title: lung, adenocarcinoma_18081

description: adenocarcinoma

tag: tissue

value: adenocarcinoma

tag: 7th tnm stage

value: Ia

tag: tumor size (cm)

value: never

value: WT

tag: death due to cancer

tag: survival after surgery (days)


title: lung, nontumor adjacent_12918

status: Public on Apr 30 2015

type: RNA

city: Bethesda

first: Ana

middle: I

last: Robles

state: MD

address: 37 Convent Dr 37/3060D

country: USA

institute: National Cancer Institute/NIH

description: nontumor adjacent

hyb_protocol: Labeled cRNA was hybridised to Illumina HumanRefseq8 v3

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

data_processing: Genome Studio v2010.3

molecule: total RNA

organism: Homo sapiens

source_name: lung, nontumor adjacent

label_protocol: Standard Illumina Protocol Illumina TotalPrep-96 RNA Amplification Kit (Life Technologies)

extract_protocol: Total cellular RNA was extracted from tumor and matching adjacent non-tumor lung using miRNA Kit (QIAGEN). RNA quality was determined using Agilent Bioanalyzer. RNA was hybridized to Illumina HumanRef-8 v3 Expression Beadchip arrays.

tag: Sex

value: Female

tag: race

value: European American

tag: age

tag: disease state

value: non-small cell lung cancer (NSCLC)

tag: histology

value: normal

tag: smoking status

value: ever

tag: smoking packyears

value: yes


title: lung, nontumor adjacent_21272

description: nontumor adjacent

hyb_protocol: Standard Nanostring Protocol

scan_protocol: Standard Nanostring Protocol

data_processing: Nanostring Nsolver

label_protocol: Standard Nanostring Protocol

extract_protocol: Total cellular RNA was extracted from tumor and matching adjacent non-tumor lung using miRNA Kit (QIAGEN), according to the manufacturer’s instructions. RNA quality was determined using Agilent Bioanalyzer.

value: lung, nontumor adjacent

tag: analysis batch

value: Male

value: African American

value: unknown

value: no


title: lung, nontumor adjacent_18133

type: genomic

description: nontumor adjacent

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2; Fluorescent signals were collated via Bead Studio software and converted into -values. Illumina Bead Studio software output data were normalized using SSN (simple scaling normalization), to correct for dye bias and transformed into M-values (M = log2 intensity of methylated probe/ intensity of unmethylated probe), using the R package lumi. Raw signals can be found on the series level in the file Unmethylated_and_methylated_signal_intensities.txt

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

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

value: lung


title: lung, adenocarcinoma_12918

description: adenocarcinoma

source_name: lung, adenocarcinoma

value: IIa

tag: kras status

tag: tp53 mutation


title: AuditoryNerve_ouabain_7d_rep2

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Targets (12.5 ug) were hybridized to Affymetrix Mouse 430 2.0 GeneChips according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner.

data_processing: CEL files imported into Affymetrix Expression Console software and data were normalized by: 1) RMA to obtain probe set expression values, and 2) MAS5 to obtain probe set detection calls.

label: biotin

organism: Mus musculus

source_name: Auditory nerve_7d post surgery_ouabain treatment

label_protocol: Total RNA (100 ng) was converted into biotin-labeled cRNA and then fragmented using the Affymetrix 3' IVT Express Kit in accordance with manufacturer protocols.

growth_protocol: CBA/CaJ mice were bred in-house in a low-noise environment at the Animal Research Facility of the Medical University of South Carolina (MUSC) with original breeding pairs purchased from The Jackson Laboratory (Bar Harbor, ME).   All mice received food and water ad libitum and were maintained on a 12-hour light/dark cycle.  Mice of both genders were used in the study.  All aspects of the animal research were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee of the MUSC.  Prior to treatment, mice were examined for signs of external ear canal and middle ear obstruction, and mice exhibiting these signs were excluded from the study.

extract_protocol: Microdissected cochlear tissues containing auditory nerves underwent total RNA preparation using the RNeasy Minikit (Qiagen). Total RNA preparations were run on an Agilent 2100 Bioanalyzer to ensure sample quality.

treatment_protocol: Adult Mice (CBA/CaJ, aged 8 to 12 weeks) were anesthetized and subjected to survival surgery to expose the bulla of the right ear. A ouabain solution (3 mM, approximately 10 ul) was administered in the round window niche. This solution was wicked away and replaced with fresh ouabain approximately every 10 min during a cummulative exposure period of 60 min. The left ears (i.e., contralateral) were not surgically manipulated and were used as controls. Mice were maintained for 3 days or 7 days following treatments, then euthanized, and the oubain-treated and contralateral cochleas were removed. Cochleas underwent microdissection to remove the outer bony cochlear shell and cochlear lateral wall, thus preserving the modiolus portion of cochlea which contains mainly the auditory nerve. All sample types were prepared in experimental triplicate (n=3).

tag: strain background

value: CBA/CaJ

value: adult; 8 to 12 weeks

tag: sample group

value: ouabain injury

tag: days after treatment

value: auditory nerve


title: lung, adenocarcinoma_18055

description: adenocarcinoma

tag: tissue

value: Female

value: adenocarcinoma

tag: 7th tnm stage

value: WT


title: lung, nontumor adjacent_18087

description: nontumor adjacent

value: European American

value: non-small cell lung cancer (NSCLC)

value: normal

tag: death due to cancer


title: lung, adenocarcinoma_18055

description: adenocarcinoma

tag: tumor size (cm)

value: ever

tag: survival after surgery (days)


title: AuditoryNerve_control_7d_rep3

source_name: Auditory nerve_7d post surgery_control

value: control


title: lung, nontumor adjacent_18193

description: nontumor adjacent

tag: Sex

value: Male

tag: race


title: AuditoryNerve_ouabain_7d_rep1

tag: age


title: lung, adenocarcinoma_21229

description: adenocarcinoma

value: lung, adenocarcinoma

value: African American

tag: disease state

tag: histology

value: Ia

value: MT


title: AuditoryNerve_control_7d_rep1

value: CBA/CaJ


title: lung, nontumor adjacent_18055

description: nontumor adjacent

tag: smoking status

tag: smoking packyears

value: unknown

value: no


title: AuditoryNerve_control_7d_rep2

value: adult; 8 to 12 weeks

value: auditory nerve


title: lung, adenocarcinoma_18011

description: adenocarcinoma

value: lung

tag: analysis batch

value: Female

value: adenocarcinoma

tag: kras status


title: AuditoryNerve_ouabain_3d_rep3

source_name: Auditory nerve_3d post surgery_ouabain treatment

tag: strain background

value: ouabain injury


title: AuditoryNerve_ouabain_3d_rep2

tag: sample group


title: lung, nontumor adjacent_18055

description: nontumor adjacent

value: European American

value: non-small cell lung cancer (NSCLC)

value: normal


title: lung, nontumor adjacent_20063

description: nontumor adjacent

value: Male


title: lung, adenocarcinoma_20336

description: adenocarcinoma

value: lung, adenocarcinoma

value: Ib

value: ever

value: WT

tag: tp53 mutation


title: lung, nontumor adjacent_18011

description: nontumor adjacent

tag: tissue


title: lung, nontumor adjacent_18081

description: nontumor adjacent

value: never


title: lung, adenocarcinoma_20063

description: adenocarcinoma

value: African American

tag: 7th tnm stage

value: Ia

value: unknown


title: lung, nontumor adjacent_21229

description: nontumor adjacent

value: lung, nontumor adjacent

tag: death due to cancer

value: no


title: lung, adenocarcinoma_21272

description: adenocarcinoma

tag: tumor size (cm)


title: lung, adenocarcinoma_17847

description: adenocarcinoma

value: lung

value: Female

tag: survival after surgery (days)


title: lung, adenocarcinoma_20063

description: adenocarcinoma

tag: Sex

value: adenocarcinoma


title: lung, nontumor adjacent_20063

description: nontumor adjacent

tag: race


title: lung, adenocarcinoma_20336

description: adenocarcinoma

value: European American

tag: age


title: AuditoryNerve_ouabain_3d_rep1

value: CBA/CaJ

value: adult; 8 to 12 weeks

value: ouabain injury

tag: days after treatment

value: auditory nerve


title: lung, adenocarcinoma_17836

description: adenocarcinoma

tag: disease state

value: non-small cell lung cancer (NSCLC)

tag: histology


title: lung, nontumor adjacent_21272

description: nontumor adjacent

value: Male

value: normal

tag: smoking status

value: ever

tag: smoking packyears


title: AuditoryNerve_control_3d_rep2

source_name: Auditory nerve_3d post surgery_control

value: unoperated contralateral control


title: lung, nontumor adjacent_17847

description: nontumor adjacent

tag: analysis batch


title: AuditoryNerve_control_3d_rep3

tag: strain background


title: AuditoryNerve_PerinatalDay21_rep2

source_name: Auditory nerve_perinatal day 21

growth_protocol: CBA/CaJ mice were bred in-house in a low-noise environment at the Animal Research Facility of the Medical University of South Carolina (MUSC) with original breeding pairs purchased from The Jackson Laboratory (Bar Harbor, ME).   All mice received food and water ad libitum and were maintained on a 12-hour light/dark cycle.  Mice of both genders were used in the study.  All aspects of the animal research were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee of the MUSC.

treatment_protocol: Cochleas were collected from euthanized mice (CBA/CaJ) at perinatal (P) stages P0, P3, P7, P10, P14 and P21. Cochleas underwent microdissection to remove the outer bony cochlear shell and cochlear lateral wall, thus preserving the modiolus portion of cochlea which contains mainly the auditory nerve. Paired cochleas (i.e., from left and right ears) from each mouse were pooled to make individual samples. All sample types were done in experimental duplicate (n=2).

