title: Stat5b-CA x Ebf1+/- Leukemia #4

city: Minneapolis

first: Lynn

last: Heltemes Harris

state: MN

address: 2101 6th St. SE

institute: University of Minnesota

description: CD19+ and/or B220+ lymph node tumor cells

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

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

data_processing: The data were analyzed with GeneSpring GX11

source_name: Leukemic cells from Stat5b-CA  x  ebf1+/- mouse #6713

label_protocol: cRNA was labeled with biotin-11-CTP (Perkin Elmer Life Sciences) and biotin-16-UTP (Roche), and cleaned up and fragmented.

growth_protocol: Mice were maintained according to IACUC protocols at the University of Minnesota.

extract_protocol: Total RNA was isolated with a Qiagen RNeasy kit.  cRNA probes were synthesized with Ambion's Message Amp II kit, biotinylated and hybridized to the Affymetrix Mouse 430 2.0 microarray chip.

treatment_protocol: Sorted preB cells (WT, Stat5, & xid) were isolated from bone marrow, negatively selected against dump antibodies with Miltenyi magnetic beads.  They were then stained with B220, CD19, CD43 and IgM antibodies, and sorted with a FacsAria for B220+ CD19+ CD43- IgM- cells.  Tumor lymph node cells were positively selected for with Miltenyi magnetic beads binding B220 and CD19.

tag: strain


title: hd2c-3_heat stress_rep3

status: Public on Dec 04 2015

type: RNA

city: Warsaw

first: Daniel

last: Buszewicz

address: Pawińskiego 5A

department: Institute of Biochemistry and Biophysics

country: Poland

institute: Polish Academy of Sciences

hyb_protocol: Labeled samples were hybridized to the Arabidopsis Gene 1.1 ST Array Strip (Affymetrix, Santa Clara, CA).

scan_protocol: The microarrays were scanned with an Affymetrix GeneAtlas Scanner and the intensity signals for each of the probe sets were written by Affymetrix software into CEL files.

data_processing: The CEL files were imported into the Partek Genomic Suite v 6.6 software with the use of RMA (Robust Multiarray Averaging). During this step, background correction was applied based on the global distribution of the PM (perfect match) probe intensities and the affinity for each of the probes (based on their sequences) was calculated. In addition, the probe intensities were quantile normalized (Bolstad et al., 2003), log2 transformed and median polish summarization was applied to each of the probe sets.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: hd2c-3_heat stress

label_protocol: Labeled cDNA was prepared using the Affymetrix GeneChip® WT Terminal Labeling Kit (Part no. 900671).

growth_protocol: Arabidopsis plants were grown on soil under long day (16h light / 8h dark) conditions at 22-23°C, with 70% humidity and 120-150 µM m-2 s-1 light intensity.

extract_protocol: RNA was isolated using MagNA Pure Compact Instrument and MagNA Pure Compact RNA Isolation Kit (Roche) according to manufacturer's insturctions.

treatment_protocol: 3-week-old plants were transferred to 38°C for 1 hour.

tag: ecotype background

tag: genotype/variation

tag: age

value: 3 weeks

tag: exposed to

value: 38°C for 1 h; heat stress


title: Stat5b-CA x Rag2-/- Leukemia #2

country: USA

organism: Mus musculus

source_name: Leukemic cells from Stat5b-CA  x  rag2-/- mouse #6353


title: Stat5b-CA x Rag2-/- Leukemia #3

source_name: Leukemic cells from Stat5b-CA  x  rag2-/- mouse #5283


title: Stat5b-CA x Ebf1+/- Leukemia #3

source_name: Leukemic cells from Stat5b-CA  x  ebf1+/- mouse #5904


title: brm-1_heat stress_rep1

source_name: brm-1_heat stress


title: Breast Cancer Sample 12

city: Monterrey

first: Hugo

last: Gomez

state: Nuevo Leon

address: Garza Sada

department: Bioinformatics

country: Mexico

institute: ITESM

description: One color per patient

hyb_protocol: Once the sample is labeled, it is dried in a Speed Vacuum Concentrator at 55ºC for 3.5 hours.The resuspension of the samples is as follows: Add 18μL of nuclease free water. Add 4.5μL of GE Blocking Agent 10x. Add 22.5μL of Hi-RPM Hybridization Buffer 2x. Agitate in vortex and heat at 100ºC for 5 minutes. Spin the samples and place them on ice. The hybridization process was made by putting 22.5μL of each sample into the array, instead the 45μL of the one color protocol. Next, put the labeled samples into the Gasket Slide. The process was the following. To hybridize the sample in the Gasket Slide. Put the Gasket Slide into the SureHyb Chamber. Add 45μL of the samples to the corresponding array (G4470B). Put the 8x15K array and close the SureHyb Chamber. Hybridize at 53ºC for 20 hours at 10RPM.

scan_protocol: Slides were scanned immediately after washing on the GenePix Scanner 4000B (Molecular DEVICES) using two color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% and Red and Red PMT is set to 100% ).

data_processing: The scanned images were analyzed with Gene Pix Software (Molecular DEVICES) using default parameters (Two color protocol and Grid:019118_D_20121224) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: Sample Tumor of Breast Cancer

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2 μL at 100ng/μL of RNA using the One-Color RNA  (Agilent, Palo Alto, CA) according to the manufacturer's instructions and employing the Cy5-pCp (Jena BioScience) following the publication of Wang et al. PMID:17105992.

extract_protocol: RNA was obtained using the  RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. The protocol includes differential tissue lysis with buffers and a tissue grinder, followed by purification using the kit columns. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Experion Automated Electrophoresis (BioRad,Technopark, Kerala, India).

treatment_protocol: Freshly obtained sample and preserved in RNA Later (Thermo Fisher Scientific). The sample was refrigerated all night at 4ºC. In the next day the RNA Later (Thermo Fisher Scientific) was removed, and the sample was putted into refrigerator at -80ºC by indeterminate time.

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Infiltrating ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

tag: her2 immunohistochemestry

value: Neg

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Father Lung Cancer

tag: personal pathological hystory

value: Dyslipidemia

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Partial

tag: final surgery date

value: Tamoxifen

value: Adriamicin

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis

tag: date at death


title: Breast Cancer Sample 29

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Right Breast Ductal carcinoma in situ Left Breast infiltrating ductal adenocarcinoma poorly differentiated

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

value: Both

value: Poor

value: Paclitaxel

value: Doxorubicin

value: Cyclophosphamide


title: hd2c-3_heat stress_rep2

tag: ecotype background

tag: genotype/variation

tag: age

value: 3 weeks

tag: exposed to

value: 38°C for 1 h; heat stress


title: hd2c-3_heat stress_rep1


title: Stat5b-CA x Rag2-/- Leukemia #1

source_name: Leukemic cells from Stat5b-CA  x  rag2-/- mouse #5279

tag: strain


title: Stat5b-CA x Ebf1+/- Leukemai #2

source_name: Leukemic cells from Stat5b-CA  x  ebf1+/- mouse #4671


title: Stat5b-CA x Ebf1+/- Leukemia #1

source_name: Leukemic cells from Stat5b-CA  x  ebf1+/- mouse #5834


title: Stat5b-CA x Ebf1+/- Leukemia #5

source_name: Leukemic cells from Stat5b-CA  x  ebf1+/- mouse #7289


title: WT_heat stress_rep2

source_name: WT_heat stress

value: WT


title: brm-1 hd2c-3_control_rep3

source_name: brm-1 hd2c-3_control

value: brm-1 hd2c-3

value: control


title: Breast Cancer Sample 134

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Neg

tag: her2 immunohistochemestry

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

tag: date at death


title: WT_heat stress_rep1

tag: ecotype background

tag: genotype/variation

tag: age

tag: exposed to


title: WT_heat stress_rep3


title: Breast Cancer Sample 57

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated infiltrating ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

value: Pos

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Complete

value: Lung


title: CP-Remission-2

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: BeadStudio software (Illumina Inc., San Diego, CA, USA) was read into R/Bioconductor and normalized using quantile normalization. A linear model was applied to the normalized data using Limma package in R/Bioconductor

source_name: CP-Remission

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

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

tag: strain

value: SJL mice (Charles River, Barcelona, Spain)

tag: gender

value: female

tag: age

value: 6–8 weeks of age adult

tag: mouse status

value: experimental autoimmune encephalomyelitis (EAE)

tag: eae phase

value: remission

tag: tissue

value: choroid plexus (CP)


title: Stat5b-CA preB #2

description: CD19+ B220+ dump- IgM- CD43- Bone marrow cells

source_name: Sorted preB cells from Stat5b-CA  mouse #3819


title: WT preB #5

source_name: Sorted preB cells from C57BL/6 mouse #6212


title: Stat5b-CA preB #1

source_name: Sorted preB cells from a Stat5b-CA  mouse


title: Stat5b-CA preB #4

source_name: Sorted preB cells from Stat5b-CA  mouse #3288


title: Breast Cancer Sample 11

description: One color per patient

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

tag: e-cadherina ihc

tag: t

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Progresive

tag: final surgery date

value: Paclitaxel

tag: radiotherapy

value: Yes

tag: date at relapse

tag: place to metastasis

tag: date at death


title: Stat5b-CA preB #3

source_name: Sorted preB cells from Stat5b-CA  mouse #6213

tag: strain


title: brm-1 hd2c-3_control_rep2

tag: ecotype background

tag: genotype/variation

value: brm-1 hd2c-3

tag: age

value: 3 weeks

tag: exposed to

value: control


title: brm-1 hd2c-3_control_rep1


title: WT preB #4

source_name: Sorted preB cells from C57BL/6 mouse #3820


title: Breast Cancer Sample 25

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Neg

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Liver Cancer

tag: personal pathological hystory

tag: tabaquism

value: Pos

tag: age at menarche

tag: birads

tag: breast affected

value: Left

tag: initial highest diameter in mm by image

value: Poor

value: Adriamicin

value: Cyclophosphamide


title: brm-1_control_rep2

tag: ecotype background

tag: genotype/variation

tag: age

tag: exposed to


title: CP-PBS-1

description: replicate 1

source_name: CP-PBS

tag: strain

value: SJL mice (Charles River, Barcelona, Spain)

tag: gender

value: female

value: 6–8 weeks of age adult

tag: mouse status

value: Control mice injected with phosphate buffer saline (PBS)

tag: tissue

value: choroid plexus (CP)


title: hd2c-3_control_rep3

value: 3 weeks


title: Breast Cancer Sample 39

description: One color per patient

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Invasive ductal carcinoma, carcinoma in situ associated with comedo necrosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

value: Hypertension and Rheumatoid Artritis

value: Both

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Progresive

tag: final surgery date

value: Trastuzumab

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis

tag: date at death


title: CP-Onset-3

description: replicate 3

source_name: CP-Onset

tag: strain

tag: gender

tag: age

tag: mouse status

value: experimental autoimmune encephalomyelitis (EAE)

tag: eae phase

value: Onset

tag: tissue


title: brm-1_control_rep1

tag: ecotype background

tag: genotype/variation

tag: exposed to

value: control


title: F1 strain, biological replicate 4

city: Singapore

first: Wee Siang

last: Lim

address: 20 Biopolis Way, Centros

country: Singapore

institute: A*STAR BTI

description: Gene expression data from F1 strain at mid-log

hyb_protocol: cDNA was hybridized onto Affymetrix GeneChip P. aeruginosa genome array at 50oC and 60 rpm.

scan_protocol: Arrays were scanned with Affymetrix GeneChip Scanner 3000.

data_processing: The data was analyzed with Partek Genomics Suite with GCRMA normalization method.

