title: Sox2mGS#1, biological rep1

value: lentivirus-mediated transfection of Sox2 in combination with knock-down of p53


title: Sox2mGS#1, biological rep2

status: Public on Oct 21 2013

type: RNA

city: Kyoto

first: Seiji

last: Takashima

address: 53 Kawahara-cho, Shogoin, Sakyo

department: Department of Molecular Genetics

country: Japan

institute: Kyoto University

description: Gene expression data from mGS cells induced from GS cells by lentivirus-mediated transfection of Sox2 in combination with knock-down of p53.

hyb_protocol: Resultant labeled-cDNA were hybridized for 17 hr at 45C on Mouse Gene 1.0 ST Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed with GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Plier normalization. Data analyses were performed using GeneSpring 12.0 software (Agilent Technologies, Inc., Santa Clara, CA). The probeset signals were calculated with the Plier algorithm. The annotation is based on na32 (mm9). The probesets that had low signals (less than 100) in all samples were excluded from the analysis. Statistical analysis was performed by one-way analysis of variance (ANOVA) with a Benjamini and Hochberg false discovery rate (BH-FDR = 0.05). The 12085 probes that showed more than 2-fold expression change in at least one pair of samples were subjected to hierarchical clustering (Distance metric: Pearson Centered, Linkage method: Average).

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Sox2 mGS cells

label_protocol: For generating whole transcript sense target with label, purified total RNA were converted to sense strand cDNA using The Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript (WT) Expression Arrays (Applied Biosystems). Resultant cDNA samples were labeled using GeneChip WT terminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: All pluripotent cell lines were maintained on MEFs in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 1000 U/ml LIF (ESGRO; Merck Millipore, Billerica, MA), non-essential amino acid mixture (Invitrogen, Carlsbad, CA), and 0.1 mM 2-mercaptoethanol (ME). GS cells were maintained on MMC-treated MEF feeder with StemPro-34 SFM (Invitrogen) supplemented with StemPro supplement (Invitrogen), 25 µg/ml insulin, 100 µg/ml transferrin, 60 µM putrescine, 30 nM sodium selenite, 6 mg/ml D-(+)-glucose, 30 µg/ml pyruvic acid, 1 µl/ml DL-lactic acid (Sigma, St Louis, MO), 5 mg/ml bovine albumin (ICN Biomedicals, Irvine, CA), 2 mM L-glutamine, 5 x 10-5 M 2-mercaptoethanol, minimal essential medium (MEM) vitamin solution (Invitrogen), MEM nonessential amino acid solution (Invitrogen), 10-4 M ascorbic acid, 10 µg/ml d-biotin, 30 ng/ml beta-estradiol, 60 ng/ml progesterone (Sigma), 10 ng/ml human basic fibroblast growth factor, 10 ng/ml recombinant rat glial cell line-derived neurotrophic factor (Peprotech, London, UK) and 1% fetal calf serum (JRH Biosciences, Lenexa, KS).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by purification with Rneasy Plus Mini kit (Qiagen).

treatment_protocol: Cultured cells were collected by trypsin-EDTA and incubated on 0.1% gelatin-coated dish for 30min to remove feeder cells. Resultant samples were pelletted and susupended in Trizol reagent (Invitrogen).

tag: strain

value: DBA/2; GFP Tg

tag: cell type

value: Sox2 mGS cells

tag: treatment


title: Sox2mGS#2, biological rep1


title: NCI10041

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

country: USA

institute: University of North Carolina at Chapel Hill

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

organism: Homo sapiens

source_name: Human Reference B

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129

extract_protocol: Qiagen Rneasy Mini

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Normal Tissue Adjacent to Breast Tumor

tag: mammographic density

tag: mammographic dense area

tag: microenvironment subtype

value: Active;Stromal proportion_tertile3;Epithelial proportion_tertile2;Adipose proportion_tertile2


title: L10_B2_19c

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

country: France

institute: INRA

description: Gene expression in sample 19c

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 016322 completed with the 39 genes from the new region of EC1118 (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plate were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software PRO7

data_processing: Data normalization and statistical analysis were performed using R 2.13.1 software and the limma package. Normalization was done by the quantile method considering all arrays

organism: Saccharomyces cerevisiae

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific)

growth_protocol: Fermentations were done in a synthetic SM425 medium (with 425mg/L of assimilate nitrogen pH3.3 and previously describe as SM300, Bely et al, 1990) which mimics natural grape must. This medium was supplemented by 1mg/L of p-aminobenzoic acid and 14.5mg/L of iron(III) chloride. Cells sample for RNA extraction was performed at 66gCO2/L release (70% of fermentation advancement) in stationary phase.

extract_protocol: Total RNA extraction were perform with Trizol reagent (Gibco BRL, Life Technologies), purified by isopropanol precipitation then with RNeasy kit (Qiagen).

treatment_protocol: For each condition, 10E9 cells were sampled, pelleted, washed with DEPC-treated water and freeze in methanol at -80°C.