tag: perinatal stage


title: AuditoryNerve_control_3d_rep1

tag: sample group


title: lung, adenocarcinoma_13130

description: adenocarcinoma

value: unknown (I or II)

tag: kras status

value: WT

tag: tp53 mutation

value: MT

value: yes


title: lung, nontumor adjacent_20336

description: nontumor adjacent

value: unknown

tag: death due to cancer

value: no


title: lung, nontumor adjacent_19840

description: nontumor adjacent

tag: tissue

value: lung, nontumor adjacent


title: lung, adenocarcinoma_19840

description: adenocarcinoma

value: lung, adenocarcinoma

value: European American

value: adenocarcinoma

tag: 7th tnm stage

value: Ib

tag: tumor size (cm)

tag: survival after surgery (days)


title: lung, adenocarcinoma_19309

description: adenocarcinoma

tag: Sex

tag: race

value: African American

tag: age


title: lung, nontumor adjacent_13130

description: nontumor adjacent

tag: disease state

value: non-small cell lung cancer (NSCLC)

tag: histology


title: lung, nontumor adjacent_20336

description: nontumor adjacent

value: Male

tag: smoking status

tag: smoking packyears


title: AuditoryNerve_PerinatalDay21_rep1

tag: strain background

value: CBA/CaJ

value: auditory nerve


title: lung, nontumor adjacent_17736

description: nontumor adjacent

value: lung

tag: analysis batch

value: Female

value: normal

value: ever


title: lung, adenocarcinoma_17736

description: adenocarcinoma

value: MT

value: WT


title: lung, adenocarcinoma_17847

description: adenocarcinoma

value: Ia

value: unknown

value: no


title: lung, adenocarcinoma_18974

description: adenocarcinoma

value: lung, adenocarcinoma

value: European American

value: yes


title: lung, nontumor adjacent_18974

description: nontumor adjacent

value: lung, nontumor adjacent


title: lung, adenocarcinoma_17716

description: adenocarcinoma

value: non-small cell lung cancer (NSCLC)

value: adenocarcinoma

value: Ib

value: never


title: lung, nontumor adjacent_17716

description: nontumor adjacent

value: lung


title: AuditoryNerve_PerinatalDay10_rep2

source_name: Auditory nerve_perinatal day 10

value: CBA/CaJ

tag: perinatal stage

value: auditory nerve


title: lung, nontumor adjacent_17847

description: nontumor adjacent

value: Female

value: normal

value: ever


title: lung, adenocarcinoma_18011

description: adenocarcinoma

value: Ia

tag: kras status

value: WT


title: AuditoryNerve_PerinatalDay10_rep1


title: lung, adenocarcinoma_18318

description: adenocarcinoma

value: Male

tag: tp53 mutation

value: unknown

value: no


title: lung, nontumor adjacent_17836

description: nontumor adjacent

value: European American

tag: death due to cancer


title: AuditoryNerve_PerinatalDay14_rep1

source_name: Auditory nerve_perinatal day 14

tag: tissue


title: lung, nontumor adjacent_18011

description: nontumor adjacent


title: lung, nontumor adjacent_18318

description: nontumor adjacent

value: lung, nontumor adjacent


title: lung, adenocarcinoma_13761

description: adenocarcinoma

value: non-small cell lung cancer (NSCLC)

tag: 7th tnm stage

value: IIa

value: MT


title: lung, adenocarcinoma_15409

description: adenocarcinoma

value: adenocarcinoma

value: IIb

tag: tumor size (cm)


title: lung, nontumor adjacent_15538

description: nontumor adjacent

value: lung

value: African American

tag: survival after surgery (days)


title: AuditoryNerve_PerinatalDay14_rep2

value: CBA/CaJ

value: auditory nerve


title: lung, nontumor adjacent_15409

description: nontumor adjacent

tag: Sex

value: normal

value: ever


title: AuditoryNerve_PerinatalDay7_rep2

source_name: Auditory nerve_perinatal day 7


title: lung, nontumor adjacent_18193

description: nontumor adjacent

tag: race


title: lung, adenocarcinoma_18133

description: adenocarcinoma

value: lung, adenocarcinoma

value: Female

tag: age

value: Ia

value: never

value: WT


title: lung, adenocarcinoma_18193

description: adenocarcinoma

value: Male

value: European American

tag: disease state

value: Ib

value: unknown

value: no


title: lung, nontumor adjacent_13761

description: nontumor adjacent

value: non-small cell lung cancer (NSCLC)

tag: histology


title: AuditoryNerve_PerinatalDay3_rep2

source_name: Auditory nerve_perinatal day 3


title: lung, adenocarcinoma_15538

description: adenocarcinoma

value: lung

value: adenocarcinoma

tag: smoking status

value: MT


title: lung, nontumor adjacent_17716

description: nontumor adjacent

tag: smoking packyears

value: yes


title: AuditoryNerve_PerinatalDay3_rep1

tag: strain background

value: CBA/CaJ

value: auditory nerve


title: lung, nontumor adjacent_18133

description: nontumor adjacent

value: lung, nontumor adjacent

tag: analysis batch

value: normal


title: lung, adenocarcinoma_14479

description: adenocarcinoma

value: Female


title: lung, adenocarcinoma_15248

description: adenocarcinoma

value: ever


title: lung, nontumor adjacent_15248

description: nontumor adjacent


title: AuditoryNerve_PerinatalDay0_rep1

source_name: Auditory nerve_perinatal day 0

tag: perinatal stage


title: lung, adenocarcinoma_13473

description: adenocarcinoma

value: Ia

tag: kras status

value: WT


title: AuditoryNerve_PerinatalDay0_rep2


title: lung, nontumor adjacent_13473

description: nontumor adjacent

value: European American


title: lung, nontumor adjacent_14479

description: nontumor adjacent

value: never


title: lung, adenocarcinoma_18193

description: adenocarcinoma

value: Male

value: Ib

value: unknown

tag: tp53 mutation


title: lung, adenocarcinoma_18087

description: adenocarcinoma

value: lung, adenocarcinoma

value: non-small cell lung cancer (NSCLC)

tag: death due to cancer

value: no


title: lung, adenocarcinoma_14468

description: adenocarcinoma

tag: tissue

value: lung

value: African American

value: adenocarcinoma


title: lung, nontumor adjacent_19309

description: nontumor adjacent

value: lung, nontumor adjacent

value: yes


title: lung, nontumor adjacent_18193

description: nontumor adjacent

value: normal


title: lung, nontumor adjacent_18087

description: nontumor adjacent

value: Female

value: ever


title: lung, adenocarcinoma_19840

description: adenocarcinoma

tag: 7th tnm stage

value: WT


title: lung, nontumor adjacent_14468

description: nontumor adjacent


title: lung, nontumor adjacent_18081

description: nontumor adjacent

value: European American


title: lung, adenocarcinoma_14440

description: adenocarcinoma

value: Ia

tag: tumor size (cm)

value: MT


title: lung, adenocarcinoma_18081

description: adenocarcinoma

value: never

tag: survival after surgery (days)


title: lung, adenocarcinoma_18055

description: adenocarcinoma

tag: Sex

value: IIa

value: unknown


title: lung, adenocarcinoma_19309

description: adenocarcinoma

value: Male

tag: race

value: non-small cell lung cancer (NSCLC)

value: Ib


title: lung, nontumor adjacent_18055

description: nontumor adjacent

tag: age

value: no


title: lung, nontumor adjacent_19309

description: nontumor adjacent

value: African American

tag: disease state


city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: CRPC mononuclear cell fraction of peripheral blood: 10SE2646.CEL (CTC's>5)

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4)  in R.2.9.1

source_name: mononuclear cell fraction of peripheral blood (PBMNC)

label_protocol: Standard Affymetrix protocol

extract_protocol: Five mL of peripheral blood samples were collected into Monovette EDTA–containing Vacutainers (Sarstedt). Blood specimens were layered onto 4 mL of Ficoll- Paque (GE Healthcare Life Sciences). Mononuclear cells were isolated and total RNA was extracted using Trizol Reagent (Invitrogen Life Technologies) according to manufacturer’s instructions. RNA was quantified by ND- 1000 Spectrophotometer (Nanodrop Technologies).

tag: ctc's group


title: lung, nontumor adjacent_14440

description: nontumor adjacent

value: lung

tag: histology

tag: smoking status


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2644.CEL (CTC's>5)


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2641.CEL (CTC's>5)


title: lung, nontumor adjacent_18011

description: nontumor adjacent

value: lung, nontumor adjacent

tag: smoking packyears


title: lung, nontumor adjacent_13761

description: nontumor adjacent

tag: analysis batch

value: normal


title: lung, adenocarcinoma_13761

description: adenocarcinoma

value: Female

value: adenocarcinoma


title: lung, nontumor adjacent_18133

description: nontumor adjacent


title: lung, adenocarcinoma_18133

description: adenocarcinoma

value: WT


title: lung, adenocarcinoma_12839

description: adenocarcinoma

value: European American

value: ever


title: lung, adenocarcinoma_17847

description: adenocarcinoma

value: lung, adenocarcinoma

value: Ia


title: lung, nontumor adjacent_13473

description: nontumor adjacent


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2631.CEL (CTC's>5)


title: lung, adenocarcinoma_18011

description: adenocarcinoma


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2634.CEL (CTC's>5)


title: lung, adenocarcinoma_13473

description: adenocarcinoma


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2638.CEL (CTC's>5)


title: lung, nontumor adjacent_14440

description: nontumor adjacent

value: yes


title: lung, nontumor adjacent_17847

description: nontumor adjacent

value: unknown


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2630.CEL (CTC's>5)


title: lung, adenocarcinoma_13172

description: adenocarcinoma


title: lung, nontumor adjacent_12839

description: nontumor adjacent


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2629.CEL (CTC's>5)


title: lung, adenocarcinoma_17836

description: adenocarcinoma


title: lung, nontumor adjacent_17836

description: nontumor adjacent


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2648.CEL (CTC's>5)


title: lung, adenocarcinoma_13172

description: adenocarcinoma


title: lung, nontumor adjacent_13172

description: nontumor adjacent


title: lung, nontumor adjacent_13172

description: nontumor adjacent


title: lung, adenocarcinoma_17736

description: adenocarcinoma

value: MT


title: lung, adenocarcinoma_13130

description: adenocarcinoma

value: Male

value: non-small cell lung cancer (NSCLC)

value: unknown (I or II)


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2639.CEL (CTC's>5)


title: lung, nontumor adjacent_17736

description: nontumor adjacent

value: no


title: lung, nontumor adjacent_20603

description: nontumor adjacent

value: African American


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2628.CEL (CTC's>5)


title: AuditoryNerve_PerinatalDay7_rep1

tag: strain background

value: CBA/CaJ

tag: perinatal stage

value: auditory nerve


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2627.CEL (CTC's>5)


title: lung, adenocarcinoma_13077

description: adenocarcinoma

value: lung

value: Ib

tag: kras status

tag: tp53 mutation


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2626.CEL (CTC's>5)


title: lung, adenocarcinoma_20603

description: adenocarcinoma

value: adenocarcinoma

value: WT

tag: death due to cancer


title: lung, nontumor adjacent_13130

description: nontumor adjacent

tag: tissue

value: European American

value: normal

value: ever


title: lung, nontumor adjacent_17716

description: nontumor adjacent

value: lung, nontumor adjacent

value: Female

value: never

value: yes


title: lung, adenocarcinoma_17716

description: adenocarcinoma

value: lung, adenocarcinoma

value: non-small cell lung cancer (NSCLC)

tag: 7th tnm stage

tag: tumor size (cm)

value: MT


title: lung, nontumor adjacent_17836

description: nontumor adjacent

tag: Sex

value: no

tag: survival after surgery (days)


title: lung, adenocarcinoma_17836

description: adenocarcinoma

tag: race

tag: age

value: Ia


title: lung, adenocarcinoma_15538

description: adenocarcinoma

value: Male

value: African American

tag: disease state


title: lung, adenocarcinoma_12918

description: adenocarcinoma

value: lung

tag: histology

value: IIa


title: lung, adenocarcinoma_15538

description: adenocarcinoma

value: adenocarcinoma

tag: smoking status

value: WT


title: lung, nontumor adjacent_13077

description: nontumor adjacent

value: European American

value: normal

tag: smoking packyears


title: lung, adenocarcinoma_17716

description: adenocarcinoma

value: Ib


title: lung, nontumor adjacent_12918

description: nontumor adjacent

tag: analysis batch

value: Female

value: ever


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2625.CEL (CTC's>5)

tag: ctc's group


title: lung, adenocarcinoma_15409

description: adenocarcinoma

value: IIb

value: unknown


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2615.CEL (CTC's>5)


title: lung, adenocarcinoma_14479

description: adenocarcinoma

value: non-small cell lung cancer (NSCLC)

value: never


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2620.CEL (CTC's>5)