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa cells harvested at mid-log

label_protocol: cDNA was fragmented with New England Biolabs DNAseI and labelled with Genechip Labelling Reagent using Promega terminal deoxynucleotidyl transferase.

growth_protocol: 1mL of overnight culture was added to 25 mL of fresh LB media and 25 mL of 20% LB media. The culture was incubated at 37oC and shaken at 225 rpm.

extract_protocol: RNA was extracted from the cells with Qiagen RNAeasy Midi Kit and treated with Ambion Turbo Dnase. RNA was reverse transcribed to cDNA with Invitrogen Superscript II reverse transcriptase.

treatment_protocol: 10 mL of mid-log cells were harvested and treated with Qiagen RNAProctect Bacteria reagent accoding to manufacturer's instructions.

value: F1 (PB1-phage resistant derivative)


title: WT preB #3

source_name: Sorted preB cells from C57BL/6 mouse #5680


title: CP-PBS-3

description: replicate 3

value: SJL mice (Charles River, Barcelona, Spain)


title: control, biological rep3

city: Beijing

first: Shuhong

last: Li

address: No.8 GongTiNanLu

country: China

institute: Beijing Chao-Yang Hospital

description: microRNA expression data from control lung tissue-3

hyb_protocol: 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array(Affymetrix, Santa Clara, CA) in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method. Values presented are log2 RMA signal intensity.

source_name: control lung tissue-3

label_protocol: Biotinylated cDNA were prepared from 250 ng total RNA by using Ambion® WT Expression Kit according to the standard Affymetrix protocol 3

growth_protocol: Lung tissue was obtained from 4 IPF patients at the time of surgical lung biopsy or lung transplantation, or obtained from 3 patients with primary spontaneous pneumothorax at the time of thoracoscopy with stapling of any air leak.

extract_protocol: Trizol extraction of total RNA was perfored according to the manufacture's instructions.

treatment_protocol: Lung tissue was harvested in optimum cutting temperature compound and frozen in liquid nitrogen

tag: tissue type

value: lung


title: WT preB #2

source_name: Sorted preB cells from 3 C57BL/6 pooled


title: F1 strain, biological replicate 3


title: F1 strain, biological replicate 2


title: brm-1_control_rep3


title: F1 strain, biological replicate 1


title: CP-Relapse-1

description: replicate 1

source_name: CP-Relapse

value: female

value: 6–8 weeks of age adult

value: relapse


title: F0 strain, biological replicate 4

description: Gene expression data from F0 strain at mid-log

value: F0 (PAO1)


title: CP-Remission-3

description: replicate 3

value: remission

value: choroid plexus (CP)


title: CP-Onset-2

description: replicate 2


title: CP-Onset-1

description: replicate 1


title: IPF, biological rep4

description: microRNA expression data from IPF lung tissue-4

source_name: Idiopathic Pulmonary Fibrosis lung tissue-4


title: IPF, biological rep3

description: microRNA expression data from IPF lung tissue-3

source_name: Idiopathic Pulmonary Fibrosis lung tissue-3


title: hd2c-3_control_rep2

value: 3 weeks


title: control, biological rep2

description: microRNA expression data from control lung tissue-2

source_name: control lung tissue-2


title: F0 strain, biological replicate 3


title: WT preB #1


title: WT_control_rep2

value: WT


title: control, biological rep1

description: microRNA expression data from control lung tissue-1

source_name: control lung tissue-1


title: Sample_85, Normal

status: Public on Dec 03 2015

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString.com) with 5 µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer's instructions.  For each assay, a high-density scan (600 fields of view) was performed

data_processing:
Raw expression data, which are proportional to copy number, were log-transformed and normalized by the quantile method after application of a manufacturer-supplied correction factors
The probes flagged with the message "+++ See Message Below" have specific level adjustment factors supplied by Nanostring. Nanostring_miRNA_Panel_V2_Special_Factors.xls: The special correction factors for the Nanostring platform (Human miRNA Expression Assay v2); functional tests indicate that probes have some level of background which may be corrected prior to normalization. This background is probe-specific and may be corrected by subtracting the background. The number of counts to be subtracted for a given probe is determined by multiplying the special correction factor by the number of counts observed for the 128fM positive control in the same lane.^SAMPLE = GSM1864051

source_name: Lung

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Ohio State Microarray Core Facility

extract_protocol: Trizol according to manufacture's instructions

tag: mutational status

value: Normal, healthy


title: F0 strain, biological replicate 2


title: Sample_81, Normal


title: Sample_83, Normal


title: Sample_82, Normal


title: Sample_84, Normal


title: Sample_79, Normal


title: Sample_80, Normal


title: Sample_78, Normal


title: F0 strain, biological replicate 1


title: CP-Relapse-2

description: replicate 2


title: Sample_76, Normal


title: IPF, biological rep1

description: microRNA expression data from IPF lung tissue-1

source_name: Idiopathic Pulmonary Fibrosis lung tissue-1


title: CP-Remission-1

description: replicate 1

source_name: CP-Remission


title: hd2c-3_control_rep1


title: WT_control_rep1


title: IPF, biological rep2

description: microRNA expression data from IPF lung tissue-2

source_name: Idiopathic Pulmonary Fibrosis lung tissue-2


title: Sample_75, ALK Fusion

value: ALK Fusion


title: Sample_72, Normal


title: Sample_74, Normal


title: Sample_73, Normal


title: Sample_67, Wild Type

value: Wild Type


title: Sample_68, Normal


title: Sample_69, Normal


title: Sample_70, Normal


title: Sample_71, Normal


title: Sample_66, Wild Type


title: CP-PBS-2

description: replicate 2

value: Control mice injected with phosphate buffer saline (PBS)


title: Sample_77, Normal


title: WT_control_rep3


title: Sample_65, Normal


title: Sample_64, Wild Type


title: Sample_57, ALK Fusion


title: Sample_55, ALK Fusion


title: Sample_61, ALK Fusion


title: Sample_60, ALK Fusion


title: Sample_58, ALK Fusion


title: Sample_56, ALK Fusion


title: Sample_63, ALK Fusion


title: Sample_59, ALK Fusion


title: Sample_62, ALK Fusion


title: Sample_54, ALK Fusion


title: Sample_51, ALK Fusion


title: Sample_50, ALK Fusion


title: Sample_47, KRAS

value: KRAS


title: Sample_46, KRAS


title: Sample_40, KRAS


title: Sample_43, KRAS


title: Sample_45, KRAS


title: Sample_41, KRAS


title: Sample_38, KRAS


title: Sample_42, KRAS


title: Sample_37, KRAS


title: Sample_39, KRAS


title: Sample_36, KRAS


title: Sample_44, KRAS

data_processing: Raw expression data, which are proportional to copy number, were log-transformed and normalized by the quantile method after application of a manufacturer-supplied correction factors


title: Sample_53, ALK Fusion


title: Sample_35, KRAS


title: Sample_52, ALK Fusion


title: Sample_48, ALK Fusion


title: Sample_49, ALK Fusion


title: Sample_32, EGFR

value: EGFR


title: Sample_33, KRAS


title: Sample_30, EGFR


title: Sample_34, KRAS


title: Sample_29, EGFR


title: Sample_31, EGFR


title: Sample_25, EGFR


title: Sample_28, EGFR


title: Sample_27, EGFR


title: Sample_26, EGFR


title: Sample_24, EGFR


title: Sample_20, Wild Type

data_processing:
The probes flagged with the message "+++ See Message Below" have specific level adjustment factors supplied by Nanostring. Nanostring_miRNA_Panel_V2_Special_Factors.xls: The special correction factors for the Nanostring platform (Human miRNA Expression Assay v2); functional tests indicate that probes have some level of background which may be corrected prior to normalization. This background is probe-specific and may be corrected by subtracting the background. The number of counts to be subtracted for a given probe is determined by multiplying the special correction factor by the number of counts observed for the 128fM positive control in the same lane.^SAMPLE = GSM1864051
Raw expression data, which are proportional to copy number, were log-transformed and normalized by the quantile method after application of a manufacturer-supplied correction factors


title: Sample_16, Wild Type


title: Sample_21, Wild Type


title: Sample_19, Wild Type


title: Sample_18, Wild Type


title: Sample_17, Wild Type


title: Sample_23, EGFR


title: Sample_11, Wild Type


title: Sample_12, Wild Type


title: Sample_13, Wild Type


title: Sample_15, Wild Type


title: Sample_14, Wild Type


title: Sample_10, Wild Type


title: Sample_9, Wild Type


title: Sample_8, Wild Type


title: Sample_22, EGFR


title: Young.Rest.LCR (26273)

city: Ann Arbor

first: Yu-yu

last: Ren

state: MI

address: 1241 Catherine St.

department: Human Genetics

institute: University of Michigan

description: Gene expression data from young rest LCR

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Rat Gene 2.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515).

