10


title: Proband 3

description: proband 3 of 33, peripheral whole blood

source_name: whole blood sample from Proband 3


title: RAS_RG_partial clear gut_-18hr_rep1

description: This sample is of RasV12 ring gland of 8hours PPF. It is the first of three wild-type biological replicates used in this experiment.


title: Proband 16

description: proband 16 of 33, peripheral whole blood

source_name: whole blood sample from Proband 16


title: Proband 19

description: proband 19 of 33, peripheral whole blood

source_name: whole blood sample from Proband 19


title: Torso_RG_blue gut_-18hr_rep1

description: This sample is of Torso-RNAi ring gland of 18hours PPF. It is the first of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster phm22_Torso-RNAi ring gland 18hr PPF

value: RNAi knockdown of Torso

value: developmental delay


title: Proband 2

description: proband 2 of 33, peripheral whole blood

source_name: whole blood sample from Proband 2


title: Proband 4

description: proband 4 of 33, peripheral whole blood

source_name: whole blood sample from Proband 4


title: RAS_RG_blue gut_-18hr_rep3

description: This sample is of RasV12 ring gland of 18hours PPF. It is the last of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster phm22_RasV12 ring gland 18hr PPF

value: Ring gland, mid third instar


title: PHMW_RG_partial clear gut_-18hr_rep1

description: This sample is of phm22Gal4 control cross ring gland of 8hours PPF. It is the first of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster phm22_w1118 ring gland 8hr PPF

value: control Gal4 driver cross to wildtype

value: normal


title: PHMW_RG_blue gut_-18hr_rep3

description: This sample is of phm22Gal4 control cross ring gland of 18hours PPF. It is the last of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster phm22_w1118 ring gland 18hr PPF


title: PHMW_RG_blue gut_-18hr_rep1

description: This sample is of phm22Gal4 control cross ring gland of 18hours PPF. It is the first of three wild-type biological replicates used in this experiment.


title: RAS_RG_blue gut_-18hr_rep1

description: This sample is of RasV12 ring gland of 18hours PPF. It is the first of three wild-type biological replicates used in this experiment.


title: PHMW_RG_blue gut_-18hr_rep2

description: This sample is of phm22Gal4 control cross ring gland of 18hours PPF. It is the second of three wild-type biological replicates used in this experiment.


title: WT_WB_36HRL3_rep2

description: This sample is of wild-type whole larvae of 36hours L3. It is the second of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster w1118 wildtype whole body 36hours L3

value: Wild-type

value: Whole larva, larval third instar


title: RAS_RG_blue gut_-18hr_rep2

description: This sample is of RasV12 ring gland of 18hours PPF. It is the second of three wild-type biological replicates used in this experiment.


title: PHMW_RG_partial clear gut_-18hr_rep3

description: This sample is of phm22Gal4 control cross ring gland of 8hours PPF. It is the last of three wild-type biological replicates used in this experiment.


title: WT_WB_36HRL3_rep3

description: This sample is of wild-type whole larvae of 36hours L3. It is the last of three wild-type biological replicates used in this experiment.


title: PHMW_RG_partial clear gut_-18hr_rep2

description: This sample is of phm22Gal4 control cross ring gland of 8hours PPF. It is the second of three wild-type biological replicates used in this experiment.


title: WT_WB_24HRL3_rep3

description: This sample is of wild-type whole larvae of 24hours L3. It is the last of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster w1118 wildtype whole body 24hours L3


title: WT_WB_36HRL3_rep1

description: This sample is of wild-type whole larvae of 36hours L3. It is the first of three wild-type biological replicates used in this experiment.


title: WT_WB_4HRL3_rep2

description: This sample is of wild-type whole larvae of 4hours L3. It is the second of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster w1118 wildtype whole body 4hours L3


title: Proband 1

description: proband 1 of 33, peripheral whole blood

source_name: whole blood sample from Proband 1


title: Unaffected twin of Proband 25

description: unaffected twin of proband 25, peripheral whole blood

source_name: whole blood sample from unaffected twin of proband 25


title: WT_RG_36HRL3_rep3

description: This sample is of wild-type ring gland of 36hours L3. It is the last of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster w1118 wildtype ring gland 36hours L3

value: Ring gland, larval third instar


title: HMVEC-L_10ng CTSL_4hr_Replicate 3

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

description:
Gene expression in HMVEC-L cells exposed to CTSL-Replicate 3
CTSL 3

hyb_protocol: 5.5 ug labeled and fragmented cDNA were hybridized onto GeneChip® Human Transcriptome Array 2.0 for 16 hrs.

scan_protocol: Chips were washed in a FS 450 fluidics station and then scanned on GeneChip® Scanner 3000 7G following Affymetrix recommendations

data_processing: Data was normalized using RMA as implemented in Partek and later analyzed using R-Bioconductor software packages

source_name: HMVEC-L, 10ng CTSL

label_protocol: 200 ng total RNA was labeled using GeneChip® WT PLUS Reagent Kit (WT PLUS Kit) from Affymetrix following manufacturer's instructions

growth_protocol: HMVEC-L cells were cultured in EGM2 MV media supplied by Lonza (CC-3202). Experiment was performed at passage # 2

extract_protocol: Total RNA was extracted using RNeasy Plus Mini from QIAGEN

treatment_protocol: To evaluate the effect of CTSL on endothelial cell signaling, human microvascular endothelial cells were exposed to 10 ng/ml of purified human Cathepsin L. 4hr later, cells were lysed

tag: cell line

value: HMVEC-L

tag: cell type

value: Primary culture of microvascular endothelial cells

tag: passage #

tag: treatment

value: CTSL


title: WT_WB_8HRL3_rep1

description: This sample is of wild-type whole larvae of 8hours L3. It is the first of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster w1118 wildtype whole body 8hours L3


title: HMVEC-L_Control_Replicate 3

description:
Gene expression in HMVEC-L cells exposed to vehicle-Replicate 3
Control 3

source_name: HMVEC-L, Control

value: Control


title: WT_WB_4HRL3_rep1

description: This sample is of wild-type whole larvae of 4hours L3. It is the first of three wild-type biological replicates used in this experiment.


title: WT_RG_8HRL3_rep2

description: This sample is of wild-type ring gland of 8hours L3. It is the second of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster w1118 wildtype ring gland 8hours L3


title: WT_RG_36HRL3_rep2

description: This sample is of wild-type ring gland of 36hours L3. It is the second of three wild-type biological replicates used in this experiment.


title: WT_WB_24HRL3_rep2

description: This sample is of wild-type whole larvae of 24hours L3. It is the second of three wild-type biological replicates used in this experiment.


title: HMVEC-L_10ng CTSL_4hr_Replicate 4

description:
Gene expression in HMVEC-L cells exposed to CTSL-Replicate 4
CTSL 4


title: WT_RG_24HRL3_rep3

description: This sample is of wild-type ring gland of 24hours L3. It is the last of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster w1118 wildtype ring gland 24hours L3


title: WT_RG_8HRL3_rep1

description: This sample is of wild-type ring gland of 8hours L3. It is the first of three wild-type biological replicates used in this experiment.


title: HMVEC-L_10ng CTSL_4hr_Replicate 2

description:
Gene expression in HMVEC-L cells exposed to CTSL-Replicate 2
CTSL 2


title: HMVEC-L_Control_Replicate 1

description:
Gene expression in HMVEC-L cells exposed to vehicle-Replicate 1
Control 1


title: HMVEC-L_Control_Replicate 2

description:
Gene expression in HMVEC-L cells exposed to vehicle-Replicate 2
Control 2


title: WT_WB_8HRL3_rep3

description: This sample is of wild-type whole larvae of 8hours L3. It is the last of three wild-type biological replicates used in this experiment.


title: RA-MSCs-3

city: Hiroshima

first: katsumi

last: Fujimoto

address: 1-2-3 Kasumi, Minami-ku

country: Japan

institute: Hiroshima University

hyb_protocol: The hybridization was performed (Hybridization Oven 640 110V, Affymetrix 800138) according to the manufacturer's instructions (Expression Analysis Technical Manual, 701021 Rev. 5, Section2 Eukaryotic Sample and Array Processing, Chapter2 Eukaryotic Target Hybridization, Affymetrix). GeneChips were washed and stained in the Fluidics Station 450 (Affymetrix 00-0079).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix 00-0074).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method (Scaling Factor = 1, Normalization Value = 1, Detection Call a1 = 0.05, a2 = 0.065, Tau = 0.015).

source_name: rheumatoid arthritis synovium MSC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

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

value: synovial

tag: Sex

value: female

tag: age

value: 72 years

tag: disease

value: rheumatoid arthritis


title: HMVEC-L_Control_Replicate 4

description:
Gene expression in HMVEC-L cells exposed to vehicle-Replicate 4
Control 4


title: WT_RG_36HRL3_rep1

description: This sample is of wild-type ring gland of 36hours L3. It is the first of three wild-type biological replicates used in this experiment.