value: segregate 19c

tag: array

tag: block


title: shRNA control R11 T5

city: Seattle

first: Nathan

last: Palpant

state: WA

address: 850 Republican St

institute: University of Washington

description: SAMPLE 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The complete set of microarray data was assessed for quality, followed by quantile normalization using the Bioconductor package lumi.  The dataset was initially filtered by flagging probes that were below a signal 'noise floor,' which was established using the 75th percentile of the negative control probe signals within each array.  We subsequently filtered the dataset by employing a variance filter using the 'shorth' function of the Bioconductor package genefilter.  Pair-wise statistical analyses was performed using Bioconductor v. 2.10, limma v.3.12.3, lumi v.2.8.0.

label: biotin

source_name: RUES2_shRNA control

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

growth_protocol: Cardiac differentiation of hES cells is as described by Laflamme et al Nature Biotechnology 2007

extract_protocol: Samples were isolated using Qiagen RNease kit

tag: cell line

value: human embryonic stem cells

tag: transduced with

value: control shRNA

tag: time point

value: Day 5 of cardiac differentiation; cardiovascular progenitor cell stage


title: NCI10319

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-215

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-210

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile3;Adipose proportion_tertile3


title: Sox2mGS#3, biological rep1


title: DmrtmGS#2, biological rep2

description: Gene expression data from mGS cells induced from GS cells by lentivirus-mediated knock-down of p53 and Dmrt1.

source_name: Dmrt mGS cells

value: Dmrt mGS cells


title: DmrtmGS#2, biological rep1

value: lentivirus-mediated knock-down of p53 and Dmrt1


title: NCI10038

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128

value: Inactive;Stromal proportion_tertile3;Epithelial proportion_tertile3;Adipose proportion_tertile1


title: NCI10043

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-135

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile3;Adipose proportion_tertile2


title: DmrtmGS#1, biological rep2


title: DnmtmGS#3, biological rep2

description: Gene expression data from mGS cells induced from GS cells by lentivirus-mediated knock-down of p53 and Dnmt1.

source_name: Dnmt mGS cells

value: Dnmt mGS cells


title: Sox2mGS#2, biological rep2


title: L10_B3_S288Cs5

description: Gene expression in sample S288C, biological rep 2, technical rep 1

value: parent S288C


title: DnmtmGS#3, biological rep1

value: lentivirus-mediated knock-down of p53 and Dnmt1


title: DmrtmGS#1, biological rep1


title: DmrtmGS#3, biological rep2


title: DmrtmGS#3, biological rep1


title: NCI10028

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

value: Active;Stromal proportion_tertile2;Epithelial proportion_tertile2;Adipose proportion_tertile2


title: L9_B8_18c

description: Gene expression in sample 18c

value: segregate 18c


title: L10_B1_20a

description: Gene expression in sample 20a

value: segregate 20a


title: L9_B7_19b

description: Gene expression in sample 19b

value: segregate 19b


title: NCI10025

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: Active


title: DnmtmGS#2, biological rep2

value: DBA/2; GFP Tg


title: DnmtmGS#2, biological rep1


title: GS cell#3, biological rep2

description: Gene expression data from GS cells.

source_name: GS cells

value: GS cells


title: GS cell#3, biological rep1

description: Gene expression data from GS cells.


title: GS cell#2, biological rep2

description: Gene expression data from GS cells.


title: DnmtmGS#1, biological rep2


title: L9_B6_17a

description: Gene expression in sample 17a

value: segregate 17a


title: NCI10019

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

value: Active;Stromal proportion_tertile2;Epithelial proportion_tertile3;Adipose proportion_tertile2


title: L9_B5_18b

description: Gene expression in sample 18b

value: segregate 18b


title: NCI10015

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128

value: Active;Stromal proportion_tertile2;Epithelial proportion_tertile1;Adipose proportion_tertile3


title: L9_B4_16d

description: Gene expression in sample 16d

value: segregate 16d


title: L9_B3_59As5

description: Gene expression in sample 59A, biological rep 2, technical rep 2

value: parent 59A


title: GS cell#2, biological rep1

description: Gene expression data from GS cells.


title: L9_B2_16b

description: Gene expression in sample 16b

value: segregate 16b


title: NCI10009

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126


title: NCI10004

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

value: Inactive


title: DnmtmGS#1, biological rep1

value: Dnmt mGS cells

value: lentivirus-mediated knock-down of p53 and Dnmt1


title: shp53/Mock (1:4) - Co-culture - biological replicate 1

city: New York

first: Thomas

middle: P.

last: Zwaka

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mt. Sinai

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChip Scanner 3000

data_processing: ArrayStar DNAStar software

source_name: RNA from shp53 ESCs and mock ESCs co-cultured for 4 days in a ratio of 1:4

label_protocol: standard Affymetrix protocol

growth_protocol: standard embyronic stem cell conditions

extract_protocol: Qiagen - RNeasy Mini protocol for RNA isolation from cultured cells, including on-column Dnase digest.

