title: Lung_C3H_P21_r3

description:
Sample name: C3H_P21_534_m534_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P21


title: Lung_C3H_P21_r2

status: Public on Jul 01 2016

type: RNA

city: Bar Harbor

first: Carol

last: Bult

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

description:
Sample name: C3H_P21_352_m352_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

hyb_protocol: As per standard Affymetrix protocol for the Mouse 1.0ST arrays.

scan_protocol: GeneChips were scanned by the GeneChip® Scanner 3000 7G (Affymetrix) using the AGCC Scan Control software program.

data_processing:
First data was processed using DeSNPer, a tool developed at the Center for Genome Dynamics (Jackson Laboratory) which removes probes with single nucleotide polymorphisms within the three strains of interest to reduce hybridization bias. Then a custom probe annotation pipeline was used to align probe sequences with the Ensembl Release 70 Mus musculus transcriptome. Next, data was log2-transformed, then probe-level hybridization intensities were quantile normalized and median polished to generate summarized expression values. Finally, transcriptome-alignment locations from the remaining probe sequences were converted to genomic locations for gene-level annotation.
RMA log2 expression values.
See supplementary files linked to the Series record.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for the Mouse 1.0ST arrays from 250-300ng total RNA.

growth_protocol: Mice were fed regular lab chow diet ad libitum until time of tissue harvest.

extract_protocol: RNA was extracted using mirVana isolation kits (Ambion) following manufacturer's instructions. An additional DNAse I (Promega) step was added before organic extraction. RNA quality was assessed using RNA 6000 LabChip assays and 2100 Bioanalyzer (Agilent Technologies). OD 260/280 and OD 260/230 ratios were also measured using nanodrop spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Immediately following dissection, whole lung tissues (or whole embryos for time point e9.5) were placed in RNAlater and stored at -80C.

tag: tissue

value: Lung

tag: strain

tag: stock

tag: age

tag: stage1 (canonical stages of lung development)

tag: stage2 (molecular divisions of lung development)


title: IGFR_100nM_IGF-1_Clone_3

city: Boston

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

description:
IGFR_stimulated_Clone_3
s18

hyb_protocol: 3.5ug of fragmented and labeled cDNA was used to make 150ul hyb cocktail, of which 130ul was injected into GeneChip Mouse Gene 2.0 ST arrays and hybridized for 16 hours at 45°C. Arrays were washed and stained using Affymetrix Fluidics Station 450 with reagents from Affymetrix.

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

data_processing: Data were analyzed using RMA, on Affymetrix Expression Console.

label_protocol: 5.5 ug of ss-cDNA was fragmented then labeled with biotin using the WT PLUS protocol from Affymetrix.

growth_protocol: The IR/IGFR double floxed mouse pups were used to collect brown preadipocytes, immortalized by SV40, and infected with adenoviral Cre to induce recombination and endogenous IR and IGF1R deletion (DKO). Normal receptors as well as chimeric receptors were then reconstituted into the DKO cells using retroviral expression system.

extract_protocol: Total RNA was extracted using an RNeasy mini kit (Qiagen) following manufacturer’s manual.

treatment_protocol: Cells were serum starved overnight with DMEM + 0.1% BSA. Cells were then treated with insulin or IGF-1 (100 nM) for 6 h and then washed once with cold 1 × PBS and resuspended in RLT lysis buffer (Qiagen).

tag: cell type

value: brown preadipocytes

tag: genotype

value: IR and IGF1R DKO

tag: reconstituted with

value: IGFR

tag: treatment


title: IR_IGFR_100nM_Insulin_Clone_2

description:
IR_IGFR_stimulated_Clone_2
s10

value: insulin


title: Ji_Batch6_55

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

description:
Baseline (day 0) = pre-vaccination
whole blood  transcripts
STANSUB_SLVP022-010-2013
protocol manuals are available on the series record

data_processing: Genespring GX 12.6., RMA normalization: median of all samples

organism: Homo sapiens

value: whole blood

tag: time point

value: day 0 (before vaccination)

tag: Sex

value: female

tag: race

value: Native Hawaiian or Other Pacific Islander


title: IR_IGFR_nostimulated_Clone_3

description:
IR_IGFR_nostimulated_Clone_3
s11

value: not stimulated


title: 190-29554-V

city: Chicago

first: Silvia

last: Kariuki

state: IL

department: Human Genetics

institute: University of Chicago

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalized and variance transformed using LUMI package in R

source_name: PBMCs

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

extract_protocol: RNA was extracted with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: PBMCs were treated with phytohemagglutinin with 1,25-dihydroxyvitamin D3, or vehicle control (EtOH) for 6hours

value: PBMC

tag: ethnic group

value: African American

value: 1,25 dihydroxyvitamin D3 + phytohemagglutinin


title: Ji_Batch6_54

description:
Baseline (day 0) = pre-vaccination
whole blood  transcripts
STANSUB_SLVP022-009-2013
protocol manuals are available on the series record

value: male

value: Asian


title: 187-29536-E

value: vehicle (EtOH) + phytohemagglutinin


title: 185-29524-E


title: Ji_Batch6_53

description:
Baseline (day 0) = pre-vaccination
whole blood  transcripts
STANSUB_SLVP022-012-2013
protocol manuals are available on the series record

value: White


title: 186-29524-V


title: Ji_Batch6_56

description:
Baseline (day 0) = pre-vaccination
whole blood  transcripts
STANSUB_SLVP022-013-2013
protocol manuals are available on the series record


title: 188-29536-V


title: Lung_C3H_P21_r1

description:
Sample name: C3H_P21_124_m124_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

value: Lung


title: Ji-Batch3-9

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-047-2011
protocol manuals are available on the series record

data_processing: Genespring GX 12.6.1, RMA normalization: median of all samples

source_name: whole blood depleted of globin transcripts

value: plasmablast

tag: timepoint

value: day 0 (before vaccine)

tag: vaccine

value: Fluzone Intradermal|49281-703-55


title: IR_IGFR_nostimulated_Clone_1

description:
IR_IGFR_nostimulated_Clone_1
s7

value: brown preadipocytes

value: IR and IGF1R DKO


title: IR_nostimulated_Clone_3

description:
IR_nostimulated_Clone_3
s5

value: IR


title: 181-29523-V


title: Ji-Batch3-8

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-021-2011
protocol manuals are available on the series record

value: female

value: FluMist Intranasal spray|66019-109-10


title: IR_IGFR_100nM_Insulin_Clone_1

description:
IR_IGFR_stimulated_Clone_1
s8

value: insulin


title: Lung_C3H_P14_r2

description:
Sample name: C3H_P14_077_m77_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P14


title: IR_100nM_Insulin_Clone_2

description:
IR_stimulated_Clone_2
s4


title: Lung_C3H_P14_r1

description:
Sample name: C3H_P14_076_m76_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: IR_100nM_Insulin_Clone_3

description:
IR_stimulated_Clone_3
s6


title: 177-29401-E

value: PBMC


title: Lung_C3H_P13_r3

description:
Sample name: C3H_P13_046_m660_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P13


title: Ji-Batch3-7

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-042-2011
protocol manuals are available on the series record

value: Other


title: 183-29523-E

value: African American


title: Lung_C3H_P13_r2

description:
Sample name: C3H_P13_045_m659_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: IR_100nM_Insulin_Clone_1

description:
IR_stimulated_Clone_1
s2


title: 178-29401-V

value: 1,25 dihydroxyvitamin D3 + phytohemagglutinin


title: IR_nostimulated_Clone_1

description:
IR_nostimulated_Clone_1
s1

value: not stimulated


title: Ji-Batch3-6

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-071-2011
protocol manuals are available on the series record


title: Lung_C3H_P13_r1

description:
Sample name: C3H_P13_044_m658_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 175-29404-V


title: Lung_C3H_P12_r3

description:
Sample name: C3H_P12_074_m774_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P12


title: 174-29404-E

value: vehicle (EtOH) + phytohemagglutinin


title: Ji-Batch3-59

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-016-2011
protocol manuals are available on the series record


title: Ji-Batch3-58

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-028-2011
protocol manuals are available on the series record

value: male


title: 170-28515-V


title: Lung_C3H_P14_r3

description:
Sample name: C3H_P14_075_m775_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

value: Lung


title: Lung_C3H_P12_r2

description:
Sample name: C3H_P12_073_m773_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 169-28515-E


title: Ji-Batch3-57

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-018-2011
protocol manuals are available on the series record

value: plasmablast

value: White


title: Ji-Batch3-60

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-005-2011
protocol manuals are available on the series record

value: day 0 (before vaccine)

value: Asian


title: 168-28947-V


title: Lung_C3H_P12_r1

description:
Sample name: C3H_P12_040_m648_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C3H_P11_r2

description:
Sample name: C3H_P11_194_m628_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P11


title: Lung_C3H_P11_r1

description:
Sample name: C3H_P11_193_m627_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Ji-Batch3-56

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-034-2011
protocol manuals are available on the series record

value: Fluzone Intradermal|49281-703-55


title: Lung_C3H_P11_r3

description:
Sample name: C3H_P11_043_m651_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Ji-Batch3-54

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-063-2011
protocol manuals are available on the series record


title: Ji-Batch3-51

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-036-2011
protocol manuals are available on the series record


title: 165-29310-E


title: Lung_C3H_P09_r2

description:
Sample name: C3H_P09_192_m625_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P09


title: 167-28947-E


title: 161-28798-V


title: Ji-Batch3-52

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-048-2011
protocol manuals are available on the series record


title: Lung_C3H_P09_r1

description:
Sample name: C3H_P09_191_m624_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Ji-Batch3-5

