title: Day3os_9002_2

description:
raw data file: Day3os_9002.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the first of 2 independent biological replicates for this sample type.  These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: Day3os_9002_1

status: Public on Dec 01 2014

type: RNA

city: San Diego

first: Ricardo

last: Zayas

state: CA

address: 5500 Campanile Dr.

department: Biology

country: USA

institute: San Diego State University

description:
raw data file: Day3os_9002.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the first of 2 independent biological replicates for this sample type.  These data are from the first of 2 technical replicates for this biological sample obtained from the same array.

hyb_protocol: Hybridization was performed by the VMRF GeneChip Microarray Core at University of California-San Diego following standard operating procedures laid out in the Nimblegen Array User's Guide for gene expression analysis.

scan_protocol: Scanning was performed by the VMRF GeneChip Microarray Core at University of California-San Diego following standard operating procedures laid out in the Nimblegen Array User's Guide for gene expression analysis.

data_processing: The raw data (.pair files) were processed with RMA (Robust Multi-Array Analysis), quantile normalization and background correction using Nimblescan software  (Roche NimbleGen, Inc.).  Replicates were normalized first within sample type, and then all samples were normalized together.

molecule: total RNA

organism: Schmidtea mediterranea

source_name: non-regenerating side of head, day 3 regenerates

label_protocol: Labeling was performed by the VMRF GeneChip Microarray Core at University of California-San Diego following standard operating procedures laid out in the Nimblegen Array User's Guide for gene expression analysis.

growth_protocol: Asexual Schmidtea mediterranea of the CIW4 strain were maintained in Montjuïc salts and fed pureed calf liver.  Animals were starved for one week prior to use in experiments.

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen), treated with Turbo DNA-free DNase (Ambion), then further purified using the Qiagen RNeasy MinElute Cleanup kit.  cDNA was synthesized with the SuperScript Double-Stranded cDNA Synthesis kit (Invitrogen).

treatment_protocol: Control samples were collected from the heads of intact (non-regenerating) planarians.  All other samples were collected from either the blastema or non-regenerating half of the head on day 2, 3 or 4 following removal of one side of the head.

tag: strain

value: asexual CIW4

tag: developmental stage

value: adult

tag: treatment

value: half-head amputation

tag: time (regeneration stage)

value: day 3 after half-head amputation

tag: tissue

value: non-regenerating side of head


title: Day2os_11422_2

description:
raw data file: Day2os_11422.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the second of 2 independent biological replicates for this sample type.  These data are from the second of 2 technical replicates for this biological sample obtained from the same array.

source_name: non-regenerating side of head, day 2 regenerates

value: day 2 after half-head amputation


title: Day3os_11424_2

description:
raw data file: Day3os_11424.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the second of 2 independent biological replicates for this sample type.  These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: Macrophage Donor 5 1 hour [2 Hy3TM]

city: Chicago

first: Jezrom

middle: Bokcaerin

last: Self-Fordham

state: IL

address: 801 S Paulina

department: Periodontics

institute: UIC

description: The samples were labeled using the miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM and hybridized on the miRCURY LNATM microRNA Array (7th Gen)

hyb_protocol: Hybridisation was performed by Exiqon.

scan_protocol: Scanning was performed by Exiqon.

data_processing:
Data normalization was performed using Quantile normalization by Exiqon.
Quantile normalized signal
Fold change (Normalized Reads)
Expression analysis (ANOVA for Time - dendritic cells)
Expression analysis (ANOVA for Time - macrophages)
Expression analysis for DC_1h vs. Monocyte
Expression analysis for MP_1h vs. Monocyte

organism: Homo sapiens

source_name: Macrophage Donor 5 1 hour

label_protocol: 250ng of total RNA was used as input for miRCURY LNATM microRNA Hi-Power Labeling Kit. Labelling was performed on an automated Tecan hybridization station.

growth_protocol: CD14+ monocytes were cultured at 3×106 cells/ml in either (a) RPMI 1640 medium supplemented with 10% FBS, 2 mmol/L L-glutamine, penicillin (100 U/ml), streptomycin (100 μg/ml), 1000U/ml IL-4, 500U/ml GM-CSF; or (b) DMEM medium supplemented with 10% FBS, 2 mmol/L L-glutamine, penicillin (100 U/ml), streptomycin (100 μg/ml), gentamicin (50ng/ml), 100ng/ml M-CSF. Media was replenished every 48 hours.

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen) following manufacturer’s protocol. The RNA was quantitated using the NanoDrop (Thermo Scientific) and integrity assessed using the 2100 Bioanalyzer.

treatment_protocol: Cells were left untreated.

tag: cell type

value: Macrophage

tag: donor

tag: time point

value: 1 hour


title: Day2os_11422_1

description:
raw data file: Day2os_11422.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the second of 2 independent biological replicates for this sample type.  These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: Monocyte Donor 5 [1 Hy3TM]

source_name: Monocyte Donor 5

value: Monocyte


title: Day2os_9001_2

description:
raw data file: Day2os_9001.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the first of 2 independent biological replicates for this sample type.  These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: EpCAM siRNA treated Y79 Replicate 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: MicroRNA expression After 48 hrs of transfection sample-2

hyb_protocol: The hybridization mixture [10X GE blocking agent (4.5 ul), 2X Hi-RPM hybridization buffer (22.5ul)] along with labeled miRNA sample was incubated for 5 min at 100 °C and immediately kept on ice. Each 45 ul sample was hybridized onto a microarray at 55 °C for 20 h. Slides were washed for 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 5 minutes.

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: The normalization was done using GeneSpring GX  Software. 90th Percentile Shift Normalization

source_name: Retinoblastoma, Y 79, 48 hr, EpCAM siRNA treated  Replicate-2

label_protocol: miRNA labeling was performed as described in Agilent miRNA microarray protocol version 2.0 using Agilent miRNA labeling kit(Agilent Technologies, Part Number: 5190-0456). 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 7 min and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 hrs. The labeled samples were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: Y 79 cells control and EpCAM siRNA treated cells was extracted using Trizol reagent. The quality of total RNA was checked using Bioanalyzer instrument.

value: EpCAM siRNA

tag: cell line

tag: growth

value: Non adherent/Suspension cells


title: Day2os_9001_1

description:
raw data file: Day2os_9001.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then tissue was collected from the non-regenerating side of the head and pooled from around 300 animals to form the first of 2 independent biological replicates for this sample type.  These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: EpCAM siRNA treated Y79 Replicate 3

description: MicroRNA expression After 48 hrs of transfection sample-3

source_name: Retinoblastoma, Y 79, 48 hr, EpCAM siRNA treated  Replicate-3


title: Day4_11425_2

description:
raw data file: Day4_11425.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then the blastema tissue was collected and pooled from around 300 animals to form the fourth of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.

source_name: half head blastema, day 4 regenerates

value: day 4 after half-head amputation

value: half head blastema


title: Control Y79 Replicate 2

description: MicroRNA expression before transfection sample-2

source_name: Retinoblastoma, Y 79, 0 hr,  Replicate-2


title: Control Y79 Replicate 1

description: MicroRNA expression before transfection sample-1

source_name: Retinoblastoma, Y 79, 0 hr,  Replicate-1


title: Normal_Prostate_HSPH0090

city: Boston

first: Kathryn

last: Penney

address: 181 Longwood Ave

department: Medicine

institute: Brigham and Women's Hospital

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: For the expression profiles generated, we regressed out technical variables including mRNA concentration, age of the block, batch (96-well plate), percent of the probes on the array detectable above the background, log transformed average background signal, and the median of the perfect match probes for each probe intensity of the raw data. The residuals were then shifted to have the original mean expression values and normalized using the RMA method. We mapped gene names to Affymetrix transcript cluster IDs using the NetAffx annotations as implemented in Bioconductor annotation package pd.hugene.1.0.st.v1; this resulted in 20,254 unique named genes.  As gene names were used in the final analysis, this is what we have included in the sample tables.

label: biotin

source_name: FFPE normal prostate

label_protocol: Not provided

extract_protocol: Not provided


title: Day4_8687_1

description:
raw data file: Day4_8687.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then the blastema tissue was collected and pooled from around 300 animals to form the third of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: Day4_11425_1

description:
raw data file: Day4_11425.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then the blastema tissue was collected and pooled from around 300 animals to form the fourth of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: 102

city: New York

first: Marsha

last: Reyngold

state: NY

address: 1275 York Ave

department: Radiation Oncology

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The raw CEL files of the samples were imported into Partek 6.1 using RMA normalization.

source_name: regional metastases

label_protocol: Expression analysis of tumors was performed using the Affymetrix U133 2.0 microarray (Affymetrix). Processing of the arrays was per the manufacturer’s protocol.

extract_protocol: RNeasy Lipid Tissue Mini Kit (Qiagen)

tag: patient id

value: AZ

tag: tissue type

value: breast tumor tissue

tag: tissue subtype

value: lymph node metastasis


title: Day4_8687_2

description:
raw data file: Day4_8687.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then the blastema tissue was collected and pooled from around 300 animals to form the third of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: Normal_Prostate_HSPH0089


title: Day4_8622_2

description:
raw data file: Day4_8622.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then the blastema tissue was collected and pooled from around 300 animals to form the second of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: Day4_8280_1

description:
raw data file: Day4_8280.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then the blastema tissue was collected and pooled from around 300 animals to form the first of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: Day4_8622_1

description:
raw data file: Day4_8622.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then the blastema tissue was collected and pooled from around 300 animals to form the second of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: 101

source_name: primary breast tumors

value: primary tumor


title: Day3_8686_2

description:
raw data file: Day3_8686.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then the blastema tissue was collected and pooled from around 300 animals to form the third of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.