value: embryonic stem cells


title: mGS cell#2, biological rep2

description: Gene expression data from mGS cells spontaneously developed during GS cell culture.

source_name: mGS cells

value: mGS cells


title: GS cell#1, biological rep1

description: Gene expression data from GS cells.


title: iPS cell#5, biological rep2

description: Gene expression data from iPS cells induced by retrovirus-mediated transfection of Oct4, Sox2, Klf4, c-myc.

source_name: iPS cells

value: iPS cells


title: shTop1/Mock (1:4) - Co-culture - biological replicate 2

source_name: RNA from shTop1 ESCs and mock ESCs co-cultured for 4 days in a ratio of 1:4


title: shp53/Mock (1:4) - Co-culture - biological replicate 2

value: shp53 ESCs and mock ESCs co-cultured for 4 days in a ratio of 1:4


title: iPS cell#5, biological rep1

value: retrovirus-mediated transfection of Oct4, Sox2, Klf4, c-myc


title: GS cell#1, biological rep2

description: Gene expression data from GS cells.

value: DBA/2; GFP Tg


title: mGS cell#2, biological rep1


title: mGS cell#1, biological rep1


title: L8_B7_16a

description: Gene expression in sample 16a

value: segregate 16a


title: L8_B8_15b

description: Gene expression in sample 15b

value: segregate 15b


title: L8_B6_14b

description: Gene expression in sample 14b

value: segregate 14b


title: iPS cell#2, biological rep2


title: shTop1/Mock (1:4) - Co-culture - biological replicate 1

value: shTop1 ESCs and mock ESCs co-cultured for 4 days in a ratio of 1:4


title: iPS cell#2, biological rep1


title: L8_B5_59As1

description: Gene expression in sample 59A, biological rep 1, technical rep 3


title: ES cell (BRC1), biological rep2

description: Gene expression data from ES cells (BRC1) cultured under condition shown below.

source_name: ES cells (BRC1)

value: ES cells (BRC1)


title: ES cell (B6-6), biological rep2

description: Gene expression data from ES cells (B6-6) cultured under condition shown below.

source_name: ES cells (B6-6)

value: ES cells (B6-6)


title: shp53/Mock (1:4) - Control - biological replicate 1

source_name: RNA from shp53 ESCs and mock ESCs grown homotypically for 4 days mixed in a ratio of 1:4


title: shTop1/Mock (1:4) - Control - biological replicate 2

source_name: RNA from shTop1 ESCs and mock ESCs grown homotypically for 4 days mixed in a ratio of 1:4


title: ES cell (BRC1), biological rep1


title: L8_B4_13b

description: Gene expression in sample 13b

value: segregate 13b


title: mGS cell#1, biological rep2


title: iPS cell#1, biological rep1


title: shp53/Mock (1:4) - Control - biological replicate 2

value: shp53 ESCs and mock ESCs grown homotypically for 4 days mixed in a ratio of 1:4


title: iPS cell#1, biological rep2


title: ES cell (B6-6), biological rep1


title: ES cell (R1), biological rep2

description: Gene expression data from ES cells (R2) cultured under condition shown below.

source_name: ES cells (R1)

value: hybrid of two 129 substrains (129X1/SvJ and 129S1/SV-+p+Tyr-cKitlSl-J/+)

value: ES cells (R1)


title: L8_B2_10b

description: Gene expression in sample 10b

value: segregate 10b


title: L8_B3_14a

description: Gene expression in sample 14a

value: segregate 14a


title: L3_B8_S288Cs1

description: Gene expression in sample S288C, biological rep 1, technical rep 2

value: parent S288C


title: shTop1/Mock (1:4) - Control - biological replicate 1

value: embryonic stem cells

value: shTop1 ESCs and mock ESCs grown homotypically for 4 days mixed in a ratio of 1:4


title: ES cell (R1), biological rep1

description: Gene expression data from ES cells (R1) cultured under condition shown below.


title: L8_B1_59As5

description: Gene expression in sample 59A, biological rep 2, technical rep 1

value: parent 59A


title: L3_B7_9c

description: Gene expression in sample 9c

value: segregate 9c


title: 11 wk C3H cerebral cortex, rep3

city: Durham

first: Douglas

middle: A

last: Marchuk

address: 213 Research Dr, 277 CARL

institute: DUKE Univ

description: 11 wk C3H-03

hyb_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA  Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® Mouse 430 2.0 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA)

data_processing: The data were analyzed with Partek Genomic Suite

source_name: 11 wk C3H cerebral cortex

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA  Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE).