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515).

data_processing: Data was processed using the oligo package of bioconductor implemented in the R-statistical environment version 3.0.0. RMA was used to fit log2 transformed expression values

organism: Rattus norvegicus

source_name: young LCR rat at rest

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

extract_protocol: Total RNA was extracted from frozen tissue with Trizol reagent (Invitrogen, Carlsbad, CA), treated with DNase-free (Invitrogen, Carlsbad, CA) and cleaned up with RNeasy columns (Qiagen, Hilden, Germany)

value: Extensor digitorum longus muscle

tag: line

value: LCR

value: young

tag: exercise

value: Rest


title: Young.Rest.LCR (26337)


title: Young.Rest.LCR (26216)


title: Young.Rest.LCR (26287)


title: Young.Rest.HCR (16764)

description: Gene expression data from young rest HCR

source_name: young HCR rat at rest

value: HCR


title: Young.Rest.HCR (16850)


title: Old.Rest.LCR (25271)

description: Gene expression data from old rest LCR

source_name: old LCR rat at rest

value: old


title: Old.Rest.HCR (16007)

description: Gene expression data from old rest HCR

source_name: old HCR rat at rest


title: Young.Rest.HCR (16849)


title: Old.Rest.HCR (15976)

description: Gene expression data from old rest HCR


title: Old.Rest.HCR (15796)

description: Gene expression data from old rest HCR


title: Young.Exhaust.LCR (26386)

description: Gene expression data from young exhausted LCR

source_name: young LCR rat exhausted

value: Exhausted


title: Old.Rest.LCR (25378)

description: Gene expression data from old rest LCR


title: Old.Rest.LCR (25356)

description: Gene expression data from old rest LCR


title: Young.Rest.LCR (26308)


title: Young.Rest.LCR (26200)


title: Young.Rest.HCR (16756&16872)


title: Young.Rest.HCR (16823)


title: Old.Rest.LCR (25246)

description: Gene expression data from old rest LCR


title: Old.Rest.HCR (15937)

description: Gene expression data from old rest HCR


title: Old.Rest.HCR (15852)

description: Gene expression data from old rest HCR


title: Old.Rest.HCR (15886)

description: Gene expression data from old rest HCR


title: Young.Exhaust.LCR (26251)


title: Young.Rest.HCR (16755)


title: Old.Rest.LCR (25300)

description: Gene expression data from old rest LCR


title: Old.Rest.LCR (25228)

description: Gene expression data from old rest LCR


title: Young.Exhaust.LCR (26174)


title: Young.Exhaust.LCR (26203)


title: Young.Exhaust.LCR (26330)


title: Young.Exhaust.HCR (16953)

description: Gene expression data from young exhausted HCR

source_name: young HCR rat exhausted


title: Young.Exhaust.HCR (16887)


title: Young.Exhaust.HCR (16847)


title: Old.Exhaust.LCR (25409)

description: Gene expression data from old exhausted LCR

source_name: old LCR rat exhausted


title: Old.Exhaust.LCR (25294)


title: Old.Exhaust.HCR (15950)

description: Gene expression data from old exhausted HCR

source_name: old HCR rat exhausted


title: Old.Exhaust.LCR (25313)


title: Young.Exhaust.HCR (16792)


title: Sample_5, Wild Type


title: Sample_7, Wild Type


title: Sample_6, Wild Type


title: Old.Exhaust.HCR (15893)


title: Young.Exhaust.HCR (16782)


title: Old.Exhaust.LCR (25323)


title: Old.Exhaust.LCR (25262)


title: Young.Exhaust.HCR (16761)


title: Wt Coler2_roottips_rep1

city: Uppsala

first: Christina

middle: Joy

last: Müller

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

hyb_protocol: Affymetrix Arabidopsis ATH1 GeneChip® expression arrays were hybridized for 16h in a 45 °C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev2, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The raw data was normalized in the free software Expression Console provided by Affymetrix (http://www.affymetrix.com) using the robust multi-array average (RMA) method (Li and Wong, 2001; Irizarry et al., 2003). Subsequent analysis of the gene expression data was carried out in R (http://www.r-project.org) using Bioconductor packages (www.bioconductor.org). To search for differentially expressed genes between the different biological replicate groups within each experiment, an empirical Bayes moderated t-test was then applied (Smyth, 2004) using the ‘limma’ package (Smyth et al., 2005). To address the problem with multiple testing, the p-values were adjusted using the method of (Benjamini and Hochberg, 1995).

source_name: Col er-2, 4 dpg, 0.5 mm of primary root tip

label_protocol: 250 ng of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® 3’ IVT Express Kit Manual.

growth_protocol: Plants were grown on square plates with 25 µm pore Sefar mesh placed on top of growth media (0.5X Murashige and Skoog (MS) medium, 1% sucrose, 1% plant agar). Plants were grown veritcally in a Sanyo MLR growth cabinet at 22ºC with 18h light and 6h dark (145-150 µmol m-2 s-1).

extract_protocol: Root tips (0.5 mm) were hand-dissected from 4 dpg seedling primary roots and collected in RLT buffer from the Plant RNeasy kit (QIAGEN) containing ß-mercaptoethanol according to kit instructions. About 200 root tips were collected per replicate. Tissue was immediately homogenized with glass beads using a FastPrep homogenizer (Savant), and RNA extraction including the on-column RNase-free DNase digestion (QIAGEN) were performed following the manufacturer’s protocol.

treatment_protocol: no treatments were applied to the plants

tag: genotype

value: Col er-2


title: Wt Coler2_roottips_rep2


title: athb811cna2phb13phv6_roottips_rep1

source_name: athb8-11 cna-2 phb-13 phv-6, 4 dpg, 0.5 mm of primary root tip

value: athb8-11 cna-2 phb-13 phv-6


title: cna2phb1 phv11rev6_rbvc_roottips_rep3

source_name: cna-2 phb-13 phv-6 rev-6, 4 dpg, 0.5 mm of primary root tip

value: cna-2 phb-13 phv-6 rev-6


title: Sample_4, Wild Type


title: Old.Exhaust.HCR (15915)


title: Old.Exhaust.HCR (15816)


title: athb811cna2phb13phv6_roottips_rep3


title: Old.Exhaust.HCR (15902)


title: Sample_3, Wild Type


title: Sample_1, Wild Type


title: Wt Coler2_roottips_rep3


title: Old.Exhaust.LCR (25278)


title: Young.Exhaust.LCR (26272)


title: athb811cna2phb13phv6_roottips_rep2


title: Sample_2, Wild Type

data_processing:
Raw expression data, which are proportional to copy number, were log-transformed and normalized by the quantile method after application of a manufacturer-supplied correction factors
The probes flagged with the message "+++ See Message Below" have specific level adjustment factors supplied by Nanostring. Nanostring_miRNA_Panel_V2_Special_Factors.xls: The special correction factors for the Nanostring platform (Human miRNA Expression Assay v2); functional tests indicate that probes have some level of background which may be corrected prior to normalization. This background is probe-specific and may be corrected by subtracting the background. The number of counts to be subtracted for a given probe is determined by multiplying the special correction factor by the number of counts observed for the 128fM positive control in the same lane.^SAMPLE = GSM1864051
Raw expression data, which are proportional to copy number, were log-transformed and normalized by the quantile method after application of a manufacturer-supplied correction factors
The probes flagged with the message "+++ See Message Below" have specific level adjustment factors supplied by Nanostring. Nanostring_miRNA_Panel_V2_Special_Factors.xls: The special correction factors for the Nanostring platform (Human miRNA Expression Assay v2); functional tests indicate that probes have some level of background which may be corrected prior to normalization. This background is probe-specific and may be corrected by subtracting the background. The number of counts to be subtracted for a given probe is determined by multiplying the special correction factor by the number of counts observed for the 128fM positive control in the same lane.^SAMPLE = GSM1864051


title: Coler2_roottips_rep1


title: pCRE1_XVE_MIR165A_24h_rep3

description: gene expression data of 24h MIR165 induced root tips in Col-0 background

source_name: Arabidopsis thaliana root tips (0.5mm) after 24h MIR165 induction

treatment_protocol: For transgenic inductions, seedlings were transferred to plates containing 5 µM ß-estradiol in ethanol, or a mock treatment containing the same amount of only ethanol for the indicated time, either 0h (mock plates), 6h, 10h, or 24h and seedlings were collected at 4 days post-germination. Each time point and genotype was collected in triplicate. Inductions and collections were staggered such that seedlings were the same age (+/- 4.5h) when collected.

value: 0.5 mm of primary root tip, 4 dpg


title: pCRE1_XVE_MIR165A_10h_rep3

description: gene expression data of 10h MIR165 induced root tips in Col-0 background

source_name: Arabidopsis thaliana root tips (0.5mm) after 10h MIR165 induction


title: pCRE1_XVE_MIR165A_24h_rep1


title: cna2phb1 phv11rev6_rbvc_roottips_rep2


title: cna2phb13phv11_bvc_roottips_rep2

source_name: cna-2 phb-13 phv-11, 4 dpg, 0.5 mm of primary root tip

value: cna-2 phb-13 phv-11


title: cna2phb13phv11_bvc_roottips_rep1


title: Coler2_roottips_rep2


title: pCRE1_XVE_MIR165A_6h_rep3

description: gene expression data of 6h MIR165 induced root tips in Col-0 background

source_name: Arabidopsis thaliana root tips (0.5mm) after 6h MIR165 induction


title: pCRE1_XVE_MIR165A_0h_rep2

description: gene expression data of non-induced root tips in Col-0 background

source_name: Arabidopsis thaliana root tips (0.5mm) before MIR165 induction


title: pCRE1_XVE_MIR165A_10h_rep2


title: pCRE1_XVE_MIR165A_10h_rep1


title: pCRE1_XVE_MIR165A_24h_rep2


title: cna2phb1 phv11rev6_rbvc_roottips_rep1


title: cna2phb13phv11_bvc_roottips_rep3


title: pCRE1_XVE_MIR165A_6h_rep1


title: pCRE1_XVE_MIR165A_6h_rep2


title: INTACT BASAL, BIOLOGICAL REPLICATE 3

first: Andrew

middle: Scott

last: Goldstein

address: 610 Charles E Young Dr East

department: Urology

institute: University of California, Los Angeles

description: Gene expression data from basal cells isolated from intact mouse prostate

hyb_protocol: Biotinylated cDNA was hybridized to the Affymetrix Mouse Genome 430 2.0 Chip

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cDNA were prepared from total RNA using the standard Affymetrix protocol.

growth_protocol: C57BL/6 mice (intact and castrated) were grown in standard conditions

extract_protocol: RNA was isolated from sorted cells using the RNeasy Micro kit (QIAGEN) and amplified with the NuGEN Pico kit according to standard manufacturer protocols.

treatment_protocol: Animals were sacrificed, prostates removed and dissociated to single cells using standard protocols described in Lukacs et al, Nature Protocols, 2010.