title: RA-MSCs-2

value: 40 years


title: WT_RG_4HRL3_rep1

description: This sample is of wild-type ring gland of 4hours L3. It is the first of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster w1118 wildtype ring gland 4hours L3


title: WT_WB_4HRL3_rep3

description: This sample is of wild-type whole larvae of 4hours L3. It is the last of three wild-type biological replicates used in this experiment.


title: HMVEC-L_10ng CTSL_4hr_Replicate 1

description:
Gene expression in HMVEC-L cells exposed to CTSL-Replicate 1
CTSL 1


title: Torso_RG_partial clear gut_-18hr_rep2

description: This sample is of Torso-RNAi ring gland of 8hours PPF. It is the second of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster phm22_Torso-RNAi ring gland 8hr PPF

value: RNAi knockdown of Torso

value: Ring gland, late third instar


title: Torso_RG_partial clear gut_-18hr_rep1

description: This sample is of Torso-RNAi ring gland of 8hours PPF. It is the first of three wild-type biological replicates used in this experiment.

value: developmental delay


title: WT_RG_8HRL3_rep3

description: This sample is of wild-type ring gland of 8hours L3. It is the last of three wild-type biological replicates used in this experiment.


title: Torso_RG_blue gut_-18hr_rep3

description: This sample is of Torso-RNAi ring gland of 18hours PPF. It is the last of three wild-type biological replicates used in this experiment.

source_name: Drosophila melanogaster phm22_Torso-RNAi ring gland 18hr PPF


title: WT_RG_24HRL3_rep1

description: This sample is of wild-type ring gland of 24hours L3. It is the first of three wild-type biological replicates used in this experiment.


title: WT_RG_24HRL3_rep2

description: This sample is of wild-type ring gland of 24hours L3. It is the second of three wild-type biological replicates used in this experiment.


title: WT_WB_8HRL3_rep2

description: This sample is of wild-type whole larvae of 8hours L3. It is the second of three wild-type biological replicates used in this experiment.


title: WT_RG_4HRL3_rep2

description: This sample is of wild-type ring gland of 4hours L3. It is the second of three wild-type biological replicates used in this experiment.


title: Torso_RG_blue gut_-18hr_rep2

description: This sample is of Torso-RNAi ring gland of 18hours PPF. It is the second of three wild-type biological replicates used in this experiment.


title: WT_WB_24HRL3_rep1

description: This sample is of wild-type whole larvae of 24hours L3. It is the first of three wild-type biological replicates used in this experiment.


title: RA-MSCs-1

value: 30 years


title: OA-MSCs-3

source_name: osteoarthritis arthritis synovium MSC

value: male

value: 61 years

value: osteoarthritis arthritis


title: OA-MSCs-2

value: 54 years


title: A-MSCs-3

source_name: adipose tissue mesenchymal stem cell

value: adipose

value: 41 years


title: OA-MSCs-1


title: H1650_GSK3A_1_knockdown

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

description:
replicate 1
H1650_GSK3A_1_HH_7196801027_G.mean

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Processing of the Illumina microarray data was performed using open source Illumina microarray pipeline lumi (Du et al. Bioinformatics 2008)

source_name: H1650 cell line

label_protocol: 100ng of total RNA was amplified and Biotin-labeled according to manufacturer’s instructions

growth_protocol: The human NSCLC cell line H1650 was purchased from ATCC (Manassas, VA) and authenticated. The single mutation was confirmed in H1650 (EGFR, E746 A750del) using MassARRAYtechnology (OncoCarta v1.0 Genotyping, Sequenom, San Diego, CA). H1650 cells were cultured in RPMI-1640 medium with10% FBS (Life Technologies, Carlsbad, CA).  Per well 2 × 105 cells were seeded on 6-well plates and cultured for 24h

extract_protocol: Total RNA from the 72 cell line extracts was isolated using RNeasy protocol (Qiagen, Hilden, Germany) according to the manufacturer’s instructions

treatment_protocol: Gene knockdown in H1650 cells was performed using pooled siRNAs (40nM) against the genes  BCL10, EGFR, ESPL1, MTOR, GSK3A, GSK3B, ITGB4, LEPR, PIK3C3, PRKAA1, PRKAB1, RAF1, RPS6KA1, RPS6KB1, SRC, STK11, TRUB2, TSC1, TSC2, and WDR3, and transfection reagent RNAiMax, including Mock and different non-template controls (DNTC, AllStar) for 48h.

tag: tumor type

value: lung adenocarcinoma

tag: gene knockdown

tag: chip experiment batch


title: Torso_RG_partial clear gut_-18hr_rep3

description: This sample is of Torso-RNAi ring gland of 8hours PPF. It is the last of three wild-type biological replicates used in this experiment.


title: H1650_GSK3A_2_knockdown

description:
replicate 1
H1650_GSK3A_2_HH_7196801027_H.mean


title: A-MSCs-2

tag: tissue

value: 37 years


title: H1650_GSK3B_1_knockdown

description:
replicate 1
H1650_GSK3B_1_HH_7196801027_D.mean


title: H1650_RAF1_2_knockdown

description:
replicate 1
H1650_RAF1_2_HH_7196801027_K.mean


title: DPCs-4

source_name: dental pulp cell

value: permanent molar

value: 24 years


title: H1650_TSC1_2_knockdown

description:
replicate 1
H1650_TSC1_2_HH_7196801027_B.mean


title: WT_RG_4HRL3_rep3

description: This sample is of wild-type ring gland of 4hours L3. It is the last of three wild-type biological replicates used in this experiment.