source_name: half head blastema, day 3 regenerates

value: asexual CIW4


title: Control Y79 Replicate 3

description: MicroRNA expression before transfection sample-3

source_name: Retinoblastoma, Y 79, 0 hr,  Replicate-3


title: EpCAM siRNA treated Y79 Replicate 1

description: MicroRNA expression After 48 hrs of transfection sample-1

source_name: Retinoblastoma, Y 79, 48 hr, EpCAM siRNA treated Replicate-1


title: Day3_11423_1

description:
raw data file: Day3_11423.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then the blastema tissue was collected and pooled from around 300 animals to form the fourth of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.

value: adult


title: Day4_8280_2

description:
raw data file: Day4_8280.pair
Following amputation of one side of the head, planarians were allowed to regenerate for four days and then the blastema tissue was collected and pooled from around 300 animals to form the first of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.

value: half-head amputation


title: 94

value: AW


title: Day3_11423_2

description:
raw data file: Day3_11423.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then the blastema tissue was collected and pooled from around 300 animals to form the fourth of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.

value: day 3 after half-head amputation


title: 97

value: AY


title: Day3_8686_1

description:
raw data file: Day3_8686.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then the blastema tissue was collected and pooled from around 300 animals to form the third of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: 98


title: 100b

value: AO


title: 96b

value: AX


title: 93


title: 95b


title: 99b


title: 86

value: AS


title: 84

value: AR


title: Day3_8621_1

description:
raw data file: Day3_8621.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then the blastema tissue was collected and pooled from around 300 animals to form the second of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: 85


title: Day3_8621_2

description:
raw data file: Day3_8621.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then the blastema tissue was collected and pooled from around 300 animals to form the second of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: 82

value: AQ


title: Day3_8339_2

description:
raw data file: Day3_8339.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then the blastema tissue was collected and pooled from around 300 animals to form the first of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: 72

value: AK


title: Day2_11421_1

description:
raw data file: Day2_11421.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then the blastema tissue was collected and pooled from around 300 animals to form the fourth of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.

source_name: half head blastema, day 2 regenerates

value: day 2 after half-head amputation

value: half head blastema


title: 81

value: breast tumor tissue


title: 70

value: AJ

value: lymph node metastasis


title: Day3_8339_1

description:
raw data file: Day3_8339.pair
Following amputation of one side of the head, planarians were allowed to regenerate for three days and then the blastema tissue was collected and pooled from around 300 animals to form the first of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.

value: asexual CIW4


title: 66

value: AH


title: 71

value: primary tumor


title: Day2_11421_2

description:
raw data file: Day2_11421.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then the blastema tissue was collected and pooled from around 300 animals to form the fourth of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.

value: adult

value: half-head amputation


title: Day2_8685_2

description:
raw data file: Day2_8685.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then the blastema tissue was collected and pooled from around 300 animals to form the third of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: 83


title: 68

value: AI


title: 67


title: 69


title: 62

value: AF


title: 65


title: Day2_8685_1

description:
raw data file: Day2_8685.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then the blastema tissue was collected and pooled from around 300 animals to form the third of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: Day2_8620_2

description:
raw data file: Day2_8620.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then the blastema tissue was collected and pooled from around 300 animals to form the second of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: 58

value: AD


title: 61


title: Day2_8620_1

description:
raw data file: Day2_8620.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then the blastema tissue was collected and pooled from around 300 animals to form the second of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: 64

value: AG


title: 63


title: 55

value: AC


title: Day2_8932_2

description:
raw data file: Day2_8932.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then the blastema tissue was collected and pooled from around 300 animals to form the first of 4 independent biological replicates for this sample type.   These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: 56


title: 52

value: AA


title: 57


title: 51


title: 50

value: Z


title: 49


title: Control_11420_2

description:
raw data file: Control_11420.pair
One side of the head was amputated and collected from around 300 large, non-regenerating Schmidtea mediterranea adults, and the tissues were pooled to form the fourth of 4 independent biological replicates for this sample type.  These data are from the second of 2 technical replicates for this biological sample obtained from the same array.

source_name: half of head, non-regenerating control

value: control (intact head)

value: non-regenerating

value: half of head


title: 48

value: Y

value: breast tumor tissue


title: 45

value: X


title: 46

value: lymph node metastasis


title: 44

value: W


title: Control_8684_2

description:
raw data file: Control_8684.pair
One side of the head was amputated and collected from around 300 large, non-regenerating Schmidtea mediterranea adults, and the tissues were pooled to form the third of 4 independent biological replicates for this sample type.  These data are from the second of 2 technical replicates for this biological sample obtained from the same array.

value: asexual CIW4

value: adult


title: Day2_8932_1

description:
raw data file: Day2_8932.pair
Following amputation of one side of the head, planarians were allowed to regenerate for two days and then the blastema tissue was collected and pooled from around 300 animals to form the first of 4 independent biological replicates for this sample type.   These data are from the first of 2 technical replicates for this biological sample obtained from the same array.

value: half-head amputation

value: day 2 after half-head amputation

value: half head blastema


title: 47

value: primary tumor


title: Control_8619_2

description:
raw data file: Control_8619.pair
One side of the head was amputated and collected from around 300 large, non-regenerating Schmidtea mediterranea adults, and the tissues were pooled to form the second of 4 independent biological replicates for this sample type.  These data are from the second of 2 technical replicates for this biological sample obtained from the same array.


title: Control_11420_1

description:
raw data file: Control_11420.pair
One side of the head was amputated and collected from around 300 large, non-regenerating Schmidtea mediterranea adults, and the tissues were pooled to form the fourth of 4 independent biological replicates for this sample type.  These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: 42

value: V


title: 43


title: Control_8684_1

description:
raw data file: Control_8684.pair
One side of the head was amputated and collected from around 300 large, non-regenerating Schmidtea mediterranea adults, and the tissues were pooled to form the third of 4 independent biological replicates for this sample type.  These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: 41


title: 39

value: U


title: 38

value: T


title: 40


title: 37


title: 36

value: S


title: Control_8931_2

description:
raw data file: Control_8931.pair
One side of the head was amputated and collected from around 300 large, non-regenerating Schmidtea mediterranea adults, and the tissues were pooled to form the first of 4 independent biological replicates for this sample type.  These data are from the second of 2 technical replicates for this biological sample obtained from the same array.

value: control (intact head)

value: non-regenerating


title: Control_8619_1

description:
raw data file: Control_8619.pair
One side of the head was amputated and collected from around 300 large, non-regenerating Schmidtea mediterranea adults, and the tissues were pooled to form the second of 4 independent biological replicates for this sample type.  These data are from the first of 2 technical replicates for this biological sample obtained from the same array.

value: half of head


title: 35

value: breast tumor tissue


title: 32

value: Q


title: Control_8931_1

description:
raw data file: Control_8931.pair
One side of the head was amputated and collected from around 300 large, non-regenerating Schmidtea mediterranea adults, and the tissues were pooled to form the first of 4 independent biological replicates for this sample type.  These data are from the first of 2 technical replicates for this biological sample obtained from the same array.


title: 34

value: R

value: lymph node metastasis


title: low prolificacy, biological replicate 9

city: Bunyola

first: Anna

last: Tomas Sangenis

state: Mallorca

address: recinte Hosp. Joan-March, ctra soller Km 12

department: Infection and Immunity

country: Spain

institute: Fundacio d'Investigacio Sanitaria Illes Balears (FISIB)

hyb_protocol: Labelled cRNA was fractioned and hybridised with the GeneChip® Porcine Genome Array following the manufacturers instructions. Subsequently, the arrays were stained with a GeneChip Fluidics Station 450 using the standard fluidics protocol.

scan_protocol: Chips were scanned with an Affymetrix GeneChip Scanner 3000 (Affymetrix) by using the GeneChip Operating Software (GCOS) to produce a *.CEL file for further data processing

data_processing: Microarray data was analysed with the Bioconductor software. Array normalization was assessed using the Robust Multichip Average (RMA) methodology

organism: Sus scrofa

source_name: uterus of low prolificacy IbxMe sow at 30-32 days gestation, biological replicate 9

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

growth_protocol: Iberian x Meishan F2 sows at day 30-32 of the fifth gestation

extract_protocol: RiboPure kit (Ambion) was used for total RNA isolation according to manufacturer's instructions

treatment_protocol: Sows were slaughtered and uterus samples were recovered and immediately frozen in liquid nitrogen

value: pregnant uterus (30d)

tag: breed

value: Iberian x Meishan

tag: phenotype

value: low prolificacy


title: 33


title: 31


title: 30

value: P


title: 21

value: L


title: 29

value: primary tumor


title: 19

value: K


title: 22


title: 9

value: E


title: 27

value: O


title: 28


title: 1

value: A


title: 18

value: J


title: low prolificacy, biological replicate 7

source_name: uterus of low prolificacy IbxMe sow at 30-32 days gestation, biological replicate 7


title: low prolificacy, biological replicate 3

source_name: uterus of low prolificacy IbxMe sow at 30-32 days gestation, biological replicate 3


title: low prolificacy, biological replicate 6

source_name: uterus of low prolificacy IbxMe sow at 30-32 days gestation, biological replicate 6


title: low prolificacy, biological replicate 5

source_name: uterus of low prolificacy IbxMe sow at 30-32 days gestation, biological replicate 5


title: 10


title: 15

value: H


title: 20


title: 16


title: 17


title: low prolificacy, biological replicate 8

source_name: uterus of low prolificacy IbxMe sow at 30-32 days gestation, biological replicate 8


title: low prolificacy, biological replicate 2

source_name: uterus of low prolificacy IbxMe sow at 30-32 days gestation, biological replicate 2


title: low prolificacy, biological replicate 1

source_name: uterus of low prolificacy IbxMe sow at 30-32 days gestation, biological replicate 1