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2614.CEL (CTC's>5)


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2619.CEL (CTC's>5)


title: lung, nontumor adjacent_14479

description: nontumor adjacent

value: no


title: lung, nontumor adjacent_15409

description: nontumor adjacent

value: lung, nontumor adjacent


title: lung, adenocarcinoma_12900

description: adenocarcinoma

value: Male

value: Ia


title: lung, adenocarcinoma_15409

description: adenocarcinoma


title: lung, nontumor adjacent_12900

description: nontumor adjacent

value: lung


title: lung, adenocarcinoma_12881

description: adenocarcinoma

value: African American

value: MT

value: yes


title: lung, adenocarcinoma_15248

description: adenocarcinoma

value: lung, adenocarcinoma

value: European American

value: adenocarcinoma

value: WT


title: lung, nontumor adjacent_15248

description: nontumor adjacent

value: Female

value: normal

value: ever


title: lung, adenocarcinoma_14479

description: adenocarcinoma

value: non-small cell lung cancer (NSCLC)

value: Ib


title: lung, nontumor adjacent_14479

description: nontumor adjacent

value: never

value: no


title: lung, adenocarcinoma_14468

description: adenocarcinoma

value: Male


title: lung, adenocarcinoma_13077

description: adenocarcinoma


title: lung, adenocarcinoma_12860

description: adenocarcinoma

value: Ia

value: unknown


title: lung, nontumor adjacent_14468

description: nontumor adjacent

value: lung, nontumor adjacent

value: African American


title: lung, adenocarcinoma_12839

description: adenocarcinoma

value: lung

value: MT


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2647.CEL (CTC's<5)


title: lung, adenocarcinoma_13761

description: adenocarcinoma

value: lung, adenocarcinoma

value: European American

value: IIa


title: lung, nontumor adjacent_13077

description: nontumor adjacent


title: lung, nontumor adjacent_15409

description: nontumor adjacent


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2605.CEL (CTC's>5)


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2640.CEL (CTC's<5)


title: lung, nontumor adjacent_14468

description: nontumor adjacent


title: lung, nontumor adjacent_21272

description: nontumor adjacent


title: lung, nontumor adjacent_18974

description: nontumor adjacent

value: yes


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2637.CEL (CTC's<5)


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2643.CEL (CTC's<5)


title: lung, adenocarcinoma_18974

description: adenocarcinoma

value: adenocarcinoma

value: WT


title: lung, nontumor adjacent_12881

description: nontumor adjacent

value: Female

value: non-small cell lung cancer (NSCLC)

value: normal

value: ever


title: lung, nontumor adjacent_12860

description: nontumor adjacent

value: no


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2642.CEL (CTC's<5)


title: lung, adenocarcinoma_14468

description: adenocarcinoma

value: Male

value: Ib


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2645.CEL (CTC's<5)


title: lung, adenocarcinoma_17736

description: adenocarcinoma

value: unknown


title: lung, adenocarcinoma_21272

description: adenocarcinoma

value: African American

value: Ia


title: lung, nontumor adjacent_13761

description: nontumor adjacent

value: lung, nontumor adjacent


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2636.CEL (CTC's<5)


title: lung, nontumor adjacent_12839

description: nontumor adjacent

value: lung


title: lung, adenocarcinoma_21229

description: adenocarcinoma

value: MT


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2635.CEL (CTC's<5)


title: lung, adenocarcinoma_13473

description: adenocarcinoma

value: lung, adenocarcinoma

value: European American


title: lung, nontumor adjacent_17736

description: nontumor adjacent


title: lung, nontumor adjacent_21229

description: nontumor adjacent


title: lung, adenocarcinoma_13172

description: adenocarcinoma

value: adenocarcinoma


title: lung, nontumor adjacent_13473

description: nontumor adjacent


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2610.CEL (CTC's>5)


title: lung, adenocarcinoma_13130

description: adenocarcinoma

value: unknown (I or II)

value: WT

value: yes


title: lung, nontumor adjacent_13172

description: nontumor adjacent

value: Female

value: non-small cell lung cancer (NSCLC)

value: normal


title: lung, adenocarcinoma_18318

description: adenocarcinoma

value: Male

value: ever

value: no


title: lung, adenocarcinoma_20603

description: adenocarcinoma

value: African American


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2632.CEL (CTC's<5)


title: lung, nontumor adjacent_20603

description: nontumor adjacent


title: lung, nontumor adjacent_13130

description: nontumor adjacent


title: lung, adenocarcinoma_20336

description: adenocarcinoma

value: Ib

value: unknown


title: lung, nontumor adjacent_18318

description: nontumor adjacent


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2623.CEL (CTC's<5)


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2633.CEL (CTC's<5)


title: lung, nontumor adjacent_18087

description: nontumor adjacent


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2624.CEL (CTC's<5)


title: lung, nontumor adjacent_20336

description: nontumor adjacent

value: lung


title: lung, adenocarcinoma_13077

description: adenocarcinoma

value: MT


title: lung, adenocarcinoma_12860

description: adenocarcinoma

value: Ia


title: lung, adenocarcinoma_20063

description: adenocarcinoma


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2621.CEL (CTC's<5)


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2622.CEL (CTC's<5)


title: lung, nontumor adjacent_15248

description: nontumor adjacent

value: European American


title: lung, adenocarcinoma_19840

description: adenocarcinoma

data_processing: BeadStudio software v3.2; Fluorescent signals were collated via Bead Studio software and converted into Beta values. Illumina Bead Studio software output data were normalized using SSN (simple scaling normalization), to correct for dye bias and transformed into M-values (M = log2 intensity of methylated probe/ intensity of unmethylated probe), using the R package lumi. Raw signals can be found on the series level in the file Unmethylated_and_methylated_signal_intensities.txt

value: adenocarcinoma


title: lung, adenocarcinoma_15248

description: adenocarcinoma


title: lung, nontumor adjacent_13077

description: nontumor adjacent

value: lung, nontumor adjacent


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2618.CEL (CTC's<5)


title: lung, nontumor adjacent_20063

description: nontumor adjacent


title: lung, adenocarcinoma_12918

description: adenocarcinoma

value: lung, adenocarcinoma

value: IIa

value: WT


title: lung, adenocarcinoma_18087

description: adenocarcinoma

value: Female

value: non-small cell lung cancer (NSCLC)


title: lung, nontumor adjacent_12918

description: nontumor adjacent

value: normal

value: yes


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2613.CEL (CTC's<5)


title: lung, nontumor adjacent_19309

description: nontumor adjacent

value: Male

value: ever


title: lung, adenocarcinoma_18081

description: adenocarcinoma

value: never

value: no


title: lung, adenocarcinoma_19309

description: adenocarcinoma

value: lung

value: African American

value: Ib

value: unknown


title: lung, nontumor adjacent_12900

description: nontumor adjacent

value: European American


title: lung, adenocarcinoma_12900

description: adenocarcinoma

value: adenocarcinoma

value: Ia


title: lung, nontumor adjacent_19840

description: nontumor adjacent


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2617.CEL (CTC's<5)


title: lung, adenocarcinoma_12860

description: adenocarcinoma

value: lung, adenocarcinoma


title: lung, nontumor adjacent_12900

description: nontumor adjacent


title: lung, nontumor adjacent_18081

description: nontumor adjacent


title: lung, nontumor adjacent_12839

description: nontumor adjacent

value: lung, nontumor adjacent


title: lung, adenocarcinoma_12839

description: adenocarcinoma

value: Female

value: WT

value: MT


title: control 1

city: Daegu

first: Heon-Jin

last: Lee

address: 2177 Dalgubeol Daero

department: School of Dentistry, Microbiology and Immunology

country: South Korea

institute: Kyungpook National University

description: Control

hyb_protocol: Each labeled Samples were prepared for hybridization by adding nuclease-free water, Hyb Spike-In solution, 10X GE Blocking Agent and 2X Hi-RPM Hybridization Buffer. 45μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human miRNA 8X60K, V19.0 Microarrays (Agilent®), and then rotated at 20 rpm for 20 h at 55°C.

scan_protocol: Agilent Gene Expression Wash Buffers 1(RT) and 2(37°C) were used after hybridization as recommended by Agilent miRNA Microarray System and were scanned on a Agilent Technologies G4900DA SureScan scanner using 3 µm resolution.

data_processing:
Raw data were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies). The raw data for same miRNA was then summarized automatically in Agilent feature extraction protocol to generate Gene view file, providing expression data for each miRNA probed on the array. Array data were filtered by gIsGeneDetected =1 in all samples (1 : detected). Selected miRNA gTotalGeneSignal value was transformed by logarithm and normalized by quantile method.
Please note that each set (i.e. set1 and set2) was analyzed independently.

source_name: control_salivary exosome

label_protocol: The miRNA Microarray System with miRNA Complete Labeling and hybridization Kit (Agilent Technologies) was used according to the manufacturer′s recommended protocol. The Agilent microRNA Spike-In Kit was used for in-process control to measure labeling and hybridization efficiency.  Briefly, 100ng total RNA was dephosphorylated at 37°C for 30 min with calf intestinal phosphatase and denatured by using 100% DMSO at 100°C for 7min. Samples were labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 2 hour. The labeled RNA samples were purified in a Vacuum Concentrator for one hour. Once samples are completely dried.

extract_protocol: RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

tag: subject status

value: healthy control

value: Saliva

tag: molecule source

value: Exsosomal RNAs


title: CD34+/CD105-, long warm ischemia (patient 2)

status: Public on Apr 29 2015

city: Boston

first: Andrew

middle: Michael

last: Siedlecki

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

description:
experimental
h2e

data_processing:
Initial signal intensity results and normalized cycle time results were analyzed using SymphoniSuite software (Life Technologies, Inc).  Cycle time thresholds were normalized by averaging three endogenous controls including U6 snRNA, RNU44, and RNU48
normalized_human.txt reports normalized signal (against housekeeping genes).
Fold Change file reports 2^ΔΔCt, where ΔΔCt = [average ΔCtcontrol-average ΔCtexperimental]

label: FAM

source_name: renal artery, radical nephrectomy, renal cell cancer

label_protocol: cDNA was analyzed using the 7900HT Fast Real-Time PCR System  (Life Technologies, Inc) following the manufacturer's instructions

growth_protocol: Renal artery tissue was extracted from human kidneys and digested with collagenase.  Individual CD34+ CD105- cells were then selected by fluorescence assisted cell sorting.

extract_protocol: mirVana miRNA Isolation Kit (Life Technologies, Inc.) was used according to the manufacturer's instructions.