value: Wild-type

value: normal

value: Ring gland, larval third instar


title: A-MSCs-1

value: female

value: 32 years


title: H1650_GSK3A_3_knockdown

description:
replicate 1
H1650_GSK3A_3_HH_7196801027_I.mean


title: H1650_RAF1_3_knockdown

description:
replicate 1
H1650_RAF1_3_HH_7196801027_L.mean


title: H1650_RAF1_1_knockdown

description:
replicate 1
H1650_RAF1_1_HH_7196801027_J.mean


title: H1650_TSC2_2_knockdown

description:
replicate 1
H1650_TSC2_2_HH_7196801025_K.mean


title: H1650_GSK3B_3_knockdown

description:
replicate 1
H1650_GSK3B_3_HH_7196801027_F.mean


title: DPCs-3

value: 25 years


title: H1650_TSC1_1_knockdown

description:
replicate 1
H1650_TSC1_1_HH_7196801027_A.mean


title: H1650_TSC2_1_knockdown

description:
replicate 1
H1650_TSC2_1_HH_7196801025_J.mean


title: DPCs-2


title: H1650_GSK3B_2_knockdown

description:
replicate 1
H1650_GSK3B_2_HH_7196801027_E.mean


title: H1650_TSC1_3_knockdown

description:
replicate 1
H1650_TSC1_3_HH_7196801027_C.mean


title: H1650_P90S6K_2_knockdown

description:
replicate 1
H1650_P90S6K_2_HH_7196801025_H.mean


title: H1650_P90S6K_1_knockdown

description:
replicate 1
H1650_P90S6K_1_HH_7196801025_G.mean


title: H1650_LEPR_1_knockdown

description:
replicate 1
H1650_LEPR_1_HH_7196801025_D.mean

value: LEPR


title: H1650_LEPR_3_knockdown

description:
replicate 1
H1650_LEPR_3_HH_7196801025_F.mean


title: H1650_TRUB2_2_knockdown

description:
replicate 1
H1650_TRUB2_2_HH_7196801025_B.mean


title: H1650_LKB1_1_knockdown

description:
replicate 1
H1650_LKB1_1_HH_7196801023_G.mean


title: H1650_LEPR_2_knockdown

description:
replicate 1
H1650_LEPR_2_HH_7196801025_E.mean


title: H1650_TRUB2_1_knockdown

description:
replicate 1
H1650_TRUB2_1_HH_7196801025_A.mean


title: H1650_PIK3C3_2_knockdown

description:
replicate 1
H1650_PIK3C3_2_HH_7196801023_K.mean


title: H1650_PIK3C3_3_knockdown

description:
replicate 1
H1650_PIK3C3_3_HH_7196801023_L.mean


title: H1650_LKB1_3_knockdown

description:
replicate 1
H1650_LKB1_3_HH_7196801023_I.mean


title: H1650_TRUB2_3_knockdown

description:
replicate 1
H1650_TRUB2_3_HH_7196801025_C.mean


title: H1650_P90S6K_3_knockdown

description:
replicate 1
H1650_P90S6K_3_HH_7196801025_I.mean


title: H1650_PIK3C3_1_knockdown

description:
replicate 1
H1650_PIK3C3_1_HH_7196801023_J.mean


title: H1650_Mock_2_control_2

description:
replicate 1
H1650_Mock_2_HH_7196801023_E.mean

value: Mock control


title: H1650_TSC2_3_knockdown

description:
replicate 1
H1650_TSC2_3_HH_7196801025_L.mean


title: H1650_DNTC_2_control

description:
replicate 1
H1650_DNTC_2_HH_7196801023_B.mean

value: DNTC non-template control


title: H1650_LKB1_2_knockdown

description:
replicate 1
H1650_LKB1_2_HH_7196801023_H.mean


title: H1650_PRKAA1_1_knockdown

description:
replicate 1
H1650_PRKAA1_1_HH_6235821042_J.mean


title: H1650_DNTC_3_control

description:
replicate 1
H1650_DNTC_3_HH_7196801023_C.mean


title: H1650_DNTC_1_control

description:
replicate 1
H1650_DNTC_1_HH_7196801023_A.mean


title: H1650_WDR3_1_knockdown

description:
replicate 1
H1650_WDR3_1_HH_6235821042_G.mean


title: H1650_PRKAA1_3_knockdown

description:
replicate 1
H1650_PRKAA1_3_HH_6235821042_L.mean


title: H1650_WDR3_2_knockdown

description:
replicate 1
H1650_WDR3_2_HH_6235821042_H.mean


title: H1650_PRKAA1_2_knockdown

description:
replicate 1
H1650_PRKAA1_2_HH_6235821042_K.mean


title: H1650_Mock_1_control_2

description:
replicate 1
H1650_Mock_1_HH_7196801023_D.mean


title: H1650_Mock_3_control_2

description:
replicate 1
H1650_Mock_3_HH_7196801023_F.mean


title: H1650_BCL10_3_knockdown

description:
replicate 1
H1650_BCL10_3_HH_6235821039_F.mean


title: H1650_p70S6K_1_knockdown

description:
replicate 1
H1650_p70S6K_1_HH_6235821042_A.mean


title: H1650_PRKAB1_2_knockdown

description:
replicate 1
H1650_PRKAB1_2_HH_6235821039_B.mean


title: H1650_mTOR_2_knockdown

description:
replicate 1
H1650_mTOR_2_HH_6235821022_K.mean

value: MTOR


title: H1650_EGFR_1_knockdown

description:
replicate 1
H1650_EGFR_1_HH_6235821039_G.mean

value: EGFR mutation


title: H1650_EGFR_2_knockdown

description:
replicate 1
H1650_EGFR_2_HH_6235821039_H.mean


title: H1650_SRC_1_knockdown

description:
replicate 1
H1650_SRC_1_HH_6235821042_D.mean

value: SRC


title: H1650_ESPL1_2_knockdown

description:
replicate 1
H1650_ESPL1_2_HH_6235821039_K.mean


title: H1650_PRKAB1_3_knockdown

description:
replicate 1
H1650_PRKAB1_3_HH_6235821039_C.mean


title: H1650_ESPL1_1_knockdown

description:
replicate 1
H1650_ESPL1_1_HH_6235821039_J.mean


title: H1650_SRC_2_knockdown

description:
replicate 1
H1650_SRC_2_HH_6235821042_E.mean


title: H1650_SRC_3_knockdown

description:
replicate 1
H1650_SRC_3_HH_6235821042_F.mean


title: H1650_ESPL1_3_knockdown

description:
replicate 1
H1650_ESPL1_3_HH_6235821039_L.mean


title: H1650_WDR3_3_knockdown

description:
replicate 1
H1650_WDR3_3_HH_6235821042_I.mean


title: H1650_PRKAB1_1_knockdown

description:
replicate 1
H1650_PRKAB1_1_HH_6235821039_A.mean


title: H1650_p70S6K_2_knockdown

description:
replicate 1
H1650_p70S6K_2_HH_6235821042_B.mean


title: H1650_EGFR_3_knockdown

description:
replicate 1
H1650_EGFR_3_HH_6235821039_I.mean


title: H1650_mTOR_1_knockdown

description:
replicate 1
H1650_mTOR_1_HH_6235821022_J.mean


title: H1650_p70S6K_3_knockdown

description:
replicate 1
H1650_p70S6K_3_HH_6235821042_C.mean


title: H1650_BCL10_2_knockdown

description:
replicate 1
H1650_BCL10_2_HH_6235821039_E.mean


title: H1650_BCL10_1_knockdown

description:
replicate 1
H1650_BCL10_1_HH_6235821039_D.mean


title: H1650_mTOR_3_knockdown

description:
replicate 1
H1650_mTOR_3_HH_6235821022_L.mean


title: H1650_ITGB4_3_knockdown

description:
replicate 1
H1650_ITGB4_3_HH_6235821022_I.mean


title: H1650_ITGB4_2_knockdown

description:
replicate 1
H1650_ITGB4_2_HH_6235821022_H.mean


title: TGFb [7911798012_E]

status: Public on Jun 19 2016

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: replicate 2

data_processing: The data were normalized using quantile normalisation in Partek Genomic Suite

organism: Mus musculus

source_name: primary microglia, TGFb treatment 48h

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit

growth_protocol: Microglia were prepared from newborn C57BL/6J mice and cultured in DMEM, containing 9 % heat-inactivated FCS, 0.9 % non-essential amino acids, 0.9 % penicillin/streptomycin, and 0.05 mM β-mercaptoethanol, at 37°C and 8 % CO2.

extract_protocol: Cells were lysed in TRIZOL (Invitrogen) and total RNA was extracted according to the manufacturers’ protocol

treatment_protocol: Microglia were either left untreated or stimulated with a combination of LPS+IFNg (100+20 ng/ml), IL4 (100U/ml), or TGFb (20ng/ml) for 16 or 48h

tag: strain

value: brain

tag: developmental stage

value: neonatal

value: microglia

value: TGFb


title: unstimuliert [7911798014_F]

description: replicate 3

source_name: primary microglia, untreated


title: H1650_AllStar_1_control

description:
replicate 1
H1650_AllStar_1_HH_6235821022_D.mean

value: lung adenocarcinoma

value: AllStar non-template control


title: H1650_ITGB4_1_knockdown

description:
replicate 1
H1650_ITGB4_1_HH_6235821022_G.mean


title: unstimuliert [7911798014_E]

description: replicate 2


title: H1650_Mock_1_control

description:
replicate 1
H1650_Mock_1_HH_6235821022_A.mean


title: unstimuliert [7911798014_C]

description: replicate 1


title: H1650_AllStar_3_control

description:
replicate 1
H1650_AllStar_3_HH_6235821022_F.mean


title: H1650_Mock_2_control

description:
replicate 1
H1650_Mock_2_HH_6235821022_B.mean


title: TGFb [7911798012_A]

description: replicate 1


title: IL-4 [7911798012_C]

description: replicate 1

source_name: primary microglia, IL-4 treatment 48h


title: LPS/IFNg [7911798012_B]

description: replicate 1

source_name: primary microglia, LPS/IFNg treatment 16h

value: LPS/IFNg


title: H1650_Mock_3_control

description:
replicate 1
H1650_Mock_3_HH_6235821022_C.mean


title: H1650_AllStar_2_control

description:
replicate 1
H1650_AllStar_2_HH_6235821022_E.mean


title: TGFb [7911798014_D]

description: replicate 3


title: LPS/IFNg [7911798014_A]

description: replicate 3


title: IL-4 [7911798014_B]

description: replicate 3


title: IL-4 [7911798012_D]

description: replicate 2


title: Unstimulated [9462063064_A]

description: replicate 2

source_name: ESdM, untreated

growth_protocol: ESdM, generated from C57BL/6-ATCC ES cells, were grown in sterile-filtered N2-medium (DMEM/F12, supplemented with 5 ml N2 supplement, 0.48 mM L-glutamine, and 100 μg/ml penicillin/streptomycin) at 37°C and 5 % CO2

treatment_protocol: ESdM were either left untreated or stimulated with a combination of LPS+IFNg (500+20 ng/ml), IL4 (100U/ml), or TGFb (50ng/ml) for 24h

value: embryonic stem cell-derived microglia


title: Unstimulated [9462063023_C]

description: replicate 1


title: Tgfb [9462063064_D]

description: replicate 2

source_name: ESdM, TGFb treatment 24h


title: Unstimulated [9462063064_F]

description: replicate 4


title: Tgfb [9462063065_C]

description: replicate 3


title: Unstimulated [9462063065_A]

description: replicate 5


title: Unstimulated [9462063065_D]

description: replicate 6


title: Unstimulated [9462063064_C]

description: replicate 3


title: Tgfb [9462063023_D]

description: replicate 1


title: Il4 [9462063065_F]

description: replicate 3

source_name: ESdM, IL-4 treatment 24h


title: LPS_Ifng [9462063023_E]

description: replicate 1

source_name: ESdM, LPS/IFNg treatment 24h


title: CT-HB3

city: Madison

first: chi

last: zhou

state: WI

address: 202 S. Park Street, PAB1, Meriter Hospital

department: Department of OB/Gyn

institute: University of Wisconsin-Madison

description: Array 8

hyb_protocol: hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: GenePix 4200 Autoloader by Molecular Devices. Software is GenePix Pro, Acuity 4.0

data_processing: Simple background submission and within array global lowess normalization. The medium value of the intensity of each spot from the microarray raw data were processed with simple background substraction and followed by a within array global lowess normalization. Only positively detected spots was used in further analysis. The threshold for positively detected spots selection from microarray data was determined by the mean value of all the negative control spots plus 2 fold of standard deviation of these negative control spots (resulting a reduced data set of 23,971 data rows).