title: 2


title: 11

value: F


title: low prolificacy, biological replicate 4

source_name: uterus of low prolificacy IbxMe sow at 30-32 days gestation, biological replicate 4


title: high prolificacy, biological replicate 5

source_name: uterus of high prolificacy IbxMe sow at 30-32 days gestation, biological replicate 5

value: high prolificacy


title: 12

source_name: regional metastases

value: breast tumor tissue


title: high prolificacy, biological replicate 4

source_name: uterus of high prolificacy IbxMe sow at 30-32 days gestation, biological replicate 4


title: DSW1200 intestinal epithelium 1

city: Taipei

first: Chiang

middle: Ting

last: Chien

address: No. 88, Tingzhou Road

department: Life Science

country: Taiwan

institute: National Taiwan Normal University

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

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

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

organism: Rattus norvegicus

source_name: DSW1200 intestinal epithelium

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

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

treatment_protocol: Rat intestinal epithelium was treated with water restriction 12 hr, tap water, 1200 hardness deep sea water, selenium water for 3 days

value: Wistar

tag: age

value: 4 month

tag: treated with

value: 1200 hardness deep sea water for 3 days

value: intestinal epithelium


title: Water restriction intestinal epithelium 2

source_name: Water restriction intestinal epithelium

tag: strain

value: water restriction for 12 hr


title: DSW1200 intestinal epithelium 2


title: high prolificacy, biological replicate 3

source_name: uterus of high prolificacy IbxMe sow at 30-32 days gestation, biological replicate 3

value: pregnant uterus (30d)

value: Iberian x Meishan


title: Selenium drinking intestinal epithelium 1

source_name: Selenium drinking intestinal epithelium

value: selenium water for 3 days


title: Selenium drinking intestinal epithelium 2


title: high prolificacy, biological replicate 2

source_name: uterus of high prolificacy IbxMe sow at 30-32 days gestation, biological replicate 2


title: Tap water intestinal epithelium 1

source_name: Tap water intestinal epithelium

value: tap water for 3 days


title: CD26-depleted mesothelioma cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: normalized log2 ratio (3/1 Cont)

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.  If Cy5(Red) signal or Cy3(Green) signal is not detected, log2 ratios are labeled as "null".

source_name: 1 Cont

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Tumor cells were maintained in RPMI 1640 supplemented with 10% heat inactivated fetal calf serum and antibiotics

extract_protocol: Total RNA was extracted by TRIZOL reagent.

treatment_protocol: ACC-MESO1 cells were transfected with CD26 shRNA and MSTO-211H cells were transfected with CD26 inserted pLNCX2 vector.

value: ACC-MESO1 cells

tag: genotype/variation

value: control

source_name: 3 CD26 depleted

value: CD26 depleted


title: Tap water intestinal epithelium 2


title: Mock 24h rep3

city: Manhattan

first: Jianfa

last: Bai

state: KS

address: 1800 Denison Ave

department: Diagnostic Medicine and Pathobiology

institute: Kansas State University

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip GCS3000g scanner.

data_processing: MAS 5.0

label: Biotin

organism: Oryza sativa Japonica Group

source_name: Rice leaves-Mock

label_protocol: Biotinylated cRNA were prepared according to Affymetrix large-sample protocol from 5 ug total RNA (Affymetrix One-Cycle Target Labeling and Control Reagents).

growth_protocol: Rice seeds were pre-geminated at 30oC for 5 days.  Uniformed seedlings were transplanted and kept in 25oC growth chambers with 14 h-light, 10 h-dark for 14 days prior to rust inoculation.

extract_protocol: Total RNA extracted by Invitrogen Trizol Reagent was further purified with Qiagen RNeasy columns according to the manufacturer's instructions.

treatment_protocol: Wheat leaf rust spores were suspended in soltrol oil, and pressure-sprayed onto rice leaves with soltrol oil along as control.  Inoculated plants were kept in the dark with 100% RH for 24 h prior to moving back to regular growth chambers.

tag: time

value: 24 h post inoculation

tag: infection

value: mock

value: leaf


title: high prolificacy, biological replicate 1

source_name: uterus of high prolificacy IbxMe sow at 30-32 days gestation, biological replicate 1

tag: tissue

value: high prolificacy


title: Control Huh7.5 cell vs HPI cell

description: Cells were harvested three days after passage.

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

growth_protocol: Control Huh7.5 cells and HPI cells were cultured in the DMEM medium with 10% FBS.

extract_protocol: Total RNA extracted using RNeasy following manufacturer's instructions.

treatment_protocol: To establish HPI cell, Huh7.5 cells were transfected with RNA of TNS2J1 HCV strain and maintained for more than a year.

value: Huh7.5 Hepatoma cell

source_name: HPI

value: HPI Hepatoma cell


title: CD4+ lymphoma cells 1

city: Tsukuba

first: Hideharu

last: Muto

state: Ibaraki

address: 1-1-1 Tennodai

department: Hematology

institute: University of Tsukuba

description: Gene expression data from CD4+ lymphoma cells in Tet2 gene trap mouse

hyb_protocol: Following fragmentatin, hybridization was performed with GeneChip Mouse Gene 1.0 ST array (Affymetrix) according to the manufacturer's instruction.

scan_protocol: mRNA expression was analyzed using a Scanner 3000 7G (Affymetrix).

data_processing: Data was standardized  using Expression Console soft ware (Affymetrix).

organism: Mus musculus

source_name: CD4+ lymphoma cells from Tet2 gene trap mouse

label_protocol: Labeling were performed by WT Expression kit (Affymetrix) according to the manufacturer's instruction.

growth_protocol: Single cell suspension from spleen was hemolyzed with the ammonium-chloride-potassium Buffer.

extract_protocol: Total RNA was extracted from each samples using RNeasy mini kit (QIAGEN) according to the manufacturer's instruction.

treatment_protocol: CD4+ splenocytes were incubated with biotinylated-CD4 antibodies for 30 minutes at 4℃, followed by incubation with streptavidin MicroBeads (Miltenyi Biotec). CD4+ cells were manuallly separated using LS Columns (Miltenyi Biotec) according to the manufacturer's instructions.

value: spleen

value: homozygous gene trap


title: Spleen iNKT

first: Lydia

last: Lynch

state: MA

address: One Jimmy Fund Way

institute: Harvard Medical School

description: Gene expression data from iNKT cells from spleen.

hyb_protocol: Hybridizations were performed at Expression Analysis, Durham, NC.

scan_protocol: Microarrays were scanned in the Affymetrix GeneChip Scanner 3000 7G instrument.

data_processing: Each new batch of .cel files returned from Expression Analysis to the Boston core team was normalized, using Affymetrix Power Tools’ “apt-probeset-summarize” executable with the rma-sketch standard method. Robust Multichip Average (RMA, ref2) was the algorithm used for feature-level normalization, the de facto standard for Affymetrix microarrays. Data were filtered by removing duplicate genes and internal controls.

source_name: Splenic iNKT

label_protocol: Probe amplification and labeling were performed at Expression Analysis, Durham, NC. RNA was first converted to sense-strand cDNA using the Ambion WT Expression Kit.

growth_protocol: Mice were ordered from Jackson Labs at 5 weeks old, rested in our facility for 7 days, and sacrificed at 6 weeks old.

extract_protocol:
Epididymal adipose tissue and spleen were harvested and single cell suspensions were generated from mincing and washing the spleen, and from mincing adipose and digesting with type 2 collagenase for 20 mins at 37 degrees celcius. Cells were strained through a nylon mesh and washed in PBS, then stained with antibodies to detect iNKT cells.
Cell suspensions from spleen and adipose tissue were stained for 30 mins at 4 degrees with aGalCer loaded CD1d tetramers conjugated with APC, obtained from the NIH, couple with TCRb-PE, and CD45-Pacific Blue, and were negative for CD19 to exclude non-specific staining on B cells.
Cells were blocked with Fc block for 10 mins before the antibodies were added.
Cells were washed with PBS to remove unbound antibody and resuspended in 1ml cold PBS, and propidium iodide was added to exclude dead cells.
Tetramer+ TCRb+ CD45+ CD19 - cells were isolated by cell sorting on a Facs Aria cell sorter, and then double sorted to >97% purity.
Cells were sorted into Trizol, frozen, and shipped to the Immgen team for RNA extraction according to their protocol (Immgen.org).

tag: strain/background

value: WT

tag: cell type

value: splenic invariant natural killer T (iNKT) cells

value: 6 weeks


title: Rust 24h rep2

source_name: Rice leaves-Rust

value: Puccinia triticina f. sp. Tritici


title: CD26-overexpressing mesothelioma cells

description: normalized log2 ratio (4/3 Cont)

source_name: 3 Cont

value: MSTO-211H cells

source_name: 4 CD26 transfected

value: CD26 transfected


title: Water restriction intestinal epithelium 1

value: Wistar

value: 4 month

value: water restriction for 12 hr

value: intestinal epithelium


title: Mock 24h rep2

value: 24 h post inoculation

value: mock


title: Mock 24h rep1

value: leaf


title: Neural precursors, midbrain precursors 2, rep2 (exon level)

city: London

first: Mina

last: Ryten

address: Queen Square

department: Department of Molecular Neuroscience

country: United Kingdom

institute: UCL Institute of Neurology

description:
A653_768
Neural precursors, midbrain precursors 2.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes. Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing:
Data were processed using Partek Genomics Suite v6.6. Arrays were preprocessed using RMA quantile normalization with GC background correction. Gene-level summary signals were generated by calculating the Winsorized mean of expression values of all probe sets annotated to a transcript.

Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.na30.hg19.probeset_core.mps
Core exons were used in the analysis.
Transcript assignments were based on genome build hg19.

source_name: Neural precursors

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol:
hESCs: CDM+FGF2(10ng/ml) + Insulin (10ng/ml) + Activin (10ng/ml).
Neural precursors: CDM (Day0-8), FGF2(10ng/ml; Day 8-16), FGF8(200ng/ml) + puromorphamine (1µM) from Day 16-24.
hESC-derived neurons: DMEM(HG)+ B27(2%)+BDNF(10ng/ml)+GDNF(10ng/ml).

extract_protocol: Total RNA was extracted from all cell samples using the RNeasy kit (Qiagen), from fetal samples using TRIzol (Invitrogen) and from adult substantia nigra using the miRNeasy kit (Qiagen). cDNA synthesis and amplification was performed using the Ambion®WT Expression Kit (Ambion).

value: neural precursors


title: CD4+ lymphoma cells 2


title: Rust 24h rep1


title: eWAT_rep3

city: Debrecen

first: Zoltan

last: Simandi

address: Egyetem ter 1

department: BMBI

country: Hungary

institute: University of Debrecen

hyb_protocol: 10 ug of ss cDNA was fragmented and labeled with biotin and were hybridized for 16 hr at 45C on GeneChip  1.0 ST Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring GX12 Software (Agilent). Cel files were imported using RMA16 algorithm and median normalization was performed.

source_name: eWAT

label_protocol: Biotinylated ss cDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA using WT Expression kit (Ambion).

growth_protocol: This study is part of a method paper. All the cell culturing condition is detailed in the manuscript.

extract_protocol: TRIzol was used for RNA extraction.

treatment_protocol: This study is part of a method paper. All the treatments and conditions are detailed in the manuscript.

value: eWAT


title: CD4+ splenocytes WT 1

description: Gene expression data from CD4+ splenocytes in wild type control mouse

source_name: CD4+ splenocytes from WT control mouse

value: spleen

value: wild type


title: Rust 24h rep3


title: Neural precursors, neural precursors 2, rep1 (exon level)

description:
A653_748
Neural precursors, neural precursors 2.


title: Neural precursors, neural precursors 1, rep2 (exon level)

description:
A653_727
Neural precursors, neural precursors 1.


title: Neural precursors, midbrain precursors 1, rep1 (exon level)

description:
A653_703
Neural precursors, midbrain precursors 1.


title: CD4+ splenocytes WT 2


title: ES_adipo_rep3

source_name: ES derived adipocyte

value: ES derived adipocyte


title: hESC, rep4 (exon level)

description:
A653_1475
hESC.

source_name: hESC

value: hESC


title: eWAT_rep1


title: ES_adipo_rep2


title: eWAT_rep2


title: PMEF_adipo_rep3

source_name: PMEF derived adipocyte

value: PMEF derived adipocyte


title: hESC, rep5 (exon level)

description:
A653_1476
hESC.


title: PMEF_adipo_rep1


title: siPRMT8 neuron, biological rep2

source_name: day16 ES derived neuron

growth_protocol: mESCs (D3, siSCR, siPRMT1 and siPRMT8) were cultured as described in the article. ES medium contained 15% ES qualified FBS.  For induction of EB formation mES cells were aggregated in 100-mm bacteriological dishes (Greiner) at a specific density (4x106 cells/ 15 ml) in the abscence of LIF.  Protocol details described Bibel et al., 2007

extract_protocol: RNeasy mini kit was used to extract total RNA (according to the manufacturer's instructions).

treatment_protocol: no treatment

tag: treatment


title: 3T3L1_adipo_rep1

source_name: 3T3-L1 derived adipocyte

value: 3T3-L1 derived adipocyte


title: hESC, rep2 (exon level)

description:
A653_717
hESC.


title: hESC, rep3 (exon level)

description:
A653_1474
hESC.


title: siPRMT8 neuron, biological rep3

tag: cell line


title: PMEF_adipo_rep2


title: siPRMT8 neuron, biological rep1


title: siPRMT1 neuron, biological rep2


title: siPRMT1 neuron, biological rep1


title: ES_adipo_rep1


title: Prostate_Tumor_HSPH0261

source_name: FFPE prostate tumor


title: hESC, rep1 (exon level)

description:
A653_691
hESC.


title: siSCR neuron, biological rep3

value: scrambled


title: D3 neuron, biological rep2


title: 3T3L1_adipo_rep2


title: hESC-derived neurons, rep2 (exon level)

description:
A653_716
hESC-derived neurons.

source_name: hESC-derived neurons

value: hESC-derived neurons


title: Adult control substantia nigra, 013/10 (exon level)

description:
A653_1441
Adult control substantia nigra.

source_name: Control adult substantia nigra

value: substantia nigra

tag: developmental stage

value: adult


title: 3T3L1_adipo_rep3


title: hESC-derived neurons, rep3 (exon level)

description:
A653_731
hESC-derived neurons.


title: siSCR neuron, biological rep2


title: hESC-derived neurons, rep1 (exon level)

description:
A653_713
hESC-derived neurons.


title: siPRMT1 neuron, biological rep3


title: Adult control substantia nigra, 016/10 (exon level)

description:
A653_1291
Adult control substantia nigra.


title: Adult control substantia nigra, 032/10 (exon level)

description:
A653_1346
Adult control substantia nigra.


title: D3 neuron, biological rep3


title: D3 neuron, biological rep1


title: siSCR neuron, biological rep1


title: Adult control substantia nigra, 015/10 (exon level)

description:
A653_1142
Adult control substantia nigra.


title: Adult control substantia nigra, 024/10 (exon level)

description:
A653_1031
Adult control substantia nigra.


title: siPRMT1 ATRA, biological rep2

description: SAMPLE 23

source_name: embryoid body_day 4 + 12h ATRA

growth_protocol: mESCs (siSCR and siPRMT1) were cultured as described in the article. ES medium contained 15% ES qualified FBS.  For induction of EB formation mES cells were aggregated in 100-mm bacteriological dishes (Greiner) at a specific density (4x10^6 cells/ 15 ml) in the abscence of LIF.

treatment_protocol: Over the span of four days, embryoid bodies were treated for 12h with DMSO or ATRA (5 mikromol final concentration).

value: PRMT1 knockdown (siPRMT)

value: 4d_old aggregated embrioid bodies

value: ATRA (5 mikromol final conc.) for 12hr


title: Adult control substantia nigra, 001/10 (exon level)

description:
A653_974
Adult control substantia nigra.


title: siPRMT1 DMSO, biological rep1

description: SAMPLE 19

source_name: embryoid body_day 4 + 12h DMSO

value: DMSO for 12hr


title: siPRMT1 day4, biological rep3

description: SAMPLE 18

source_name: embryoid body_day 4


title: siPRMT1 DMSO, biological rep2

description: SAMPLE 20


title: siPRMT1 ATRA, biological rep3

description: SAMPLE 24


title: siPRMT1 ES, biological rep3

description: SAMPLE 15

source_name: undifferentiated

value: undifferentiated embryonic stem cells


title: siPRMT1 ES, biological rep2

description: SAMPLE 14


title: Adult control substantia nigra, 010/10 (exon level)

description:
A653_964
Adult control substantia nigra.


title: siPRMT1 ATRA, biological rep1

description: SAMPLE 22


title: Adipose tissue iNKT

description: Gene expression data from iNKT cells from adipose.

source_name: Adipose iNKT

value: WT

value: epididymal adipose invariant natural killer T (iNKT) cells

value: 6 weeks


title: siSCR ATRA, biological rep1

description: SAMPLE 10

value: scrambled sequence control (siSCR)


title: siPRMT1 day4, biological rep2

description: SAMPLE 17


title: Adult control substantia nigra, 025/10 (exon level)

description:
A653_1090
Adult control substantia nigra.


title: siPRMT1 ES, biological rep1

description: SAMPLE 13


title: siSCR DMSO, biological rep3

description: SAMPLE 9


title: Adult control substantia nigra, 007/10 (exon level)

description:
A653_890
Adult control substantia nigra.


title: siPRMT1 DMSO, biological rep3

description: SAMPLE 21


title: siPRMT1 day4, biological rep1

description: SAMPLE 16


title: siSCR ATRA, biological rep2

description: SAMPLE 11


title: siSCR day4, biological rep3

description: SAMPLE 6


title: Adult control substantia nigra, 006/10 (exon level)

description:
A653_950
Adult control substantia nigra.


title: siSCR DMSO, biological rep1

description: SAMPLE 7


title: siSCR ATRA, biological rep3

description: SAMPLE 12


title: siSCR DMSO, biological rep2

description: SAMPLE 8


title: Adult control substantia nigra, 011/10 (exon level)

description:
A653_874
Adult control substantia nigra.


title: Adult control substantia nigra, 012/10 (exon level)

description:
A653_917
Adult control substantia nigra.


title: Adult control substantia nigra, 003/10 (exon level)

description:
A653_875
Adult control substantia nigra.


title: Adult control substantia nigra, 008/10 (exon level)

description:
A653_883
Adult control substantia nigra.


title: siSCR ES, biological rep2

description: SAMPLE 2


title: siSCR ES, biological rep3

description: SAMPLE 3


title: siSCR day4, biological rep1

description: SAMPLE 4


title: Adult control substantia nigra, 034/09 (exon level)

description:
A653_800
Adult control substantia nigra.


title: chronic SAHA rep2

first: Javier

last: Gonzalez-Maeso

address: One Gustave L. Levy Place

department: Psychiatry

institute: Mount Sinai School of Medicine

description: Gene expression data from frontal cortex of mice chronically treated with SAHA

hyb_protocol: 2.5 ug of ST-cDNA were made into hyb cocktail and hybridized for 18 hr at 45C on GeneChip Gene ST 1.0  Array according to the Nugen Appluse WT-Amp ST protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol FS450_0007.