tag: cell type

tag: warm ischemia time

value: long, 30minutes


title: CD34+/CD105-, long warm ischemia (patient 3)

description:
experimental
h3e


title: control 2

label_protocol: The miRNA Microarray System with miRNA Complete Labeling and hybridization Kit (Agilent Technologies) was used according to the manufacturer′s recommended protocol. The Agilent microRNA Spike-In Kit was used for in-process control to measure labeling and hybridization efficiency.  Briefly, 50~60ng total RNA was dephosphorylated at 37°C for 30 min with calf intestinal phosphatase and denatured by using 100% DMSO at 100°C for 7min. Samples were labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 2 hour. The labeled RNA samples were purified in a Vacuum Concentrator for one hour. Once samples are completely dried.

tag: tissue


title: patient 1

description: Patient

source_name: patient_salivary exosome

value: patients with oral lichen planus


title: patient 2


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2616.CEL (CTC's<5)


title: lung, adenocarcinoma_18974

description: adenocarcinoma

value: lung

value: Male

value: non-small cell lung cancer (NSCLC)

tag: 7th tnm stage

value: ever

tag: kras status

tag: tp53 mutation

tag: death due to cancer

value: yes


title: CD34+/CD105-, short warm ischemia (patient 4)

description:
control
h4c

source_name: renal artery, living donor kidney transplant

value: short, 5minutes


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2612.CEL (CTC's<5)


title: CD34+/CD105-, short warm ischemia (patient 2)

description:
control
h2c


title: CD34+/CD105-, short warm ischemia (patient 1)

description:
control
h1c


title: CD34+/CD105-, short warm ischemia (patient 3)

description:
control
h3c


title: CD34+/CD105-, long warm ischemia (patient 4)

description:
experimental
h4e


title: RNA-Seq HET Naïve

type: SRA

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: hippocampus

growth_protocol: Hippocampal tissue was dissected from 3 months old mice.

extract_protocol: Total RNA was exctracted with the Qiagen RNAeasy kit

treatment_protocol: Hippocampal tissue was dissected from mice that were trained in a fear conditioning paradigm.

value: hippocampal tissue


title: RNA-Seq WT FC 24h


title: RNA-Seq HET 24h


title: RNA-Seq WT Naïve


title: lung, adenocarcinoma_12900

description: adenocarcinoma

source_name: lung, adenocarcinoma

tag: Sex

tag: race

value: European American

value: adenocarcinoma

value: Ia

tag: tumor size (cm)

value: no

tag: survival after surgery (days)


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2607.CEL (CTC's<5)


title: CD34+/CD105-, long warm ischemia (patient 1)

description:
experimental
h1e


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2609.CEL (CTC's<5)


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2606.CEL (CTC's<5)


description: CRPC mononuclear cell fraction of peripheral blood: 10SE2608.CEL (CTC's<5)


title: plep-1-reference-rep-1 hyb3

city: New York

first: Luke

middle: Mackley

last: Noble

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

hyb_protocol: as per Agilent protocol. Arrays were strippped by incubation with 20u RNAseH in 1x buffer for 6 hours at 37C, followed by 5' in 0.1X Agilent Wash Buffer 2 at 62C.

scan_protocol: Agilent G256CA Scanner and Feature Extraction Software.

data_processing: Raw data were imported into the R package limma, background corrected (method=normexp, offset=50), and normalized within (method=loess, span = 0.05) and across (method=Gquantile) arrays.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: reference

label_protocol: Labeled cRNA was in vitro transcribed from 1 μg total RNA  with the Agilent Low Input Quick Amp Labeling Kit.

growth_protocol: worms were synchronised by bleaching and L1 arrest, ~5000 L1 were added to 9cm NGM agarose plate seeded with OP50-1 E. coli and grown to young adult stage at 20C.

extract_protocol: Plates were washed with M9 buffer, worms were transferred to 1.5mL tubes, briefly centrifuged, excess buffer was aspirated, and samples were snap frozen in liquid nitrogen and stored at -80C until RNA extraction. 0.5mL Trizol reagent was added, tubes were thawed, mixed, and freeze/thaw was repeated before following the manufacturer's protocol./

tag: sample type

value: YA hermaphrodites

tag: genotype


title: Renal Cell Carcinoma_Specimen_CGI-186

city: Rutherford

first: Jane

last: Houldsworth

state: NJ

address: 201 Route 17 North

institute: Cancer Genetics, Inc.

description: CGI-186 RCC specimen as test DNA and Promega normal male DNA as reference

hyb_protocol: Labeled DNA was hybridized to custom designed targeted oligoarray in a mixture of hybridization buffer, block (both from Agilent In Situ Hybridization Kit Plus), and Cot-1 DNA (Life Technologies) were added to each sample prior to application to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization for 24 hours, slides were washed sequentially as described by the manufacturer.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B.

data_processing: Data extraction was performed using Feature Extraction Version 10.7.3.1 (Agilent Technologies).

source_name: Human RCC specimen

label_protocol: 1 ug of genomic DNA samples were heat fragmented, labeled using the Enzo array-CGH Labeling Kit, according to the manufacturer's protocol

extract_protocol: Extraction of genomic DNA was performed using PureGene DNA extraction kit according to the manufacturer's instructions.

value: Formalin Fixed Paraffin Embedded (FFPE)

value: renal cell carcinoma specimen

tag: histology

value: pRCC

tag: gender

value: M

tag: age

tag: furhman nuclear grade

tag: tnm stage

tag: tumor size (mm)

source_name: Reference human normal male genomic DNA (Promega).

value: Promega normal female DNA


title: plep-1-reference-rep-2 hyb3


title: Renal Cell Carcinoma_Specimen_CGI-192

description: CGI-192 RCC specimen as test DNA and Promega normal male DNA as reference

tag: tissue

value: ccRCC


title: Renal Cell Carcinoma_Specimen_CGI-185

description: CGI-185 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-189

description: CGI-189 RCC specimen as test DNA and Promega normal male DNA as reference


title: plep-1-reference-rep-4 hyb3


title: Renal Cell Carcinoma_Specimen_CGI-184

description: CGI-184 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-190

description: CGI-190 RCC specimen as test DNA and Promega normal male DNA as reference

value: T3a N1


title: wild-type-reference-rep-4 hyb2

value: wild-type


title: Renal Cell Carcinoma_Specimen_CGI-181

description: CGI-181 RCC specimen as test DNA and Promega normal male DNA as reference


title: wild-type-reference-rep-1 hyb3


title: wild-type-reference-rep-2 hyb3


title: plep-1-reference-rep-3 hyb3


title: plep-1-reference-rep-3 hyb2


title: Renal Cell Carcinoma_Specimen_CGI-188

description: CGI-188 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-191

description: CGI-191 RCC specimen as test DNA and Promega normal male DNA as reference


title: wild-type-reference-rep-4 hyb3


title: plep-1-reference-rep-2 hyb2


title: wild-type-reference-rep-1 hyb2


title: Renal Cell Carcinoma_Specimen_CGI-178

description: CGI-178 RCC specimen as test DNA and Promega normal male DNA as reference


title: plep-1-reference-rep-4 hyb2


title: plep-1-reference-rep-1 hyb2


title: Renal Cell Carcinoma_Specimen_CGI-179

description: CGI-179 RCC specimen as test DNA and Promega normal male DNA as reference


title: wild-type-reference-rep-3 hyb2


title: wild-type-reference-rep-2 hyb2


title: Renal Cell Carcinoma_Specimen_CGI-182

description: CGI-182 RCC specimen as test DNA and Promega normal male DNA as reference


title: wild-type-reference-rep-3 hyb3


title: Renal Cell Carcinoma_Specimen_CGI-180

description: CGI-180 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-183

description: CGI-183 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-162

description: CGI-162 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-158

description: CGI-158 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-165

description: CGI-165 RCC specimen as test DNA and Promega normal male DNA as reference


title: wild-type-reference-rep-2 hyb1


title: Renal Cell Carcinoma_Specimen_CGI-169

description: CGI-169 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-168

description: CGI-168 RCC specimen as test DNA and Promega normal male DNA as reference


title: plep-1-reference-rep-4 hyb1


title: plep-1-reference-rep-2 hyb1


title: Renal Cell Carcinoma_Specimen_CGI-175

description: CGI-175 RCC specimen as test DNA and Promega normal male DNA as reference

value: T2 M1


title: Renal Cell Carcinoma_Specimen_CGI-177

description: CGI-177 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-176

description: CGI-176 RCC specimen as test DNA and Promega normal male DNA as reference


title: wild-type-reference-rep-4 hyb1


title: Renal Cell Carcinoma_Specimen_CGI-156

description: CGI-156 RCC specimen as test DNA and Promega normal male DNA as reference


title: wild-type-reference-rep-1 hyb1


title: Renal Cell Carcinoma_Specimen_CGI-157

description: CGI-157 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-160

description: CGI-160 RCC specimen as test DNA and Promega normal male DNA as reference


title: 1052 D Tum Muc

first: Ho-Chou

last: Tu

state: MA - Massachusetts

address: One Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description: replicate 2

hyb_protocol: standard Illumina hybridization protocol

scan_protocol: standard Illumina scanning protocol

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

source_name: APC+B small intestinal tumor rep 2

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

growth_protocol: mouse intestinal mucosa or tumors, dissected and snap frozen in liquid nitrogen

extract_protocol: TRIZOL method for RNA extraction

treatment_protocol: transgenic animals de novo tumor formation

tag: strain

value: mix background B6/129/Balbc/CD1

value: 3 months

tag: treatment

value: doxycycline from 6-7 weeks old

value: iLIN28B; Apcmin/+

tag: tumor histology

value: adenoma


title: 2216 D Tum

description: replicate 1

source_name: APC+B small intestinal tumor rep 1


title: Renal Cell Carcinoma_Specimen_CGI-163

description: CGI-163 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-164

description: CGI-164 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-155

description: CGI-155 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-167

description: CGI-167 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-152

description: CGI-152 RCC specimen as test DNA and Promega normal male DNA as reference


title: wild-type-reference-rep-3 hyb1


title: Renal Cell Carcinoma_Specimen_CGI-149

description: CGI-149 RCC specimen as test DNA and Promega normal male DNA as reference


title: plep-1-reference-rep-1 hyb1


title: Renal Cell Carcinoma_Specimen_CGI-166

description: CGI-166 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-161

description: CGI-161 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-151

description: CGI-151 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-148

description: CGI-148 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-144

description: CGI-144 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-145

description: CGI-145 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-147

description: CGI-147 RCC specimen as test DNA and Promega normal male DNA as reference


title: plep-1-reference-rep-3 hyb1


title: 2218 D Tum

description: replicate 1

source_name: Apcmin small intestinal tumor rep 1

value: Apcmin/+


title: Renal Cell Carcinoma_Specimen_CGI-139

description: CGI-139 RCC specimen as test DNA and Promega normal male DNA as reference


title: MCF7_Xeno_BYL day 7_1

first: Aleix

last: Prat

address: Passeig Vall d´Hebron 119

department: Translational Genomics

institute: VHIO

hyb_protocol: Hybridization was conducted by the gene expression analysis service at MSKCC, (New York, NY, USA).  Briefly, Agilent Bioanalyzer nano chip was used to check the RNA quality and integrity. cRNA amplification and labeling with biotin were performed using Illumina TotalPrep RNA amplification kit (Ambion, Inc., Austin, TX) with 200ng of total RNA as input material. cRNA yields were quantified with Agilent Bioanalyzer, and 750ng of cRNAs were hybridized to the HumanHT-12 v4 Expression BeadChip. All reagents and equipment used for hybridization were purchased from Illumina. The cRNA was hybridized to arrays for 16 h at 58°C, washed and stained with streptavidin-Cy3 according to the manufacturer's protocol.