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-013-2011
protocol manuals are available on the series record


title: 163-29310-V


title: Ji-Batch3-50

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-058-2011
protocol manuals are available on the series record


title: Lung_C3H_P09_r3

description:
Sample name: C3H_P09_039_m642_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 160-28798-E


title: Ji-Batch3-53

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-014-2011
protocol manuals are available on the series record


title: 159-28652-V


title: Lung_C3H_P07_r3

description:
Sample name: C3H_P07_078_m778_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P07


title: Lung_C3H_P07_r2

description:
Sample name: C3H_P07_077_m777_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 158-28652-E


title: Lung_C3H_P07_r1

description:
Sample name: C3H_P07_041_m649_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C3H_P05_r2

description:
Sample name: C3H_P05_393_m393_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P05


title: Lung_C3H_P05_r1

description:
Sample name: C3H_P05_392_m392_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C3H_P05_r3

description:
Sample name: C3H_P05_076_m776_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Ji-Batch3-49

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-001-2011
protocol manuals are available on the series record


title: Lung_C3H_P04_r3

description:
Sample name: C3H_P04_519_m519_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P04


title: 153-28355-V


title: 156-28355-E


title: 149-28797-E


title: Ji-Batch3-44

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-009-2011
protocol manuals are available on the series record


title: Lung_C3H_P04_r2

description:
Sample name: C3H_P04_518_m518_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 150-28797-V


title: Ji-Batch3-42

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-010-2011
protocol manuals are available on the series record


title: Ji-Batch3-47

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-040-2011
protocol manuals are available on the series record


title: Ji-Batch3-45

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-044-2011
protocol manuals are available on the series record


title: Ji-Batch3-48

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-020-2011
protocol manuals are available on the series record

value: American Indian or Alaska Native


title: Lung_C3H_P04_r1

description:
Sample name: C3H_P04_517_m517_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Ji-Batch3-39

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-025-2011
protocol manuals are available on the series record

value: female


title: 139-28642-E


title: Ji-Batch3-40

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-002-2011
protocol manuals are available on the series record


title: 147-28221-V


title: Ji-Batch3-46

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-082-2011
protocol manuals are available on the series record


title: Ji-Batch3-41

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-006-2011
protocol manuals are available on the series record

value: FluMist Intranasal spray|66019-109-10


title: 144-28499-E


title: 140-28642-V


title: 146-28221-E


title: 142-28499-V


title: Ji-Batch3-38

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-035-2011
protocol manuals are available on the series record


title: 138-28776-V


title: Lung_C3H_P03_r2

description:
Sample name: C3H_P03_067_m732_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P03


title: Ji-Batch3-43

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-017-2011
protocol manuals are available on the series record

value: Fluzone multi-dose vial|49281-388-15


title: Lung_C3H_P03_r1

description:
Sample name: C3H_P03_066_m731_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C3H_P03_r3

description:
Sample name: C3H_P03_068_m733_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Ji-Batch3-4

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-057-2011
protocol manuals are available on the series record


title: Lung_C3H_P02_r1

description:
Sample name: C3H_P02_540_m540_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P02


title: Lung_C3H_P02_r3

description:
Sample name: C3H_P02_064_m729_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C3H_P02_r2

description:
Sample name: C3H_P02_063_m728_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C3H_P0_r1

description:
Sample name: C3H_P0_397_m397_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P0


title: 135-29439-E

value: PBMC


title: 137-28776-E


title: Lung_C3H_P0_r3

description:
Sample name: C3H_P0_072_m755_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 133-29439-V


title: Ji-Batch3-37

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-061-2011
protocol manuals are available on the series record


title: 129-28688-V


title: Ji-Batch3-36

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-079-2011
protocol manuals are available on the series record


title: Ji-Batch3-35

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-060-2011
protocol manuals are available on the series record


title: IR_nostimulated_Clone_2

description:
IR_nostimulated_Clone_2
s3

value: brown preadipocytes

value: IR and IGF1R DKO

value: IR


title: Ji-Batch3-34

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-024-2011
protocol manuals are available on the series record


title: 130-28598-E

value: African American


title: 131-28598-V

value: 1,25 dihydroxyvitamin D3 + phytohemagglutinin


title: Ji-Batch3-3

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-067-2011
protocol manuals are available on the series record


title: Ji-Batch3-31

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-046-2011
protocol manuals are available on the series record

value: male

value: Other


title: 126-28684-E

value: vehicle (EtOH) + phytohemagglutinin


title: Lung_C3H_P0_r2

description:
Sample name: C3H_P0_398_m398_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

value: Lung


title: Ji-Batch3-32

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-029-2011
protocol manuals are available on the series record

value: plasmablast

value: day 0 (before vaccine)

value: White


title: Ji-Batch3-30

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-003-2011
protocol manuals are available on the series record


title: 128-28688-E


title: Lung_C3H_e18.5_r2

description:
Sample name: C3H_e18.5_250_m250_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, e18.5


title: Lung_C3H_e18.5_r1

description:
Sample name: C3H_e18.5_248_m248_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C3H_e18.5_r3

description:
Sample name: C3H_e18.5_251_m251_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 122-29443-V


title: Ji-Batch3-29

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-065-2011
protocol manuals are available on the series record

value: Fluzone Intradermal|49281-703-55


title: Lung_C3H_e17.5_r2

description:
Sample name: C3H_e17.5_013_m13_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, e17.5


title: Ji-Batch3-27

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-052-2011
protocol manuals are available on the series record

value: female


title: Ji-Batch3-26

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-081-2011
protocol manuals are available on the series record


title: 121-29443-E


title: 120-28657-V


title: Lung_C3H_e17.5_r1

description:
Sample name: C3H_e17.5_012_m12_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 124-28684-V


title: Lung_C3H_e16.5_r3

description:
Sample name: C3H_e16.5_329_m329_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, e16.5


title: Lung_C3H_e17.5_r3

description:
Sample name: C3H_e17.5_014_m14_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C3H_e16.5_r2

description:
Sample name: C3H_e16.5_223_m223_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C3H_e16.5_r1

description:
Sample name: C3H_e16.5_009_m9_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Ji-Batch3-24

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-038-2011
protocol manuals are available on the series record


title: Ji-Batch3-25

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-080-2011
protocol manuals are available on the series record


title: Lung_C3H_e15.5_r3

description:
Sample name: C3H_e15.5_460_m460_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, e15.5


title: Ji-Batch3-28

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-084-2011
protocol manuals are available on the series record


title: Lung_C3H_e15.5_r2

description:
Sample name: C3H_e15.5_459_m459_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Ji-Batch3-23

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-030-2011
protocol manuals are available on the series record


title: CCK_50 nM_D21 Repl tech1

city: Bagnols sur Cèze

first: Odette

last: Prat

address: Site de Marcoule

department: Life Science

country: France

institute: CEA

description:
ex-vivo
Gene expression at D21
Sample 81

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µL of 2X Gex Hybridization Buffer Hi-RPM was added to the fragmentation mixture and hybridized to Human V2 4x44K oligo microarrays (Agilent) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent), then dried at ambiant atmosphere.

scan_protocol: Microarrays were scanned immediately after washing on the Agilent Scanner using one color scan setting.

data_processing:
The scanned images were analyzed with Feature Extraction software (Agilent technologies) using one-color treatment to obtain background subtracted and spatially detrended Processed Signal intensities.  Non-uniform outliers were excluded. Data were statistically analyzed with Genespring GX12 software (Agilent technologies).
Normalized signal intensities in Series supplementary file processed_data.txt

organism: Rattus norvegicus

source_name: seminiferous tubules, D21, 50 nM CCK

label_protocol: RNA samples were amplified and labeled with cyanine-3 fluorophore using a Low Input Quick Amp Labeling Kit (Agilent), according to the supplier’s protocol. The efficiency of fluorescent labelling was controlled by UV spectroscopy (Nanodrop 1000).

growth_protocol: The entire study was performed ex vivo using three cultures of seminiferous tubules. For these cultures, Male 23-day-old Sprague Dawley rats from Charles River, having undergone no treatment, were used. Testes from eight rats were pooled in every culture, and used immediately. The same population was seeded for control cultures and cultures exposed to toxicant. Analyses were performed at days 7 (D7), 14 (D14) and 21 (D21) of the cultures.

extract_protocol: Total RNAs were extracted using the RNeasy Mini Kit (Qiagen). RNAs were quantified with the NanoDrop 1000 spectrophotometer and their qualities were assessed with the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Cultures were performed with and without fungicides. When required, CBZ, IPR or mixture was added beginning from day 2, at 50 nM or 500 nM for CBZ and at 50 nM or 500 nM for IPR; 50 nM each or 500 nM each for the mixture. For microarray experiments, three different pools of seminiferous tubules were exposed to two concentrations of CBZ, IPR or their mixture (50 nM and 500 nM) or to complete medium with vehicle (control cells) for 7, 14, and 21 days. Each condition of exposure to fungicides was compared with control cells at the same time point.