organism: Sus scrofa

source_name: CT-HB

label_protocol:
amp protocol: amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol: total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.

tag: sample type

value: Chromatin transfer (CT)

value: hatched_blastocyst (HB)

tag: embryo collection time point

value: 7 hpf (hours post-in-vitro fertilization)

source_name: RefPool

value: Reference RNA pool

value: pooled_preimplantation porcine emrbyos (GV to Day11)

value: day0 to day 11 post-in-vivo insemination)


title: 1-IVV-HB1

description: Array 1

source_name: IVV-HB

value: In vivo (IVV)

value: 5.5 dpi (days post-in-vivo insemination)


title: 1-PA-HB1

description: Array 3

source_name: PA-HB

value: Parthenogenetic activation (PA)


title: LPS_Ifng [9462063064_B]

description: replicate 2


title: 1-IVV-HB2

description: Array 2


title: CT-HB1

description: Array 6


title: 1-IVV-HB3

description: Array 9


title: IVV-XB2

description: Array 3

data_processing: Simple background submission and within array global lowess normalization. The medium value of the intensity of each spot from the microarray raw data were processed with simple background substraction and followed by a within array global lowess normalization. Only positively detected spots was used in further analysis. The threshold for positively detected spots selection from microarray data was determined by the mean value of all the negative control spots plus 2 fold of standard deviation of these negative control spots (resulting a reduced data set of 24,908 data rows).

source_name: IVV-XB

label_protocol:
amp protocol: Amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

value: 5 dpi (days post-in-vivo insemination)

tag: embryo collection timepoint


title: Il4 [9462063023_B]

description: replicate 1


title: PA-XB3

description: Array 9

source_name: PA-XB

value: 6 hpf (hours post-in-vitro fertilization)


title: PA-HB1

description: Array 6


title: IVV-XB1

description: Array 1


title: PA-XB2

description: Array 7


title: PA-XB1

description: Array 5

value: 5 hpf (hours post-in-vitro fertilization)


title: CT-HB2

description: Array 7


title: HCS_6 (SCC control) [circRNA]

status: Public on Jun 18 2016

city: Bochum

first: Michael

last: Sand

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

institute: Ruhr-University Bochum

description: A total of 322 circRNAs (143 up- and 179 down-regulated; fold change ≥2 and p<0.05) were identified as being differentially expressed in cSCC.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, next heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the hybridization gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C (Agilent Technologies, Santa Clara, USA).

data_processing: Scanned array images were imported into Agilent Feature Extraction software (version 11.0.1.1; Agilent Technologies, Santa Clara, USA) for raw data extraction and analysis. Quantile normalization of raw data and subsequent data processing were performed using the R software package (version 2.15, http://www.r-project.org/). After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least in 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analysis. The normalized and log2 transformed data were averaged across the samples, and a group-wise comparison was performed between cSCC and non-lesional epithelial skin as a control.

source_name: skin

label_protocol: Sample labeling and array hybridization was performed according to the manufacturer’s protocol (Arraystar, Rockville, USA). In order to remove linear RNAs and enrich circRNA, total RNA was digested with RNase R (Epicentre, Madison, USA). Random priming method (Arraystar Super RNA Labeling Kit; Arraystar, Rockville, USA) was used to amplify and transcribe the enriched circRNA into fluorescent cRNA. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen, Hilden, Germany). Concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: During micrographic controlled excision of cSCCs with cold steel under local anaesthesia, 4-mm punch biopsies were taken from the centre of the tumor and from non-lesional epithelial skin of healthy individuals serving as control (NLES, control). The samples were subsequently placed in RNAlater (Qiagen, Hilden, Germany) and stored at - 80 °C. After extraction of total RNA with TRIzol (Life Technologies, Carlsbad, USA) according to the manufacturer's protocol, NanoDrop ND-1000 (NanoDrop, Wilmington, USA) was used for measuring RNA quantity and quality.

tag: gender

value: Male

value: non-lesional skin (control)


title: PA-HB2

description: Array 8


title: HCS_11 (SCC control) [circRNA]

value: Female


title: 1-PA-HB2

description: Array 4


title: IVV-HB1

description: Array 2


title: IVV-HB3

description: Array 12


title: PA-HB3

description: Array 10


title: IVV-XB3

description: Array 11

value: 6dpi (days post-in-vivo insemination)


title: HCS_8 (SCC control) [circRNA]


title: IVV-HB2

description: Array 4


title: 1-PA-HB3

description: Array 5


title: SCC_29T [circRNA]

source_name: cutaneous squamous cell carcinoma

value: cutaneous squamous cell carcinoma


title: SCC_18T [circRNA]


title: SCC_13T [circRNA]


title: Il4 [9462063064_E]

description: replicate 2

value: embryonic stem cell-derived microglia


title: 20% protein 1wk G121_H09_rat79

city: Groningen

first: vincent

last: bloks

department: Pediatrics

institute: UMCG

description: RMA - affy (unlogged scale): G121_H09_rat79.CEL (18_1)

hyb_protocol: Hybridisation of 5.5ug labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual

scan_protocol: Washing and staining of the arrays was done on a Affymetrix 450 fluidics stations using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual. Arrays where then scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual

data_processing: The data where normalized using RMA normalisation strategies using the MADMAX analysis pipeline pmid:21778530

label: Biotin

organism: Rattus norvegicus

source_name: Liver

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 500ng of total RNA without rRNA reduction

growth_protocol: RNA was extracted out the liver after 1wk or 4wks feeding an dieet with 5 or 20% protein

extract_protocol: total RNA

value: 20% protein 1wk

value: Wistar

value: liver


title: 5% protein 1wk G121_G09_rat76

description: RMA - affy (unlogged scale): G121_G09_rat76.CEL (4_1)

treatment_protocol: RNA was extracted out the liver after 1wk or 4wks feeding an dieet with 5 or 20% protein

value: 5% protein 1wk


title: 5% protein 4wks G121_C05_rat32

description: RMA - affy (unlogged scale): G121_C05_rat32.CEL (4_4)

value: 5% protein 4wks


title: 20% protein 1wk G121_H05_rat77

description: RMA - affy (unlogged scale): G121_H05_rat77.CEL (18_1)


title: 5% protein 1wk G121_E05_rat54

description: RMA - affy (unlogged scale): G121_E05_rat54.CEL (4_1)


title: 5% protein 1wk G121_C07_rat49

description: RMA - affy (unlogged scale): G121_C07_rat49.CEL (4_1)


title: 20% protein 1wk G121_D07_rat52

description: RMA - affy (unlogged scale): G121_D07_rat52.CEL (18_1)


title: 20% protein 4wks G121_F09_rat73

description: RMA - affy (unlogged scale): G121_F09_rat73.CEL (18_4)

value: 20% protein 4wks


title: 20% protein 1wk G121_D05_rat51

description: RMA - affy (unlogged scale): G121_D05_rat51.CEL (18_1)


title: 5% protein 1wk G121_G07_rat75

description: RMA - affy (unlogged scale): G121_G07_rat75.CEL (4_1)


title: 20% protein 4wks G121_F07_rat72

description: RMA - affy (unlogged scale): G121_F07_rat72.CEL (18_4)


title: 20% protein 4wks G121_F05_rat67

description: RMA - affy (unlogged scale): G121_F05_rat67.CEL (18_4)


title: 20% protein 1wk G121_H07_rat78

description: RMA - affy (unlogged scale): G121_H07_rat78.CEL (18_1)


title: 20% protein 1wk G121_D09_rat53

description: RMA - affy (unlogged scale): G121_D09_rat53.CEL (18_1)


title: pancreatic head cancer 3

city: Hangzhou

first: Qi

last: Ling

state: Zhejiang

address: 79 Qingchun road

department: Suegery

country: China

institute: Zhejiang University

description: pancreatic head cancer 3

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Slides were scanned by an Agilent Microarray Scanner and Feature Extraction software 10.7 (Agilent Technologies) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent Technologies). The data were analyzed by SBC analysis system (ShanghaiBio Corp., China)

source_name: pancreatic head cancer

label_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using a miRNA Complete Labeling and Hyb Kit (Agilent Technologies) in a hybridization oven (Agilent Technologies) at 55°C, 20rpm for 20 h

growth_protocol: Frozen fresh tissues were used.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: No treatment.