tag: age

value: post-natal 11 weeks (11 wk)

tag: tissue

value: cerebral cortex

tag: gender

value: male


title: 11 wk B6 cerebral cortex, rep3

description: 11 wk B6-03

source_name: 11 wk B6 cerebral cortex


title: L3_B5_9a

description: Gene expression in sample 9a

value: segregate 9a


title: 1638455

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: control

hyb_protocol: Hybridized onto Agilent whole human genome 8x60k gene expression microarrays (Agilent Technologies, Santa Clara, CA) according to Agilent standard procedures. After hybridization for 17 h at 65 C and 10 rpm, the arrays were washed

scan_protocol: Scanned with the Agilent G3 high-resolution scanner

data_processing: Probe features were extracted from the microarray scan data using Feature Extraction software v.10.7.3.1 (Agilent Technologies). Microarray data was read and processed with R/Bioconductor (version 2.15.1/2.16) statistical software environment using the limma package (version 3.12.1).

source_name: Knee

label_protocol: Twenty-five nanograms of total RNA from each sample was used for amplification, and then was fluorescently labeled using Cy3

extract_protocol: RNA was isolated from 18 AS and normal human RNA was isolated from 3 kidney and 2 skeletal muscle OCT frozen sections and 3 samples of frozen whole blood.

tag: diagnosis

value: eptithelioid hemangioendothelioma of right popliteal fossa

value: F

tag: prior radiation

value: U


title: 11 wk C3H cerebral cortex, rep2

description: 11 wk C3H-02

tag: strain


title: pooled ctrl 02

description: control

source_name: misc

value: pooled RNA from normal tissues used in this study  (i.e. skeletal muscle, kidney epithelial tissue, and peripheral blood)

value: misc


title: 11 wk C3H cerebral cortex,rep1

description: 11 wk C3H-01


title: UM-AS2

description: AS

source_name: L. Arm

value: angiosarcoma

value: M

value: N


title: 11 wk B6 cerebral cortex, rep1

description: 11 wk B6-01


title: L3_B6_7c

description: Gene expression in sample 7c

value: segregate 7c


title: pooled ctrl 01

description: control

value: pooled RNA from normal tissues used in this study (i.e. skeletal muscle, kidney epithelial tissue, and peripheral blood)


title: 1640967

description: AS

source_name: Peri-Anal

value: Y


title: 11 wk B6 cerebral cortex, rep2

description: 11 wk B6-02


title: p1 C3H cerebral cortex, rep3

description: P1 C3H-03

source_name: p1 C3H cerebral cortex

value: post-natal day 1 (p1)


title: L3_B3_7b

description: Gene expression in sample 7b

value: segregate 7b


title: L3_B4_59As1

description: Gene expression in sample 59A, biological rep 1, technical rep 2

value: parent 59A


title: 1638158.002

description: control

source_name: LMS

value: Kidney epithelial tissue; normal, uninvolved, resected from patient with leiomyosarcoma

value: u


title: p1 C3H cerebral cortex, rep2

description: P1 C3H-02

value: cerebral cortex

value: male


title: 1634723.001

description: control

source_name: brain

value: hemangiopericytoma of the brain

value: F

value: n


title: 1653196

description: control

source_name: LPS

value: Kidney epithelial tissue; normal, uninvolved, resected from patient with liposarcoma


title: L3_B2_6d

description: Gene expression in sample 6d

value: segregate 6d


title: p1 B6 cerebral cortex, rep3

description: P1 B6-03

source_name: p1 B6 cerebral cortex


title: 1630962.002

description: control

source_name: Chondrosarcoma

value: Peripheral blood from patient diagnosed with chondrosarcoma

value: M


title: 1653194

description: control

source_name: neck-spine

value: metastatic hemangiopericytoma of the liver, right lobe


title: 1643447.002

description: control

value: skeletal muscle; normal, uninvolved, resected from a patient with liposarcoma


title: p1 B6 cerebral cortex, rep2

description: P1 B6-02


title: L2_B8_5a

description: Gene expression in sample 5a

value: segregate 5a


title: 1630960.002

description: control


title: L2_B6_3a

description: Gene expression in sample 3a

value: segregate 3a


title: p1 C3H cerebral cortex, rep1

description: P1 C3H-01

value: post-natal day 1 (p1)


title: L2_B7_6b

description: Gene expression in sample 6b

value: segregate 6b


title: L3_B1_7a

description: Gene expression in sample 7a

value: segregate 7a


title: 1633972.002

description: control

value: Kidney epithelial tissue; normal, uninvolved, resected from patient with leiomyosarcoma

value: u


title: 1631441

description: AS

value: angiosarcoma

value: U


title: UM-AS7

description: AS

source_name: Breast

value: F

value: Y


title: E00003

description: AS

source_name: L. Breast

value: N


title: p1 B6 cerebral cortex, rep1

description: P1 B6-01

value: cerebral cortex

value: male


title: 1630942

description: AS

source_name: Spleen


title: D01460

description: control

source_name: R Abdomen

value: hemangiopericytoma of the right abdomen


title: D01556

description: AS

source_name: R. Parotid


title: 1630961.002

description: control

source_name: DermatoFS

value: Peripheral blood from patient diagnosed with dermatofibrosarcoma

value: n


title: 1630753.001

description: control

source_name: Mal. FH

value: skeletal muscle; normal, uninvolved, resected from a patient with Malignant fibrous histiocytoma