value: Sprague-Dawley

value: Seminiferous tubules


title: 117-28230-E

source_name: PBMCs

value: PBMC


title: 115-28230-V


title: 113-28643-V


title: 112-28643-E


title: Ji-Batch3-22

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-023-2011
protocol manuals are available on the series record

source_name: whole blood depleted of globin transcripts

value: Asian

value: FluMist Intranasal spray|66019-109-10


title: Ji-Batch3-2

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-055-2011
protocol manuals are available on the series record


title: Ji-Batch3-21

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-031-2011
protocol manuals are available on the series record


title: CCK_50 nM_D21 Repl tech2

description:
ex-vivo
Gene expression at D21
Sample 82


title: 110-28203-E


title: Ji-Batch3-19

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-007-2011
protocol manuals are available on the series record


title: Lung_C3H_e15.5_r1

description:
Sample name: C3H_e15.5_455_m455_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CCK_50 nM_D21 Repl tech3

description:
ex-vivo
Gene expression at D21
Sample 83


title: 119-28657-E


title: 108-28772-E


title: CCK_500 nM_D21 Repl tech2

description:
ex-vivo
Gene expression at D21
Sample 79

source_name: seminiferous tubules, D21, 500 nM CCK


title: Lung_C3H_e14.5_r2

description:
Sample name: C3H_e14.5_237_m237_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, e14.5


title: CCK_500 nM_D21 Repl tech1

description:
ex-vivo
Gene expression at D21
Sample 78


title: CCK_500 nM_D21 Repl tech3

description:
ex-vivo
Gene expression at D21
Sample 80


title: 111-28203-V


title: Lung_C3H_e14.5_r3

description:
Sample name: C3H_e14.5_183_m552_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Ji-Batch3-18

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-027-2011
protocol manuals are available on the series record


title: CCK_500 nM_D14 Repl tech3

description:
ex-vivo
Gene expression at D14
Sample 77

source_name: seminiferous tubules, D14, 500 nM CCK


title: Lung_C3H_e14.5_r1

description:
Sample name: C3H_e14.5_175_m175_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CCK_500 nM_D14 Repl tech2

description:
ex-vivo
Gene expression at D14
Sample 76


title: Lung_C3H_e13.5_r2

description:
Sample name: C3H_e13.5_402_m402_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, e13.5


title: 106-28772-V


title: Ji-Batch3-17

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-062-2011
protocol manuals are available on the series record


title: Lung_C3H_e13.5_r3

description:
Sample name: C3H_e13.5_036_m615_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CCK_500 nM_D14 Repl tech1

description:
ex-vivo
Gene expression at D14
Sample 75


title: Lung_C3H_e13.5_r1

description:
Sample name: C3H_e13.5_219_m219_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CTRL_CCK_D21 Repl tech3

description:
ex-vivo
Gene expression at D21
Sample 74

source_name: seminiferous tubules, D21, no treatment


title: 104-28779-V


title: Lung_C3H_e12.5_r3

description:
Sample name: C3H_e12.5_332_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, e12.5


title: CTRL_CCK_D21 Repl tech2

description:
ex-vivo
Gene expression at D21
Sample 73


title: Ji-Batch3-16

description:
Baseline (day 0)
LAIV
STANSUB_SLVP021-069-2011
protocol manuals are available on the series record


title: Ji-Batch3-15

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-059-2011
protocol manuals are available on the series record


title: Lung_C3H_e12.5_r2

description:
Sample name: C3H_e12.5_331_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 103-28779-E


title: 102-28686-V


title: CTRL_CCK_D14 Repl tech3

description:
ex-vivo
Gene expression at D14
Sample 71

source_name: seminiferous tubules, D14, no treatment


title: CTRL_CCK_D14 Repl tech2

description:
ex-vivo
Gene expression at D14
Sample 70


title: Lung_C3H_e12.5_r1

description:
Sample name: C3H_e12.5_327_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C3H_e11.5_r1

description:
Sample name: C3H_e11.5_372374_pooled_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, e11.5


title: Ji-Batch3-14

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-050-2011
protocol manuals are available on the series record


title: Lung_C3H_e11.5_r3

description:
Sample name: C3H_e11.5_316_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CTRL_CCK_D14 Repl tech1

description:
ex-vivo
Gene expression at D14
Sample 69


title: Ji-Batch3-12

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-068-2011
protocol manuals are available on the series record


title: 95-28898-V


title: 97-28513-V


title: CCK_50 nM_D14 Repl tech3

description:
ex-vivo
Gene expression at D14
Sample 68

source_name: seminiferous tubules, D14, 50 nM CCK


title: Ji-Batch3-13

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-026-2011
protocol manuals are available on the series record


title: Ji-Batch3-11

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-022-2011
protocol manuals are available on the series record


title: Ji-Batch3-10

description:
Baseline (day 0)
TIVID
STANSUB_SLVP021-054-2011
protocol manuals are available on the series record


title: CTRL_CCK_D21 Repl tech1

description:
ex-vivo
Gene expression at D21
Sample 72


title: Lung_C3H_e11.5_r2

description:
Sample name: C3H_e11.5_060_m654_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 94-28898-E


title: 101-28686-E


title: CCK_50 nM_D14 Repl tech2

description:
ex-vivo
Gene expression at D14
Sample 67


title: Ji-Batch3-1

description:
Baseline (day 0)
TIVIM
STANSUB_SLVP021-019-2011
protocol manuals are available on the series record


title: 92-28911-E


title: 88-28218-V


title: Embryo_C3H_e09.5_r3

description:
Sample name: C3H_e09.5_305_m305_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Embryo, C3H, e09.5

value: Embryo

value: REF-EMB


title: 90-28218-E

value: African American


title: CCK_50 nM_D14 Repl tech1

description:
ex-vivo
Gene expression at D14
Sample 66


title: 93-28911-V

value: 1,25 dihydroxyvitamin D3 + phytohemagglutinin


title: 99-28513-E


title: Embryo_C3H_e09.5_r2

description:
Sample name: C3H_e09.5_304_m304_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CCK_500 nM_D7 Repl tech3

description:
ex-vivo
Gene expression at D7
Sample 65

source_name: seminiferous tubules, D7, 500 nM CCK


title: CCK_500 nM_D7 Repl tech1

description:
ex-vivo
Gene expression at D7
Sample 63


title: Lung_C57B6_P56_r2

description:
Sample name: B6_P56_073_m73_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P56


title: Lung_C57B6_P56_r1

description:
Sample name: B6_P56_072_m72_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 85-28949-E


title: Lung_C57B6_P56_r3

description:
Sample name: B6_P56_034_m538_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CCK_50 nM_D7 Repl tech3

description:
ex-vivo
Gene expression at D7
Sample 62

source_name: seminiferous tubules, D7, 50 nM CCK


title: CCK_50 nM_D7 Repl tech2

description:
ex-vivo
Gene expression at D7
Sample 61


title: Lung_C57B6_P30_r2

description:
Sample name: B6_P30_071_m71_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P30


title: CCK_50 nM_D7 Repl tech1

description:
ex-vivo
Gene expression at D7
Sample 60


title: 86-28949-V


title: Embryo_C3H_e09.5_r1

description:
Sample name: C3H_e09.5_182_m300_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CCK_500 nM_D7 Repl tech2

description:
ex-vivo
Gene expression at D7
Sample 64


title: CTRL_CCK_D7 Repl tech3

description:
ex-vivo
Gene expression at D7
Sample 59

source_name: seminiferous tubules, D7, no treatment


title: Lung_C57B6_P30_r1

description:
Sample name: B6_P30_070_m70_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C57B6_P30_r3

description:
Sample name: B6_P30_042_m650_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 79-28689-V

source_name: PBMCs


title: 83-28676-E


title: 84-28676-V


title: 77-28257-V


title: NonTu_AKTCAT_CCl4_3

city: Basel

first: Matthias

middle: Sebastian

last: Matter

state: BS

address: Schönbeinstrasse 40

department: Institute of Pathology

country: Switzerland

institute: University of Basel

scan_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with Genome Studio

source_name: Liver non-tumoral tissue

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

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: Liver non-tumoral

tag: cell type/treatment

value: FVB/n


title: NonTu_AKTCAT_CCl4_2

tag: tissue


title: Lung_C57B6_P24_r3

description:
Sample name: B6_P24_489_m489_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P24

value: Lung

tag: strain


title: CTRL_CCK_D7 Repl tech1

description:
ex-vivo
Gene expression at D7
Sample 57


title: CTRL_CCK_D7 Repl tech2

description:
ex-vivo
Gene expression at D7
Sample 58


title: 81-28689-E

value: vehicle (EtOH) + phytohemagglutinin


title: Lung_C57B6_P24_r2

description:
Sample name: B6_P24_488_m488_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

tag: stock


title: NonTu_AKTCAT_CCl4_4


title: 76-28257-E


title: IPR_500 nM_D21 Repl tech4

description:
ex-vivo
Gene expression at D21
Sample 56

source_name: seminiferous tubules, D21, 500 nM IPR


title: IPR_500 nM_D21 Repl tech3

description:
ex-vivo
Gene expression at D21
Sample 55


title: 75-28249-V


title: Tu_AKTCAT_CCl4_4

source_name: Liver tumor tissue

value: Liver tumor


title: Lung_C57B6_P21_r3

description:
Sample name: B6_P21_200_m641_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P21

tag: age


title: 74-28249-E


title: NonTu_AKTCAT_CCl4_1


title: 72-28923-E


title: Tu_AKTCAT_CCl4_2


title: IPR_500 nM_D21 Repl tech2

description:
ex-vivo
Gene expression at D21
Sample 54


title: Tu_AKTCAT_CCl4_3


title: 70-28923-V


title: Lung_C57B6_P21_r2

description:
Sample name: B6_P21_067_m67_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

tag: stage1 (canonical stages of lung development)