value: PDAC

value: male

tag: differentiation

value: Moderate-poor

tag: tnm


title: 5% protein 4wks G121_B09_rat31

description: RMA - affy (unlogged scale): G121_B09_rat31.CEL (4_4)


title: pancreatic head cancer 4

description: pancreatic head cancer 4

value: poor


title: 20% protein 4wks G121_E09_rat63

description: RMA - affy (unlogged scale): G121_E09_rat63.CEL (18_4)


title: 5% protein 1wk G121_G05_rat74

description: RMA - affy (unlogged scale): G121_G05_rat74.CEL (4_1)


title: pancreatic head cancer 2

description: pancreatic head cancer 2


title: Equine sarcoids: lesional samples vs. tumour-distant skin samples 1

city: Balice

first: Ewelina

last: Semik-Gurgul

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

description: Biological replicate 1 of 4.

hyb_protocol: Gene Expression Blocking Agent, Fragmentation Buffer and then 2× Hi-RPM Hybridization Buffer (Agilent) were added, and later samples were applied to microarray enclosed in Agilent SureHyb-enabled hybridization chamber. After hybridization, slide was washed.

scan_protocol: Scanned on an Agilent Microarray Scanner System G2565CA at settings recommended for the AgilentHD_Gx_2color array format.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1). This array was pre-processed using linear lowess normalization. Genes showing differences in expression level (DEGs) between the control and sarcoid tissue groups were identified using GeneSpring GX software (Agilent Technologies, USA).

organism: Equus caballus

source_name: sarcoid 1

label_protocol: 100 ng of total RNA  was amplified and labelled with the use of Low Input QuickAmp Labeling Two-Color Kit (Agilent Technologies, USA) according to Two-Color Microarray-Based Gene Expression Analysis v. 6.6 protocol.

extract_protocol: Total RNA extracted using Direct-zol RNA MiniPrep Kit (Zymo Research). ). The obtained RNA was additionally purified and concentrated with RNA Clean & Concentrator™-5 (Zymo Research)

treatment_protocol: The collected material was frozen at -80°C  in tubes with RNAlater (Qiagen).

tag: individual

value: horse 1

value: tumour tissue

source_name: tumour distan skin 1

value: control


title: 20% protein 4wks G121_B07_rat30

description: RMA - affy (unlogged scale): G121_B07_rat30.CEL (18_4)

tag: treatment

value: Male


title: Equine sarcoids: lesional samples vs. tumour-distant skin samples 4

description: Biological replicate 4 of 4. Control embryonic stem cells, untreated, harvested after several passages.

source_name: sarcoid 4

value: horse 4

source_name: tumour distan skin 4


title: 5% protein 4wks G121_E07_rat59

description: RMA - affy (unlogged scale): G121_E07_rat59.CEL (4_4)


title: pancreatic head cancer 1

description: pancreatic head cancer 1

value: female


title: Equine sarcoids: lesional samples vs. tumour-distant skin samples 2

description: Biological replicate 2 of 4. Control embryonic stem cells, untreated, harvested after several passages.

source_name: sarcoid 2

value: horse 2

source_name: tumour distan skin 2


title: 5% protein 4wks G121_A09_rat26

description: RMA - affy (unlogged scale): G121_A09_rat26.CEL (4_4)


title: Equine sarcoids: lesional samples vs. tumour-distant skin samples 3

description: Biological replicate 3 of 4. Control embryonic stem cells, untreated, harvested after several passages.

source_name: sarcoid 3

value: horse 3

source_name: tumour distan skin 3


title: pancreatic body/tail cancer 4

description: pancreatic body/tail cancer 4

source_name: pancreatic body/tail cancer


title: pancreatic body/tail cancer 2

description: pancreatic body/tail cancer 2


title: 20% protein 4wks G121_B05_rat29

description: RMA - affy (unlogged scale): G121_B05_rat29.CEL (18_4)

value: Wistar


title: pancreatic body/tail cancer 3

description: pancreatic body/tail cancer 3


title: 5% protein 4wks G121_A05_rat22

description: RMA - affy (unlogged scale): G121_A05_rat22.CEL (4_4)

value: liver


title: pancreatic body/tail cancer 1

description: pancreatic body/tail cancer 1


title: LPS_Ifng [9462063065_B]

description: replicate 3

source_name: ESdM, LPS/IFNg treatment 24h

tag: cell type

value: embryonic stem cell-derived microglia

value: LPS/IFNg


title: 5% protein 4wks G121_A07_rat23

description: RMA - affy (unlogged scale): G121_A07_rat23.CEL (4_4)

value: 5% protein 4wks


title: Huh-7-HBV-1

city: Xuzhou

first: Fanyun

last: Kong

state: Jiangsu

address: 209 Tongshan Road

department: Department of Pathogenic Biology and Immunology

institute: Xuzhou Medical University

description: Gene expression data from Huh-7 cells transfected with pUC18-HBV.12 plasmid

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hour at 45°C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The analysis of microarray data was performed with Affymetrix expression console as well as Affymetrix transcriptome analysis console. Using Affymetrix expression console, probe signal values were converted to log2 values, and genes annotated by the probes were analyzed according to Affymetrix Human Gene 1.0 ST array annotation files. Sequentially, the data were normalized with the robust multi-array average (RMA) algorithm.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: The cells were cultured in DMEM medium supplemented with 100 mL/L fetal bovine serum at 37°C in 5% CO2

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

treatment_protocol: When the cell fusion rate reached 80%, in the presence of the liposome Lipofectamin2000,Huh-7 cells were transfected with pUC18-HBV1.2 plasmid and control plasmid,according to the manufacturer’s instructions.

tag: cell line

value: Hepatoma cells


title: Huh-7-Mock-1

description: Gene expression data from Huh-7 cells transfected with control plasmid


title: Tgfbeta1 ligand_rep3

status: Public on Jun 17 2016

city: Portland

first: Jared

middle: Michael

last: Fischer

state: OR

address: 3181 SW Sam Jackson Park Road

department: Molecular and Medical Genetics

institute: Oregon Health and Science University

description: Gene expression data from organoids treated with Tgfbeta 1 ligand (0.04ng/mL

hyb_protocol: Each sample was hybirdized to Affymetrix Human Genome U133 plus 2.0 GeneChip array

scan_protocol: Image processing with Affymetrix GeneChip Command Console v 3.1.1 Expression analysis with Affymetrix Expression Console v 1.1

data_processing: Data were analyzed with Microarray Suite version 5.0.  The absolute analyses were rerun using global scaling to an average target intensity of 350.  The parameters alpha1 = 0.05 and alpha2 = 0.065.

source_name: Intestinal enteroid

label_protocol: RNA samples were amplified and labeled with NuGEN Pico WTA system v2.0 and Encore Biotin Module for the 3' IVT assay

growth_protocol: Enteroids were grown for 6 days

extract_protocol: RNA was extracted with RNeasy Micro Kit from Qiagen

treatment_protocol: Enteroids were continuously treated with either nothing, TgfbR1/2 inhibitor or Tgfb1 ligand in triplicate

value: small intestine


title: Tgfbeta inhibitor_rep3

description: Gene expression data from organoids treated with Tgfbeta inhibitor (20uM)


title: 5% protein 1wk G121_C09_rat50

description: RMA - affy (unlogged scale): G121_C09_rat50.CEL (4_1)

value: 5% protein 1wk


title: Tgfbeta inhibitor_rep1


title: Tgfbeta1 ligand_rep2


title: no treatment_rep3

description: Gene expression data from organoids with no treatment


title: Tgfbeta1 ligand_rep1


title: Tgfbeta inhibitor_rep2


title: Old HSC, biological rep13

city: Lund

first: Alexandra

last: Rundberg Nilsson

address: Klinikgatan 26

department: Experimental Hematology

country: Sweden

institute: Lund University

hyb_protocol: 3.0 µg of fragmented and labeled SPIA cDNA were hybridized to Affymetrix Human Gene 1.1 ST Array Plates. For hybridization, washing and staining an Affymetrix GeneTitan system was used.

scan_protocol: GeneChips were scanned using an Affymetrix GeneTitan system controlled by the Affymetrix GeneChip Command Console software v3.3 (AGCC).