scan_protocol: The bead chips were centrifuged to dry and scanned on the Illumina BeadArray Reader confocal scanner. The data were analyzed with GenomeStudio using Illumina default analysis settings.

label: Biotin

source_name: Breast cancer cell line

extract_protocol: For microarray-gene expression analyisis total RNA was extracted from MCF7, T47D, CAMA1 cell lines using the QIAGEN RNeasy kit. Total RNA from MCF7 xenografts and patient derived xenografts was obtained using the same kit preceded by tissue homogenization with TRIzol® (Thermo Fisher Scientific Inc).

tag: cell line

value: MCF7 xenograft

tag: treatment (drug)

value: PI3K inhibitor (BYL719)

tag: cell type

value: Breast cancer cell line


title: MCF7_Xeno_Control_3

value: Ctrl


title: 1737 Jej T1

description: replicate 2

source_name: iLIN28B intestinal tumor rep 2

value: 8 months

value: adenoma/adenocarcinoma


title: Renal Cell Carcinoma_Specimen_CGI-134

description: CGI-134 RCC specimen as test DNA and Promega normal male DNA as reference

value: Formalin Fixed Paraffin Embedded (FFPE)

value: renal cell carcinoma specimen

value: chrRCC

value: M

value: Promega normal female DNA


title: 1737 D T1

description: replicate 1

source_name: iLIN28B intestinal tumor rep 1

value: mix background B6/129/Balbc/CD1


title: MCF7_Xeno_Control_2


title: PDX131_BYL_3

value: Patient derived xenograft


title: 1032 D Muc

description: replicate 2

source_name: wt small intestinal mucosa rep 2

value: 3 months

value: doxycycline from 6-7 weeks old

value: wt

value: normal


title: MCF7_Xeno_BYL day 7_2

value: MCF7 xenograft


title: Renal Cell Carcinoma_Specimen_CGI-131

description: CGI-131 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-132

description: CGI-132 RCC specimen as test DNA and Promega normal male DNA as reference


title: 2215 D Tum

description: replicate 2

source_name: Apcmin small intestinal tumor rep 2

value: Apcmin/+

value: adenoma


title: 1053 Col T2

description: replicate 4

source_name: APC+B colon tumor rep 4

value: iLIN28B; Apcmin/+


title: 1028 D Muc

description: replicate 1

source_name: wt small intestinal mucosa rep 1


title: Renal Cell Carcinoma_Specimen_CGI-136

description: CGI-136 RCC specimen as test DNA and Promega normal male DNA as reference

value: ccRCC


title: Renal Cell Carcinoma_Specimen_CGI-128

description: CGI-128 RCC specimen as test DNA and Promega normal male DNA as reference

value: pRCC


title: MCF7_Xeno_Control_1

value: Ctrl

value: Breast cancer cell line


title: PDX131_BYL_2

value: PI3K inhibitor (BYL719)


title: Renal Cell Carcinoma_Specimen_CGI-133

description: CGI-133 RCC specimen as test DNA and Promega normal male DNA as reference

value: Formalin Fixed Paraffin Embedded (FFPE)

value: renal cell carcinoma specimen

value: chrRCC

value: M


title: Renal Cell Carcinoma_Specimen_CGI-141

description: CGI-141 RCC specimen as test DNA and Promega normal male DNA as reference

value: Promega normal female DNA


title: Renal Cell Carcinoma_Specimen_CGI-143

description: CGI-143 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-138

description: CGI-138 RCC specimen as test DNA and Promega normal male DNA as reference


title: PDX131_BYL_1

value: Patient derived xenograft


title: Renal Cell Carcinoma_Specimen_CGI-125

description: CGI-125 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-126

description: CGI-126 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-124

description: CGI-124 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-130

description: CGI-130 RCC specimen as test DNA and Promega normal male DNA as reference


title: 2135 Col T4

description: replicate 3

source_name: APC+B colon tumor rep 3

value: mix background B6/129/Balbc/CD1

value: 3 months

value: doxycycline from 6-7 weeks old


title: PDX131_Control_3


title: 2135 Col T2

description: replicate 2

source_name: APC+B colon tumor rep 2


title: Renal Cell Carcinoma_Specimen_CGI-122

description: CGI-122 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-116

description: CGI-116 RCC specimen as test DNA and Promega normal male DNA as reference


title: T47D_BYL48h_3

tag: treatment (time)


title: Renal Cell Carcinoma_Specimen_CGI-117

description: CGI-117 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-113

description: CGI-113 RCC specimen as test DNA and Promega normal male DNA as reference


title: PDX131_Control_2


title: 1030 Col T

description: replicate 2

source_name: Apcmin colon tumor rep 2

value: Apcmin/+


title: 1032 Col Muc

description: replicate 2

source_name: wt colon mucosa rep 2

value: wt

value: normal


title: Renal Cell Carcinoma_Specimen_CGI-120

description: CGI-120 RCC specimen as test DNA and Promega normal male DNA as reference

value: ccRCC

value: T3a M1


title: T47D_BYL48h_2


title: Renal Cell Carcinoma_Specimen_CGI-112

description: CGI-112 RCC specimen as test DNA and Promega normal male DNA as reference


title: PDX131_Control_1

value: Ctrl


title: Renal Cell Carcinoma_Specimen_CGI-107

description: CGI-107 RCC specimen as test DNA and Promega normal male DNA as reference


title: 1028 Col Muc

description: replicate 1

source_name: wt colon mucosa rep 1


title: Renal Cell Carcinoma_Specimen_CGI-108

description: CGI-108 RCC specimen as test DNA and Promega normal male DNA as reference

source_name: Human RCC specimen


title: T47D_BYL24h_3

value: Breast cancer cell line


title: Renal Cell Carcinoma_Specimen_CGI-104

description: CGI-104 RCC specimen as test DNA and Promega normal male DNA as reference

value: pRCC

source_name: Reference human normal male genomic DNA (Promega).


title: Renal Cell Carcinoma_Specimen_CGI-103

description: CGI-103 RCC specimen as test DNA and Promega normal male DNA as reference

value: Formalin Fixed Paraffin Embedded (FFPE)


title: Renal Cell Carcinoma_Specimen_CGI-105

description: CGI-105 RCC specimen as test DNA and Promega normal male DNA as reference

value: renal cell carcinoma specimen


title: T47D_BYL48h_1

value: PI3K inhibitor (BYL719)


title: Renal Cell Carcinoma_Specimen_CGI-100

description: CGI-100 RCC specimen as test DNA and Promega normal male DNA as reference

value: M


title: 1029 Col T

description: replicate 1

source_name: Apcmin colon tumor rep 1

value: adenoma


title: Renal Cell Carcinoma_Specimen_CGI-114

description: CGI-114 RCC specimen as test DNA and Promega normal male DNA as reference

value: Promega normal female DNA


title: 2135 Col T1

description: replicate 1

source_name: APC+B colon tumor rep 1

value: mix background B6/129/Balbc/CD1

value: iLIN28B; Apcmin/+


title: Renal Cell Carcinoma_Specimen_CGI-092

description: CGI-092 RCC specimen as test DNA and Promega normal male DNA as reference


title: T47D_BYL24h_2


title: Renal Cell Carcinoma_Specimen_CGI-097

description: CGI-097 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-094

description: CGI-094 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-099

description: CGI-099 RCC specimen as test DNA and Promega normal male DNA as reference


title: Low yield line at Stage 2, biological rep2, in 2007

city: St Paul

first: Susan

last: Gibson

state: MN

address: 1500 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: Expresion data for developing seeds of low yield line at length 3.5 mm

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Soybean Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

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

data_processing: The data were analyzed using GCRMA function in the GCRMA package in R environment.

organism: Glycine max

source_name: Developing seeds for low yield line at Stage 2, biological rep2, in 2007

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

growth_protocol: Soybean plants were grown and maintained under regular field conditions.

extract_protocol: Extraction of total RNA was performed using Sigma Spectrum Plant Total RNA kit according to the manufacturer's instructions.

treatment_protocol: Developing soybean seeds were collected, put on dry ice, and then transferred to -80 C until RNA extraction.

value: seeds

tag: developmental stage

value: Developing seeds, 3.5 mm in length


title: Renal Cell Carcinoma_Specimen_CGI-091

description: CGI-091 RCC specimen as test DNA and Promega normal male DNA as reference

tag: sample type


title: Low yield line at Stage 2 , biological rep3, in 2007

description: Expresion data for developing seeds of high yield line at length 3.5 mm

source_name: Developing seeds for low yield line at Stage 2 , biological rep3, in 2007

tag: genotype


title: T47D_BYL12h_1

source_name: Breast cancer cell line


title: T47D_BYL12h_3


title: T47D_BYL12h_2


title: Low yield line at Stage 2, biological rep1, in 2007

source_name: Developing seeds for low yield line at Stage 2, biological rep1, in 2007


title: High yield line at Stage 1, biological rep3, in 2007

description: Expresion data for developing seeds of high yield line at length 2 mm

source_name: Developing seeds for high yield line at Stage 1, biological rep3, in 2007

value: Developing seeds, 2 mm in length


title: Renal Cell Carcinoma_Specimen_CGI-095

description: CGI-095 RCC specimen as test DNA and Promega normal male DNA as reference

tag: histology


title: Renal Cell Carcinoma_Specimen_CGI-087

description: CGI-087 RCC specimen as test DNA and Promega normal male DNA as reference

tag: gender


title: T47D_BYL24h_1


title: Renal Cell Carcinoma_Specimen_CGI-088

description: CGI-088 RCC specimen as test DNA and Promega normal male DNA as reference

value: chrRCC

tag: age


title: Renal Cell Carcinoma_Specimen_CGI-089

description: CGI-089 RCC specimen as test DNA and Promega normal male DNA as reference

tag: furhman nuclear grade


title: High yield line at Stage 1, biological rep2, in 2007

source_name: Developing seeds for high yield line at Stage 1, biological rep2, in 2007


title: T47D_BYL8h_2


title: Low yield line at Stage 1, biological rep2, in 2007

description: Expresion data for developing seeds of low yield line at length 2 mm

source_name: Developing seeds for low yield line at Stage 1, biological rep2, in 2007


title: T47D_BYL8h_3


title: Renal Cell Carcinoma_Specimen_CGI-085

description: CGI-085 RCC specimen as test DNA and Promega normal male DNA as reference

tag: tnm stage


title: Renal Cell Carcinoma_Specimen_CGI-080

description: CGI-080 RCC specimen as test DNA and Promega normal male DNA as reference