title: IPR_500 nM_D21 Repl tech1

description:
ex-vivo
Gene expression at D21
Sample 53


title: Lung_C57B6_P21_r1

description:
Sample name: B6_P21_066_m66_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

tag: stage2 (molecular divisions of lung development)


title: Lung_C57B6_P18_r3

description:
Sample name: B6_P18_203_m645_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P18


title: Lung_C57B6_P24_r1

description:
Sample name: B6_P24_487_m487_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: IPR_50 nM_D21 Repl tech2

description:
ex-vivo
Gene expression at D21
Sample 51

source_name: seminiferous tubules, D21, 50 nM IPR


title: IPR_50 nM_D21 Repl tech3

description:
ex-vivo
Gene expression at D21
Sample 52


title: 68-29328-V

tag: cell type


title: 67-29328-E


title: Lung_C57B6_P18_r2

description:
Sample name: B6_P18_202_m644_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C57B6_P18_r1

description:
Sample name: B6_P18_201_m643_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: IPR_50 nM_D21 Repl tech1

description:
ex-vivo
Gene expression at D21
Sample 50


title: CTRL_IPR_D21 Repl tech3

description:
ex-vivo
Gene expression at D21
Sample 49

source_name: seminiferous tubules, D21, no treatment


title: Lung_C57B6_P14_r2

description:
Sample name: B6_P14_112_m112_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P14


title: Tu_AKTNRAS_DDC_3


title: CTRL_IPR_D21 Repl tech2

description:
ex-vivo
Gene expression at D21
Sample 48


title: Tu_AKTCAT_CCl4_1


title: 66-29420-V


title: 65-29420-E


title: Lung_C57B6_P14_r1

description:
Sample name: B6_P14_111_m111_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Tu_AKTNRAS_DDC_4


title: Tu_AKTNRAS_4

value: AKTNRAS


title: 61-29442-V


title: CTRL_IPR_D21 Repl tech1

description:
ex-vivo
Gene expression at D21
Sample 47


title: Tu_AKTNRAS_DDC_1


title: Tu_AKTNRAS_DDC_2


title: Tu_AKTNRAS_3


title: Tu_AKTNRAS_2


title: 58-29306-E


title: Lung_C57B6_P14_r3

description:
Sample name: B6_P14_061_m714_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 63-29442-E


title: 59-29306-V


title: 57-28687-V


title: Lung_C57B6_P13_r3

description:
Sample name: B6_P13_055_m713_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P13


title: Lung_C57B6_P13_r2

description:
Sample name: B6_P13_054_m712_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: IPR_500 nM_D14 Repl tech3

description:
ex-vivo
Gene expression at D14
Sample 46

source_name: seminiferous tubules, D14, 500 nM IPR


title: IPR_500 nM_D14 Repl tech1

description:
ex-vivo
Gene expression at D14
Sample 44


title: Lung_C57B6_P13_r1

description:
Sample name: B6_P13_053_m711_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: NonTu_AKTCAT_3

value: AKTCAT


title: IPR_50 nM_D14 Repl tech3

description:
ex-vivo
Gene expression at D14
Sample 43

source_name: seminiferous tubules, D14, 50 nM IPR


title: Tu_AKTNRAS_1


title: Lung_C57B6_P12_r3

description:
Sample name: B6_P12_071_m736_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P12


title: IPR_50 nM_D14 Repl tech2

description:
ex-vivo
Gene expression at D14
Sample 42


title: NonTu_AKTCAT_1


title: Lung_C57B6_P12_r2

description:
Sample name: B6_P12_070_m735_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 56-28687-E


title: Lung_C57B6_P12_r1

description:
Sample name: B6_P12_069_m734_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: IPR_50 nM_D14 Repl tech1

description:
ex-vivo
Gene expression at D14
Sample 41


title: IPR_500 nM_D14 Repl tech2

description:
ex-vivo
Gene expression at D14
Sample 45


title: Lung_C57B6_P11_r3

description:
Sample name: B6_P11_052_m697_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P11


title: CTRL_IPR_D14 Repl tech2

description:
ex-vivo
Gene expression at D14
Sample 39

source_name: seminiferous tubules, D14, no treatment


title: Lung_C57B6_P11_r2

description:
Sample name: B6_P11_051_m696_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: NonTu_AKTCAT_2


title: Lung_C57B6_P11_r1

description:
Sample name: B6_P11_050_m695_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Tu_AKTCAT_2


title: 54-28517-E


title: CTRL_IPR_D14 Repl tech1

description:
ex-vivo
Gene expression at D14
Sample 38


title: CTRL_IPR_D14 Repl tech3

description:
ex-vivo
Gene expression at D14
Sample 40


title: Lung_C57B6_P09_r3

description:
Sample name: B6_P09_317_m796_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P09


title: Tu_AKTCAT_4


title: 52-28517-V

source_name: PBMCs


title: 50-28248-V


title: Tu_AKTCAT_1


title: Tu_AKTCAT_3


title: Lung_C57B6_P09_r2

description:
Sample name: B6_P09_049_m694_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: NonTu_AKTCAT_DDC_1

source_name: Liver non-tumoral tissue


title: NonTu_AKTCAT_DDC_2


title: 49-28248-E


title: 47-28585-E


title: 45-29510-E


title: NonTu_AKTCAT_DDC_3


title: 43-29510-V


title: 48-28585-V


title: IPR_500 nM_D7 Repl tech1

description:
ex-vivo
Gene expression at D7
Sample 35

source_name: seminiferous tubules, D7, 500 nM IPR


title: Lung_C57B6_P09_r1

description:
Sample name: B6_P09_048_m693_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: IPR_50 nM_D7 Repl tech3

description:
ex-vivo
Gene expression at D7
Sample 34

source_name: seminiferous tubules, D7, 50 nM IPR


title: Lung_C57B6_P07_r3

description:
Sample name: B6_P07_197_m633_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P07


title: IPR_500 nM_D7 Repl tech3

description:
ex-vivo
Gene expression at D7
Sample 37


title: Tu_AKTCAT_DDC_4

source_name: Liver tumor tissue


title: Tu_AKTCAT_DDC_3


title: IPR_50 nM_D7 Repl tech2

description:
ex-vivo
Gene expression at D7
Sample 33


title: 41-29399-V


title: 40-29399-E


title: IPR_500 nM_D7 Repl tech2

description:
ex-vivo
Gene expression at D7
Sample 36


title: Lung_C57B6_P07_r2

description:
Sample name: B6_P07_190_m609_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 39-29441-V


title: Lung_C57B6_P07_r1

description:
Sample name: B6_P07_189_m608_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CTRL_IPR_D7 Repl tech3

description:
ex-vivo
Gene expression at D7
Sample 31

source_name: seminiferous tubules, D7, no treatment


title: IPR_50 nM_D7 Repl tech1

description:
ex-vivo
Gene expression at D7
Sample 32


title: Lung_C57B6_P05_r2

description:
Sample name: B6_P05_551_m551_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P05


title: 38-29441-E


title: CTRL_IPR_D7 Repl tech2

description:
ex-vivo
Gene expression at D7
Sample 30


title: Lung_C57B6_P05_r1

description:
Sample name: B6_P05_265_m265_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CTRL_IPR_D7 Repl tech1

description:
ex-vivo
Gene expression at D7
Sample 29


title: Tu_AKTCAT_DDC_1


title: Lung_C57B6_P04_r3

description:
Sample name: B6_P04_550_m550_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P04


title: 36-28943-E


title: PBS_only_2

source_name: Liver tissue

value: liver


title: 34-28943-V


title: CBZ_500 nM_D21 Repl tech3

description:
ex-vivo
Gene expression at D21
Sample 28

source_name: seminiferous tubules, D21, 500 nM CBZ

value: Sprague-Dawley


title: PBS_only_1


title: Tu_AKTCAT_DDC_2


title: PBS_only_3


title: Lung_C57B6_P04_r2

description:
Sample name: B6_P04_513_m513_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 32-28256-V


title: DDC_only_2


title: Lung_C57B6_P04_r1

description:
Sample name: B6_P04_512_m512_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 30-29225-V


title: 31-28256-E


title: 29-29225-E


title: CBZ_500 nM_D21 Repl tech2

description:
ex-vivo
Gene expression at D21
Sample 27

value: Seminiferous tubules


title: Lung_C57B6_P03_r2

description:
Sample name: B6_P03_547_m547_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P03


title: CBZ_500 nM_D21 Repl tech1

description:
ex-vivo
Gene expression at D21
Sample 26


title: CBZ_50 nM_D21 Repl tech3

description:
ex-vivo
Gene expression at D21
Sample 25

source_name: seminiferous tubules, D21, 50 nM CBZ


title: CBZ_50 nM_D21 Repl tech2

description:
ex-vivo
Gene expression at D21
Sample 24


title: Lung_C57B6_P03_r1

description:
Sample name: B6_P03_546_m546_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: DDC_only_1


title: CBZ_50 nM_D21 Repl tech1

description:
ex-vivo
Gene expression at D21
Sample 23


title: Lung_C57B6_P02_r2

description:
Sample name: B6_P02_545_m545_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P02


title: 27-28511-E

value: PBMC


title: AC RLN injury 3

city: Carmel

first: Stacey

last: Halum

state: IN

address: 1185 Carmel Dr.