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using the RMA algorithm (Irizarry et al., 2003) in the Affymetrix GeneChip Expression Console v1.3 software.

source_name: Old HSC, >70 years

label_protocol: SPIA cDNA was generated from 0.6 to 20 ng of total RNA, followed by fragmentation and biotin labeling according to the NuGEN Ovation PicoSL WTA System V2 and NUGEN Encore Biotin Module manuals.

growth_protocol: Freshly isolated human bone marrow.

extract_protocol: Total RNA was extracted from cells stabilized in RLT buffer according to the Purification of total RNA from animal and human cells protocol of the QIAGEN RNeasy Micro Kit.

treatment_protocol: Human hemaotpoietic stem and progenitor populations (HSPCs) were isolated be means of FACS and sorted into RLT buffer, after which they were immediatly frozen on dry ice. Samples were shipped on dry ice to KFB Center of Excellence for Fluorescent Bioanalytics, Regensburg, Germany, prepared and subjected to the Affymetrix Human Gene 1.1 ST array (www.kfb-regensburg.de)

value: Bone marrow

tag: genotype

value: Healthy donors

tag: age

value: >70 years


title: Metastatic clear cell renal cell carcinoma Caki-1_1

city: Warsaw

first: Mohammed

middle: Imran

last: Khan

address: ul. Szaserów 128

department: Department of Oncology

institute: Military Institute of Medicine

description: Gene expression of metastatic ccRCC

hyb_protocol: Resulting cRNA was hybridized (Gene Expression Hybridization Kit, Agilent, USA) on Agilent’s Mouse GE 4x44K v2 microarrays  as manufacturer protocol.

scan_protocol: Data were extracted using G2505C Microarray Scanner (Agilent, USA) and Agilent Feature Extraction Software (version 10.7.3.1) (Agilent, USA) on default settings.

data_processing: Data processing for differential gene expression levels between healthy control kidney cell line ASE and metastatic ccRCC cell line Caki-1 were estimated with moderate T-test using limma package. P values were corrected with Benjamini-Hochberg algorithm (False Discovery Rate – FDR). Genes were considered as differentially expressed if adjusted p value was less than 0.05 and absolute fold change was greater or equal 2.

source_name: Derived from metastatic site: skin

label_protocol: 50 ng of total RNA from each pool was converted to cDNA, then amplified and labeled with cyanine 3 (One-Color Low Input Quick Amp Labeling Kits, Agilent, USA) as manufacturer protocol.

growth_protocol: Human metastatic clear cell renal carcinoma cell line Caki-1 and human healthy kidney epithelial cell line (ASE-5063) were maintained in RPMI-1640 + GlutaMAX-I  media with 10% FBS and 1% PenStrep (100 U/mL penicillin and 100μg/mL Streptomycin). Cells were expanded in T-75 flask before isolation of total RNA. Cells were dissociated using Accutase cell detachment solution.

extract_protocol: Total RNA was isolated using Total RNA Mini Plus from A&A Biotechnology as described in manufactural protocol. RNA quality and integrity was measured by 2100 Bioanalyzer. The isolated RNA was stored in -80ºC until the microarray experiment was carried out.

treatment_protocol: No treatment

value: clear cell renal cell carcinoma

value: 49 years


title: Metastatic clear cell renal cell carcinoma Caki-1_3

description: Gene expression of metastatic ccRCC


title: Healthy kidney epithelial cells ASE_2

description: Gene expression of healthy kidney

source_name: Derived from whole kidney

value: Human normal kidney epithelial cells

value: Prenatal


title: Healthy kidney epithelial cells ASE_3

description: Gene expression of healthy kidney


title: Metastatic clear cell renal cell carcinoma Caki-1_2

description: Gene expression of metastatic ccRCC


title: Healthy kidney epithelial cells ASE_1

description: Gene expression of healthy kidney


title: Old HSC, biological rep11


title: Old HSC, biological rep10


title: Old HSC, biological rep8


title: Old HSC, biological rep12


title: no treatment_rep2


title: Young HSC, biological rep13

source_name: Young HSC, 20-26 years

value: 20-26 years


title: Young HSC, biological rep14


title: Old HSC, biological rep14


title: Old HSC, biological rep7


title: no treatment_rep1


title: Young HSC, biological rep10


title: Old HSC, biological rep9


title: Young HSC, biological rep11


title: Young CLP, biological rep6

source_name: Young CLP, 20-26 years


title: Young HSC, biological rep12


title: day6, NET39 shRNA, rep3

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

description: replicate 3

scan_protocol: Standard Protocols (Clinical Research Facility Edinburgh), Scanner: HiScan H166

data_processing: Data were log2 transformed and quantile normalised using the BioConductor package Limma.

source_name: C2C12 myoblast cell line

label_protocol: Ambion Illumina TotalPrep kit

growth_protocol: C2C12 Myoblasts (MBs) were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 20% fetal calf serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin and passaged every 2 days in a 1:7 dilution by trypsinisation. Critically, cells were never permitted to reach more than 80% confluency, i.e. ~2.5 million cells on an 8.5 cm diameter tissue culture plate.

extract_protocol: total RNA extraction was performed using Trizol reagent (Invitrogen) according to the manufacturer's instructions

treatment_protocol: To generate stable cell lines, MBs were transduced with VSV-G coated shRNA lentiviruses for two days followed by 1 µg/ml puromycin for 3 days. For differentiation of MBs to myotubes (MTs), MBs were plated at 90% confluency in complete media (~3 million cells/8.5 cm plate or 350,000 cells/3.5 cm plate) and permitted to proliferate for 48 h prior to washing in PBS and induction of differentiation by the addition of pre-warmed differentiation media. Differentiation media was changed every 48 h up to 6 days and tetrodotoxin (TTX, Abcam ab120054) was added to a final concentration of 1 µM to prevent muscle contraction 72 h post-serum withdrawl. TTX stocks are generated at 10 mM in 0.1M citrate buffer, pH 4.8 and are stored at -80°C. To specifically isolate differentiated MTs partial trypsinization was performed. Briefly, differentiation media was aspirated and cells subsequently washed once in PBS. TrypLE Express trypsin diluted 1:5 in PBS was then incubated with washed cells for 1 min at 37oC or until MTs, but not mono-nuclear MBs, were released from the growth surface, after which differentiation medium was added to block further trypsin activity and cell detachment. MTs were then carefully extracted by aspirating the cell-containing supernatant after which plates were gently washed in further differentiation medium to gather remaining MTs. To further deplete the sample of MBs, MTs were then preferentially pelleted by limited centrifugation at 500 rpm for 1 min.

tag: time

value: day 6

value: differentiation

value: NET39 shRNA


title: Young MEP, biological rep6

source_name: Young MEP, 20-26 years


title: Young HSC, biological rep8


title: Young HSC, biological rep9


title: day6, NET39 shRNA, rep2

description: replicate 2

hyb_protocol: Standard Protocols (Clinical Research Facility Edinburgh)


title: day6, NET39 shRNA, rep1

description: replicate 1


title: day6, WFS1 shRNA, rep3

description: replicate 3

value: WFS1 shRNA


title: day6, TMEM214 shRNA, rep1

description: replicate 1

value: TMEM214 shRNA


title: Young HSC, biological rep7


title: day6, WFS1 shRNA, rep2

description: replicate 2


title: day6, TMEM214 shRNA, rep3

description: replicate 3


title: day6, TMEM38A shRNA, rep3

description: replicate 3

value: TMEM38A shRNA


title: Young HSC, biological rep6


title: day6, WFS1 shRNA, rep1

description: replicate 1


title: Young GMP, biological rep5

source_name: Young GMP, 20-26 years


title: Young MEP, biological rep5


title: day6, control  shRNA, rep2

description: replicate 2

value: control shRNA vector


title: Young GMP, biological rep6


title: Young CLP, biological rep5


title: day6, TMEM214 shRNA, rep2

description: replicate 2


title: day6, TMEM38A shRNA, rep1

description: replicate 1


title: day6, control  shRNA, rep1

description: replicate 1


title: day6, TMEM38A shRNA, rep2

description: replicate 2


title: day6, untransduced, rep3

description: replicate 3

value: untransduced


title: day6, control  shRNA, rep3

description: replicate 3


title: nevil-00068: FVB_Lac9_105333_mammary gland

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Whole Mammary tissue, less lymph node

tag: tissue name

value: Mammary Gland

tag: celltype

value: Epithelial

tag: phenotype

value: Wild Type

tag: developmentalstage

value: Lactation Day 9

tag: Sex

value: female

value: FVB

tag: disease state

value: Normal


title: nevil-00068: FVB_Lac9_105332_mammary gland

scan_protocol: See mage-tab files linked to series entry for additional details

tag: strain


title: nevil-00068: FVB_Lac9_105331_mammary gland

data_processing: See mage-tab files linked to series entry for additional details


title: nevil-00068: FVB_Lac2_105324_Mammary Gland

label_protocol: See mage-tab files linked to series entry for additional details

value: Lactation Day 2


title: day6, untransduced, rep1

description: replicate 1


title: nevil-00068: FVB_Lac2_105325_Mammary Gland

extract_protocol: See mage-tab files linked to series entry for additional details


title: Young CLP, biological rep4

tag: tissue

value: Bone marrow

value: Healthy donors

value: 20-26 years


title: nevil-00068: FVB_Lac2_105323_Mammary Gland


title: Young MEP, biological rep4


title: Young GMP, biological rep4


title: day0, untransduced, rep3

description: replicate 3

value: day 0

value: untreated


title: nevil-00068: FVB Lac2 105322_Mammary Gland


title: Young HSC, biological rep5


title: nevil-00068: FVB_Lac9_105327_mammary gland


title: [4] the population enriched with CPCs after FACS at day 4_rep1

city: Seoul

first: Choon-Soo

last: Lee

address: 28 Yongon-Dong, Jongno-gu

country: South Korea

institute: Seoul National University Hospital

description: 4-1. double positive

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Mouse Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

extract_protocol: The sample preparation was performed according to the instructions and recommendations provided by the manufacturer. Total RNA was isolated using RNeasy Mini Kit columns as described by the manufacturer (Qiagen, Hilden, Germany).