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

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and RMA as normalization method. The number was log 2 transformed.

source_name: SAHA-treated

label_protocol: Biotinylated ST-cDNA were prepared after amplification and fragmentation according to the standard Nugen Appluse WT-Amp ST protocol from 200 ng total RNA (Manual, 2010, Nugen).

growth_protocol: Mice were housed at 12 h light/dark cycle at 23C with food and water ad libitum

extract_protocol: Total RNA was extracted from mouse frontal cortex using RNeasy lipid tissue mini kit (Qiagen)

treatment_protocol: Mice were chronicaly (21 days) injected with SAHA (20 mg/kg) or vehicle, and sacrificed on day after the last injection

value: frontal cortex

tag: genotype

value: wild type

value: 8-12 weeks


title: chronic SAHA rep1


title: chronic saline rep3

description: Gene expression data from frontal cortex of mice chronically treated with saline

source_name: saline-treated


title: siSCR ES, biological rep1

description: SAMPLE 1


title: Adult control substantia nigra, 036/09 (exon level)

description:
A653_794
Adult control substantia nigra.


title: Adult control substantia nigra, 027/09 (exon level)

description:
A653_762
Adult control substantia nigra.


title: chronic saline rep1


title: chronic SAHA rep3


title: Adult control substantia nigra, 022/08 (exon level)

description:
A653_772
Adult control substantia nigra.


title: G2_replicate_12

city: Berkeley

first: David

middle: H

last: Nguyen

address: 1 Cyclotron Road, MS-977

department: Cell & Molecular Biology

institute: Lawrence Berkeley National Laboratory

description:
8546243195_F
#36

hyb_protocol: Standard protocol of Illumina Whole-Genome Gene Expression Direct Hybridization Assay onto Mouse WG-6 v2.0 Expression Beadchips.

scan_protocol: Standard protocol using Illumina iScan array scanner.

data_processing: Data were log2-transformed and quantile normalized in R with the lumi package in Bioconductor. Fold-change analysis and t-tests were performed in R with the limma package in Bioconductor.

source_name: mammary tumor

label_protocol: Standard protocol of Ambion Illumina TotalPrep RNA Amplification Kit (Life Technologies, Cat# AMIL1791). Labeled cRNA quantified using Quant-iT RiboGreen RNA Assay Kit (Life Technologies, Cat# R11490)

growth_protocol: Chimeric mice were grown on normal chow for over a year and housed four per cage under standard mouse husbandry conditions. Food and water available to ad libidum consumption. Enrichment materials (igloo huts and bedding material) were provided in each cage.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit according to manufacturer's instructions. RNA was frozen at -80 degrees Celsius until it was prepared for microarray analysis.

treatment_protocol: Transplantations were done on host mice that were either 5-weeks old or 10-weeks old. Each mouse was palpated 2-3 times per week to detect and track tumor growth.

value: BALB/c

tag: host age at transplant

value: Adult Host (10wk-old)


title: Adult control substantia nigra, 030/09 (exon level)

description:
A653_522
Adult control substantia nigra.


title: Adult control substantia nigra, 035/09 (exon level)

description:
A653_719
Adult control substantia nigra.


title: G2_replicate_11

description:
8546243195_E
#35


title: G1_replicate_15

description:
8546243171_D
#12

value: Juvenile Host (5wk-old)


title: G2_replicate_10

description:
8546243195_D
#34


title: Adult control substantia nigra, 025/05 (exon level)

description:
A653_381
Adult control substantia nigra.

value: substantia nigra


title: G2_replicate_9

description:
8546243195_C
#30


title: G2_replicate_8

description:
8546243195_B
#29


title: Adult control substantia nigra, 028/09 (exon level)

description:
A653_534
Adult control substantia nigra.

value: adult


title: G2_replicate_7

description:
8546243195_A
#28


title: G1_replicate_14

description:
8546243171_C
#11


title: G1_replicate_13

description:
8546243171_B
#10


title: Adult control substantia nigra, 022/09 (exon level)

description:
A653_380
Adult control substantia nigra.


title: G1_replicate_12

description:
8546243171_A
#9


title: G1_replicate_11

description:
8546243168_E
#42


title: Adult control substantia nigra, 025/09 (exon level)

description:
A653_297
Adult control substantia nigra.


title: Prostate_Tumor_HSPH0231


title: G1_replicate_10

description:
8546243168_D
#41


title: Adult control substantia nigra, 018/06 (exon level)

description:
A653_286
Adult control substantia nigra.


title: G2_replicate_6

description:
8546243168_B
#39


title: G1_replicate_9

description:
8546243168_C
#40


title: G2_replicate_5

description:
8546243168_A
#38


title: G1_replicate_8

description:
8451105024_F
#7


title: siSCR day4, biological rep2

description: SAMPLE 5


title: Prostate_Tumor_HSPH0227


title: G1_replicate_5

description:
8451105024_C
#4


title: Prostate_Tumor_HSPH0225


title: G2_replicate_4

description:
8451105019_F
#37


title: G2_replicate_2

description:
8451105019_D
#32


title: G1_replicate_4

description:
8451105024_B
#2


title: G1_replicate_7

description:
8451105024_E
#6


title: Adult control substantia nigra, 017/09 (exon level)

description:
A653_283
Adult control substantia nigra.


title: G1_replicate_6

description:
8451105024_D
#5


title: Adult control substantia nigra, 016/07 (exon level)

description:
A653_248
Adult control substantia nigra.


title: Adult control substantia nigra, 033/08 (exon level)

description:
A653_238
Adult control substantia nigra.


title: G1_replicate_3

description:
8451105024_A
#1


title: G2_replicate_3

description:
8451105019_E
#33


title: Adult control substantia nigra, 021/09 (exon level)

description:
A653_243
Adult control substantia nigra.


title: Adult control substantia nigra, 037/08 (exon level)

description:
A653_239
Adult control substantia nigra.


title: Adult control substantia nigra, 032/08 (exon level)

description:
A653_234
Adult control substantia nigra.


title: G2_replicate_1

description:
8451105019_C
#27


title: Adult control substantia nigra, 038/08 (exon level)

description:
A653_223
Adult control substantia nigra.


title: G1_replicate_2

description:
8451105019_B
#8


title: G1_replicate_1

description:
8451105019_A
#3


title: Adult control substantia nigra, 014/09 (exon level)

description:
A653_219
Adult control substantia nigra.


title: Empty Vector Control for transient transfection replicate 2

city: Los Angeles

first: Wolf

last: Wiedemeyer

state: California

address: 8700 Beverly Blvd.

department: BMS

institute: Cedars-Sinai

description: 2_V2_Akop_(HuGene-1_0-st-v1).plier-gene-default-Signal

hyb_protocol: 10 ug of cRNA was used for second-cycle cDNA synthesis and was purified, fragmented, labeled, and hybridized to GeneChip Human Gene 1.0 ST Arrays at 45C for 16.5 hours per manufacturer's instructions.  GeneChips were washed and stained per manufacturer's instructions in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips scanned with GeneChip Scanner 3000 7G System

data_processing: The data were analyzed with Expression Console software (1.3.1.187). Gene level analysis, PLIER summarization method, PM-GCBG background correction, sketch-quantile normalized.

source_name: MCF-7_vector control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7,  cells were maintained in DMEM containing 10% fetal bovine serum (FBS). For experiments involving estrogen depletion, media was replaced by phenol-free DMEM containing 5% charcoal/dextran-treated FBS.

extract_protocol: RNA extraction was performed using the RNAeasy kit(Qiagen)

treatment_protocol: MCF- 7 cells upon transient expression of TOX3

value: breast cancer cells

tag: transfected with

value: Empty vector


title: chronic saline rep2

description: Gene expression data from frontal cortex of mice chronically treated with saline


title: Empty Vector Control for transient transfection replicate 1

description: 1_V1_Akop_(HuGene-1_0-st-v1).plier-gene-default-Signal


title: Experiment TOX3 transient transfection replicate 2

description: 4_T2_Akop_(HuGene-1_0-st-v1).plier-gene-default-Signal

source_name: MCF-7_TOX3 expression

value: TOX3 Vector


title: Adult control substantia nigra, 035/06 (exon level)

description:
A653_149
Adult control substantia nigra.


title: Experiment TOX3 transient transfection replicate 1

description: 3_T1_Akop_(HuGene-1_0-st-v1).plier-gene-default-Signal


title: Adult control substantia nigra, 016/09 (exon level)

description:
A653_157
Adult control substantia nigra.


title: Adult control substantia nigra, 039/06 (exon level)

description:
A653_165
Adult control substantia nigra.


title: Adult control substantia nigra, 005/09 (exon level)

description:
A653_112
Adult control substantia nigra.


title: Adult control substantia nigra, 025/08 (exon level)

description:
A653_072
Adult control substantia nigra.


title: Adult control substantia nigra, 010/09 (exon level)

description:
A653_142
Adult control substantia nigra.


title: Adult control substantia nigra, 023/09 (exon level)

description:
A653_121
Adult control substantia nigra.


title: Adult control substantia nigra, 016/08 (exon level)

description:
A653_102
Adult control substantia nigra.


title: Adult control substantia nigra, 013/09 (exon level)

description:
A653_040
Adult control substantia nigra.


title: Adult control substantia nigra, 021/08 (exon level)

description:
A653_140
Adult control substantia nigra.


title: Adult control substantia nigra, 009/09 (exon level)

description:
A653_147
Adult control substantia nigra.


title: Adult control substantia nigra, 018/08 (exon level)

description:
A653_055
Adult control substantia nigra.


title: Adult control substantia nigra, 018/09 (exon level)

description:
A653_034
Adult control substantia nigra.


title: Adult control substantia nigra, 020/08 (exon level)

description:
A653_141
Adult control substantia nigra.


title: Adult control substantia nigra, 004/08 (exon level)

description:
A653_093
Adult control substantia nigra.