department: Voice Clinic of Indiana

institute: Purdue

hyb_protocol: each sample was hybridized to an Affymetrix Rat Gene 1.0 ST array using the standard Affymetrix protocol

scan_protocol: Scanned using the affymetrix GS30007G using Affymetrix Command Console (AGCC)

data_processing: Cel files were generated by AGCC and imported into Partek Genomics Suite  RMA (robust multi-array average) signals were generated using the RMA background correction, Quantile normalization and summarization by Median Polish. RMA data was log base 2 transformed.   RMA was generated only for core probe sets as designated by Affymetrix.

molecule: polyA RNA

source_name: laryngeal adductor complex

label_protocol: 100ng of total RNA was labeled using the Ambion WT Expression kit combined with the Affymetrix GeneChip® WT Terminal Labeling and Controls Kit

extract_protocol: For each adductor or PCA specimen, 30-50 mg of tissue was disrupted and homogenized using zirconia 1 mm beads (BioSpec Producers Inc, Bartlesville, OK) with density of 3.7 g/ml in a tissue homogenizer (Min-bead Beater-8, BioSpec Products Inc, Bartlesville, OK) for 3 min at 4°C. The total RNA was extracted and purified using RNeasy Fibrous Tissue MiniKit (QIAGEN, Austin, Texas). RNA concentrations were determined using a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific Inc.). The quality of purified total RNA was determined by optical density (A260/A280 ratio between 1.8 and 2.1) and electrophoresis on 1% agarose gel (ensuring the 18S and 28S bands are clearly distinguished), with a minimum of 5μg total RNA as starting material.

treatment_protocol: All animals underwent anesthesia with intraperitoneal (IP) ketamine (75 mg/kg) and xylazine (10 mg/kg).  Study animals underwent unilateral recurrent laryngeal nerve (RLN) transection with removal of a 1 cm nerve segment, while control animals underwent the same surgical approach with no nerve injury.  Before awakening from anesthesia, unilateral vocal fold motion immobility and normal motion were confirmed in the study and control animals, respectively. At one week following the denervation surgery, all 10 animals from each group were euthanized.

tag: gender

value: male

value: denervated

value: laryngeal adductor complex


title: 25-28511-V


title: Lung_C57B6_P03_r3

description:
Sample name: B6_P03_035_m548_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CTRL_CBZ_D21 Repl tech3

description:
ex-vivo
Gene expression at D21
Sample 22

source_name: seminiferous tubules, D21, no treatment


title: Lung_C57B6_P02_r1

description:
Sample name: B6_P02_544_m544_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C57B6_P02_r3

description:
Sample name: B6_P02_038_m632_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CTRL_CBZ_D21 Repl tech2

description:
ex-vivo
Gene expression at D21
Sample 21


title: DDC_only_3


title: 22-28641-E


title: Lung_C57B6_P0_r3

description:
Sample name: B6_P0_539_m539_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C57B6, P0


title: AC RLN injury 1


title: 23-28641-V

source_name: PBMCs


title: PCA RLN injury 3

source_name: abducting posterior cricoarytenoid muscle


title: AC RLN injury 2


title: CBZ_500 nM_D14 Repl tech4

description:
ex-vivo
Gene expression at D14
Sample 19

source_name: seminiferous tubules, D14, 500 nM CBZ


title: PCA RLN injury 2

value: abducting posterior cricoarytenoid muscle


title: 21-28592-V

value: African American


title: PCA RLN injury 1


title: Lung_C57B6_P0_r2

description:
Sample name: B6_P0_116_m116_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 20-28592-E


title: CBZ_500 nM_D14 Repl tech3

description:
ex-vivo
Gene expression at D14
Sample 18


title: 16-28498-V

value: 1,25 dihydroxyvitamin D3 + phytohemagglutinin


title: Lung_C57B6_P0_r1

description:
Sample name: B6_P0_115_m115_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CBZ_500 nM_D14 Repl tech2

description:
ex-vivo
Gene expression at D14
Sample 17


title: AC control 2

value: control


title: 14-28344-V


title: AC control 1


title: CTRL_CBZ_D21 Repl tech1

description:
ex-vivo
Gene expression at D21
Sample 20


title: Lung_C57B6_e18.5_r2

description:
Sample name: B6_e18.5_241_m241_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 13-28344-E


title: PCA control 3


title: CBZ_500 nM_D14 Repl tech1

description:
ex-vivo
Gene expression at D14
Sample 16


title: Lung_C57B6_e18.5_r1

description:
Sample name: B6_e18.5_240_m240_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CBZ_50 nM_D14 Repl tech3

description:
ex-vivo
Gene expression at D14
Sample 15

source_name: seminiferous tubules, D14, 50 nM CBZ


title: Lung_C57B6_e18.5_r3

description:
Sample name: B6_e18.5_062_m717_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: AC control 3


title: 12-29516-V


title: 18-28498-E


title: 11-29516-E


title: 9-29514-E


title: PCA control 1


title: CBZ_50 nM_D14 Repl tech1

description:
ex-vivo
Gene expression at D14
Sample 13


title: CBZ_50 nM_D14 Repl tech2

description:
ex-vivo
Gene expression at D14
Sample 14


title: CTRL_CBZ_D14 Repl tech3

description:
ex-vivo
Gene expression at D14
Sample 12

source_name: seminiferous tubules, D14, no treatment


title: Lung_C57B6_e17.5_r1

description:
Sample name: B6_e17.5_339_m339_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 7-29514-V


title: Lung_C57B6_e16.5_r3

description:
Sample name: B6_e16.5_232_m232_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CTRL_CBZ_D14 Repl tech2

description:
ex-vivo
Gene expression at D14
Sample 11


title: Lung_C57B6_e16.5_r2

description:
Sample name: B6_e16.5_036_m36_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C57B6_e16.5_r1

description:
Sample name: B6_e16.5_035_m35_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 5-28354-V


title: CTRL_CBZ_D14 Repl tech1

description:
ex-vivo
Gene expression at D14
Sample 10


title: CBZ_500 nM_D7 Repl tech3

description:
ex-vivo
Gene expression at D7
Sample 9

source_name: seminiferous tubules, D7, 500 nM CBZ


title: Lung_C57B6_e17.5_r2

description:
Sample name: B6_e17.5_342_m342_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C57B6_e15.5_r3

description:
Sample name: B6_e15.5_486_m486_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: PCA control 2


title: siOrm1

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: Gene expression of Orm knockdown mouse livers

hyb_protocol: Oligonucleotide microarray experiments were performed using Affymetrix GeneChip Mouse Genome 430A 2.0 Array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The arrays were scanned using an GenePix 4000B microarray scanner (Axon Instruments, Union City, CA, USA).

data_processing: Data normalization and analysis was performed with GeneSpring GX13.0 (Agilent Technologies). The signal intensities for each probe were normalized to the 75th percentile without baseline transformation and filtered by percentile (1 out of 4 samples have values between 20.0 and 100 percentile).

source_name: siOrm

label_protocol: RNA was amplified into cRNA and labeled with Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies).

extract_protocol: Total RNA was isolated from the culture cells using an RNeasy Kit (Qiagen, Valencia, CA) in accordancewith the manufacturer’s instructions. Quantification and quality assessment of theisolated RNA samples were performed and verified using a NanoDrop spectrophotometer (NanoDrop products, Wilmington, DE) in accordancewith the manufacturer’s instructions.

value: Male

value: 6-13 weeks


title: siCtl2

description: Gene expression of control mouse livers

source_name: siControl


title: siOrm2


title: siCtl1

description: Gene expression of control mouse livers


title: Lung_C57B6_e15.5_r2

description:
Sample name: B6_e15.5_485_m485_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

value: Lung


title: 3-29422-V


title: CBZ_500 nM_D7 Repl tech1

description:
ex-vivo
Gene expression at D7
Sample 7


title: CBZ_500 nM_D7 Repl tech2

description:
ex-vivo
Gene expression at D7
Sample 8


title: Prom1-positive cells_MACS sorted LQZ340

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: primary cells, normal

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix array per manufacturer's instructions.

scan_protocol: Standard HT TITAN scanning protocol

data_processing: The data were analyzed with Partek Genomics suite 6.6 and in STATA/SE 11.2.

label: Biotin

source_name: uterus

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

extract_protocol: Total RNA of mouse tumor tissues was extract using RNeasy Mini Kit (Qiagen). Total RNA of isolated mouse primary cells were extracted using PicoPure™ extraction kit (Arcturus).

treatment_protocol: For Prom1 MACS sorting, mouse tissues were dissociated into single cells followed by red blood cell lysis and dead cells removal (Miltenyi Biotec, Dead Cell Removal Kit #130-090-101). Cells were then mixed with anti-Prominin1 MicroBeads (Miltenyi Biotec, #130-092-333) for 10 min at 4°. Cells were washed with MACS buffer (Miltenyi Biotec) and sorted according to the manufacturer’s instruction.

tag: sample type

value: Mouse primary cells

value: Prom1-positive cells MACS sorted


title: Prom1-positive cells_MACS sorted LQZ342

description: primary cells, normal


title: 4-28354-E

tag: treatment

value: vehicle (EtOH) + phytohemagglutinin


title: PC9 cocu_yGef_3_WH

city: Heidelberg

first: Sajo

last: Kaduthanam

state: BW

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: DKFZ

description: SAMPLE 12

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

source_name: PC9_MRC-5 co-culture_Gefitinib

growth_protocol: Cells were cultured in RPMI 1640 (10% FCS without antibiotics) medium until experiment. For co-culture experiment with MRC-5 cells EMEM (10% FCS without antibiotics) medium was used