title: L2_B4_1b

description: Gene expression in sample 1b

value: segregate 1b


title: L2_B3_2a

description: Gene expression in sample 2a

value: segregate 2a


title: 1638162

description: AS

source_name: Adrenal

value: M


title: 1653169-70

description: AS

source_name: medial


title: L2_B5_4c

description: Gene expression in sample 4c

value: segregate 4c


title: 1643575

description: AS

source_name: L. Leg


title: L2_B1_S288cs1

description: Gene expression in sample S288C, biological rep 1, technical rep 1

value: parent S288C


title: Intestine infected 2

city: Washington

first: Steven

last: Singer

state: DC

address: 37th & O Sts, NW

department: Biology

institute: Georgetown University

description: Gene expression data from mice infected for 10 days with G. lambblis strain GS

hyb_protocol: 20 µg of fragmented cRNA was hybridized MG_UV74Av2 chips.

scan_protocol: The detection and quantitation of target hybridization were performed with a GeneArray Scanner 3000 set to the manufacturer's defaults (Affymetrix, Santa Clara, CA).

data_processing: Affymetrix MicroArray Suite Version 5.0 (Affyemtrix, Santa Clara, CA) was used to pre-process the data files. The resulting CHP files were imported into GeneSpring GX version 7.3.1

source_name: Duodenum from C57BL/6 mouse infected 10 days with G. lamblia strain GS

label_protocol: 5-10 μg of total RNA from each sample was used to generate double stranded cDNA using a T7 oligo (dT) primer; 1 μg of this product was then used in an in vitro transcription reaction in the presence of biotinylated dNTPs using a transcript labeling kit to yield 50-100 μg of biotin labeled cRNA target. 20 μg of full-length cRNA was subjected to metal catalyzed acid hydrolysis to a length of 20–200 bp

growth_protocol: Female C57BL/6 mice were purchased from Jackson Laboratories

extract_protocol: Total RNA was prepared by extraction with RNA-STAT-60 followed by Qiagen RNeasy columns.

treatment_protocol: Four mice were infected with 1 million trophopzites of G. lmblia strain GS by gavage. 10 days; ater mice were euthanized with CO2 and duodenum was removed.

value: duodenum

tag: infection

value: G. lamblia GS

value: 7 weeks


title: 1638137

description: AS

source_name: Nose

value: angiosarcoma


title: L9_B1_16c

description: Gene expression in sample 16c

value: segregate 16c


title: Intestine uninfected 2

description: Gene expression data from uninfected mice

source_name: Duodenum from C57BL/6 mouse uninfected


title: Intestine uninfected 4


title: Intestine uninfected 3


title: L2_B2_59As1

description: Gene expression in sample 59A, biological rep 1, technical rep 1

value: parent 59A


title: Intestine infected 3


title: Intestine infected 1


title: 1633227

description: AS

source_name: R. Leg

value: U


title: UM-AS1

description: AS

value: F

value: Y


title: UM-AS8

description: AS


title: UM-AS3

description: AS

source_name: Heart

value: N


title: STOP2-complemented lline vs. stop1-mutant low pH Replicate 3

city: Gifu

first: Yuriko

last: Kobayashi

address: 1-1, Yanagido Gifu

department: Faculty of Applied Biological Sciences

institute: Gifu University

description: Biological replicate 3 of 3. 10 day-old seedlings of STOP2-complemented line and stop1-mutant were treated with low pH (pH4.5) for 24 h, and the roots were harvested.

hyb_protocol: 0.825 micro g of Cy3- and Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5 per micro g cRNA) were fragmented with Gene Expression Hybridization Kit (5188-5242, Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 micro litter of 2x GE hybridization buffer HI-PRM was added to the fragmentation mixture and hybridized to Agilent Arabidopsis 3 Oligo Microarray (G2519F) 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: Scanned on the Agilent G2508B scanner

data_processing: Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: STOP2-complemented line, low pH 24 h

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA were prepared from 1 micro g of total RNA using the Two-Color Quick Amp Labeling kit (5190-0444, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

growth_protocol: STOP2-complemented line (CaMV35s driven STOP2 in the stop1-mutant)  and stop1-mutant of Arabidopsis were grown hydroponically in the 2% modified MGRL solution  (0 µM AlCl3, pH 5.5, 2% MGRL containing 200 µM CaCl2)  for 10 days. All seedlings were kept under 12 h illuminations per day (30 µmol m–2 s–1) at 25°C .

extract_protocol: Total RNA was isolated by the method of Suzuki et al. (2004).

treatment_protocol: Root of the seedlings were exposed to toxic solutions containing 10 µM Al (pH5.0) or low pH (no Al at pH 4.5) for 24 hrs at growth conditions.

tag: background

value: root

source_name: stop1-mutant, low pH 24 h


title: STOP2-complemented lline vs. stop1-mutant Al Replicate 3

description: Biological replicate 3 of 3. 10 day-old seedlings of STOP2-complemented line and stop1-mutant were treated with Al for 24 h, and the roots were harvested.