title: Adult control substantia nigra, 015/09 (exon level)

description:
A653_058
Adult control substantia nigra.


title: Adult control substantia nigra, 031/08 (exon level)

description:
A653_145
Adult control substantia nigra.


title: Adult control substantia nigra, 036/08 (exon level)

description:
A653_092
Adult control substantia nigra.


title: Adult control substantia nigra, 022/06 (exon level)

description:
A653_111
Adult control substantia nigra.


title: Adult control substantia nigra, 017/07 (exon level)

description:
A653_115
Adult control substantia nigra.


title: Adult control substantia nigra, 004/06 (exon level)

description:
A653_043
Adult control substantia nigra.


title: Adult control substantia nigra, 024/08 (exon level)

description:
A653_146
Adult control substantia nigra.


title: cKO 24h E::3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
Gene expression after 24h E2 treatment in cKO female mouse uterine tissue.
Replicate 3

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

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

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

source_name: uterine sample from cKO female mouse, 24h E2 treated

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

growth_protocol: cKO females at the age of 8 to 10 weeks were ovariectomized and housed for 10 days before the treatment.

extract_protocol: Uterine samples were collected at 2 or 24 h after the injection. Tissues were immediately frozen in liquid nitrogen. RNA was extracted by using RNeasy Mini Kit (Qiagen, Valencia, CA) and treated with DNaseI (Qiagen) according to the manufacturer's protocol.

treatment_protocol: cKO females were injected intraperitoneally with vehicle (saline) or E2 (0.25 ug of 17beta-estradiol) for 2 h or 24 h.

value: Wnt7aCre+;Esr1f/f (uterine epithelial ERα conditional knockout)

value: 8-10 weeks

tag: gender

value: female

value: uterus

tag: time point


title: cKO 24h E::2

description:
Gene expression after 24h E2 treatment in cKO female mouse uterine tissue.
Replicate 2

tag: age


title: cKO 24h V1::2

description:
Gene expression after 24h vehicle treatment in cKO female mouse uterine tissue.
Replicate 2

source_name: uterine sample from cKO female mouse, 24h vehicle treated

value: saline


title: cKO 2h E::3

description:
Gene expression after 2h E2 treatment in cKO female mouse uterine tissue.
Replicate 3

source_name: uterine sample from cKO female mouse, 2h E2 treated


title: cKO 2h E::2

description:
Gene expression after 2h E2 treatment in cKO female mouse uterine tissue.
Replicate 2


title: cKO 24h E::1

description:
Gene expression after 24h E2 treatment in cKO female mouse uterine tissue.
Replicate 1


title: Adult control substantia nigra, 006/09 (exon level)

description:
A653_002
Adult control substantia nigra.


title: cKO 24h V1::3

description:
Gene expression after 24h vehicle treatment in cKO female mouse uterine tissue.
Replicate 3


title: cKO 24h V1::1

description:
Gene expression after 24h vehicle treatment in cKO female mouse uterine tissue.
Replicate 1


title: MCF7-DMSO-10d-rep1

city: Cambridge

first: Marc

last: Mendillo

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Sample name: Control.10days.rep1
Gene Expression after 10 days in the presence of indicated drug

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (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 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MCF-7 breast cancer cells treated with DMSO for 10 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: In vitro cultured in DMEM with 10% FCS

extract_protocol: Qiagen RNeasy kit

treatment_protocol: MCF-7 cells were treated with indicated drug for 10 days.

value: DMSO


title: MCF7-TAM-1µM-STA9090-10nM-10d

description:
Sample name: Tam.STA.10days
Gene Expression after 10 days in the presence of indicated drug

source_name: MCF-7 breast cancer cells treated with STA9090 and Tamoxifen for 10 days


title: MCF7-TAM-1µM-10d

description:
Sample name: Tam.10days
Gene Expression after 10 days in the presence of indicated drug

source_name: MCF-7 breast cancer cells treated with Tamoxifen for 10 days


title: PKC theta KO - N4 Erep 2

city: Tampa

first: Amer

last: Beg

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

description: PKC theta KO Experimental

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C to the Affymetrix Mouse 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scaner.

data_processing: The data were analyzed with the Affymetrix GCOS 1.4 software using the MAS 5.0 alorighthm with default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: primary T-cell

label_protocol: Biotinylated cRNA were prepared according to the Ambion Message Amp Premier protocl using 100 ng of total RNA (Ambion).

growth_protocol: Mice were maintained in pathogen free conditions and in accordance with IACUC regulations.  CD8 T-cells were isolated from spleens using Miltenyi beads (positive selection) and LS magnetic columns.

extract_protocol: DCs were removed from the culture with positive selection for CD11c, and Isolation of total RNA from T-cells only was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

treatment_protocol: The T-cells were either cultured with non-pulsed DC  (WT only and signified as "WT - UN") or with BMDCs pulsed with the OVA peptide SIINFEKL (N4)  (WT, PKCθ theta KO, and p50 cRel DKO and signified as 'genotype - N4') at a ratio of 1:10 (DC:T-cell) for 18 hours.

value: primary T-cell

tag: condition

value: PKC theta KO Experimental

value: PKC theta KO

tag: genetic background


title: CTRL cKO 02

city: Brussels

first: benjamin

last: beck

address: route de Lennik 808

country: Belgium

institute: ULB

description: CTRL 1915-07

hyb_protocol: The microarrays have been performed by facilities (IRB FGC Barcelona)

source_name: FACS sorted tumor epithelial cells CTRL from cKO 02

growth_protocol: DMBA/TPA induced skin tumors

extract_protocol: Qiagen RNA purification microkit

treatment_protocol: TAM 5x2mg

tag: genotype/variation

value: 5x 2mg TAMOXIFEN

tag: isolation

value: FACS

tag: staining

value: Epcam+/Lin-/DAPI-

value: tumor epithelial cells


title: Control rep.2

city: Salamanca

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

institute: University of Salamanca

description:
2.C2_(HuGene-1_0-st-v1).chp
2.C2_(HuGene-1_0-st-v1).CEL

hyb_protocol: Hybridization was carried out according to protocols described in the Gene Expression Analysis Technical Manual (http://www.affymetrix.com) using the Genechip Fluidics Station 450 (Affymetrix).

scan_protocol: Chips were washed, stained and scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Affymetrix Expression Console:  Background correction, normalization, and expression analysis from the data were performed using the RMA algorithm (Irizarry et al., 2003).
The significance of the differential expression under the two conditions compared was determined by statistical analysis performed with the T-test algorithm (Baldi and Long, 2001).
Transcripts showing significantly differential expression (FC≥2) were annotated Gene Ontology (GO) terms, and analyzed using the Genespring GX program.

source_name: MCF-7 cells grown in the absence of trichodermin

label_protocol: cDNAs were synthesized from 1 gµ of total RNA using the ‘‘Reverse Transcription System’’ kit (Promega Biotech Iberica, Alcobendas, Spain), and used for hybridization to Human Gene 1.0 ST expression chips using the Genechip Fluidics Station 450 (Affymetrix) and according to protocols described in the Gene Expression Analysis Technical Manual (http://www.affymetrix.com).

growth_protocol: MCF-7 cells were cultured in ATCC-formulated Eagle’s Mininum Essential Medium with 10% FBS. Cell cultures were maintained at 37 ºC in a humidified 5% CO2 incubator.

extract_protocol: Total RNA was isolated from MCF-7 cells grown for 8 h in the absence (C) or presence of 10 µM trichodermin (T), using the Mini RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's protocol. The quality of the RNA was assessed on the Agilent 2100 Bioanalyser (Agilent Technologies, Germany).

treatment_protocol: MCF-7 cells grown for 8 h in without trichodermin (C, control) or presence of 10 µM trichodermin (T).

value: MCF-7 human breast cancer cell line

tag: agent

value: Control


title: Trichodermin rep.3

description:
6.T3_(HuGene-1_0-st-v1).chp
6.T3_(HuGene-1_0-st-v1).CEL

source_name: MCF-7 cells grown in the presence of 10 µM of trichodermin

value: Trichodermin


title: cKO 02

description: Twist1cKO 1915-04

scan_protocol: The microarrays have been performed by facilities (IRB FGC Barcelona)

source_name: FACS sorted tumor epithelial cells Twist1 cKO 02


title: cKO 01

description: Twist1cKO 1808-02

data_processing: The microarrays have been performed by facilities (IRB FGC Barcelona)

source_name: FACS sorted tumor epithelial cells Twist1 cKO 01


title: Trichodermin rep.1

description:
4.T1_(HuGene-1_0-st-v1).chp
4.T1_(HuGene-1_0-st-v1).CEL


title: WT - N4 Erep 2

description: WT Activation Control

value: WT Activation Control

value: WT


title: Trichodermin rep.2

description:
5.T2_(HuGene-1_0-st-v1).chp
5.T2_(HuGene-1_0-st-v1).CEL


title: MCF7-STA9090-10nM-10d

description:
Sample name: STA9090.10days
Gene Expression after 10 days in the presence of indicated drug

source_name: MCF-7 breast cancer cells treated with STA9090 for 10 days


title: MCF7-DMSO-10d-rep2

description:
Sample name: Control.10days.rep2
Gene Expression after 10 days in the presence of indicated drug


title: WT - UN Erep 2

description: Unstimulated Control

value: Unstimulated Control


title: p50 cRel DKO - N4 Erep 2

description: p50 cRel DKO Experimental

value: p50 cRel DKO Experimental

value: p50 cRel DKO


title: CTRL cKO 01

description: CTRL 1915-03

source_name: FACS sorted tumor epithelial cells CTRL from cKO 01

label_protocol: The microarrays have been performed by facilities (IRB FGC Barcelona)


title: Control rep.1

description:
1.C1_(HuGene-1_0-st-v1).chp
1.C1_(HuGene-1_0-st-v1).CEL


title: Control rep.3

description:
3.C3_(HuGene-1_0-st-v1).chp
3.C3_(HuGene-1_0-st-v1).CEL


title: p50 cRel DKO - N4

description: p50 cRel DKO Experimental


title: Nr 1_AX-S

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

description: Gene expression data from axonal compartment from cultured Smn knockdown motoneurons