value: adult

tag: Sex

value: male

tag: protocol

value: intact

tag: cell type

value: Basal cells


title: pCRE1_XVE_MIR165A_0h_rep1


title: INTACT LUMINAL, BIOLOGICAL REPLICATE 3

description: Gene expression data from luminal cells isolated from intact mouse prostate

tag: strain

value: Luminal cells


title: INTACT LUMINAL, BIOLOGICAL REPLICATE 1

source_name: luminal cells isolated from intact mouse prostate


title: INTACT LUMINAL, BIOLOGICAL REPLICATE 2


title: pCRE1_XVE_MIR165A_0h_rep3


title: Hum_4_M

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

library_source: genomic

data_processing:
Submitter states that sequence data are being deposited at EBI-EGA.
Sequencing data were processed with illumina2bam-tools v. 1.12
BAM files were converted to fastq format using SamToFastq.jar (picard-tools v1.100) with the INCLUDE_NON_PF_READS parameter set to FALSE
All reads were trimmed for adapter sequences and low-quality sequences using trimgalore v0.3.3 with the following command: trim_galore -q 20 --phred33 -a "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" --stringency 1 -e 0.1 --length 16 --output_dir $output_dir $input_fastq.
Reference-free processing (creation of the deduced genomes and processing) was performed using the RefFreeDMA software/pipeline (http://RefFreeDMA.computational-epigenetics.org)
Bisulfite alignment of the RRBS reads to the deduced genomes and to the reference genomes was performed using BSMAP v2.74 with the following command line: bsmap -a $input_fastq -d $ref_genome_fasta -o $output_bam -D C-CGG -w 100 -v 0.08 -r 1 -p 4 -n 0 -S 1 -f 5 –u.
DNA methylation calling was performed using the biseqMethCalling.py software (Bock, 2010)
Genome_build: hg19, bosTau6, GCA_000951615.1, human_deduced_genome.fa, bovine_deduced_genome.fa, carp_deduced_genome.fa
Supplementary_files_format_and_content: Tab-delimited text files include CpG methylation calls for each sample. Files ending with "_ded" were produced using the deduced genomes (human_deduced_genome.fa, bovine_deduced_genome.fa, carp_deduced_genome.fa) as reference. Files ending with "_ref" were produced using the published reference genomes (hg19, bosTau6, GCA_000951615.1) as reference.

molecule: genomic DNA

source_name: peripheral blood

extract_protocol:
The Allprep DNA/RNA Mini kit (Qiagen) was used for DNA isolation. Cells were lysed in 600 µl Buffer RLT Plus supplemented with 1% β-Mercaptoethanol and vortexed thoroughly for at least five minutes. The procedure of isolating DNA and RNA was performed according to protocol. DNA was stored at -20˚C.
For RRBS, 100 ng of genomic DNA was digested for 12 hours at 37°C with 20 units of MspI (New England Biolabs, R0106L) in 30 μl of 1x NEB buffer 2. To retain even the smallest fragments and to minimize the loss of material, end preparation and adaptor ligation were performed in a single-tube setup. End fill-in and A-tailing were performed by addition of Klenow Fragment 3’ > 5’ exo- (New England Biolabs, M0212L) and dNTP mix (10 mM dATP, 1 mM dCTP, 1 mM dGTP). After ligation to methylated Illumina TruSeq LT v2 adaptors using Quick Ligase (New England Biolabs, M2200L), the libraries were size selected by performing a 0.75x clean-up with AMPure XP beads (Beckman Coulter, A63881). The libraries were pooled in combinations of six based on qPCR data and subjected to bisulfite conversion using the EZ DNA Methylation Direct Kit (Zymo Research, D5020) with the following changes to the manufacturer’s protocol: conversion reagent was used at 0.9x concentration, incubation performed for 20 cycles of 1 min at 95°C, 10 min at 60°C and the desulphonation time was extended to 30 min. These changes increase the number of CpG dinucleotides covered, by reducing double-strand break formation in larger library fragments. Bisulfite-converted libraries were enriched using PfuTurbo Cx Hotstart DNA Polymerase (Agilent, 600412). The minimum number of enrichment cycles was estimated based on a qPCR experiment. After a 2x AMPure XP clean-up, quality control was performed by a Qubit dsDNA HS (Life Technologies, Q32854) and Experion DNA 1k assay (BioRad, 700-7107). The RRBS libraries were sequenced on the Illumina HiSeq 2000 platform in 50 bp single read mode.

treatment_protocol: Leukocytes were isolated from whole blood by removing the erythrocytes through hypotonic lysis. Specifically, 5 ml of whole blood was incubated with 9 ml ddH2O for one minute. The lysis was stopped by adding 1 ml of 10x phosphate buffered saline (PBS) to the sample. Leukocytes were pelleted by centrifuging for five minutes at 550g. If the pellet was still red, a second round of lysis was initiated by resuspending the pellet in 1 ml 1x PBS. Subsequently, 4.5 ml of ddH2O was added and after 30 seconds the lysis reaction was stopped by adding 0.5 ml 10x PBS. Leukocytes were pelleted by centrifuging for three minutes at 550g. Finally, the pellet was washed in 1 ml 1x PBS and then resuspended in 500-800 µl RPMI-1640 medium supplemented with 10% fetal calf serum (FCS). The cell suspension was then filtered into a FACS tube, and cell populations were sorted by FACS based on their forward and side scatter properties. Sorting was performed on a BD FACS Aria 1 with a 70 µm nozzle, which allowed for a maximum sorting speed of 30,000 events per second. For each population, between 500,000 and three million cells were obtained. Giemsa stained cytospins were produced for each sorted cell population, and the purity was assessed at 100x magnification.

value: monocyte

value: M


title: Hum_4_L

value: lymphocyte


title: INTACT BASAL, BIOLOGICAL REPLICATE 1

source_name: basal cells isolated from intact mouse prostate


title: Hum_4_G

value: granulocyte


title: Dose 2-2

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

description: Biological replicate 2 of 3.

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (MetricSet in use: GE2_QCMT_Feb07 ).

data_processing: Limma (Bioconductor).  Series supplementary file Matrix_table.xlsx includes logFC data. Sample 9 is an outlier and was not used in the final analyses.

organism: Daphnia magna

source_name: Complete organism

label_protocol: Agilent Quick-AMP kit 2 color protocol

growth_protocol: Environment Canada test method (1990).  20oC, 16 hr light/8 hr dark photoperiod; fed daily on green algae and YCT preparation

extract_protocol: RNEasy Plus Mini kit (Qiagen); Experion Automated Electrophoresis System (BioRad)

treatment_protocol: OECD Guidelines 2008; 21-day exposures

tag: dose

source_name: Reference

value: Pooled controls


title: INTACT BASAL, BIOLOGICAL REPLICATE 2

tag: age


title: CASTRATED LUMINAL, BIOLOGICAL REPLICATE 1

description: Gene expression data from luminal cells isolated from mouse prostate 4-weeks post-castration

value: castrated


title: Dose 3-3

description: Biological replicate 3 of 3.

value: 6 mg/L


title: Dose 3-1

description: Biological replicate 1 of 3.


title: Dose 2-1

description: Biological replicate 1 of 3.


title: Dose 3-2

description: Biological replicate 2 of 3.


title: Dose 2-3

description: Biological replicate 3 of 3.


title: CASTRATED LUMINAL, BIOLOGICAL REPLICATE 3

source_name: luminal cells isolated from mouse prostate 4-weeks post-castration


title: Hum_3_M

value: F


title: CASTRATED BASAL, BIOLOGICAL REPLICATE 2

description: Gene expression data from basal cells isolated from mouse prostate 4-weeks post-castration


title: CASTRATED LUMINAL, BIOLOGICAL REPLICATE 2


title: Hum_3_L


title: CASTRATED BASAL, BIOLOGICAL REPLICATE 3

source_name: basal cells isolated from mouse prostate 4-weeks post-castration


title: CASTRATED BASAL, BIOLOGICAL REPLICATE 1


title: Hum_3_G


title: Hum_2_M


title: Dose 1-2

description: Biological replicate 2 of 3.


title: Dose 1-3

description: Biological replicate 3 of 3.


title: Dose 1-1

description: Biological replicate 1 of 3.


title: Hum_2_L


title: Control 1

description: Biological replicate 1 of 3.

value: Culture media only


title: Hum_2_G


title: Control 3

description: Biological replicate 3 of 3 -- This became an outlier and was not used in the final analysis.


title: Hum_1_M


title: Control 2

description: Biological replicate 2 of 3.


title: Hum_1_G


title: Old.Exhaust.HCR (15833)

value: Extensor digitorum longus muscle

value: HCR

value: old

value: Exhausted


title: Hum_1_L


title: bev 1

city: Tokushima

first: atsushi

last: mitsuhashi

address: 3-18-15 Kuramoto-cho

department: Department of Respiratory Medicine and Rheumatology

country: Japan

institute: Tokushima university

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65℃in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Y-14, bev, day28, mouse 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color  (Agilent, 5190-2305) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human malignant pleural mesothelioma cell line Y-MESO-14 (1.0 × 106 per mouse) cells suspended in 0.1mL PBS were injected into the thoracic cavity of the SCID mice under anesthesia.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Y-MESO-14 bearing mice were treated twice a week with 10µg/mouse bevacizumab (bev) or vehicle (control) by intraperitoneal injection, beginning 1 week after inoculation.The mice were killed humanely under anesthesia and thoracic tumors were removed 28 days after tumor cell inoqulation. Y-MESO-14 tumor tissue was

tag: cell line

value: Human malignant pleural mesothelioma

tag: treatment

value: 10µg/mouse bevacizumab


title: bev 2

source_name: Y-14, bev, day28, mouse 2

tag: tissue


title: control 2

source_name: Y-14, vehicle, day28, mouse 2

value: vehicle


title: control 1

source_name: Y-14, vehicle, day28, mouse 1


title: Coler2_roottips_rep3

source_name: Col er-2, 4 dpg, 0.5 mm of primary root tip

value: Col er-2


title: human placental trophoblasts subjected to 4 hours in vitro Enterococcus faecalis Symbioflor 1

city: Nanchang

first: qianglai

last: tan

state: Jiangxi

address: 235 Nanjing Donglu

institute: State Key Laboratory of Food Science and Technology

description: replicate 1

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

source_name: placental choriocarcinoma cell line

value: BeWo


title: untreated control

description: replicate 1

value: untreated


title: human placental trophoblasts subjected to 4 hours in vitro Enterococcus faecalis OG1RF

description: replicate 1


title: human placental trophoblasts subjected to 4 hours in vitro Enterococcus faecalis V583

description: replicate 1


title: ARK_61 European

type: genomic

city: Gliwice

first: Aleksandra

last: Pfeifer

address: Wybrzeze Armii Krajowej 15

institute: MSC Memorial Cancer Center and Institute of Oncology

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450 BeadChip Arrays using standard Illumina protocol