source_name: STOP2-complemented line, Al 24 h

source_name: stop1-mutant, Al 24 h


title: WT_rep11

first: Bin

last: XU

state: NY

address: 1051 Riverside Drive

institute: columbia university

hyb_protocol: Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing:
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (R, v.2.12.0).
probe group file: MoGene-1_1-st-v1.r4.pgf
meta-probeset file: MoGene-1_1-st-v1.r4.mps

source_name: wild type_prefrontal cortex

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit was used for the preparation of labelled cDNA from 100ng of total RNA

extract_protocol: Qiagen miRNeasy Kit

tag: strain background

tag: genotype/variation

value: WT

value: 8 week old

value: male

value: prefrontal cortex


title: MUT_rep12

source_name: mutant_prefrontal cortex


title: STOP2-complemented lline vs. stop1-mutant Al Replicate 2

description: Biological replicate 2 of 3. 10 day-old seedlings of STOP2-complemented line and stop1-mutant were treated with Al for 24 h, and the roots were harvested.


title: UM-AS4

description: AS

source_name: Bladder

value: M


title: UM-AS10

description: AS


title: UM-AS6

description: AS

source_name: Breast


title: Intestine uninfected 1


title: WT_rep10


title: STOP2-complemented lline vs. stop1-mutant Al Replicate 1

description: Biological replicate 1 of 3. 10 day-old seedlings of STOP2-complemented line and stop1-mutant were treated with Al for 24 h, and the roots were harvested.


title: WT_rep12


title: MUT_rep11


title: STOP2-complemented lline vs. stop1-mutant low pH Replicate 2

description: Biological replicate 2 of 3. 10 day-old seedlings of STOP2-complemented line and stop1-mutant were treated with low pH (pH4.5) for 24 h, and the roots were harvested.


title: WT_rep9


title: STOP2-complemented lline vs. stop1-mutant low pH Replicate 1

description: Biological replicate 1 of 3. 10 day-old seedlings of STOP2-complemented line and stop1-mutant were treated with low pH (pH4.5) for 24 h, and the roots were harvested.


title: MCF7_AGO2-IP_2

city: Memphis

first: Meiyun

last: Fan

address: 19 S. Manassas Street

institute: University of Tennessee

description:
4763734046_H
Replicate 2 of 3.

hyb_protocol: Biotinylated cRNA were hybridized to the Illumina array per manufacturer's instructions.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Illumina GenomeStudio software was used for data processing: background subtraction and quantile normalization.

source_name: MCF7, AGO2-IP

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol.

growth_protocol: Cells were maintained in MEM medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS and 100 units/ml penicillin.

extract_protocol: Total RNA in cell lysates or immunoprecipitated-AGO2 complexes was prepared using Trizol according to the manufacturer's instructions.

treatment_protocol: Cells were untreated.

tag: cell type

value: luminal breast cancer cells

tag: chip antibody

value: anti-human Ago2

value: Clone 2E12-1C9

tag: antibody catalog #

tag: antibody vendor

value: Abnova


title: MDA-MB-231_AGO2-IP_3

description:
4763734046_J
Replicate 3 of 3.

source_name: MDA-MB-231, AGO2-IP

tag: cell line

value: basal-like breast cancer cells


title: MCF7_AGO2-IP_3

description:
4763734046_L
Replicate 3 of 3.


title: MUT_rep8


title: MUT_rep10


title: WT_rep6


title: WT_rep7


title: Intestine infected 4

value: duodenum

value: G. lamblia GS

value: 7 weeks


title: MCF7_input_3

description:
4763734046_K
Replicate 3 of 3.

source_name: MCF7, cell lysate

value: control IgG


title: WT_rep8


title: MDA-MB-231_input_3

description:
4763734046_I
Replicate 3 of 3.

source_name: MDA-MB-231, cell lysate


title: MDA-MB-231_AGO2-IP_2

description:
4763734046_F
Replicate 2 of 3.


title: MDA-MB-231_input_2

description:
4763734046_E
Replicate 2 of 3.


title: WT_rep5


title: MCF7_input_2

description:
4763734046_G
Replicate 2 of 3.


title: MUT_rep9


title: MUT_rep6


title: MUT_rep7


title: MDA-MB-231_AGO2-IP_1

description:
4763734046_B
Replicate 1 of 3.


title: Phytophthora sojae mycelium small RNA

type: SRA

city: Saint Louis

first: James

middle: C

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: Small RNA isolated from total RNA extracted from Phytophthora sojae mycelium

library_source: transcriptomic

data_processing:
Sequencing reads from small RNA libraries were computationally processed to remove 5' and 3’ adaptor sequences, and sequences were consolidated to generate read counts per unique small RNA.
Unique small RNAs were aligned to the Phytophthora infestans genome using Bowtie v0.12.8 with settings allowing for perfect matches only (bowtie –f –v 0 –a –S –p 10).
Genome_build: Phytophthora sojae, version 3.0; http://www.ncbi.nlm.nih.gov/assembly/GCA_000149755.2/
Supplementary_files_format_and_content: GFF (version 3) files are provided that contain small RNA mapping data and read abundances (non-normalized) used in our study. GFF formats are specified in the header of each file.