value: enriched cardiac progenitor cells after FACS (FLK1+/PDGFRα+)

tag: time point

value: day 4


title: Young CLP, biological rep3


title: day6, untransduced, rep2

description: replicate 2

value: day 6

value: differentiation


title: day0, untransduced, rep2

description: replicate 2

value: untransduced


title: Young HSC, biological rep4


title: [3] cells that underwent optimized cardiac differentiation at day 4_rep2

description: 3-2. EB + ck

value: optimized cardiac-differentiated cells from iPSC


title: Young GMP, biological rep3


title: day0, untransduced, rep1

description: replicate 1


title: [3] cells that underwent optimized cardiac differentiation at day 4_rep3

description: 3-3. EB + ck


title: Young MEP, biological rep3


title: nevil-00068: Mike_Val_Lac1_D_U74Av2_Aug01_rep_Mammary gland

value: Mammary Gland

value: Epithelial

value: Wild Type

value: Lactation Day 1


title: [4] the population enriched with CPCs after FACS at day 4_rep2

description: 4-2. double positive


title: Young HSC, biological rep3


title: nevil-00068: Mike_Val_Lac1_C_U74Av2_Aug01_rep_Mammary gland

value: female

value: FVB

value: Normal


title: [2] spontaneously differentiated cells at day 4_rep3

description: 2-3. spontaneous differentiation

value: spontaneously differentiated cells from iPSC


title: [2] spontaneously differentiated cells at day 4_rep2

description: 2-2. spontaneous differentiation


title: nevil-00068: Mike_Val_Lac1_A_U74Av2_Aug01_Mammary gland


title: Young CLP, biological rep2

value: Bone marrow

value: Healthy donors

value: 20-26 years


title: Young GMP, biological rep2


title: [3] cells that underwent optimized cardiac differentiation at day 4_rep1

description: 3-1. EB + ck


title: nevil-00068: Mike_Val_P17_I_U74Av2_rescan_Mammary Gland

value: Pregnant Day 12


title: nevil-00068: Mike_Val_Lac1_B_U74Av2_Aug01_rep2_Mammary gland


title: nevil-00068: Mike_Val_P17_G_U74Av2_Aug01_Mammary Gland

value: Pregnant Day 17


title: nevil-00068: Mike_Val_P17_H_U74Av2_Aug01_rep_Mammary gland


title: nevil-00068: FVB_P12_112182_2_Mammary gland


title: nevil-00068: Mike_Val_P17_F_U74Av2_Aug01_Mammary gland


title: Young CLP, biological rep1


title: nevil-00068: FVB_P12_105330_mammary gland


title: nevil-00068: FVB_P12_113529_1_mammary gland


title: Young HSC, biological rep2


title: [2] spontaneously differentiated cells at day 4_rep1

description: 2-1. spontaneous differentiation

value: day 4


title: nevil-00068: FVB_P12_105329_mammary gland


title: [1] undifferentiated iPSCs at day 0_rep3

description: 1-3. piPS cell_0day

source_name: undifferentiated iPSCs at day 0

value: pluripotent stem cells

value: day 0


title: 5AVA vs NaCl_3

city: Bielefeld

first: João

middle: M. P.

last: Jorge

address: Universitätsstraße 25

institute: University of Bielefeld

description: Technical replicate 3 of 3

hyb_protocol: DNA microarray hybridization was performed as described previously with modification (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ). Hybridization and washing was performed with HS4800 (Tecan).

scan_protocol: Image was attained with LS200 (Tecan).

data_processing: Normalization and evaluation of the microarray data was done with the software package EMMA 2 (Dondrup, M., Albaum, S. P., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C. K., Küster, H., Linke, B., Mertens, D., et al. (2009). EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10, 50.). Genes which were up- or downregulated inWT with 200 mM 5AVA in at least two of the three replicates were taken into account for further analysis (p-value < 0.05, mRNA value > 2).

organism: Corynebacterium glutamicum

source_name: growth of C. glutamicum supplemented with 200 mM NaCl

label_protocol: cDNA synthesis from total RNA and labeling were performed as described previously (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ).

growth_protocol: LB seed culture was inoculated from an agar plate and grown overnight. The cells were harvested by centrifugation (4000 x g, 10 min) and washed once with CGXII medium lacking the carbon source. Finally, 50 mL of CGXII medium containing 4% of glucose, the necessary supplements, and either 200 mM NaCl or 200 mM 5AVA was inoculated to an OD600 of 1.0. Cells were grown until mid-exponential phase (OD between 15 and 26) and were spilled in two falcons (half filled with ice) and centrifuged (4000 x g, 10 minutes, 4ºC). Supernatant was discarded and cells were kept at -80ºC.

extract_protocol: RNA isolation was performed as described previously with some modification (Wendisch, V. F. (2003). Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J. Biotechnol. 104, 273–285.). Total RNA was isolated using the RNeasy Mini Kit(Qiagen). The purified RNA was analyzed by spectrophotometer (NanoDrop) for quantity and gel electrophoresis for quality. The RNA sample was stored at −80 °C until further use.

treatment_protocol: 200 mM NaCl or 200 mM 5AVA were added to CGXII medium  from the beginning of the growth

value: 200 mM NaCl

source_name: growth of C. glutamicum supplemented with 200 mM 5AVA

value: 200 mM 5AVA


title: Young MEP, biological rep1


title: 5AVA vs NaCl_2

description: Technical replicate 2 of 3


title: 5AVA vs NaCl_1

description: Technical replicate 1 of 3


title: Young HSC, biological rep1


title: [1] undifferentiated iPSCs at day 0_rep2

description: 1-2. piPS cell_0day


title: Young GMP, biological rep1


title: [4] the population enriched with CPCs after FACS at day 4_rep3

description: 4-3. double positive

value: enriched cardiac progenitor cells after FACS (FLK1+/PDGFRα+)


title: [1] undifferentiated iPSCs at day 0_rep1

description: 1-1. piPS cell_0day


title: LNCAP_TH_3

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

description: Biological replicate 3 of 3.

hyb_protocol: 1650 ng of the labeled cRNA were hybridised onto a custom Agilent oligo microarray at 65⁰C for 17 hours.

scan_protocol: Arrays were scanned on an Agilent scanner (G2565CA) using the Agilent Scan Control Software (A.8.4.1), and feature extraction was performed using the Agilent Feature Extraction Software (10.7).

data_processing: A quantile between array normalization was applied and differential expression was determined using the Bayesian adjusted t-statistic linear model of the 'Linear Models for Microarray Data' (LIMMA) package in R.

source_name: LNCaP, TH

label_protocol: 150 ng of total RNA was amplified and labelled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: LNCaP cells were seeded at 1.5 x 10^5 cells per well into 6-well plates in phenol-red free RPMI-1640 medium + 5% FBS and cultured at 37°C in an atmosphere containing 5% CO2 for 24 h before treatment.

extract_protocol: Total cellular RNA was extracted using the Qiagen RNeasy Mini Kit including on-column DNase-I treatment.

treatment_protocol: LNCaP cells were treated for 24 h with 15 µM Thalicthuberine (TH). 3 biological repeats were processed for microarray analysis.

value: LNCaP

value: prostate cancer cell line

value: Thalicthuberine (TH)


title: PBS_4rd_rep2

status: Public on Jun 16 2016

city: Guangzhou

first: Ai

middle: bin

last: Liu

address: 74 Zhongshan Road II

institute: SUN YAT-SEN UNIVERSITY

description: RNA extraction from PBS-treatd tumors for 4 rounds.

hyb_protocol: Hybridization was performed by loading a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Slowly dispense all of the volume of the hybridization sample onto thegasket well in the center: sample 17μl; Hyb Spike-In 1μl; 10×GE Blocking Agent 4.5μl; 2×Hi-RPM Hybridization Buffer 22.5μl; total 45μl. Place assembled slide chamber in rotisserie in a hybridization oven set to 55°C. Set hybridization rotator to rotate at 20rpm. Reaction condition: Hybridize at 55°C for 20 hours.

scan_protocol: Arrays were scanned with Agilent SureScan Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) and the images obtained were then analyzed using the Agilent Feature Extraction (FE) software (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US).

data_processing: Data normalization and transformation was performed on Genespring GX 11 (Agilent) in shanghai oebiotech corporation (http://www.oebiotech.com/).