tag: tumor size (mm)


title: High yield line at Stage 1, biological rep1, in 2007

source_name: Developing seeds for high yield line at Stage 1, biological rep1, in 2007

tag: tissue


title: Renal Cell Carcinoma_Specimen_CGI-082

description: CGI-082 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-083

description: CGI-083 RCC specimen as test DNA and Promega normal male DNA as reference


title: Low yield line at Stage 1, biological rep1, in 2007

source_name: Developing seeds for low yield line at Stage 1, biological rep1, in 2007


title: T47D_BYL8h_1


title: Low yield line at Stage 1, biological rep3, in 2007

source_name: Developing seeds for low yield line at Stage 1, biological rep3, in 2007


title: T47D_BYL4h_3


title: Renal Cell Carcinoma_Specimen_CGI-078

description: CGI-078 RCC specimen as test DNA and Promega normal male DNA as reference

value: ccRCC


title: T47D_BYL4h_2


title: High yield line at Stage 3, biological rep3, in 2007

description: Expresion data for developing seeds of high yield line at length 5-6 mm

source_name: Developing seeds for high yield line at Stage 3, biological rep3, in 2007

value: Developing seeds, 5-6 mm in length


title: Renal Cell Carcinoma_Specimen_CGI-072

description: CGI-072 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-075

description: CGI-075 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-067

description: CGI-067 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-090

description: CGI-090 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-071

description: CGI-071 RCC specimen as test DNA and Promega normal male DNA as reference


title: T47D_DMSO_3

value: Ctrl

value: Control


title: High yield line at Stage 3, biological rep1, in 2007

source_name: Developing seeds for high yield line at Stage 3, biological rep1, in 2007


title: T47D_DMSO_2

value: Breast cancer cell line


title: High yield line at Stage 3, biological rep2, in 2007

source_name: Developing seeds for high yield line at Stage 3, biological rep2, in 2007


title: Low yield line at Stage 3, biological rep1, in 2007

description: Expresion data for developing seeds of low yield line at length 5-6 mm

source_name: Developing seeds for low yield line at Stage 3, biological rep1, in 2007


title: Renal Cell Carcinoma_Specimen_CGI-066

description: CGI-066 RCC specimen as test DNA and Promega normal male DNA as reference

source_name: Human RCC specimen

value: Formalin Fixed Paraffin Embedded (FFPE)

value: pRCC

source_name: Reference human normal male genomic DNA (Promega).


title: Renal Cell Carcinoma_Specimen_CGI-062

description: CGI-062 RCC specimen as test DNA and Promega normal male DNA as reference

value: renal cell carcinoma specimen


title: Low yield line at Stage 3, biological rep3, in 2007

source_name: Developing seeds for low yield line at Stage 3, biological rep3, in 2007


title: MCF7_BYL_1uM_48h_3

value: PI3K inhibitor (BYL719)


title: T47D_BYL4h_1


title: Renal Cell Carcinoma_Specimen_CGI-061

description: CGI-061 RCC specimen as test DNA and Promega normal male DNA as reference

value: M


title: Renal Cell Carcinoma_Specimen_CGI-056

description: CGI-056 RCC specimen as test DNA and Promega normal male DNA as reference

value: Promega normal female DNA


title: Renal Cell Carcinoma_Specimen_CGI-065

description: CGI-065 RCC specimen as test DNA and Promega normal male DNA as reference


title: Low yield line at Stage 3, biological rep2, in 2007

source_name: Developing seeds for low yield line at Stage 3, biological rep2, in 2007


title: Renal Cell Carcinoma_Specimen_CGI-055

description: CGI-055 RCC specimen as test DNA and Promega normal male DNA as reference


title: MCF7_BYL_1uM_48h_2


title: High yield line at Stage 2, biological rep2, in 2007

description: Expresion data for developing seeds of high yield line at length 3.5 mm

source_name: Developing seeds for high yield line at Stage 2, biological rep2, in 2007


title: T47D_DMSO_1

source_name: Breast cancer cell line


title: Renal Cell Carcinoma_Specimen_CGI-057

description: CGI-057 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-059

description: CGI-059 RCC specimen as test DNA and Promega normal male DNA as reference


title: High yield line at Stage 2, biological rep3, in 2007

source_name: Developing seeds for high yield line at Stage 2, biological rep3, in 2007


title: Renal Cell Carcinoma_Specimen_CGI-052

description: CGI-052 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-051

description: CGI-051 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-074

description: CGI-074 RCC specimen as test DNA and Promega normal male DNA as reference


title: High yield line at Stage 2, biological rep1, in 2007

source_name: Developing seeds for high yield line at Stage 2, biological rep1, in 2007


title: Renal Cell Carcinoma_Specimen_CGI-069

description: CGI-069 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-049

description: CGI-049 RCC specimen as test DNA and Promega normal male DNA as reference


title: MCF7_BYL_1uM_24h_3


title: Renal Cell Carcinoma_Specimen_CGI-050

description: CGI-050 RCC specimen as test DNA and Promega normal male DNA as reference


title: MCF7_BYL_1uM_48h_1


title: Minsoy at Stage 3, biological rep3, in 2008

description: Expresion data for developing seed of Minsoy at length 5-6 mm

source_name: Minsoy developing seeds at Stage 3, biological rep3, in 2008

value: MInsoy


title: Renal Cell Carcinoma_Specimen_CGI-042

description: CGI-042 RCC specimen as test DNA and Promega normal male DNA as reference


title: Minsoy at Stage 2, biological rep3, in 2008

description: Expresion data for developing seed of Minsoy at length 3.5 mm

source_name: Minsoy developing seeds at Stage 2, biological rep3, in 2008

value: Minsoy


title: MCF7_BYL_1uM_24h_2


title: Renal Cell Carcinoma_Specimen_CGI-046

description: CGI-046 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-043

description: CGI-043 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-038

description: CGI-038 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-040

description: CGI-040 RCC specimen as test DNA and Promega normal male DNA as reference


title: MCF7_BYL_1uM_24h_1


title: Renal Cell Carcinoma_Specimen_CGI-041

description: CGI-041 RCC specimen as test DNA and Promega normal male DNA as reference


title: MCF7_BYL_1uM_12h_3


title: Renal Cell Carcinoma_Specimen_CGI-037

description: CGI-037 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-044

description: CGI-044 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-034

description: CGI-034 RCC specimen as test DNA and Promega normal male DNA as reference

value: OC


title: Archer at Stage 3, biological rep3, in 2008

description: Expresion data for developing seed of Archer at length 5-6 mm

source_name: Archer developing seeds at Stage 3, biological rep3, in 2008

value: seeds

value: Archer


title: Archer at Stage 1, biological rep3, in 2008

description: Expresion data for developing seed of Archer at length 2 mm

source_name: Archer developing seeds at Stage 1, biological rep3, in 2008

value: Developing seeds, 2 mm in length


title: Renal Cell Carcinoma_Specimen_CGI-036

description: CGI-036 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-035

description: CGI-035 RCC specimen as test DNA and Promega normal male DNA as reference


title: MCF7_BYL_1uM_12h_2


title: Renal Cell Carcinoma_Specimen_CGI-032

description: CGI-032 RCC specimen as test DNA and Promega normal male DNA as reference


title: MCF7_BYL_1uM_8h_3


title: MCF7_BYL_1uM_8h_2


title: Minsoy at Stage 3, biological rep2, in 2008

source_name: Minsoy developing seeds at Stage 3, biological rep2, in 2008


title: MCF7_BYL_1uM_12h_1


title: Archer at Stage 2, biological rep3, in 2008

description: Expresion data for developing seed of Archer at length 3.5 mm

source_name: Archer developing seeds at Stage 2, biological rep3, in 2008

value: Developing seeds, 3.5 mm in length


title: Renal Cell Carcinoma_Specimen_CGI-027

description: CGI-027 RCC specimen as test DNA and Promega normal male DNA as reference


title: Minsoy at Stage 1, biological rep3, in 2008

description: Expresion data for developing seed of Minsoy at length 2 mm

source_name: Minsoy developing seeds at Stage 1, biological rep3, in 2008


title: Renal Cell Carcinoma_Specimen_CGI-031

description: CGI-031 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-033

description: CGI-033 RCC specimen as test DNA and Promega normal male DNA as reference


title: Minsoy at Stage 2, biological rep2, in 2008

description: Expresion data for developing seed of Minsoy at length 3.5 mm

source_name: Minsoy developing seeds at Stage 2, biological rep2, in 2008


title: Renal Cell Carcinoma_Specimen_CGI-028

description: CGI-028 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-023

description: CGI-023 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-021

description: CGI-021 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-025

description: CGI-025 RCC specimen as test DNA and Promega normal male DNA as reference


title: MCF7_BYL_1uM_4h_3


title: MCF7_BYL_1uM_8h_1


title: Minsoy at Stage 1, biological rep2, in 2008

source_name: Minsoy developing seeds at Stage 1, biological rep2, in 2008


title: Renal Cell Carcinoma_Specimen_CGI-022

description: CGI-022 RCC specimen as test DNA and Promega normal male DNA as reference

source_name: Human RCC specimen


title: Renal Cell Carcinoma_Specimen_CGI-018

description: CGI-018 RCC specimen as test DNA and Promega normal male DNA as reference

source_name: Reference human normal male genomic DNA (Promega).


title: Archer at Stage 3, biological rep2, in 2008

description: Expresion data for developing seed of Archer at length 5-6 mm

source_name: Archer developing seeds at Stage 3, biological rep2, in 2008

value: Developing seeds, 5-6 mm in length


title: Archer at Stage 2, biological rep2, in 2008

source_name: Archer developing seeds at Stage 2, biological rep2, in 2008


title: MCF7_BYL_1uM_4h_2


title: Archer at Stage 1, biological rep2, in 2008

description: Expresion data for developing seed of Archer at length 2 mm

source_name: Archer developing seedsat Stage 1, biological rep2, in 2008


title: Renal Cell Carcinoma_Specimen_CGI-015

description: CGI-015 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-009

description: CGI-009 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-013

description: CGI-013 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-014

description: CGI-014 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-008

description: CGI-008 RCC specimen as test DNA and Promega normal male DNA as reference


title: Minsoy at Stage 2, biological rep1, in 2008

source_name: Minsoy developing seeds at Stage 2, biological rep1, in 2008


title: MCF7_Control_3

source_name: Breast cancer cell line

value: Ctrl


title: Renal Cell Carcinoma_Specimen_CGI-007

description: CGI-007 RCC specimen as test DNA and Promega normal male DNA as reference


title: Minsoy at Stage 1, biological rep1, in 2008

description: Expresion data for developing seed of Minsoy at length 2 mm

source_name: Minsoy developing seeds at Stage 1, biological rep1, in 2008


title: Renal Cell Carcinoma_Specimen_CGI-017

description: CGI-017 RCC specimen as test DNA and Promega normal male DNA as reference


title: MCF7_Control_2

value: Control


title: Minsoy at Stage 3, biological rep1, in 2008

description: Expresion data for developing seed of Minsoy at length 5-6 mm

source_name: Minsoy developing seeds at Stage 3, biological rep1, in 2008


title: Renal Cell Carcinoma_Specimen_CGI-010

description: CGI-010 RCC specimen as test DNA and Promega normal male DNA as reference


title: Archer at Stage 3, biological rep1, in 2008

source_name: Archer developing seedsat Stage 3, biological rep1, in 2008


title: Renal Cell Carcinoma_Specimen_CGI-005

description: CGI-005 RCC specimen as test DNA and Promega normal male DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-187

description: CGI-187 RCC specimen as test DNA and Promega normal female DNA as reference

value: ccRCC

value: F

value: 3 and 4

source_name: Reference human normal female genomic DNA (Promega).