organism: Phytophthora sojae

source_name: mycelium

growth_protocol: Mycelium was grown from Phytophthora sojae P6497 maintained on cleared 10% V8 agar medium (100 mL V8 juice; 1 g CaCO3; 30 mg/L β-sitosterol; 15 g agar; 900 mL deionized water) in a 20°C incubator in the dark. Mycelia were grown in V8 broth (V8 agar medium without agar) on a rotating shaker in flasks and collected after 7 days.

extract_protocol:
Mycelium samples were frozen in liquid nitrogen, ground into a fine powder and homogenized in Trizol (1g:10mL, Life Technologies). After adding 2 mL chloroform per 10 mL Trizol, samples were mixed, incubated at room temperature for 5 minutes and centrifuged at 8400 x g for 10 minutes. Two additional chloroform extractions were done before RNA was precipitated in 0.7 volumes isopropanol for 20 minutes at room temperature and spun for 30 minutes at 8400 x g. Minimally dried pellets were resuspended in 200 μL 0.1X TE, extracted 2 times with phenol:chloroform:isoamyl alcohol (50:49:1), and once with chloroform. Total RNA was precipitated with 5M ammonium acetate and ethanol at -80°C overnight, spun at 12000 x g for 30 minutes at 4°C, resuspended in 100 microliters 0.1X TE and quantitated by Nanodrop (Thermo Scientific).
Small RNA was extracted from total RNA (100 μg) by size fractionation and converted to DNA amplicons by serial adaptor ligation followed by RT-PCR as in (Kasschau et al., PLoS Biology 2007). The 3' adaptor sequence was 5'- CTGTAGGCACCATCAATC-3'. The 5' adaptor sequence was 5'-ATCGTAGGCUGCUGAUA-3'.

value: mycelium

tag: molecule subtype

value: small RNA


title: Phytophthora ramorum mycelium small RNA

description: Small RNA isolated from total RNA extracted from Phytophthora ramorum mycelium

data_processing:
Sequencing reads from small RNA libraries were computationally processed to remove 5' and 3’ adaptor sequences, and sequences were consolidated to generate read counts per unique small RNA.
Unique small RNAs were aligned to the Phytophthora infestans genome using Bowtie v0.12.8 with settings allowing for perfect matches only (bowtie –f –v 0 –a –S –p 10).
Genome_build: Phytophthora ramorum, version 1.1 http://www.ncbi.nlm.nih.gov/assembly/GCA_000149735.1/
Supplementary_files_format_and_content: GFF (version 3) files are provided that contain small RNA mapping data and read abundances (non-normalized) used in our study. GFF formats are specified in the header of each file.

organism: Phytophthora ramorum

growth_protocol: Mycelium was grown from Phytophthora ramorum Pr-102 maintained on cleared 10% V8 agar medium (100 mL V8 juice; 1 g CaCO3; 30 mg/L β-sitosterol; 15 g agar; 900 mL deionized water) in a 20°C incubator in the dark. Mycelia were grown in V8 broth (V8 agar medium without agar) on a rotating shaker in flasks and collected after 7 days.

extract_protocol:
Mycelium samples were frozen in liquid nitrogen, ground into a fine powder and homogenized in Trizol (1g:10mL, Life Technologies). After adding 2 mL chloroform per 10 mL Trizol, samples were mixed, incubated at room temperature for 5 minutes and centrifuged at 8400 x g for 10 minutes. Two additional chloroform extractions were done before RNA was precipitated in 0.7 volumes isopropanol for 20 minutes at room temperature and spun for 30 minutes at 8400 x g. Minimally dried pellets were resuspended in 200 μL 0.1X TE, extracted 2 times with phenol:chloroform:isoamyl alcohol (50:49:1), and once with chloroform. Total RNA was precipitated with 5M ammonium acetate and ethanol at -80°C overnight, spun at 12000 x g for 30 minutes at 4°C, resuspended in 100 microliters 0.1X TE and quantitated by Nanodrop (Thermo Scientific).
Small RNA was extracted from total RNA (100 μg) by size fractionation and converted to DNA amplicons by serial adaptor ligation followed by RT-PCR as in (Kasschau et al., PLoS Biology 2007). The 3' adaptor sequence was 5'- CTGTAGGCACCATCAATC-3'. The 5' adaptor sequence was 5'-ATCGTAGGCCACUGAUA-3'.


title: MCF7_input_1

description:
4763734046_C
Replicate 1 of 3.


title: MDA-MB-231_input_1

description:
4763734046_A
Replicate 1 of 3.


title: MUT_rep4


title: WT_rep4


title: MUT_rep5


title: WT_rep3


title: Liver_pool_acetate_infusion

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.22.0).