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and quantile-quantile as normalization method

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual,  Affymetrix).

growth_protocol: Spinal cords were dissected from E12.5 mouse embryos and, following removal of dorsal root ganglia and meninges, motoneurons were isolated and enriched via p75-panning as described previously (Wiese et al. 2010). Following lentiviral transfection, one million motoneurons were plated into one compartment of a microfluidic chamber (Xona Microfluidics, SND 150) precoated with polyornithine and laminin-111 (Invitrogen, 23017–015). To achieve a directed growth of the axons through the microchannels of the microfluidic chamber towards the axonal compartment a BDNF gradient was established by adding this neurotrophic factor at 20 ng/ml only to the axonal compartment. CNTF (5 ng/ml) was applied to both compartments for survival. Motoneurons were grown for 7 days at 37°C and 5% CO2 in neurobasal medium (Invitrogen) containing 500 µM GlutaMAX (Invitrogen), 2% horse serum (Linaris), 2% B27 supplement (Invitrogen). 50% of culture medium was exchanged on day 1 and then every second day.

extract_protocol: Total RNA of the somatodendritic and axonal compartment was extracted with the Pico Pure RNA Isolation Kit (Arcturus, KIT0204), according to the manufacturer´s protocol. Extracted RNA was directly used for linear amplification with the RiboAmp® HSPlus Amplification Kit (Arcturus, KIT0525). Linear amplification was done according to the manufacturer´s protocol with labelling of antisense RNA after two rounds of amplification. The biotin-labeled antisense RNA was then hybridised to a microarray chip (Affymetrix Gene Chip ® Mouse Genome 430 2.0 Array, 900496).

treatment_protocol: Motoneurons were treated with lentiviruses expressing an shRNA against Smn, empty vector control or left untreated (wild-type).

value: motoneurons

tag: subcellular compartment

value: axonal

value: Smn knockdown


title: Gr1_5_AX-WT

description: Gene expression data from axonal compartment from cultured wild-type motoneurons

tag: cell type

value: wild-type


title: WT - UN

description: Unstimulated Control

value: primary T-cell


title: WT - N4

description: WT Activation Control


title: Gr3_5_AX-WT

source_name: axonal compartment from cultured wild-type motoneurons


title: Gr3_6_AX-G

description: Gene expression data from axonal compartment from cultured empty vector control motoneurons

value: empty vector control


title: PKC theta KO - N4

description: PKC theta KO Experimental

value: PKC theta KO Experimental

value: PKC theta KO


title: Gr2_5_AX-WT


title: Gr1_6_AX-G

source_name: axonal compartment from cultured empty vector control motoneurons


title: Nr 2_AX-S

source_name: axonal compartment from cultured Smn knockdown motoneurons


title: Nr 4_ZK-S

description: Gene expression data from somatodendritic compartment from cultured Smn knockdown motoneurons

value: somatodendritic


title: Nr 6_ZK-S

source_name: somatodendritic compartment from cultured Smn knockdown motoneurons


title: cKO 2h E::1

description:
Gene expression after 2h E2 treatment in cKO female mouse uterine tissue.
Replicate 1

tag: strain/background

value: Wnt7aCre+;Esr1f/f (uterine epithelial ERα conditional knockout)

value: 8-10 weeks

value: female

tag: tissue

value: uterus

tag: treatment


title: Gr1_2_ZK-G

description: Gene expression data from somatodendritic compartment from cultured empty vector control motoneurons


title: Nr 5_ZK-S


title: Gr3_1_ZK-WT

description: Gene expression data from somatodendritic compartment from cultured wild-type motoneurons


title: Gr2_2_ZK-G

source_name: somatodendritic compartment from cultured empty vector control motoneurons


title: Gr2_6_AX-G


title: Prostate_Tumor_HSPH0162

city: Boston

first: Kathryn

last: Penney

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: For the expression profiles generated, we regressed out technical variables including mRNA concentration, age of the block, batch (96-well plate), percent of the probes on the array detectable above the background, log transformed average background signal, and the median of the perfect match probes for each probe intensity of the raw data. The residuals were then shifted to have the original mean expression values and normalized using the RMA method. We mapped gene names to Affymetrix transcript cluster IDs using the NetAffx annotations as implemented in Bioconductor annotation package pd.hugene.1.0.st.v1; this resulted in 20,254 unique named genes.  As gene names were used in the final analysis, this is what we have included in the sample tables.

source_name: FFPE prostate tumor

label_protocol: Not provided

extract_protocol: Not provided


title: Gr2_1_ZK-WT

source_name: somatodendritic compartment from cultured wild-type motoneurons


title: non-transformed KSLs sorted from normal mouse, rep 1non-transformed KSLs sorted from leukemic mouse, rep 2

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description: Gene expression data from embryos in slow phase of cellularisation.

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

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

data_processing: The data were analyzed using RMA in the bioconducter and normalized using cross correlation.  The trimmed mean target intensity of each array was set to 10.

source_name: CD45.1+ KSL

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

growth_protocol: Leukemic mice were generated by transplanting equal numbers of CD45.2+ BCR-ABL x SCL-tTA transgenic murine bone marrow along with CD45.1+ (leukemic-exposed) bone marrow into CD45.1+ hosts, while control (normal) mice were generated without the BCR-ABL transgene.

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

treatment_protocol: HSC or KSL cells from leukemic mice compared with those from normal (healthy) mice

tag: diseaste state

value: leukemic mouse

value: CD45.1+ KSL


title: Gr3_2_ZK-G


title: non-transformed KSLs sorted from normal mouse, rep 2

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

value: Normal mouse


title: non-transformed KSLs sorted from normal mouse, rep 1non-transformed KSLs sorted from leukemic mouse, rep 1


title: Adult control substantia nigra, 023/08 (exon level)

description:
A653_003
Adult control substantia nigra.

source_name: Control adult substantia nigra

value: substantia nigra

tag: developmental stage

value: adult


title: non-transformed KSLs sorted from normal mouse, rep 1


title: Gr1_1_ZK-WT

value: motoneurons


title: non-transformed HSCs sorted from leukemic mouse, rep 2


title: non-transformed HSCs sorted from normal mouse, rep 2


title: non-transformed HSCs sorted from normal mouse, rep 1


title: non-transformed HSCs sorted from leukemic mouse, rep 1


title: constitutive_MLL-ENL_cell line_DOX treated_48h cME3+DOX

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

institute: UCL GOS ICH

description: constitutive MLL-ENL cell line, control for Tet-off system

hyb_protocol: Samples were hybridised on GeneChip Mouse Genome 430 2.0 Array using Affymetrix’s GeneChip Hybridisation Wash and Stain Kit (900720) according to manufacturer’s instructions using fluidics protocol FS450_0004 and Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Operating Software (GCOS) on an Affymetrix GeneChip Scanner 3000 (GCS 3000).

data_processing: The hybridisation intensity data from the GeneChips was analysed with Affymetrix Microarray Suite version 5.0 (MAS 5.0). 1. Data were filtered by selecting for a probe set detection p-value smaller than 0.07 in at least two out of 16 samples. Probe sets with a fold change > 2 in the constitutive cell line controls were excluded.

source_name: MLL-ENL immortalised haematopoietic progenitor cells

label_protocol: Biotinylated antisense RNA were prepared using Ambion’s MessageAMPII – Biotin Enhanced Kit (AM1791) according to manufacturer’s instructions.

growth_protocol: Immortalised cell lines were cultured in RPMI-1640 with 10% FCS, 100 U/ml Penicillin, 100 µg/ml Streptomycin, 2 mM L-glutamine and 50 µM2-ME supplemented with 100 ng/ml SCF, 10 ng/ml IL-3, 10 ng/ml IL-6.

extract_protocol: A maximum of 1x10^7 cells were lysed in 1 ml TRIzol reagent. Total RNA was extracted according to manufacturer’s instructions.

treatment_protocol: Tetracycline controlled transcriptional activation of MLL-AF9 or MLL-ENL expression was turned off in the presence of Doxycycline. Immortalised cell lines were treated without or with 2µg/ml Doxycycline for 48 hours.

value: immortalised HPC

tag: oncogene

value: MLL-ENL

tag: type

value: constitutive

value: Doxycycline treated


title: conditional_MLL-ENL_cell line_DOX treated_48h ME7+DOX

description: MLL-ENL cell line, repeat 3

value: conditional


title: conditional_MLL-ENL_cell line_untreated ME5-DOX

description: MLL-ENL cell line, repeat 2

value: untreated


title: conditional_MLL-ENL_cell line_untreated ME7-DOX

description: MLL-ENL cell line, repeat 3


title: conditional_MLL-ENL_cell line_DOX treated_48h ME5+DOX

description: MLL-ENL cell line, repeat 2


title: conditional_MLL-AF9_cell line_untreated MA3-DOX

description: MLL-AF9 cell line, repeat 2

source_name: MLL-AF9 immortalised haematopoietic progenitor cells


title: conditional_MLL-ENL_cell line_untreated ME4-DOX

description: MLL-ENL cell line, repeat 1


title: Prostate_Tumor_HSPH0147


title: conditional_MLL-AF9_cell line_DOX treated_48h MA4+DOX

description: MLL-AF9 cell line, repeat 3


title: Prostate_Tumor_HSPH0145


title: constitutive_MLL-AF9_cell line_DOX treated_48h cMA3+DOX

description: constitutive MLL-AF9 cell line, control for Tet-off system


title: tthb068-3-sta

city: Toyonaka

first: Hiromasa

last: Ohyama

address: Machikaneyamachou 1-1

institute: Osaka University

hyb_protocol: 2 μg of 3’-terminal-labeled cDNA was hybridized to a TTHB8401a520105F GeneChip (Affymetrix). The array was incubated for 16 h at 50°C in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 1 mg of herring sperm DNA (Promega), 0.5 mg of bovine serum albumin, the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix).  Then the array was automatically washed and stained with streptavidin, biotin anti-streptavidin, and streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.4 (Affymetrix). Scaled probe value was calculated as Sc = 500 according to Statistical Algorithms Description Document (Affymetrix).