title: Renal Cell Carcinoma_Specimen_CGI-174

description: CGI-174 RCC specimen as test DNA and Promega normal female DNA as reference

value: Formalin Fixed Paraffin Embedded (FFPE)

value: renal cell carcinoma specimen


title: MCF7_Control_1

value: Breast cancer cell line


title: Renal Cell Carcinoma_Specimen_CGI-173

description: CGI-173 RCC specimen as test DNA and Promega normal female DNA as reference

value: T3a M1

value: Promega normal female DNA


title: Renal Cell Carcinoma_Specimen_CGI-170

description: CGI-170 RCC specimen as test DNA and Promega normal female DNA as reference

value: pRCC


title: Archer at Stage 2, biological rep1, in 2008

description: Expresion data for developing seed of Archer at length 3.5 mm

source_name: Archer developing seeds at Stage 2, biological rep1, in 2008


title: Renal Cell Carcinoma_Specimen_CGI-154

description: CGI-154 RCC specimen as test DNA and Promega normal female DNA as reference


title: CAMA1_MK48h_1

value: AKT inhibitor (MK2206)


title: CAMA1_MK24h_3


title: CAMA1_MK48h_3


title: Renal Cell Carcinoma_Specimen_CGI-159

description: CGI-159 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-171

description: CGI-171 RCC specimen as test DNA and Promega normal female DNA as reference


title: CAMA1_MK48h_2


title: Renal Cell Carcinoma_Specimen_CGI-172

description: CGI-172 RCC specimen as test DNA and Promega normal female DNA as reference


title: Minsoy at Stage 3, biological rep3, in 2007

description: Expresion data for developing seeds of Minsoy at length 5-6 mm

source_name: Minsoy developing seeds at Stage 3, biological rep3, in 2007

value: seeds

value: MInsoy


title: Archer at Stage 1, biological rep1, in 2008

description: Expresion data for developing seed of Archer at length 2 mm

source_name: Archer developing seeds at Stage 1, biological rep1, in 2008

value: Archer

value: Developing seeds, 2 mm in length


title: Renal Cell Carcinoma_Specimen_CGI-153

description: CGI-153 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-150

description: CGI-150 RCC specimen as test DNA and Promega normal female DNA as reference


title: Minsoy at Stage 3, biological rep1, in 2007

source_name: Minsoy developing seeds at Stage 3, biological rep1, in 2007

value: Developing seeds, 5-6 mm in length


title: Renal Cell Carcinoma_Specimen_CGI-140

description: CGI-140 RCC specimen as test DNA and Promega normal female DNA as reference


title: Minsoy at Stage 3, biological rep2, in 2007

source_name: Minsoy developing seeds at Stage 3, biological rep2, in 2007

value: Minsoy


title: CAMA1_MK24h_2


title: Renal Cell Carcinoma_Specimen_CGI-146

description: CGI-146 RCC specimen as test DNA and Promega normal female DNA as reference


title: Archer at Stage 3, biological rep3, in 2007

description: Expresion data for developing seeds of Archer at length 5-6 mm

source_name: Archer developing seeds at Stage 3, biological rep3, in 2007


title: Renal Cell Carcinoma_Specimen_CGI-137

description: CGI-137 RCC specimen as test DNA and Promega normal female DNA as reference

source_name: Human RCC specimen


title: CAMA1_MK24h_1


title: CAMA1_MK12h_3


title: Renal Cell Carcinoma_Specimen_CGI-135

description: CGI-135 RCC specimen as test DNA and Promega normal female DNA as reference

value: chrRCC


title: Renal Cell Carcinoma_Specimen_CGI-127

description: CGI-127 RCC specimen as test DNA and Promega normal female DNA as reference


title: Archer at Stage 3, biological rep2, in 2007

source_name: Archer developing seeds at Stage 3, biological rep2, in 2007


title: Archer at Stage 3, biological rep1, in 2007

source_name: Archer developing seeds at Stage 3, biological rep1, in 2007


title: Renal Cell Carcinoma_Specimen_CGI-142

description: CGI-142 RCC specimen as test DNA and Promega normal female DNA as reference

value: ccRCC


title: Renal Cell Carcinoma_Specimen_CGI-129

description: CGI-129 RCC specimen as test DNA and Promega normal female DNA as reference

value: F


title: Renal Cell Carcinoma_Specimen_CGI-123

description: CGI-123 RCC specimen as test DNA and Promega normal female DNA as reference


title: CAMA1_MK8h_2


title: CAMA1_MK8h_3


title: Minsoy at Stage 2, biological rep2, in 2007

description: Expresion data for developing seeds of Minsoy at length 3.5 mm

source_name: Minsoy developing seeds at Stage 2, biological rep2, in 2007

value: Developing seeds, 3.5 mm in length


title: CAMA1_MK12h_1


title: Renal Cell Carcinoma_Specimen_CGI-119

description: CGI-119 RCC specimen as test DNA and Promega normal female DNA as reference

value: Formalin Fixed Paraffin Embedded (FFPE)


title: CAMA1_MK12h_2


title: Renal Cell Carcinoma_Specimen_CGI-110

description: CGI-110 RCC specimen as test DNA and Promega normal female DNA as reference

value: renal cell carcinoma specimen


title: Renal Cell Carcinoma_Specimen_CGI-121

description: CGI-121 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-115

description: CGI-115 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-111

description: CGI-111 RCC specimen as test DNA and Promega normal female DNA as reference


title: CAMA1_MK8h_1

value: Breast cancer cell line


title: Renal Cell Carcinoma_Specimen_CGI-118

description: CGI-118 RCC specimen as test DNA and Promega normal female DNA as reference


title: Minsoy at Stage 2, biological rep1, in 2007

source_name: Minsoy developing seeds at Stage 2, biological rep1, in 2007


title: Renal Cell Carcinoma_Specimen_CGI-109

description: CGI-109 RCC specimen as test DNA and Promega normal female DNA as reference


title: Minsoy at Stage 1, biological rep3, in 2007

description: Expresion data for developing seeds of Minsoy at length 2 mm

source_name: Minsoy developing seeds at Stage 1, biological rep3, in 2007


title: Minsoy at Stage 1, biological rep2, in 2007

source_name: Minsoy developing seeds at Stage 1, biological rep2, in 2007


title: MCF7_BYL_1uM_4h_1

source_name: Breast cancer cell line

value: PI3K inhibitor (BYL719)


title: Renal Cell Carcinoma_Specimen_CGI-101

description: CGI-101 RCC specimen as test DNA and Promega normal female DNA as reference

value: Promega normal female DNA


title: Renal Cell Carcinoma_Specimen_CGI-102

description: CGI-102 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-098

description: CGI-098 RCC specimen as test DNA and Promega normal female DNA as reference


title: Minsoy at Stage 2, biological rep3, in 2007

source_name: Minsoy developing seeds at Stage 2, biological rep3, in 2007


title: CAMA1_MK4h_2


title: CAMA1_MK4h_1


title: Minsoy at Stage 1, biological rep1, in 2007

source_name: Minsoy developing seeds at Stage 1, biological rep1, in 2007


title: Renal Cell Carcinoma_Specimen_CGI-106

description: CGI-106 RCC specimen as test DNA and Promega normal female DNA as reference

source_name: Reference human normal female genomic DNA (Promega).


title: Archer at Stage 2, biological rep3, in 2007

description: Expresion data for developing seeds of Archer at length 3.5 mm

source_name: Archer developing seeds at Stage 2, biological rep3, in 2007


title: Renal Cell Carcinoma_Specimen_CGI-086

description: CGI-086 RCC specimen as test DNA and Promega normal female DNA as reference

value: pRCC


title: CAMA1_DMSO_3

value: Ctrl

value: Control


title: CAMA1_MK4h_3

value: AKT inhibitor (MK2206)


title: Renal Cell Carcinoma_Specimen_CGI-084

description: CGI-084 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-096

description: CGI-096 RCC specimen as test DNA and Promega normal female DNA as reference


title: CAMA1_DMSO_2


title: Renal Cell Carcinoma_Specimen_CGI-081

description: CGI-081 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-079

description: CGI-079 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-093

description: CGI-093 RCC specimen as test DNA and Promega normal female DNA as reference


title: CAMA1_DMSO_1


title: Renal Cell Carcinoma_Specimen_CGI-076

description: CGI-076 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-073

description: CGI-073 RCC specimen as test DNA and Promega normal female DNA as reference


title: Archer at Stage 1, biological rep3, in 2007

description: Expresion data for developing seeds of Archer at length 2 mm

source_name: Archer developing seeds at Stage 1, biological rep3, in 2007

value: seeds

value: Archer


title: Archer at Stage 2, biological rep1, in 2007

source_name: Archer developing seeds at Stage 2, biological rep1, in 2007


title: Archer at Stage 1, biological rep2, in 2007

source_name: Archer developing seeds at Stage 1, biological rep2, in 2007

value: Developing seeds, 2 mm in length


title: Renal Cell Carcinoma_Specimen_CGI-068

description: CGI-068 RCC specimen as test DNA and Promega normal female DNA as reference


title: X R3

city: Subang Jaya

first: Melissa

middle: Su Wei

last: Poh

state: Malaysia

address: No.1, Jln Taylor’s

country: Malaysia

institute: Taylor's University

description: Combination of Glabridin 10-7M with 17β-E2 10-9M, replicate 3

hyb_protocol: Following fragmentation, hybridisation was performed on Affymetrix GeneChip® PrimeViewTM array for 16 hr at 450C in Affeymetrix GeneChip® hybridization oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000

data_processing:
The data were analysed using Genespring GX 12.6.1 software (Agilent, USA). The CEL files together with the ARR files were uploaded to the software and subjected to robust multi-array analysis. The chips were then normalised via quantile normalisation and summarised into expression measures to obtain a single expression measure for each probe-set as represented by their individual probe-set ID’s per chip. The baseline option chosen for the samples was baseline to median of control samples. The samples were grouped together with its replicates which were subjected to the same treatment and averaged.
Processed data includes averaged fold-change values of the treated samples against the untreated control e.g. Fold-change (Gla vs Untreated)

source_name: Ishikawa cells, Combination of Glabridin 10-7M with 17β-E2 10-9M

label_protocol: Biotinylated cRNA was prepared with 250ng of RNA using GeneChip®3’IVT Express kit (Affymetrix, USA) as per manufacturer’s protocol

growth_protocol: Ishikawa cells were grown in DMEM/F-12 media (without phenol red) for 24 hours prior to seeding into T-75 flasks at 1 x 106 cells/ flask and grown for 24 hours before treatiing with the drugs

extract_protocol: RNA extraction was performed using the RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions

treatment_protocol: The drugs were treated to the Ishikawa cells for 72 hours prior to RNA extraction

value: Ishikawa

tag: tag


title: X R1

description: Combination of Glabridin 10-7M with 17β-E2 10-9M, replicate 1


title: Renal Cell Carcinoma_Specimen_CGI-064

description: CGI-064 RCC specimen as test DNA and Promega normal female DNA as reference

value: chrRCC


title: Renal Cell Carcinoma_Specimen_CGI-077

description: CGI-077 RCC specimen as test DNA and Promega normal female DNA as reference

value: ccRCC


title: Renal Cell Carcinoma_Specimen_CGI-054

description: CGI-054 RCC specimen as test DNA and Promega normal female DNA as reference

value: F

value: 3 and 4


title: OE33 Combined rep3

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using Illumina's BeadStudio Data Analysis Software.