source_name: Subcutaneously transplanted tumor, PBS_4rd, replicate2

label_protocol: Label, hybridization and scanning was performed using miRNA complete Labeling and Hyb Kit（24×）(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US).100 ng of RNA was labeled with 5'-phosphate-cytidyl-uridyl-cy3-3'(Cy3-pCp) with 0.5 μl  T4 RNA ligase. . The labeling reaction was incubated at 16°C in a circulating water bath or cool block for 2 hours. The labeled RNA was purified according to the manufacturer’s manual.

extract_protocol: Total RNA from cultured cells was extracted using the mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to the manufacturer’s manual.

treatment_protocol: Primary ESCC cells were isolated from fresh ESCC tissues, minced into 1 mm3 cubes and incubated with type IV collagenase(Sigma, St. Louis, MO) for 5-10 min at 37°C, then filtered supernatant through a 100 μm cell strainer(BD Biosciences), and the number of viable cells was counted and analyzed using trypan blue staining. Primary ESCC cells were injected subcutaneously into NOG mice,and NOG mice bearing subcutaneous tumor xenografts derived from clinical ESCC cells were intraperitoneally treated with CDDP(Selleck Chemicals, Houston, TX) or PBS twice weekly for three weeks.  Tumor cells were then isolated and re-inoculated subcutaneously into NOG mice for the same treatment for 4 rounds. The CDDP-resistant ESCC  cells isolated from CDDP–treated tumors were named EC-CR cells, and the CDDP-untreated ESCC  cells isolated from PBS-treated tumors were named EC-UT cells.

value: Subcutaneously transplanted tumor

value: esophageal squamous cell carcinoma cells

tag: gender

value: male


title: CDDP_4rd_rep1

description: RNA extraction from cisplatin-treatd tumors for 4 rounds.

source_name: Subcutaneously transplanted tumor, CDDP_4rd, replicate1


title: PBS_4rd_rep1

source_name: Subcutaneously transplanted tumor, PBS_4rd, replicate1


title: LNCAP_TH_2

description: Biological replicate 2 of 3.


title: Cpt2KO Liver, fasted for 24 hours, biological rep3

city: Baltimore

middle: J.

last: Wolfgang

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file:
MoEx-1_0-st-v1.na33.1.mm9.probeset_extended.mps

source_name: Cpt2KO Liver

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: Mouse Liver dissected from 9 week old mice

extract_protocol: Albumin-Cre; Cpt2f/f and Cpt2f/f (control) mice were identified by pcr genotyping and confirmed by qRT-PCR analysis of mRNA extracted from liver.   All samples were prepared using Trizol followed by RNeasy cleanup (Qiagen).

treatment_protocol: All mice were fasted for 24 hours.

tag: strain background

tag: genotype/variation

value: Cpt2 Knockout Albumin-Cre;Cpt2f/f)

value: 14 weeks

tag: feeding

value: 24 hour fast

value: liver


title: embryonic mouse dermal fibroblast progenitors 2

city: Cleveland

first: Radhika

middle: Paresh

last: Atit

state: Ohio

address: 2074 Adelbert Road, Millis 316

department: Biology

institute: Case Western Reserve University

hyb_protocol: standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

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

source_name: E12.5 laser capture microdissected embryonic mouse dermal fibroblast progenitors

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 Bioanalyser.

value: Embryonic day 12.5

value: dorsal dermal fibroblast progenitors


title: embryonic mouse dermal fibroblast progenitors 3


title: Cpt2KO Liver, fasted for 24 hours, biological rep1

value: 12 weeks


title: LNCAP_TH_1

description: Biological replicate 1 of 3.

tag: cell line

tag: cell type

tag: treatment


title: WT Liver, fasted for 24 hours, biological rep3

source_name: WT Liver

value: Wild-type control (Cpt2f/f)

tag: age

value: 11 weeks


title: WT Liver, fasted for 24 hours, biological rep1

value: 9 weeks


title: Cpt2KO Liver, fasted for 24 hours, biological rep2

value: 13 weeks


title: WT Liver, fasted for 24 hours, biological rep2

value: 10 weeks


title: CDDP_4rd_rep2

source_name: Subcutaneously transplanted tumor, CDDP_4rd, replicate2


title: Human_islet_1_1B4_100mM_H2O2_4hr_2

city: Minato-ku

first: Yuzuru

last: Otsuka

state: Tokyo

department: Department of Nutrition

institute: Toita Women's College

description: Gene expression after 4hr in 100mM H2O2 human panceatic islet drived 1.1B4 cell by Agilent human GE 4X44Kv2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60 C for 30 minutes in a reaction volume of 55 microl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 microl of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome microarray arrays 4x44K v2(G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven with 10rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_feb07 and Grid: 014850_D_F_20101031) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity, and average of 2 samples of H2O2 added group was compared with a control sample.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared with 100 ng RNA from 3 dishes using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the Hitachi UV Spectrophotometer.

growth_protocol: Human Islet derived hybrid cell of 1.1B4 was cultured in RPMI-1640 medium supplemented with 10% FBS with Penicilin (50 IU/ml) - Streptomycine (50 micro g/ml) in humidified air at 37 C with 5% CO2.

extract_protocol: Total RNA was prepared using RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations.  The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The cells of 1.1B4 was cultured (1.5 x 100000 cells/ml) in 9 dishes and after 24hr, 100mM H2O2 was added to 6 dishes and incubated 4hr, then RNA was isolated. The RNA of 3 dishes combined and allpied to an array.

value: pancreatic islet derived cell


title: Human_islet_1_1B4_100mM_H2O2_4hr_1


title: embryonic mouse dermal fibroblast progenitors 1

tag: genotype


title: HCC parental non-treated spheres (HpP5NA)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: HCC xenograft derived parental non-treated spheres (HpP5NA)

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4) in R.3.0.1

source_name: HCC parental non-treated spheres

label_protocol: Standard Affymetrix protocol

extract_protocol: At least three subcutaneous Huh7-derived tumors corresponding to each experimental group; sorafenib-resistant, sorafenib-sensitive and non-treated control group, were excised and subjected to isolation and spheroid assays after being mechanically dissociated by gentle pipetting in Ca/Mg-free PBS on ice, and filtered through a 40 µm cell strainer (BD Falcon) to obtain single cell suspension. Cells were exposed to red cell lysis buffer (Sigma-Aldrich) to remove red blood cells. No enzymatic digestion was used to isolate cells. Cell viability was quantified in a Neubauer cytometer using the trypan blue (1%; Sigma Aldrich) exclusion method. After tumor harvest and generation of single cell suspensions tumor cells where directly cultured into non-adherent conditions to allow the formation of spheroids. Briefly, cells were grown in serum free epithelial growth medium (MEGM, BioWhittaker) supplemented with B27 (Invitrogen), 20 ng/mL EGF and 20 ng/mL bFGF (BD Biosciences), and 4 μg/mL insulin (Sigma). Live cells were then plated in 96-well ultra-low attachment plates (Corning) at limiting dilution (10, 102, 103 and 104 cells) and sphere formation was assessed microscopically after 10 days of growth.

value: not treated


title: HCC sorafenib-acquired resistant spheres (HpRE2NA)

description: HCC xenograft derived sorafenib-acquired resistant spheres (HpRE2NA)

value: sorafenib-acquired resistant


title: HCC parental non-treated spheres (HpP1NA)

description: HCC xenograft derived parental non-treated spheres (HpP1NA)


title: Human_islet_1_1B4_cell_control

description: Gene expression after 4hr in 0mM H2O2 human panceatic islet drived 1.1B4 cell by Agilent human GE 4X44Kv2


title: HCC xenograft mice treated with sorafenib (RES168D)

description: HCC xenograft mice with acquired sorafenib resistance (RES168D)


title: HCC sorafenib-acquired resistant spheres (HpRE1NA)

description: HCC xenograft derived sorafenib-acquired resistant spheres (HpRE1NA)


title: HCC sorafenib-acquired resistant spheres (HpRE3NA)

description: HCC xenograft derived sorafenib-acquired resistant spheres (HpRE3NA)


title: HCC xenograft mice treated with sorafenib (BRI710D)

description: HCC xenograft mice brivanib treated after resistance (BRI710D)

value: brivanib treated after resistance


title: HCC xenograft mice treated with sorafenib (BRI34D)

description: HCC xenograft mice brivanib treated after resistance (BRI34D)


title: HCC parental non-treated spheres (HpP2NA)

description: HCC xenograft derived parental non-treated spheres (HpP2NA)


title: HCC xenograft mice treated with sorafenib (SEN410D)

description: HCC xenograft mice sorafenib sensitive (SEN410D)

value: sorafenib sensitive


title: HCC xenograft mice treated with sorafenib (SEN14D)

description: HCC xenograft mice sorafenib sensitive (SEN14D)


title: HCC xenograft mice treated with sorafenib (RES74D)

description: HCC xenograft mice with acquired sorafenib resistance (RES74D)