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

treatment_protocol: Cell were treated with 0.5µM Gefitinib after 24h, washed with PBS twice, thereafter cultured in EMEM medium (10% FCS) and co-cultured with MRC-5 cells for 48h using transwell inserts (1µm pore)

tag: cell line

value: NSCLC cell line

tag: co-cultured with

value: MRC-5 cells

tag: treated with

value: 0.5µM Gefitinib


title: 2-29422-E

value: PBMC

tag: ethnic group


title: Prom1-positive cells_MACS sorted LQZ338

description: primary cells, normal


title: PC9 cocu_yGef_2_WH

description: SAMPLE 11


title: Lung_C57B6_e14.5_r3

description:
Sample name: B6_e14.5_047_m662_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CBZ_50 nM_D7 Repl tech2

description:
ex-vivo
Gene expression at D7
Sample 5

source_name: seminiferous tubules, D7, 50 nM CBZ

value: Sprague-Dawley

value: Seminiferous tubules


title: PC9 cocu_yGef_1_WH

description: SAMPLE 10


title: Prom1-positive cells_MACS sorted LQZ334

description: primary cells, normal


title: PC9 cocu_nGef_3_WH

description: SAMPLE 9

source_name: PC9_MRC-5 co-culture


title: Lung_C57B6_e14.5_r2

description:
Sample name: B6_e14.5_030_m30_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Prom1-positive cells_MACS sorted LQZ332

description: primary cells, normal

source_name: stomach


title: Lung_C57B6_e12.5_r2

description:
Sample name: B6_e12.5_439_m439_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CBZ_50 nM_D7 Repl tech3

description:
ex-vivo
Gene expression at D7
Sample 6


title: CTRL_CBZ_D7 Repl tech3

description:
ex-vivo
Gene expression at D7
Sample 3

source_name: seminiferous tubules, D7, no treatment


title: Lung_C57B6_e15.5_r1

description:
Sample name: B6_e15.5_483_m483_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CBZ_50 nM_D7 Repl tech1

description:
ex-vivo
Gene expression at D7
Sample 4


title: Lung_C57B6_e12.5_r3

description:
Sample name: B6_e12.5_079_m786_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C57B6_e14.5_r1

description:
Sample name: B6_e14.5_029_m29_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CTRL_CBZ_D7 Repl tech1

description:
ex-vivo
Gene expression at D7
Sample 1


title: Lung_C57B6_e12.5_r1

description:
Sample name: B6_e12.5_032_m433_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CTRL_CBZ_D7 Repl tech2

description:
ex-vivo
Gene expression at D7
Sample 2


title: Lung_C57B6_e11.5_r3

description:
Sample name: B6_e11.5_336_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Prom1-positive cells_MACS sorted LQZ302

description: primary cells, normal

source_name: small intestine


title: Prom1-positive cells_MACS sorted LQZ326

description: primary cells, normal


title: PC9 cocu_nGef_2_WH

description: SAMPLE 8


title: Prom1-positive cells_MACS sorted LQZ297

description: primary cells, normal


title: PC9 cocu_nGef_1_WH

description: SAMPLE 7


title: PC9 ctrl_yGef_2

description: SAMPLE 5


title: Prom1-positive cells_MACS sorted LQZ159

description: primary cells, normal


title: Lung_C57B6_e11.5_r2

description:
Sample name: B6_e11.5_330_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_C57B6_e11.5_r1

description:
Sample name: B6_e11.5_328_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: PC9 ctrl_yGef_3

description: SAMPLE 6


title: Prom1-positive cells_MACS sorted LQZ479

description: primary cells, normal

source_name: salivary gland


title: Embryo_C57B6_e09.5_r3

description:
Sample name: B6_e09.5_314_m314_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Embryo, C57B6, e09.5

value: Embryo

value: REF-EMB


title: Embryo_C57B6_e09.5_r2

description:
Sample name: B6_e09.5_311_m311_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: PC9 ctrl_nGef_3

description: SAMPLE 3

value: DMSO


title: Embryo_C57B6_e09.5_r1

description:
Sample name: B6_e09.5_144_m144_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Prom1-positive cells_MACS sorted LQZ478

description: primary cells, normal


title: Lung_AJ_P56_r3

description:
Sample name: AJ_P56_549_m549_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P56

value: A/J


title: PC9 ctrl_nGef_1

description: SAMPLE 1


title: Lung_AJ_P56_r2

description:
Sample name: AJ_P56_107_m107_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: PC9 ctrl_yGef_1

description: SAMPLE 4


title: PC9 ctrl_nGef_2

description: SAMPLE 2


title: Lung_AJ_P56_r1

description:
Sample name: AJ_P56_106_m106_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: HCC827 cocu_yGef_3_WH

description: SAMPLE 12

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
First six and last six samples were separately quantile normalized as they were measured on different Chips

source_name: HCC827_MRC-5 co-culture_Gefitinib


title: Prom1-positive cells_MACS sorted LQZ419

description: primary cells, normal

source_name: neonatal liver


title: Prom1-positive cells_MACS sorted LQZ402

description: primary cells, normal


title: Lung_AJ_P30_r3

description:
Sample name: AJ_P30_541_m541_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P30


title: HCC827 cocu_nGef_2_WH

description: SAMPLE 8

source_name: HCC827_MRC-5 co-culture


title: Prom1-positive cells_MACS sorted LQZ481

description: primary cells, normal


title: HCC827 cocu_yGef_1_WH

description: SAMPLE 10


title: Prom1-positive cells_MACS sorted LQZ167

description: primary cells, normal

source_name: prostate


title: Prom1-positive cells_MACS sorted LQZ133

description: primary cells, normal


title: Prom1-positive cells_MACS sorted LQZ161

description: primary cells, normal


title: Prom1-positive cells_MACS sorted LQZ400

description: primary cells, normal


title: Lung_AJ_P30_r2

description:
Sample name: AJ_P30_166_m166_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P30_r1

description:
Sample name: AJ_P30_089_m89_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Prom1-positive cells_MACS sorted LQZ163

description: primary cells, normal

source_name: lung


title: Prom1-positive cells_MACS sorted LQZ220

description: primary cells, normal


title: HCC827 ctrl_yGef_3

description: SAMPLE 6


title: HCC827 cocu_nGef_1_WH

description: SAMPLE 7


title: HCC827 cocu_yGef_2_WH

description: SAMPLE 11


title: Prom1-positive cells_MACS sorted LQZ157

description: primary cells, normal


title: HCC827 cocu_nGef_3_WH

description: SAMPLE 9


title: Lung_AJ_P24_r3

description:
Sample name: AJ_P24_501_m501_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P24


title: Lung_AJ_P24_r2

description:
Sample name: AJ_P24_500_m500_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P21_r2

description:
Sample name: AJ_P21_080_m80_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P21


title: Lung_AJ_P24_r1

description:
Sample name: AJ_P24_499_m499_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P21_r3

description:
Sample name: AJ_P21_542_m542_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Prom1-positive cells_MACS sorted LQZ153

description: primary cells, normal


title: Prom1-positive cells_MACS sorted LQZ436

description: primary cells, DDC-treated

source_name: liver


title: HCC827 ctrl_nGef_2

description: SAMPLE 2


title: HCC827 ctrl_yGef_1

description: SAMPLE 4


title: Lung_AJ_P21_r1

description:
Sample name: AJ_P21_079_m79_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: HCC827 ctrl_nGef_3

description: SAMPLE 3


title: HCC827 ctrl_yGef_2

description: SAMPLE 5


title: Prom1-positive cells_MACS sorted LQZ434

description: primary cells, DDC-treated


title: HCC827 ctrl_nGef_1

description: SAMPLE 1


title: Prom1-positive cells_MACS sorted LQZ435

description: primary cells, DDC-treated


title: Lung_AJ_P18_r3

description:
Sample name: AJ_P18_326_m806_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P18


title: Prom1-positive cells_MACS sorted LQZ440

description: primary cells, DDC-treated


title: Prom1-positive cells_MACS sorted LQZ397

description: primary cells, DDC-treated


title: Lung_AJ_P18_r2

description:
Sample name: AJ_P18_205_m647_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Prom1-positive cells_MACS sorted LQZ393

description: primary cells, DDC-treated


title: Lung_AJ_P18_r1

description:
Sample name: AJ_P18_204_m646_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Prom1-positive cells_MACS sorted LQZ392

description: primary cells, DDC-treated


title: F-4872

city: oslo

first: Francesca

last: Micci

address: Ullernchausseen 70

department: Institute for medical informatics

country: Norway

institute: Oslo Universitetssykehus

hyb_protocol: 750 ng of biotin-labeled cRNA was hibridized to the HumanHT-12 v.4 Illumina Sentrix BeadCHip according to the manufacturer's instructions.

data_processing: Bead summary data was imported into GenomeStudio to remove control probes and to produce a text file containing the signal and detection p-values per probe for all samples.

source_name: tumor

extract_protocol: RNA was extracted with Trizol reagent. Using the Illumina TotalPrep RNA Amplification Kit, 500ng were reversely transcribed, amplified and Biotin-16-UTP-labeled. The amount and quality of labeled CDNA were measured using both a NanoDrop spectrophotometer and an Agilent 2100 Bioanalyzer.

tag: histology

value: LG

tag: rearrangment

tag: arraylocation

value: endometrial stroma sarcoma tumor


title: F-5376

label_protocol: Using the Illumina TotalPrep RNA Amplification Kit, 500ng were reversely transcribed, amplified and Biotin-16-UTP-labeled.