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

data_processing: The data were preprocessed using the quantile normalization method SWAN (Subset-quantile Within Array Normalisation) [Maksimovic et al. 2012], implemented in the minfi Bioconductor package.

label: Cy5 and Cy3

source_name: B-lymphocyte cell line from European male

label_protocol: Standard Illumina Protocol

growth_protocol: Human B-lymphocyte cells were cultured under the same standard conditions and harvested at 1 mln cell per 1 ml.

extract_protocol: Standard Qiagen Protocol, Dnasy Blood&Tissue Kit

treatment_protocol: Cell lines stored at -70°C

tag: gender

value: male

value: B-lymphocyte cell line

tag: population

value: European (Caucasian from Georgia)


title: ARK_81 European


title: ARK_72 European


title: ARK_70 East Asian

source_name: B-lymphocyte cell line from East Asian male

value: East Asian (Chinese from Bejing)


title: ARK_49 European


title: ARK_75 European


title: ARK_69 East Asian


title: ARK_65 East Asian


title: ARK_74 European


title: ARK_26 East Asian


title: ARK_60 East Asian


title: ARK_50 European


title: ARK_57 East Asian


title: ARK_84 European


title: ARK_25 East Asian


title: Trophectoderm_Rep4

status: Public on Dec 02 2015

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Biological replicate 1 of 4. ICM  tissues of day 7.5 in vivo generated blastocysts were compared to TE as reference  in a dye swap design.

hyb_protocol: Antisense RNA (825 ng per replicate) was hybridized on the Agilent-manufactured EmbryoGENE® slides in a two-color dye-swap design. The microarray chip used is EmbryoGENE®. After 17 h of hybridization at 65 °C, microarray slides were washed for 1 min in gene expression wash buffer 1 (RT), 3 min in gene expression wash buffer 2 (42 °C), 10 sec in 100% acetonitrile (RT) and 30 sec in Stabilization and Drying Solution (Agilent).

scan_protocol: Slides were scanned with Power Scanner (Tecan) and features extraction was done with Array-pro6.3 (MediaCybernetics).

data_processing: Intensity files were analyzed with FlexArray 1.6.1 (Michal Blazejczyk, Mathieu Miron, Robert Nadon (2007), FlexArray: statistical Data analysis software for gene expression microarrays. Genome Quebec, Montreal, Canada, URL:http://genomequebec.mcgill.ca/FlexArray). Specifically, raw Data were corrected by background subtraction, and then normalized within and between each array (Loess and quantile, respectively). Statistical comparison between treatments (CTR-NT vs. IVF and TSA-NT vs. IVF) was done with the Limma algorithm. In pairwise comparisons among transcripts with a p-value < 0.01, a false discovery rate (FDR) of 20%, and a fold change >2.0 were considered differentially expressed.

organism: Bos taurus

source_name: Trophectoderm

label_protocol: Amplified RNA was labeled with Cy3 and Cy5 using the ULS Fluorescent Labeling Kit (Kreatech).

growth_protocol: Embryo production protocol: Production of in vivo embryos was carried out using 26 superovulated Holstein cows and semen prepared from seven bulls as described previously  by Vallée et al. (Reproduction. 2009;138:95–105).

extract_protocol:
Total RNA from each replicate was extracted and purified using the PicoPure RNA Isolation Kit (Life Science). After DNase digestion (Qiagen), quality and concentration of extracted RNA was analyzed by bioanalyzer (Agilent). All extracted samples showed good quality with an RNA integrity number ≥7.0.
Amp protocol: Purified RNA was amplified by in vitro transcription by T7 RNA amplification using the RiboAmp HSPlus RNA Amplification Kit (Life Science).

tag: time of embryo collection

value: 7.5 dpi (days post-insemination)

source_name: Inner Cell Mass


title: ARK_45 East Asian


title: ARK_51 European


title: Trophectoderm_Rep3


title: PAO1planktonic_rep2

city: Bozeman

first: Kerry

middle: S

last: Williamson

state: Montana

address: 109 Lewis Hall

department: Microbiology and Immunology

institute: Montana State University

description: PAO1 planktonic samples at 0 and 10 mM calcium, biological replicate 2

hyb_protocol: All hybridization steps were carried out with slight modifications to SOP#M008 (TIGR).  Briefly, slides were soaked at 42°C in 50 mls prehybridization solution (5x SSC, 0.1% SDS, 1% BSA) for a minimum of 60 minutes to block non-specific hybridization.  Slides were then transferred to a falcon tube containing 50 mls of filtered, autoclaved deionized (FAD) water, which was shaken by hand for 30 seconds.  This was repeated a minimum of three times before the slides were transferred to 50 mls isopropyl alcohol and shaken at room temperature for two minutes.  Slides were then dried by centrifugation for 30 seconds in a slide spinner and visually confirmed to be free from streaking and all residue. A master mix of hybridization solution containing 50 µl formamide, 25 µl 20X SSC, 5 µl 2% SDS, 1 µl DTT and 19 ul FAD water was prepared.  To each combined, labeled cDNA probe (which consists of Cy 5 labeled test RNA and Cy 3 labeled reference RNA, and vice versa), 35 µl of hybridization mixture, 1 µl tRNA, and 1 µl of herring sperm DNA was added.  This mixture was denatured at 95°C for three minutes and allowed to cool slightly before being slowly injected by pipette onto the surface of the slide array under a carefully positioned and cleaned LifterSlip™ (Erie Scientific).  The slide was then placed in a prewarmed hybridization chamber (Corning, cat # 2551), sealed, wrapped with aluminum foil, and submerged in a 43°C water bath for 16 to 20 hours. All subsequent steps were performed while keeping the slide protected from light.  Following hybridization, LifterSlips™ were removed from the slide by gentle immersion in 43°C buffer containing 2X SSC, 0.2% SDS, and 0.01 mM DTT.  Next, slides were placed in this 43°C low stringency buffer and shaken for four minutes.  Slides were then transferred to room temperature medium stringency buffer containing 1x SSC, 0.1% SDS, and 0.01 mM DTT and shaken for four minutes.  This was repeated before slides were again transferred to room temperature high stringency (0.1x SSC, 0.01 mM DTT) buffer and shaken for four minutes.  This high stringency wash was repeated twice for two minutes each before slides were dipped in FAD/0.01 mM DTT water twice, dried in a slide spinner for one minute, and immediately scanned.

scan_protocol: Slides were scanned using the GenePix 4000B scanner (Molecular Devices) and emissions at 532 and 650 nm were recorded. Genepix Pro V 6.0 software (Molecular Devices) was used to obtain median pixel intensity values for each spot on the array and generate GenePix Results (gpr) files.

data_processing: Gpr files were imported into Flexarray v 1.6.1 for normalization and analysis. Background correction was performed using the normexp algorithm. The Loess algorithm was used for within-array normalization, followed by scaling for between-array normalization. The Limma TREAT (t-tests relative to a threshold) method was used to generate symmetrical fold change to conservatively assess differential expression due to calcium addition. Empty and reserved spots were not included in the dataset. Replicate spots were averaged and genes with greater than two-fold change at p< 0.05 were selected for further analysis.

source_name: strain PAO1 planktonic at 0 mM calcium

label_protocol: 8 micrograms of total RNA were primed with 1 ul random hexamers (Invitrogen) during a 10 minute 70°C incubation in the presence of 1 µl RNase-in plus (Promega).  After a thirty second incubation on ice, RNA was then reverse transcribed at 42°C overnight using the following reagents from Invitrogen:  5.5 µl 5x first strand buffer, 3 µl 0.1 M DTT, 0.6 µl 25mM modified dNTP mix (2:1 ratio of amino-allyl dUTP to dTTP), and 2 µl Superscript II.  After synthesis, the remaining RNA was hydrolyzed by the addition of 0.5 M EDTA and 1 N sodium hydroxide.  Next, resulting cDNA samples were neutralized with 1 N HCl and 1 M sodium acetate and cleaned on MinElute columns (Qiagen) according to the manufacturer’s instructions with the substitution of non-tris containing buffers as specified in SOP#M007 (JCVI).  The resulting cDNA was assessed for quantity and purity using the Nanodrop1000 (Thermo Scientific).  It was then dried to completion with 40°C heat in an RC10-10 speed vac (Jouan) and resuspended in 9.0 µl sodium carbonate buffer, pH 9.0.  Each cDNA sample was divided into two equal portions and labeled with either Cy 3 or Cy 5 dye (GE Healthcare), again according to SOP#M007 (JCVI), for 90 minutes.  Unincorporated dye molecules were removed with the Qiagen MinElute clean-up kit and labeled samples were eluted with 25 µl EB buffer.  Corresponding samples co-hybridized to the same array were combined into a 0.5 ml centrifuge tube.

growth_protocol:
planktonic_samples: Cells were cultured planktonically for 18 hours in BMM at 37°C with shaking, as described in detail in the related publication.
biofilm_samples: Cells were also cultured in biofilms on the interior surface of silicone tubing for 72 hours at 37°C with BMM flowing at 2 mls per minute, as described in detail in the related publication.

extract_protocol: Total RNA was extracted using a hot phenol method. Pelleted cells were suspended in 1.5 mls lysis buffer (0.15 M sucrose, 0.01 M sodium acetate, pH 4.5) and 1.5 mls 2% sodium dodecyl sulfate.  Following the addition of 3 mls of water-saturated phenol, the mixture was incubated for 5 minutes at 65°C with frequent vortexing. 3 mls of chloroform were added, and the mixture was centrifuged for 30 minutes at 4°C. The aqueous phase was precipitated overnight, washed, and resuspended in RNase-free water.  The RNA was cleaned on an RNeasy column (Qiagen) following the manufacturer’s mini cleanup protocol and then subjected to two 30 minute Turbo DNase (Ambion) treatments before precipitation and resuspension in RNase free water.

treatment_protocol: Cells were cultured in BMM with no added calcium, or with 10 mM added calcium.

tag: mode of growth

value: Planktonic

tag: calcium level

value: 0 mM

source_name: strain PAO1 planktonic at 10 mM calcium

value: 10 mM


title: Trophectoderm_Rep2


title: Trophectoderm_Rep1


title: ARK_52 European


title: PAO1planktonic_rep1

description: PAO1 planktonic samples at 0 and 10 mM calcium, biological replicate 1


title: PAO1planktonic_rep2_DyeSwap

description: PAO1 planktonic samples at 0 and 10 mM calcium, biological replicate 2 dye swap


title: ARK_24 East Asian


title: PAO1planktonic_rep1_DyeSwap

description: PAO1 planktonic samples at 0 and 10 mM calcium, biological replicate 1 dye swap


title: ARK_22 East Asian


title: Inner_Cell_Mass_Rep3


title: ARK_62 European


title: ARK_56 East Asian


title: ARK_23 East Asian


title: Inner_Cell_Mass_Rep2


title: ARK_44 East Asian


title: ARK_47 European


title: ARK_20 East Asian


title: ARK_48 European


title: Inner_Cell_Mass_Rep1

description: Biological replicate 1 of 4. ICM  tissues of day 7.5 in vivo generated blastocysts were compared to TE as reference in a dye swap design.