growth_protocol: Esophageal cell lines Het-1A, OE21 and OE33 (European Collection of Cell Cultures, Salisbury, UK) were cultured in GIBCO™ RPMI 1640 medium (Invitrogen, Karlsruhe, Germany) supplemented with 10% FBS and 2 mM GIBCO™ L-Glutamine (Invitrogen) at 37 °C in a 5 % CO2 atmosphere

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

treatment_protocol: Het-1A, OE33 and OE22 were treated independently with the HDAC (histone deacetylase) inhibtor MS-275 (0.5 μM), the DNMT1 inhibtor AZA (Azacytidine, 50 μM) and in the combination of both (MS-275 and AZA) for 24 hours. DMSO were used as the respective control. For ech condition was a triplicate performed. After 24 hours stimulation time  from all treated samples were the total mRNA isolated.

tag: cell ine

tag: tissue origin

value: Esophagus

value: cell line from adenocarcinoma of the lower oesophagus (Barrett′s metaplasia)

tag: treated with

value: 50 μM AZA + 0.5 μM MS-275 for 24 hrs

tag: array id


title: X R2

description: Combination of Glabridin 10-7M with 17β-E2 10-9M, replicate 2

tag: cell type


title: Renal Cell Carcinoma_Specimen_CGI-048

description: CGI-048 RCC specimen as test DNA and Promega normal female DNA as reference

value: Formalin Fixed Paraffin Embedded (FFPE)

value: renal cell carcinoma specimen


title: E2 R3

description: 17β-E2 10-9M, replicate 3

source_name: Ishikawa cells, 17β-E2 10-9M


title: Renal Cell Carcinoma_Specimen_CGI-063

description: CGI-063 RCC specimen as test DNA and Promega normal female DNA as reference

source_name: Human RCC specimen

value: Promega normal female DNA


title: OE33 MS275 rep3

value: 0.5 μM MS-275 (histone deacetylase inhibtor) for 24 hrs


title: Renal Cell Carcinoma_Specimen_CGI-058

description: CGI-058 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-070

description: CGI-070 RCC specimen as test DNA and Promega normal female DNA as reference


title: OE33 AZA rep3

value: 50 μM AZA (Azacytidine) for 24 hrs


title: OE33 DMSO rep3

value: DMSO for 24 hrs


title: Archer at Stage 1, biological rep1, in 2007

source_name: Archer developing seeds at Stage 1, biological rep1, in 2007

value: seeds


title: Renal Cell Carcinoma_Specimen_CGI-053

description: CGI-053 RCC specimen as test DNA and Promega normal female DNA as reference


title: OE21 MS275 rep3

value: cell line from squamous carcinoma of mid oesophagus


title: E2 R1

description: 17β-E2 10-9M, replicate 1


title: Renal Cell Carcinoma_Specimen_CGI-047

description: CGI-047 RCC specimen as test DNA and Promega normal female DNA as reference

value: pRCC


title: OE21 Combined rep3


title: Renal Cell Carcinoma_Specimen_CGI-045

description: CGI-045 RCC specimen as test DNA and Promega normal female DNA as reference


title: E2 R2

description: 17β-E2 10-9M, replicate 2

value: Ishikawa


title: Renal Cell Carcinoma_Specimen_CGI-030

description: CGI-030 RCC specimen as test DNA and Promega normal female DNA as reference

value: OC


title: OE21 AZA rep3


title: Renal Cell Carcinoma_Specimen_CGI-029

description: CGI-029 RCC specimen as test DNA and Promega normal female DNA as reference


title: S R2

description: Glabridin 10-5M, replicate 2

source_name: Ishikawa cells, Glabridin 10-5M

value: Glabridin 10-5M


title: S R1

description: Glabridin 10-5M, replicate 1


title: Renal Cell Carcinoma_Specimen_CGI-020

description: CGI-020 RCC specimen as test DNA and Promega normal female DNA as reference

value: F


title: Renal Cell Carcinoma_Specimen_CGI-024

description: CGI-024 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-039

description: CGI-039 RCC specimen as test DNA and Promega normal female DNA as reference


title: Het Combined rep3

value: non-neoplastic esophageal epithlial cells


title: OE21 DMSO rep3

value: Esophagus


title: S R3

description: Glabridin 10-5M, replicate 3


title: Het AZA rep3


title: Renal Cell Carcinoma_Specimen_CGI-011

description: CGI-011 RCC specimen as test DNA and Promega normal female DNA as reference


title: Gla R3

description: Glabridin 10-7M, replicate 3

source_name: Ishikawa cells, Glabridin 10-7M

value: Glabridin 10-7M


title: Renal Cell Carcinoma_Specimen_CGI-012

description: CGI-012 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-016

description: CGI-016 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-019

description: CGI-019 RCC specimen as test DNA and Promega normal female DNA as reference


title: Renal Cell Carcinoma_Specimen_CGI-026

description: CGI-026 RCC specimen as test DNA and Promega normal female DNA as reference


title: Het MS275 rep3


title: Renal Cell Carcinoma_Specimen_CGI-006

description: CGI-006 RCC specimen as test DNA and Promega normal female DNA as reference


title: Gla R1

description: Glabridin 10-7M, replicate 1


title: Untreated R3

description: Untreated control, replicate 3

source_name: Ishikawa cells, Untreated control

value: Untreated control


title: Gla R2

description: Glabridin 10-7M, replicate 2


title: Renal Cell Carcinoma_Specimen_CGI-003

description: CGI-003 RCC specimen as test DNA and Promega normal female DNA as reference

value: Formalin Fixed Paraffin Embedded (FFPE)


title: Het DMSO rep3


title: Untreated R1

description: Untreated control, replicate 1


title: Renal Cell Carcinoma_Specimen_CGI-002

description: CGI-002 RCC specimen as test DNA and Promega normal female DNA as reference

value: renal cell carcinoma specimen


title: Renal Cell Carcinoma_Specimen_CGI-004

description: CGI-004 RCC specimen as test DNA and Promega normal female DNA as reference

value: Promega normal female DNA


title: OE33 MS275 rep2

value: cell line from adenocarcinoma of the lower oesophagus (Barrett′s metaplasia)

value: 0.5 μM MS-275 (histone deacetylase inhibtor) for 24 hrs


title: Renal Cell Carcinoma_Specimen_CGI-001

description: CGI-001 RCC specimen as test DNA and Promega normal female DNA as reference


title: OE33 Combined rep2

value: 50 μM AZA + 0.5 μM MS-275 for 24 hrs


title: OE33 AZA rep2

value: 50 μM AZA (Azacytidine) for 24 hrs


title: Untreated R2

description: Untreated control, replicate 2


title: OE33 DMSO rep2

value: DMSO for 24 hrs


title: AuditoryNerve_neurospheres_rep3

data_processing: CEL files imported were into Affymetrix Expression Console software and data were normalized by: 1) RMA to obtain probe set expression values, and 2) MAS5 to obtain probe set detection calls.

source_name: Auditory nerve cultured neurospheres

growth_protocol: CBA/CaJ mice were bred in-house in a low-noise environment at the Animal Research Facility of the Medical University of South Carolina (MUSC) with original breeding pairs purchased from The Jackson Laboratory (Bar Harbor, ME).  All mice received food and water ad libitum and were maintained on a 12-hour light/dark cycle.  Mice of both genders were used in the study.  All aspects of the animal research were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee of the MUSC.  Prior to treatment, mice were examined for signs of external ear canal and middle ear obstruction, and mice exhibiting these signs were excluded from the study.

extract_protocol: Total RNA was prepared using the miRNeasy Kit (Qiagen). Total RNA preparations were run on an Agilent 2100 Bioanalyzer to ensure sample quality.

treatment_protocol: Adult Mice (CBA/CaJ, aged 8 to 12 weeks) were euthanized, decapitated under a sterile conditions, and auditory nerves removed from the temporal bones. For cell and neurosphere samples, auditory nerves were incubated with 0.25% trypsin for 5 min at 37oC and then with DNase I (final concentration of 5mg/ml) for 5 min at 37oC.  10% fetal bovine serum (FBS) containing DMEM/F12 medium was added to stop trypsin reaction. Tissues were triturated with pipet tips and centrifuged at 1000 rpm for 5 min.  The pellet was resuspended in DMEM/F12 medium with 10% FBS and B27 supplements and filtered through a 70 µm cell strainer.  Cells were counted, plated on poly-L-ornithine and fibronectin coated plates, and grown to full confluency (5-7 days).  For neurosphere cultures, media was removed and replaced with serum-free proliferation medium (NeuroCultTM proliferation supplement, Stem Cell Technologies) containing 20 ng/ml rh EGF, 10 ng/ml FGF and 2 µg/ml heparin.

tag: strain

value: CBA/CaJ

value: 8 to 12 weeks

value: cultured auditory nerve neurospheres

tag: treatment

value: tissue dissociation, cell culture and neurosphere formation


title: AuditoryNerve_neurospheres_rep1


title: OE21 DMSO rep2

value: cell line from squamous carcinoma of mid oesophagus


title: OE21 Combined rep2


title: AuditoryNerve_neurospheres_rep2


title: AuditoryNerve_cells_rep1

source_name: Auditory nerve cultured cells

value: cultured auditory nerve cells

value: tissue dissociation and cell culture


title: AuditoryNerve_cells_rep3


title: AuditoryNerve_cells_rep2


title: AuditoryNerve_tissue_rep1

source_name: Auditory nerve tissue

value: auditory nerve


title: OE21 AZA rep2

value: Esophagus


title: AuditoryNerve_tissue_rep3


title: Het Combined rep2

value: non-neoplastic esophageal epithlial cells


title: Archer at Stage 2, biological rep2, in 2007

description: Expresion data for developing seeds of Archer at length 3.5 mm

source_name: Archer developing seeds at Stage 2, biological rep2, in 2007

value: seeds

value: Archer

tag: developmental stage

value: Developing seeds, 3.5 mm in length


title: Het AZA rep2


title: Het MS275 rep2

value: 0.5 μM MS-275 (histone deacetylase inhibtor) for 24 hrs