tag: tissue


title: Lung_AJ_P14_r1

description:
Sample name: AJ_P14_473_m473_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P14

tag: strain


title: Lung_AJ_P14_r2

description:
Sample name: AJ_P14_037_m631_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

tag: stock


title: Lung_AJ_P13_r3

description:
Sample name: AJ_P13_196_m630_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P13

tag: age


title: Lung_AJ_P13_r2

description:
Sample name: AJ_P13_195_m629_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

tag: stage1 (canonical stages of lung development)


title: Lung_AJ_P13_r1

description:
Sample name: AJ_P13_184_m567_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

tag: stage2 (molecular divisions of lung development)


title: Prom1-positive cells_MACS sorted LQZ376

description: primary cells, DDC-treated

tag: cell type


title: F-5154

value: 6p-rearrangement t(6;7)


title: Prom1-positive cells_MACS sorted LQZ378

description: primary cells, DDC-treated


title: Lung_AJ_P12_r3

description:
Sample name: AJ_P12_329_m828_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P12

value: Lung


title: F-5028

value: other


title: Lung_AJ_P12_r2

description:
Sample name: AJ_P12_325_m805_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 1302-0413


title: F-4293


title: 1202-0855


title: 1102-1002


title: Prom1-positive cells_MACS sorted LQZ228

description: primary cells, normal

value: Mouse primary cells

value: Prom1-positive cells MACS sorted


title: Prom1-positive cells_MACS sorted LQZ473

description: primary cells, normal

source_name: kidney


title: 1102-0850

value: 6p-rearrangement t(1;6)


title: Prom1-positive cells_MACS sorted LQZ246

description: primary cells, normal


title: Prom1-positive cells_MACS sorted LQZ226

description: primary cells, normal


title: F-2421


title: 11-06930

value: HG


title: Prom1-positive cells_MACS sorted LQZ145

description: primary cells, normal


title: Prom1-positive cells_MACS sorted LQZ222

description: primary cells, normal


title: Lung_AJ_P12_r1

description:
Sample name: AJ_P12_321_m801_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Prom1-positive cells_MACS sorted LQZ472

description: primary cells, normal


title: Lung_AJ_P11_r3

description:
Sample name: AJ_P11_324_m804_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P11


title: 1102-0663


title: 10-06719


title: 10-10175


title: Lung_AJ_P11_r1

description:
Sample name: AJ_P11_322_m802_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P11_r2

description:
Sample name: AJ_P11_323_m803_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P09_r3

description:
Sample name: AJ_P09_320_m800_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P09


title: Prom1-positive cells_MACS sorted LQZ470

description: primary cells, normal


title: Lung_AJ_P09_r1

description:
Sample name: AJ_P09_198_m634_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: uterine carcinoma_dissected LQZ203

description: primary tumor

source_name: uterus

value: Mouse tumor

value: uterine carcinoma dissected


title: Lung_AJ_P09_r2

description:
Sample name: AJ_P09_199_m635_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 10-04821


title: Prom1-positive cells_MACS sorted LQZ471

description: primary cells, normal


title: 09-0130


title: 07-0721


title: Lung_AJ_P07_r3

description:
Sample name: AJ_P07_319_m799_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P07


title: uterine carcinoma_dissected LQZ089

description: primary tumor


title: uterine carcinoma liver metastasis_dissected LQZ064

description: metastatic tumor

value: uterine carcinoma liver metastasis dissected


title: 10-01637


title: uterine carcinoma_dissected LQZ061

description: primary tumor


title: 06-0185

value: 6p-rearrangement t(6;10)


title: 06-0983


title: Lung_AJ_P05_r2

description:
Sample name: AJ_P05_350_m350_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P05


title: Lung_AJ_P05_r1

description:
Sample name: AJ_P05_181_m181_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P07_r2

description:
Sample name: AJ_P07_318_m798_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P04_r3

description:
Sample name: AJ_P04_516_m516_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P04


title: uterine carcinoma abdomen metastasis_dissected LQZ062

description: metastatic tumor

source_name: abdomen

value: uterine carcinoma abdomen metastasis dissected


title: Lung_AJ_P07_r1

description:
Sample name: AJ_P07_206_m797_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P04_r2

description:
Sample name: AJ_P04_515_m515_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: small intestinal adenoma_dissected LQZ042

description: primary tumor

source_name: duodenum

value: small intestinal adenoma dissected


title: HK2_JQ1_TNF

city: Oviedo

first: Beatriz

last: Suarez-Alvarez

state: Oviedo

address: Celestino Villamil s/n

country: Spain

institute: Hospital Universitario Central de Asturias

description: Human renal proximal tubular epithelail cells (ATCC CRL-2190) treated with JQ1(+) and stimulated with TNF-α

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Illumina Inc.'s protocol

scan_protocol: BeadScan Illumina Inc.

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.14.2). It was log2 transformed and quantile normalized.

source_name: Kidney-derived cell line, JQ1 (+)treated and TNF-α stimulated

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System, Epicentre (Cat.Num. TAN07924)

growth_protocol: HK2 cells were grown in RPMI medium with 10% FBS, 5mg/ml Insulin Tranferrin Selenito and 36 ng/ml hzdrocortisone in 5% CO2 at 37C. At 60% confluence, cells were growth-arrested in serum-free medium for 24h before the experiments.

extract_protocol: RNAqueous Micro kit (Ambion)

treatment_protocol: For in vitro experiments, JQ1(+) and its enantiomer (-)JQ1 were used at 500nM for 1h, and further cells were stimulated with TNF-α (5ng/ml) for additional 3 hours.

value: JQ1 (+)treated and TNF-α stimulated

tag: gender

value: male


title: 06-0115

value: LG


title: prostatic adenocarcinoma_dissected LQZ174

description: primary tumor

source_name: prostate

tag: sample type

value: prostatic adenocarcinoma dissected


title: prostatic adenocarcinoma_dissected LQZ209

description: primary tumor


title: small intestinal adenoma_dissected LQZ028

description: primary tumor


title: RNA from PBMC purified from a 30 year old female

city: Haifa

first: Ariel

last: Miller

address: Efron 1

department: Medicine

country: Israel

institute: Technion

data_processing: Data after log2 transformation, filter for transcripts with expression at background level or for transcripts with less than 5% variation, and normalized using batch normalization  embedded within JMP genomics software.

source_name: Human blood

label_protocol: Biotinylated cRNA were prepared with the TargetAmp™- Nano Labeling Kit for  Illumina® Expression BeadChip®

extract_protocol: PBMCs were purified from 60 ml blood by Ficoll density gradient centrifugation (U16 NovaMed). Some PBMC's were set aside, and the rest were used for subset isolation. The CD14 subset was isolated using EasySep™ Human Monocyte Enrichment Kit (#19059 Stemcell). B and T cell subsets were purified by FACS ARIA sorting (Becton Dickinson) using anti-CD19 antibody (Ab) (R0808, DAKO), anti-CD4 Ab (556345,BD Pharmingen), and anti-CD8 Ab (F0765,Dako). Recovery was 65-80% with a purity > 95% for all cell-subsets.  FoxpP3+ CD4 cells (Tregs) were also sorted by the FACS ARIA, but not used in this analysis, therefore the CD4 T cells included in the study are Foxp3-. From each sample both RNA and DNA was extracted using AllPrep kit (#80204 QIAGENE) according to manufacturer's protocol. DNA concentration was measured by picogreen and stored at 4°C until use. RNA quantity and quality was measured by NanoDrop and Agilent BioAnalyzer respectively and stored at -80°C until use.

tag: individual

value: 30 years

value: Blood

tag: cell subset

value: PBMC

value: Female


title: 05-0422

value: endometrial stroma sarcoma tumor


title: HK2_TNF

description: Human renal proximal tubular epithelail cells (ATCC CRL-2190) treated with the enantiomer (-)JQ1 and stimulated with TNF-α

source_name: Kidney-derived cell line, (-)JQ1 treated and TNF-α stimulated

tag: cell line

tag: treatment

value: (-)JQ1 treated and TNF-α stimulated


title: 05-0484

source_name: tumor

value: HG


title: 04-0568

value: other


title: small intestinal adenoma_dissected LQZ008

description: primary tumor

value: Mouse tumor


title: prostatic adenocarcinoma_dissected LQZ172

description: primary tumor


title: HK2

description: Human renal proximal tubular epithelail cells (ATCC CRL-2190)

source_name: Kidney-derived cell line, Control


title: prostatic adenocarcinoma_dissected LQZ171

description: primary tumor


title: prostatic adenocarcinoma_dissected LQZ170

description: primary tumor


title: Lung_AJ_P03_r3

description:
Sample name: AJ_P03_537_m537_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P03

value: Lung

value: A/J


title: Lung_AJ_P03_r2

description:
Sample name: AJ_P03_536_m536_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P03_r1

description:
Sample name: AJ_P03_535_m535_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P04_r1

description:
Sample name: AJ_P04_514_m514_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P02_r3

description:
Sample name: AJ_P02_522_m522_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P02


title: Lung_AJ_P02_r2

description:
Sample name: AJ_P02_521_m521_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_P02_r1

description:
Sample name: AJ_P02_520_m520_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: RNA from PBMC purified from a 41 year old female

value: 41 years


title: RNA from PBMC purified from a 52 year old female

value: 52 years


title: RNA from PBMC purified from a 49 year old female

value: 49 years


title: RNA from CD4 T cells purified from a 30 year old female

value: CD4 T cells


title: prostatic adenocarcinoma_dissected LQZ020

description: primary tumor


title: RNA from CD4 T cells purified from a 43 year old female

value: 43 years


title: periorbital squamous cell carcinoma_dissected LQZ509

description: primary tumor

source_name: periorbital skin

value: periorbital squamous cell carcinoma dissected


title: Lung_AJ_P0_r2

description:
Sample name: AJ_P0_469_m469_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, P0