title: PAO1biofilm_rep2_DyeSwap

description: PAO1 biofilms at 0 and 10 mM calcium, biological replicate 2 dye swap

source_name: strain PAO1 biofilm at 10 mM calcium

value: Biofilm

source_name: strain PAO1 biofilm at 0 mM calcium


title: PAO1biofilm_rep2

description: PAO1 biofilms at 0 and 10 mM calcium, biological replicate 2


title: PAO1biofilm_rep1_DyeSwap

description: PAO1 biofilms at 0 and 10 mM calcium, biological replicate 1 dye swap


title: Inner_Cell_Mass_Rep4


title: PAO1biofilm_rep1

description: PAO1 biofilms at 0 and 10 mM calcium, biological replicate 1


title: ARK_34 European


title: FRD1planktonic_rep1_DyeSwap

description: FRD1 planktonic samples at 0 and 10 mM calcium, biological replicate 1 dye swap

source_name: strain FRD1 planktonic at 10 mM calcium

source_name: strain FRD1 planktonic at 0 mM calcium


title: FRD1planktonic_rep1

description: FRD1 planktonic samples at 0 and 10 mM calcium, biological replicate 1


title: FRD1planktonic_rep2

description: FRD1 planktonic samples at 0 and 10 mM calcium, biological replicate 2


title: Whole testes_3

city: Okazaki

first: Shosei

last: Yoshida

state: Aichi prefecture

address: 5-1,Higashiyama, Myodaiji-cho

department: Division of Germ Cell Biology

institute: National Institute for Basic Biology

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned using an Agilent Technologies Scanner (G2505C and G2565CA) with the default settings for 8 × 60k-format one-color arrays, or entrusted to Hokkaido system science. Images were analyzed using Feature Extraction ver.10.7.3.1 (Agilent Technologies).

data_processing: Images were analyzed using Feature Extraction ver.10.7.3.1 (Agilent Technologies) using default parameters. I performed a 75% percentile shift as a normalize (I did not use any control genes), and it carried out using gene spring GX11-13 for my microarray data.

source_name: whole testes, sample3

label_protocol: cRNA synthesis from 25 ng total RNA and Cyanine 3 (Cy3)-CTP labeling was carried out using Low Input Quick Amp Labeling Kit (Agilent) according to manufacture’s protocol. Purification of labeled cRNA was performed using RNeasy Mini Kit (Qiagen). The concentration and quality of labeling cRNA was determined using the NanoDropand using RNA Pico 6000 LabChip kits (Agilent) and 2100 Bioanalyzer (Agilent).

extract_protocol: GFRα1+ population was purified as GFP+ fraction from GFRα1-EGFP mice. Whilst, NGN3+ and KIT+ populations were collected as GFP+/KIT- fraction and GFP+/KIT+ fraction from Ngn3-EGFP mice in which GFP fluorescence persists. Microarray analysis was done in triplicate, using RNA samples purified from about 10,000-20,000 cells (500,000 cells were used for WT) for each single microarray analysis. Three samples from different animal were used for GFRα1+ and KIT+ spermatogonia, while cells purified from two mice were pooled for a single RNA preparation of NGN3+ spermatogonia. An extraction of total RNA was curried out by using RNeasy Micro Kit (Qiagen), with DNase digestion performed on a column. Recovered RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: testes

value: 10-11 weeks old


title: FRD1planktonic_rep2_DyeSwap

description: FRD1 planktonic samples at 0 and 10 mM calcium, biological replicate 2 dye swap


title: Whole testes_1

source_name: whole testes, sample1


title: NGN3+_3

source_name: NGN3+ cells, sample3


title: KIT+_1

source_name: KIT+ cells, sample1


title: KIT+_2

source_name: KIT+ cells, sample2


title: Whole testes_2

source_name: whole testes, sample2


title: ARK_33 European


title: ARK_28 European


title: KIT+_3

source_name: KIT+ cells, sample3


title: ARK_17 East Asian


title: FRD1biofilm_rep2_DyeSwap

description: FRD1 biofilms at 0 and 10 mM calcium, biological replicate 2 dye swap

source_name: strain FRD1 biofilm at 10 mM calcium

source_name: strain FRD1 biofilm at 0 mM calcium


title: FRD1biofilm_rep2

description: FRD1 biofilms at 0 and 10 mM calcium, biological replicate 2


title: ARK_19 East Asian

source_name: B-lymphocyte cell line from East Asian male


title: ARK_21 East Asian


title: FRD1biofilm_rep1

description: FRD1 biofilms at 0 and 10 mM calcium, biological replicate 1


title: ARK_32 European

source_name: B-lymphocyte cell line from European male


title: FRD1biofilm_rep1_DyeSwap

description: FRD1 biofilms at 0 and 10 mM calcium, biological replicate 1 dye swap


title: NGN3+_2

source_name: NGN3+ cells, sample2


title: ARK_46 European


title: GFRα1+_3

source_name: GFRa1+ cells, sample3


title: GFRα1+_2

source_name: GFRa1+ cells, sample2


title: ARK_18 East Asian


title: gDNA_Spo_5hr_rep1

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

hyb_protocol: Samples were co-hybridized to custom Agilent arrays in 1X Agilent hybridization buffer at 65 degrees for 16 hours. Samples were washed according to manufacturer's instructions.

scan_protocol: Agilent scanner using the AgilentHD_CGH protocol (5μM resolution, 100% PMT for each laser). Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing: Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the marrray package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).

organism: Saccharomyces cerevisiae

source_name: cells

label_protocol: 1.5 μg of ssDNA was labeled with Cy3-dUTP or Cy5-dUTP (GE Healthcare) by random priming without denaturation using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

growth_protocol: Cells were pre-grown in presporulation medium (BYTA) and transferred into sporulation medium (SPO) at 0 hours. Samples were isolated at the indicated timepoints.

extract_protocol: To isolate ssDNA, fixed cells were removed from –20°C and thawed. Cells were spheroplasted in sorbitol buffer (1M sorbitol, 1% beta-mercaptoethanol, 0.2 mg/ml zymolyase 100T, 0.1M EDTA, pH 7.4), lysed in NDS (0.6% SDS, 300mM EDTA, 10mM Tris.HCl, pH 9.5). DNA deproteinated with proteinase K (0.25mg/ml; Roche) at 50°C, twice phenol extracted, treated with RNase A, and stored in TE (1mM EDTA, 10mM Tris.HCl, pH 7.5) at 4°C. 25 μg DNA were digested to completion with EcoRI (New England Biolabs). ssDNA was enriched by batch absorption to BND cellulose. Briefly, a 50% slurry of BND-cellulose was equilibrated in NET (1M NaCl, 10mM Tris, pH 7.6, 1mM EDTA). Digested DNA was adjusted to 1M NaCl and ssDNA was incubated with a 500 μl bed volume of BND-cellulose for 5 minutes. Resin was washed with five bed volumes of NET. ssDNA was eluted five times with 600 μl NET + 1.8% caffeine. DNA was precipitated and concentrated for microarray analysis.

treatment_protocol: Harvested cells were pelleted, fixed in 70% ethano and stored at –20°C until further processing.

tag: cycle stage

value: meiotic

value: pre-meiotic


title: GFRα1+_1

source_name: GFRa1+ cells, sample1


title: gDNA_Spo_5hr_rep1 dye-swap


title: NGN3+_1

source_name: NGN3+ cells, sample1


title: gDNA_Spo_0hr_rep1 dye-swap


title: A2058_Vemur_rep3

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

description: BRAF (V600E)

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affzmetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing: Arrays were normalized and probeset-level expression values were calculated with R (v 3.0.1)/Bioconductor's 'affy' package using the rma() function

label: Biotin

source_name: A2058 human melanoma cell line

label_protocol: 100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: A375 and A2058 human melanoma cells are cultured in DMEM medium supplied with 10% FBS, MEM NEAA (Cat No. 11140-035), GENT (Cat No. 15710-049), MEM Vitamins (Cat No. 11120-037), Sodium Pyruvate (Cat No. 11360-039) and HEPES (Cat No. 15630-056). The supplements are from Invitrogen.

extract_protocol: Total RNA was extracted with Qiagen kit (Rneasy mini kit). The protocl was according to the manual.

treatment_protocol: A375p cells were treated with Vemurafenib (Selleck, final concentration: 1μM) for 72 hours in total, refreshed every 24 hours. Control groups were treated with equal volume of DMSO.

value: melanoma

tag: agent

value: Vemurafenib


title: gDNA_Spo_0hr_rep1

tag: genotype


title: A2058_Vemur_rep2

description: BRAF (V600E)


title: A375_Vemur_rep1

description: BRAF (V600E)

source_name: A375p human melanoma cell line

growth_protocol: AA375 and A2058 human melanoma cells are cultured in DMEM medium supplied with 10% FBS, MEM NEAA (Cat No. 11140-035), GENT (Cat No. 15710-049), MEM Vitamins (Cat No. 11120-037), Sodium Pyruvate (Cat No. 11360-039) and HEPES (Cat No. 15630-056). The supplements are from Invitrogen.


title: A375_Vemur_rep2

description: BRAF (V600E)


title: A2058_DMSO_rep3

description: BRAF (V600E)

value: DMSO


title: A2058_DMSO_rep2

description: BRAF (V600E)


title: A2058_Vemur_rep1

description: BRAF (V600E)


title: A375_Vemur_rep3

description: BRAF (V600E)


title: A2058_DMSO_rep1

description: BRAF (V600E)


title: genomic DNA from C0028T

city: Harbin

first: Jiufeng

last: Wei

address: Yiyuan street

institute: the Fourth Affiliated Hospital of Harbin Medical University

description: cancer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: GenomeStudio Methylation v1.8

source_name: rectal cancer

extract_protocol: genomic DNA was extracted and purified from rectum samples using QIAamp DNA Mini Kit according to standard instructions

tag: subject id

tag: tissue type

value: rectum

tag: tissue subtype

value: rectal cancer

tag: node metastasis state

value: yes

tag: t

tag: n

tag: m

tag: Stage

value: IIIB

tag: differentiation

value: moderate


title: genomic DNA from R0006T

description: cancer

tag: gender

value: female

tag: age

value: poor


title: A375_DMSO_rep1

description: BRAF (V600E)

tag: cell type

tag: cell line


title: A375_DMSO_rep3

description: BRAF (V600E)


title: A375_DMSO_rep2

description: BRAF (V600E)


title: appendiceal cancer, validation series, 2011-1087

city: Winston-Salem

first: Lance

middle: David

last: Miller

state: North Carolina

address: Medical Center Blvd

department: Cancer Biology

institute: Wake Forest School of Medicine

hyb_protocol: 6 ug biotinylated cRNA was hybridized to the array according to current Affymetrix standard operating procedures

scan_protocol: Arrays were scanned according to Affymetrix standard operating procedures

data_processing: Raw data (CEL files) were generated using Affymetrix AGCC software and quantile normalized by the RMA method.