organism: Thermus thermophilus HB8

source_name: the sample of tthb068 gene disruptant during the stationary phase

label_protocol: 10 μg of total RNA was mixed with 750 ng of random primers (Invitrogen), incubated at 70°C for 10 min, and 25°C for 10 min.  The RNA/primer solution was reacted with SuperScript II reverse transcriptase (Invitrogen) to synthesize cDNA.  The reaction was performed in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen).  The synthesized DNA was purified by ethanol precipitation, and 3 μg of cDNA was fragmented with 35 units of DNase I (GE Healthcare) at 37°C for 10 min.  The reaction was stopped by incubation of the reaction solution at 98°C for 10 min.  3 μg of fragmented cDNA was labeled with GeneChip DNA Labeling Reagent (Affymetrix), using terminal transferase according to the manufacturer’s instructions (Affymetrix).  Gel-shift assay using NeutrAvidin (Invitrogen) as a probe confirmed that the majority of cDNA was successfully labeled with biotin.

growth_protocol: The T. thermophilus HB8 wild-type strain and disruptants were cultured in TT medium at 70°C until the cells reached to OD600 of 0.8 or to stationary phase.

extract_protocol: Collected cells were mixed with 1.4 ml of 5 mM Tris-HCl (pH 7.5) containing 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol to the cell pellet. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C.  Aqueous phase (0.2 ml) was collected and mixed with 0.75 ml of TRIZOL LS (Invitrogen, Carlsbad, CA), and incubated at room temperature for 5 min.  Then, 0.2 ml of chloroform was added, and the mixture was vortexed for 10 sec.  After centrifugation, aqueous phase was collected, mixed with 0.5 ml of chloroform, and vortexed for 10 min.   The aqueous phase was collected and mixed with 0.5 ml of isopropanol to precipitate RNA.  After incubation at -20°C for 60 min and centrifugation, aqueous phase was removed.  The pellet was dissolved in 0.2 ml of nuclease-free water, and further purified through the ethanol precipitation, and then resuspended in 0.2 ml of water.  The obtained RNA solution was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25 μl reaction mixture. The reaction was terminated by the addition of 1 μl of 0.5 M EDTA, followed by incubation at 70°C for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

treatment_protocol: In the case of TTHA0137, TTHA0540 and TTHA1817, an equal volume of hot medium was added to the culture.  In the other disruptants, cultures were added to an equal volume of 100% ethanol and stored at -80°C.

tag: genotype

tag: growth phase

value: stationary


title: Prostate_Tumor_HSPH0195


title: tthb068-2-sta

description: cultures were added to an equal volume of 100% ethanol and stored at -80°C.


title: tthb068-1-log

source_name: the sample of tthb068 gene disruptant during the log phase

value: log


title: tthb068-1-sta


title: constitutive_MLL-ENL_cell line_untreated cME3-DOX


title: ttha1817-2-sta

source_name: the sample of ttha1817 gene disruptant during the stationary phase


title: tthb068-2-log


title: tthb068-3-log


title: conditional_MLL-AF9_cell line_untreated MA4-DOX

description: MLL-AF9 cell line, repeat 3


title: constitutive_MLL-AF9_cell line_untreated cMA3-DOX


title: conditional_MLL-AF9_cell line_DOX treated_48h MA3+DOX

description: MLL-AF9 cell line, repeat 2


title: conditional_MLL-ENL_cell line_DOX treated_48h ME4+DOX

description: MLL-ENL cell line, repeat 1


title: ttha1817-3-sta


title: ttha1817-1-sta


title: conditional_MLL-AF9_cell line_DOX treated_48h MA1+DOX

description: MLL-AF9 cell line, repeat 1


title: ttha1817-2-log

description: An equal volume of hot medium was added to the culture, when the culture was harvested.

source_name: the sample of ttha1817 gene disruptant during the log phase


title: conditional_MLL-AF9_cell line_untreated MA1-DOX

description: MLL-AF9 cell line, repeat 1


title: ttha1818-1-log


title: ttha1817-3-log


title: ttha1556-3-sta

source_name: the sample of ttha1556 gene disruptant during the stationary phase


title: ttha1556-2-sta


title: Glioma stem cells (GSC) rep3

city: Saint Louis

first: Yi-Hsien

last: Chen

state: Missouri

address: 4566 Scott Avenue

department: Neurology

institute: Washington University School of Medicine

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 plus 2/Mouse 430 2.0  Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.

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

source_name: optic gliomas

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

growth_protocol: Dissociated cells were plated into low-attachment dishes and cultured with DMEM/Neurobasal medium containing N2, B27, FGF (20 ng/ml) and EGF (20 ng/ml) at 37°C.

tag: strain

value: Nf1+/-GFAP CKO

tag: tissue source

value: optic nerve

tag: age

value: cultured stem cells


title: ttha1534-3-sta

source_name: the sample of ttha1534 gene disruptant during the stationary phase


title: ttha1534-1-sta


title: ttha1556-3-log

source_name: the sample of ttha1556 gene disruptant during the log phase


title: ttha1556-1-log


title: ttha1556-2-log


title: Glioma stem cells (GSC) rep2


title: ttha1534-2-sta


title: TVZ NSCs transdcued with Cre virus rep2

source_name: third ventricle neural stem cells

value: brains

value: postnatal day 1

value: cultured neural stem cells


title: ttha1556-1-sta


title: TVZ NSCs transdcued with Cre virus rep1


title: Glioma stem cells (GSC) rep1


title: TVZ NSCs transdcued with Cre virus rep3


title: ttha1139-2-sta

source_name: the sample of ttha1139 gene disruptant during the stationary phase


title: ttha1139-3-sta


title: ttha1046-2-log

source_name: the sample of ttha1046 gene disruptant during the log phase


title: Nr 3_AX-S

source_name: axonal compartment from cultured Smn knockdown motoneurons

value: axonal

tag: genotype/variation

value: Smn knockdown


title: ttha1046-3-log


title: ttha1046-1-log


title: ttha1534-1-log

source_name: the sample of ttha1534 gene disruptant during the log phase


title: ttha1534-2-log


title: ttha1534-3-log


title: ttha1045-3-log

source_name: the sample of ttha1045 gene disruptant during the log phase


title: ttha1045-2-log


title: ttha1045-1-log


title: ttha0910-3-sta

source_name: the sample of ttha0910 gene disruptant during the stationary phase


title: ttha0910-2-sta


title: ttha1045-3-sta

source_name: the sample of ttha1045 gene disruptant during the stationary phase


title: ttha1045-2-sta


title: ttha1045-1-sta


title: ttha0910-1-sta


title: liver_male ko_rep3

city: Ann Arbor

first: Malcolm

last: Low

state: MI

address: 1000 Wall Street

institute: University of Michigan

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Data was analyzed using the affy bioconductor package implemented in the R-statistical environment version 2.12.2. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: liver

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

growth_protocol: Mice were housed in a temperature-controlled environment with a 12:12 hour light:dark cycle and free access to food and water. At 16 weeks of age, mice were euthanized and liver tissue was collected and stored at -80.

extract_protocol: RNA was extracted using the Trizol reagent (Invitrogen) from 100 mg of liver tissue according to the manufacturer's instructions. Quality of RNA was checked with the Agilent 2100 BioAnalyzer.

tag: Sex

value: male

value: sst -/-

value: liver

tag: genetic background


title: ttha0910-3-log

source_name: the sample of ttha0910 gene disruptant during the log phase


title: TVZ NSCs transduced with control LacZ virus rep3


title: liver_male ko_rep2


title: TVZ NSCs transduced with control LacZ virus rep1


title: liver_male wt_rep2

value: sst +/+


title: liver_female ko_rep2

value: female


title: ttha0540-3-sta

source_name: the sample of ttha0540 gene disruptant during the stationary phase


title: ttha0910-1-log


title: ttha0910-2-log


title: liver_female wt_rep3


title: liver_male wt_rep1


title: Prostate_Tumor_HSPH0127

department: Medicine

source_name: FFPE prostate tumor


title: ttha0540-3-log

source_name: the sample of ttha0540 gene disruptant during the log phase


title: ttha0540-1-sta


title: Prostate_Tumor_HSPH0123


title: liver_female ko_rep3


title: ttha0540-2-sta


title: liver_male ko_rep1


title: liver_male wt_rep3


title: liver_female ko_rep1


title: ttha0540-2-log


title: ttha0540-1-log


title: ttha0252-3-sta

source_name: the sample of ttha0252 gene disruptant during the stationary phase


title: liver_female wt_rep2


title: ttha0252-2-sta


title: TVZ NSCs transduced with control LacZ virus rep2


title: ttha1139-1-sta


title: ttha1046-3-sta

source_name: the sample of ttha1046 gene disruptant during the stationary phase


title: ttha0252-1-sta


title: ttha1139-3-log

source_name: the sample of ttha1139 gene disruptant during the log phase


title: ttha1139-2-log


title: ttha1139-1-log


title: ttha0252-3-log

source_name: the sample of ttha0252 gene disruptant during the log phase