title: Lung_AJ_P0_r3

description:
Sample name: AJ_P0_543_m543_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: prostatic adenocarcinoma_dissected LQZ168

description: primary tumor

value: prostatic adenocarcinoma dissected


title: RNA from CD4 T cells purified from a 33 year old female

value: 33 years

value: Blood


title: Lung_AJ_P0_r1

description:
Sample name: AJ_P0_468_m468_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: perioral squamous cell carcinoma_dissected LQZ502

description: primary tumor

source_name: perioral skin

value: perioral squamous cell carcinoma dissected


title: prostatic adenocarcinoma_dissected LQZ009

description: primary tumor


title: perioral squamous cell carcinoma_dissected LQZ210

description: primary tumor


title: perineal squamous cell carcinoma_dissected LQZ504

description: primary tumor

source_name: perineal skin

value: perineal squamous cell carcinoma dissected


title: perineal squamous cell carcinoma_dissected LQZ505

description: primary tumor


title: perioral squamous cell carcinoma_dissected LQZ068

description: primary tumor


title: RNA from CD4 T cells purified from a 52 year old female

value: Female


title: Lung_AJ_e19.5_r3

description:
Sample name: AJ_e19.5_262_m262_b3
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, e19.5


title: Lung_AJ_e19.5_r2

description:
Sample name: AJ_e19.5_258_m258_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_e18.5_r2

description:
Sample name: AJ_e18.5_296_m296_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, e18.5


title: RNA from CD4 T cells purified from a 41 year old female


title: Lung_AJ_e19.5_r1

description:
Sample name: AJ_e19.5_257_m257_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: RNA from CD8 T cells purified from a 30 year old female

value: 30 years

value: CD8 T cells


title: RNA from CD8 T cells purified from a 43 year old female


title: Runx1Δ/Δ+RUNX1-ERt2 GMP rep 2

city: Hamburg

first: Kira

last: Behrens

address: Martinistrasse 52

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

description:
Gene expression of Runx1fl/fl-Tg(vav-Cre)-RUNX1-ERt2 GMP + tamoxifen
RUNX1-ERt2+4-OHT_2

hyb_protocol: Hybridization was peformed according to manufacturer´s protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). 1.65 µg Cy3-labeled fragmented cRNA was hybridized overnight (17 hrs., 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44Kv2 by Miltenyi Biotec.

scan_protocol: Fluorescence signals were scanned using the Agilent´s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (EFS) was used to read out and process the microarray image files.

data_processing: The scanned images were analyzed by the Agilent G2567AA Feature Extraction Software v.9.1 using default parameters

source_name: GMP, Runx1fl/fl-Tg(vav-Cre)+RUNX1-ERt2

label_protocol: Cy3-labeled cRNA was prepared using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following manufacturer´s protocol. The amount of cRNA and the dye-incorporation rate were checked by using the ND-1000 Spectrophotometer (NanoDrop Technologies) by Miltenyi Biotec.

extract_protocol: RNA was extracted (NucleoSpin® RNA II; Agilent Technologies) according to the manufacturer's instructions by Miltenyi Biotec.

treatment_protocol: GMP from Runx1+/+-Tg(vav-Cre) and Runx1fl/fl-Tg(vav-Cre) BM were isolated according to Bryder et al., 2007. For GMP ectopically expressing RUNX1-ERt2 or ERt2 BM cells from Runx1fl/fl-Tg(vav-Cre) mice were isolated on day 3 post-injection of 150mg/kg 5-fluorouracil, infected twice with ecotropic pseudotypes of MIG retroviral vectors expressing GFP with RUNX1-ERt2 or ERt2 and transplanted into lethally irradiated recipient mice. After 6 weeks, RUNX1-ERt2 was induced in half of the mice by i.p. tamoxifen injection (49.5 μg/g body weight on 3 consecutive days. BM cells were harvested 24hrs later and viable GFP+GMP cells were sorted.

value: bone marrow

value: GMP

tag: genotype/variation


title: RNA from CD8 T cells purified from a 33 year old female


title: Runx1Δ/Δ+RUNX1-ERt2 GMP rep 1

description:
Gene expression of Runx1fl/fl-Tg(vav-Cre)-RUNX1-ERt2 GMP + tamoxifen
RUNX1-ERt2+4-OHT_1


title: Runx1Δ/Δ+ERt2 GMP rep 2

description:
Gene expression of Runx1fl/fl-Tg(vav-Cre)-ERt2 GMP + tamoxifen
ERt2+4-OHT_2

source_name: GMP, Runx1fl/fl-Tg(vav-Cre)+ERt2


title: Runx1Δ/Δ+ERt2 GMP rep 1

description:
Gene expression of Runx1fl/fl-Tg(vav-Cre)-ERt2 GMP + tamoxifen
ERt2+4-OHT_1


title: perineal squamous cell carcinoma_dissected LQZ503

description: primary tumor

value: Mouse tumor


title: RNA from CD4 T cells purified from a 49 year old female


title: perineal squamous cell carcinoma_dissected LQZ052

description: primary tumor


title: RNA from CD8 T cells purified from a 52 year old female


title: Lung_AJ_e18.5_r1

description:
Sample name: AJ_e18.5_293_m293_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

value: Lung

value: A/J


title: RNA from CD8 T cells purified from a 49 year old female

value: 49 years


title: Runx1Δ/Δ GMP rep 2

description:
Gene expression of Runx1fl/fl-Tg(vav-Cre) GMP
fl/fl_2

source_name: GMP, Runx1fl/fl-Tg(vav-Cre)


title: Lung_AJ_e18.5_r3

description:
Sample name: AJ_e18.5_058_m600_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Runx1Δ/Δ GMP rep 3

description:
Gene expression of Runx1fl/fl-Tg(vav-Cre) GMP
fl/fl_3


title: large intestinal adenoma_dissected LQZ511

description: primary tumor

source_name: colon

value: large intestinal adenoma dissected


title: Lung_AJ_e17.5_r2

description:
Sample name: AJ_e17.5_060_m60_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, e17.5


title: RNA from B cells purified from a 30 year old female

source_name: Human blood

value: B cells


title: RNA from B cells purified from a 43 year old female

value: 43 years


title: Lung_AJ_e17.5_r3

description:
Sample name: AJ_e17.5_059_m616_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Runx1+/+ GMP rep 4

description:
Gene expression of Runx1+/+-Tg(vav-Cre) GMP
wt/wt_4

source_name: GMP, Runx1+/+-Tg(vav-Cre)


title: Runx1Δ/Δ GMP rep 4

description:
Gene expression of Runx1fl/fl-Tg(vav-Cre) GMP
fl/fl_4


title: Runx1Δ/Δ GMP rep 1

description:
Gene expression of Runx1fl/fl-Tg(vav-Cre) GMP
fl/fl_1


title: large intestinal adenoma_dissected LQZ491

description: primary tumor


title: large intestinal adenoma_dissected LQZ488

description: primary tumor


title: large intestinal adenoma_dissected LQZ494

description: primary tumor


title: Lung_AJ_e17.5_r1

description:
Sample name: AJ_e17.5_058_m58_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: large intestinal adenoma_dissected LQZ497

description: primary tumor


title: Runx1+/+ GMP rep 3

description:
Gene expression of Runx1+/+-Tg(vav-Cre) GMP
wt/wt_3


title: Lung_AJ_e16.5_r2

description:
Sample name: AJ_e16.5_189_m189_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, e16.5


title: Lung_AJ_e16.5_r1

description:
Sample name: AJ_e16.5_186_m186_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_e16.5_r3

description:
Sample name: AJ_e16.5_185_m581_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: RNA from Monocyte purified from a 52 year old female

value: 52 years

value: Monocyte


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ500

description: primary tumor

source_name: liver


title: Lung_AJ_e15.5_r3

description:
Sample name: AJ_e15.5_188_m588_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, e15.5


title: RNA from Monocyte purified from a 33 year old female

value: 33 years

value: Blood


title: RNA from B cells purified from a 49 year old female


title: RNA from B cells purified from a 52 year old female


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ493

description: primary tumor


title: Lung_AJ_e15.5_r2

description:
Sample name: AJ_e15.5_187_m586_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: RNA from Monocyte purified from a 41 year old female

value: 41 years


title: RNA from Monocyte purified from a 30 year old female

value: Female


title: Lung_AJ_e15.5_r1

description:
Sample name: AJ_e15.5_186_m585_b7
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Runx1+/+ GMP rep 1

description:
Gene expression of Runx1+/+-Tg(vav-Cre) GMP
wt/wt_1


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ499

description: primary tumor


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ490

description: primary tumor


title: RNA from Monocyte purified from a 49 year old female


title: Runx1+/+ GMP rep 2

description:
Gene expression of Runx1+/+-Tg(vav-Cre) GMP
wt/wt_2


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ495

description: primary tumor


title: Lung_AJ_e14.5_r2

description:
Sample name: AJ_e14.5_323_m323_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, e14.5


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ489

description: primary tumor


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ486

description: primary tumor


title: Lung_AJ_e14.5_r1

description:
Sample name: AJ_e14.5_290_m290_b1
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Lung_AJ_e13.5_r2

description:
Sample name: AJ_e13.5_360_m360_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, e13.5


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ415

description: primary tumor