source_name: cancer of the appendix

label_protocol: 250 ng total RNA was amplified and labeled according to the Affymetrix 3’-IVT labeling protocol

extract_protocol: total RNA was isolated using the Qiagen RNeasy kit according to the manufacturer’s instructions

value: Female

tag: age at diagnosis

tag: cancer grade

value: Low

tag: surgical score

tag: ecog status

tag: disease-specific survival time (years)

tag: disease-specific survival event

tag: progression-free survival time (years)

tag: progression-free survival event

tag: molecular subtype

value: Unfavorable


title: appendiceal cancer, validation series, 2009-1061

value: Male


title: genomic DNA from R0008P

description: normal

source_name: adjacent normal tissue

tag: subject id

value: male

tag: tissue type

tag: tissue subtype

value: adjacent normal tissue

tag: node metastasis state

value: no


title: genomic DNA from R0006P

description: normal

tag: gender


title: genomic DNA from R0007P

description: normal

tag: age


title: genomic DNA from R0007T

description: cancer

tag: t

tag: n

tag: m

tag: Stage

tag: differentiation


title: genomic DNA from R0004P

description: normal


title: genomic DNA from R0004T

description: cancer

value: IIA


title: appendiceal cancer, original series, 2006-813

tag: age at diagnosis

tag: cancer grade

tag: surgical score

tag: ecog status


title: genomic DNA from R0008T

description: cancer


title: genomic DNA from C0028P

description: normal


title: appendiceal cancer, original series, 2006-677

tag: disease-specific survival time (years)

tag: disease-specific survival event

tag: progression-free survival time (years)

tag: progression-free survival event


title: Developmental wheat seed at P2_biological rep3

first: Yonglong

last: Yu

address: 105 Xisanhuan North Road

institute: College of Life Science, Capital Normal University

description: Gene expression data from Wheat seed_15 days post-anthesis

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

organism: Triticum aestivum

source_name: Wheat seed_15 days post-anthesis

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

growth_protocol: The collection of developmental seed which developed naturally according to the different developmental phases (P1-P3).

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

treatment_protocol: Wheat cultivar Jimai 20 was planted in the experimental station of Chinese Agricultural University, Beijing, from 2013 to 2014 growing season. Experiments were performed in three biological replicates (each plot with 50 square meter). The cultivation and management were same as local field production conditions. Grain samples were harvested from 11, 15 and 20 days post-anthesis (DPA) of grain filling stages. The collected samples were immediately put in liquid nitrogen and then stored in -80℃ prior to use.

tag: tissue

value: developmental seeds

tag: cultivar

value: Jimai 20


title: appendiceal cancer, validation series, 2008-844

tag: gender

tag: molecular subtype

value: Favorable


title: appendiceal cancer, original series, 2006-612


title: appendiceal cancer, validation series, 2008-866

value: High


title: appendiceal cancer, original series, 2006-473


title: Developmental wheat seed at P3_biological rep1

description: Gene expression data from Wheat seed_20 days post-anthesis

source_name: Wheat seed_20 days post-anthesis


title: genomic DNA from R0012P

description: normal

tag: subject id

tag: age

tag: tissue type

value: rectum

tag: tissue subtype

tag: node metastasis state


title: appendiceal cancer, validation series, 2008-731

tag: age at diagnosis


title: appendiceal cancer, original series, 2006-73

tag: cancer grade


title: appendiceal cancer, validation series, 2008-1510

tag: surgical score


title: Developmental wheat seed at P3_biological rep3


title: Developmental wheat seed at P2_biological rep2


title: Developmental wheat seed at P3_biological rep2


title: appendiceal cancer, validation series, 2008-756

tag: ecog status


title: appendiceal cancer, original series, 2006-482

tag: disease-specific survival time (years)


title: appendiceal cancer, validation series, 2009-404

tag: disease-specific survival event


title: appendiceal cancer, validation series, 2008-365

tag: progression-free survival time (years)


title: Developmental wheat seed at P1_biological rep3

description: Gene expression data from Wheat seed_11 days post-anthesis

source_name: Wheat seed_11 days post-anthesis


title: appendiceal cancer, original series, 2006-469

tag: progression-free survival event


title: appendiceal cancer, original series, 2006-1050


title: appendiceal cancer, original series, 2006-372


title: Developmental wheat seed at P2_biological rep1

tag: tissue


title: appendiceal cancer, validation series, 2009-1526


title: appendiceal cancer, original series, 2005-760


title: Developmental wheat seed at P1_biological rep2

tag: cultivar


title: appendiceal cancer, original series, 2006-149

tag: gender


title: appendiceal cancer, validation series, 2008-1428

tag: molecular subtype


title: appendiceal cancer, validation series, 2008-1181


title: mda603

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

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

scan_protocol: Standard HT TITAN scanning protocol

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

source_name: retinae

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

extract_protocol: Trizol

tag: background strain

value: mixed breed

tag: genotype/variation

value: wt

value: retina


title: mda604

tag: age


title: Developmental wheat seed at P1_biological rep1

city: Beijing


title: appendiceal cancer, validation series, 2008-1494


title: appendiceal cancer, validation series, 2008-1171


title: appendiceal cancer, original series, 2004-800


title: appendiceal cancer, original series, 2005-427


title: appendiceal cancer, validation series, 2008-136


title: appendiceal cancer, validation series, 2007-59


title: appendiceal cancer, validation series, 2007-473


title: appendiceal cancer, original series, 2005-1129


title: appendiceal cancer, validation series, 2007-866


title: mda601


title: genomic DNA from R0012T

description: cancer

tag: subject id

value: female

tag: tissue type

tag: tissue subtype

value: rectal cancer

tag: t

tag: n

tag: m

tag: Stage

tag: differentiation

value: moderate


title: appendiceal cancer, original series, 2005-685

tag: age at diagnosis

tag: cancer grade

value: Low

tag: surgical score

tag: ecog status

tag: disease-specific survival time (years)

tag: disease-specific survival event

tag: progression-free survival time (years)

value: Unfavorable


title: mda602

tag: background strain

tag: genotype/variation

tag: tissue


title: appendiceal cancer, original series, 2004-786

tag: gender

value: Female

tag: progression-free survival event

tag: molecular subtype


title: appendiceal cancer, validation series, 2007-365

value: Male


title: mda599

tag: age


title: mda600


title: appendiceal cancer, validation series, 2007-327


title: mda597


title: appendiceal cancer, original series, 2004-650


title: appendiceal cancer, original series, 2000-90


title: appendiceal cancer, original series, 2000-178


title: appendiceal cancer, original series, 2002-318


title: mda596


title: appendiceal cancer, original series, 2002-222


title: appendiceal cancer, validation series, 2007-30


title: appendiceal cancer, original series, 2004-522


title: appendiceal cancer, original series, 2000-140


title: appendiceal cancer, original series, 2002-191


title: appendiceal cancer, validation series, 2005-859


title: mda598


title: appendiceal cancer, validation series, 2007-1116


title: appendiceal cancer, validation series, 2006-1183


title: mda582

value: Brg -/-


title: appendiceal cancer, validation series, 2006-1067


title: appendiceal cancer, validation series, 2005-722


title: appendiceal cancer, validation series, 2007-352


title: appendiceal cancer, validation series, 2005-584


title: mda581


title: mda595


title: mda578


title: appendiceal cancer, validation series, 2007-278


title: appendiceal cancer, validation series, 2005-527


title: mda583


title: mda579


title: mda580


title: appendiceal cancer, validation series, 2005-295


title: appendiceal cancer, validation series, 2005-279


title: appendiceal cancer, validation series, 2004-847


title: mda577


title: appendiceal cancer, validation series, 2005-128


title: mda574


title: appendiceal cancer, validation series, 2004-751


title: total RNA from C0028P

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, Quality control was performed with NanoDrop 2000C.

tag: subject id

value: male

tag: age (yrs)

tag: tissue type

tag: tissue subtype

value: adjacent normal tissue

tag: node metastasis state

value: yes


title: appendiceal cancer, validation series, 2001-41

tag: age at diagnosis

tag: cancer grade

tag: surgical score

value: Favorable


title: mda575


title: total RNA from R0007T

tag: t

tag: n

tag: m

tag: Stage

value: IIIB

tag: differentiation


title: mda573

tag: background strain

tag: genotype/variation

tag: tissue


title: appendiceal cancer, validation series, 2004-661

tag: gender

tag: ecog status

tag: disease-specific survival time (years)

tag: disease-specific survival event

tag: progression-free survival time (years)

tag: progression-free survival event

tag: molecular subtype


title: mda572

tag: age


title: appendiceal cancer, validation series, 2004-650

tag: age at diagnosis

tag: cancer grade

tag: surgical score


title: mda571


title: total RNA from C0028T

tag: subject id

tag: age (yrs)

tag: tissue type

value: rectum

tag: tissue subtype

tag: node metastasis state

tag: t

tag: n

tag: m


title: wild-type +/+ 2

city: Zurich

first: Meliana

last: Riwanto

address: Winterthurerstrasse 190

department: Nephrology

institute: University of Zurich

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® rat genome 230 2.0 array.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing:
The data were analyzed with Affymetrix GCOSTM 1.2 software using default analysis settings and global scaling as normalization method.
The analysis of Genechip MAS5 normalized expression values was performed using GeneSpring 6.1.1 (Agilent, CA, USA). A t-test was carried out between the groups (Cy/+ and +/+), and p-values <0.05 were considered statistically significant.

source_name: kidney tissue from wild-type +/+ rat

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: not applicable

extract_protocol: Kidney tissues were homogenized in lysis buffer (RNeasy; Qiagen). Total RNA extraction was performed from the homogenates according to the manufacturer's instructions (RNeasy; Qiagen).

treatment_protocol: not applicable

tag: tissue

value: kidney

value: ten-week old

tag: gender

tag: genotype

value: wild-type +/+


title: mda570

tag: background strain

value: mixed breed

tag: genotype/variation

value: retina


title: mda569

tag: age


title: wild-type +/+ 1


title: heterozygous Han:SPRD Cy/+ 3

source_name: kidney tissue from Han:SPRD Cy/+ rat

value: heterozygous Han:SPRD Cy/+


title: heterozygous Han:SPRD Cy/+ 1


title: wild-type +/+ 3


title: 5°C gill-TCO-replicate2

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

country: Germany

institute: Research Institute for Farm Animal Biology

description: Pool of 5 individual RNAs

hyb_protocol: The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Equal amount of fragmented Cy3-labeled cRNA (0.6 µg) in hybridization buffer was hybridized at 65 °C for 17 h to 8×60 K Whole Salmon Genome Oligo Microarrays (AMADID 049158; Agilent Technologies) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37 °C for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using the Microarray Scanner System G2505C (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software 10.7.3.1 was used to read out and process the microarray image files using default settings. FES corrected the background based on a two-sided Student t-test.

organism: Oncorhynchus mykiss

source_name: 5°C gill-TCO

label_protocol: Five individual RNA samples from the same tissue (liver, gills, kidney), strain (Born or TCO) and temperature (5°C, 0°C) were pooled. 100 ng of each total RNA samples was amplified and labeled with the fluorescent dye cyanine 3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured.

growth_protocol: Fish were grown under standard aquauculture conditions in brackish water. When a temperature of 5°C was reached the treatment was performed.

extract_protocol: Liver, kidney and gill were taken from BORN and TCO. RNeasy Mini Kit (Qiagen, Hilden, Germany) in complement with the RNase-free DNase Set (Qiagen) allowed us to obtain high-quality RNA suitable for microarray hybridizations and quantitative real-time PCR (qPCR) assays.

treatment_protocol: Fish were put in basins containing either 5°C or 0°C cold water and incubated for 30 minutes. Fish were randomly sampled using hand nets. Anaesthetization of fish with was done using phenoxyethanol prior to tissue sampling.

value: gill

tag: strain

value: TCO

value: female

value: 8 months


title: dye302

value: Brg -/-


title: total RNA from R0008P

value: male

value: no


title: 0°C gill-BORN-replicate1

description: Pool of 5 individual RNAs

source_name: 0°C gill-BORN

value: BORN

value: mixed


title: total RNA from R0006T

value: rectal cancer

value: yes

tag: Stage

value: IIIB

tag: differentiation

value: poor


title: dye275

value: wt


title: appendiceal cancer, validation series, 2004-527

value: Female

tag: age at diagnosis

tag: cancer grade

value: Low

tag: surgical score

tag: ecog status

tag: disease-specific survival time (years)

tag: disease-specific survival event

tag: progression-free survival time (years)

tag: progression-free survival event

tag: molecular subtype

value: Unfavorable


title: dye301

value: mixed breed

tag: tissue

value: retina


title: total RNA from R0006P

tag: subject id

tag: gender

value: female

tag: age (yrs)

tag: tissue type

value: rectum

tag: tissue subtype

value: adjacent normal tissue

tag: node metastasis state


title: total RNA from R0007P


title: 5°C gill-BORN-replicate2

description: Pool of 5 individual RNAs

source_name: 5°C gill-BORN

value: gill

tag: strain

tag: age

value: 8 months


title: total RNA from R0012P

value: no


title: dye300

tag: background strain

tag: genotype/variation

value: Brg -/-


title: total RNA from R0012T

value: rectal cancer

tag: t

tag: n

tag: m

tag: Stage

value: IIA

tag: differentiation

value: moderate


title: heterozygous Han:SPRD Cy/+ 2

value: kidney

value: ten-week old

value: male

tag: genotype

value: heterozygous Han:SPRD Cy/+


title: 0°C gill-TCO-replicate1

description: Pool of 5 individual RNAs

source_name: 0°C gill-TCO

tag: tissue

value: TCO


title: dye298

value: mixed breed


title: dye299

value: retina


title: 0°C gill-TCO-replicate2

description: Pool of 5 individual RNAs

value: female


title: dye274

value: wt


title: total RNA from R0004P

tag: subject id

value: rectum

value: adjacent normal tissue


title: total RNA from R0004T

tag: gender


title: dye273


title: 0°C gill-BORN-replicate2

description: Pool of 5 individual RNAs

value: gill

value: BORN

value: mixed

value: 8 months


title: 5°C gill-TCO-replicate1

description: Pool of 5 individual RNAs


title: total RNA from R0008T

tag: age (yrs)

value: rectal cancer

value: no

value: IIA


title: 5°C gill-BORN-replicate1

description: Pool of 5 individual RNAs


title: 0°C kidney-TCO-replicate1

description: Pool of 5 individual RNAs

source_name: 0°C kidney-TCO

value: kidney


title: THP-1 Infected with MtbΔwhiB3  W3_24 hrs

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: replicate 3

scan_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation using GeneSpring Gx v12.5

source_name: THP-1 Infected with MtbΔwhiB3

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

growth_protocol: Human THP-1 monocytic cells (ATCC TIB 202) were grown in RPMI-1640 supplemented with 10% FBS, L-glutamine, sodium carbonate and HEPES.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance to manufacturer's instructions. Quality control was performed with BioRad Bioanalyser EXPERION.

treatment_protocol: 6 million THP-1 monocytic cells were seeded in 6-well plates. Cells were allowed to differentiate with 20 ng/mL phorbol myristate acetate and were allowed to rest for 3 days. After 3 days, differentiated THP-1 were infected with Mtb and Mtb∆whiB3 mutant at an MOI of 10 for 4 h, followed by amikacin treatment for 2 h. After 2 h, cells were washed to remove any extracellular bacteria. For 0 h time point, cells were lysed and RNA was isolated. Cells of 12 h, 24 h, 36 h, 48 h time points were kept in fresh RPMI with 10% FBS till time point.

tag: infected strain

value: WhiB3 mutant of strain H37Rv

tag: time

value: 24 hrs

tag: cell line


title: 0°C kidney-TCO-replicate2

description: Pool of 5 individual RNAs

tag: strain

value: TCO


title: 5°C kidney-TCO-replicate1

description: Pool of 5 individual RNAs

source_name: 5°C kidney-TCO

tag: age


title: dye271

tag: background strain

value: mixed breed


title: THP-1 Infected with MtbΔwhiB3  W1_24 hrs

description: replicate 1


title: dye268

tag: genotype/variation

value: Brg -/-

value: retina


title: 0°C kidney-BORN-replicate1

description: Pool of 5 individual RNAs

source_name: 0°C kidney-BORN


title: dye270


title: 5°C kidney-BORN-replicate2

description: Pool of 5 individual RNAs

source_name: 5°C kidney-BORN


title: 5°C kidney-TCO-replicate2

description: Pool of 5 individual RNAs

value: female


title: dye267


title: THP-1 Infected with MtbΔwhiB3  W2_12 hrs

description: replicate 2

value: 12 hrs


title: THP-1 Infected with MtbΔwhiB3  W2_24 hrs

description: replicate 2


title: 5°C kidney-BORN-replicate1

description: Pool of 5 individual RNAs


title: dye272

value: wt


title: 0°C liver-TCO-replicate2

description: Pool of 5 individual RNAs

source_name: 0°C liver-TCO

value: liver


title: THP-1 Infected with MtbΔwhiB3  W3_12 hrs

description: replicate 3


title: dye269


title: THP-1 Infected with MtbΔwhiB3  W1_12 hrs

description: replicate 1


title: THP-1 Infected with MtbΔwhiB3  W3_0 hrs

description: replicate 3

value: 0 hrs


title: mda576


title: dye266


title: 0°C liver-TCO-replicate1

description: Pool of 5 individual RNAs


title: 0°C kidney-BORN-replicate2

description: Pool of 5 individual RNAs

value: BORN

value: mixed


title: THP-1 Infected with MtbΔwhiB3  W1_0 hrs

description: replicate 1


title: dye265


title: THP-1 Infected with MtbΔwhiB3  W2 0 hrs

description: replicate 2


title: 5°C liver-TCO-replicate2

description: Pool of 5 individual RNAs

source_name: 5°C liver-TCO

value: 8 months


title: dye263


title: 5°C liver-TCO-replicate1

description: Pool of 5 individual RNAs


title: dye261


title: 0°C liver-BORN-replicate2

description: Pool of 5 individual RNAs

source_name: 0°C liver-BORN


title: THP-1 Uninfected control 19 UC 19

description: replicate 3

source_name: THP-1 Uninfected control 19

value: no infection


title: THP-1 Uninfected control 5 UC 5

description: replicate 1

source_name: THP-1 Uninfected control 5


title: THP-1 Uninfected control 13 UC 13

description: replicate 2

source_name: THP-1 Uninfected control 13


title: dye262

source_name: retinae


title: TA biological rep3 (array)

first: Sebastian

last: Poliak

address: 701 West 168st

department: Neuroscience and Biochemistry and Molecular Biophysics

institute: Columbia University

hyb_protocol: The Affymetrix GeneChip Hybridization control kit and GeneChip Hybridization, Wash, and Stain kit were used to hybridize samples to Affymetrix 430 2.0 GeneChip arrays, with fluidics performed on the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Data analysis was performed in Partek Genomics Suite version 6.6 using the GC Robust Multi-array Average (GCRMA) normalization algorithm, followed by one-way ANOVA to analyze relative fold-enrichment in TA vs GS proprioceptors.  TAvsGS_affy_PartekAnalysis.txt is linked as a supplementary file on the Series record.

source_name: proprioceptors supplying TAmuscle

label_protocol: cDNA was prepared from 5 µg of total RNA using the WT-Ovation One-Direct RNA Amplification system (Nugen)

growth_protocol: Dissection and purification of individual proprioceptors, following TA or GS ctb-555 muscle injections,  were done following Malin et al., 2007; and Hempel et al., 2007

extract_protocol: total RNA was extracted using a PicoPure RNA isolation kit (Arcturus).

value: TA muscle

tag: cell type

value: neuron


title: TA biological rep2 (array)

source_name: proprioceptors supplying TA muscle


title: TA biological rep1 (array)


title: THP-1 Infected with MtbΔwhiB3  W4 48 Hrs

description: replicate 3

value: WhiB3 mutant of strain H37Rv

value: 48 hrs