source_name: liver, pooled RNA of 6 mice, 6 hrs after infusion with 0.3 M sodium [1-13C]acetate

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Male C57Bl/6J mice (Charles River, L’Arbresle Cedex, France), 2 months of age, were housed in a light- and temperature-controlled facility (lights on 6:30 a.m. to 6:30 p.m., 21 °C). Mice were fed a semi-synthetic diet based on Research Diets’ formulations D12450B, with adaptations regarding type of fat (palm oil instead of lard) and carbohydrates,  for 6 weeks and had free access to drinking water.

extract_protocol: Total RNA was prepared from livers using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For array analysis, RNA of 4-8 mice per group was subsequently pooled at a concentration of 500 ng/mouse.

treatment_protocol: Mice were equipped with a permanent cecum catheter and allowed a recovery period of at least 5 days. Cecal cannulas were flushed daily with phosphate buffered saline. On the day of the experiment, mice were individually housed and fasted from 6:00 to 10:00 a.m. All infusion experiments were performed in conscious, unrestrained mice. Four different groups received either a control phosphate-buffered saline solution, a 0.3 M sodium [1-13C]acetate (99 atom %, Sigma-Aldrich) solution, a 0.3 M sodium [2-13C]propionate (99 atom %, Sigma-Aldrich) solution or a 0.3 M sodium [2,4-13C2]butyrate (99 atom %, Sigma-Aldrich) solution infused via the cecum catheter at an infusion rate of 0.2 ml/h. The resulting rate of infusion of labeled SCFA was 2.4 mmol/h/kg. After 6 h of infusion, animals were killed by cardiac puncture under isoflurane anesthesia. Livers were removed, freeze-clamped, and stored at -80 °C for RNA isolation.

value: 16-17 weeks

value: liver

tag: treatment

value: infused with 0.3 M sodium [1-13C]acetate


title: WT_rep1

value: WT

tag: age

value: 8 week old

value: male


title: MUT_rep3

tag: tissue

value: prefrontal cortex


title: MUT_rep1

tag: gender


title: enf1-1, apex, replicate 2

city: Okazaki

first: Koichi

last: Toyokura

state: Aichi

address: myodaiji-cho

institute: Nationali institute for basic biology

description: Shoot apex of enf1-1

hyb_protocol: The labeled probes were hybridized to an Agilent Arabidopsis 3 Oligo Microarray (Agilent Technologies).

scan_protocol: Agilent Technologies Scanner G2505B US22502551

data_processing: Feature extraction software (GeneSpring; Agilent Technologies) was used to locate and delineate every spot in the array and to integrate the intensity, filtering, and normalization of each spot.

source_name: Shoot apex of enf1-1

label_protocol: Total RNA was used to produce Cy3-labeled cRNA probes.

growth_protocol: 6-day-after-sowing seedlings grown on the 1/2 MS, 1% sucrose, 1% agar plate. Light condition is constant light of around 50 umol photon m-2 s-1.

extract_protocol: Isolated apexes were collected in the tube containing RNAlater (Ambion). And then, RNA was prepared using RNeasy plant mini kit (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Apexes were isolated by cut the cotyledon and hypocotyl from seedling shoot.

value: shoot apex

value: 6 days after sowing


title: enf1-6, apex, replicate 2

description: Shoot apex of enf1-6

source_name: Shoot apex of enf1-6


title: WT_rep2


title: MUT_rep2


title: Col, apex, replicate 1

description: Shoot apex of Col.

source_name: Shoot apex of Col.

value: Col


title: enf1-1, apex, replicate 1

description: Shoot apex of enf1-1


title: enf1-6, apex, replicate 1

description: Shoot apex of enf1-6


title: Liver_pool_butyrate_infusion

source_name: liver, pooled RNA of 4 mice, 6 hrs after infusion with 0.3 M sodium [2,4-13C2]butyrate

value: infused with 0.3 M sodium [2,4-13C2]butyrate


title: Col, apex, replicate 4

description: Shoot apex of Col.


title: Col, apex, replicate 3

description: Shoot apex of Col.


title: Liver_pool_propionate_infusion

source_name: liver, pooled RNA of 6 mice, 6 hrs after infusion with 0.3 M sodium [2-13C]propionate

value: infused with 0.3 M sodium [2-13C]propionate


title: enf1-1, apex, replicate 3

description: Shoot apex of enf1-1


title: enf1-6, apex, replicate 3

description: Shoot apex of enf1-6


title: Liver_pool_control_infusion

source_name: liver, pooled RNA of 6 mice, 6 hrs after infusion with phosphate-buffered saline (control)

value: infused with phosphate-buffered saline (control)


title: Col, apex, replicate 2

description: Shoot apex of Col.


title: Dermal papilla cells-cultured, passage 5-donor D6

status: Public on Oct 20 2013

first: Claire

last: Higgins

address: 1150 St Nicholas Avenue, Russ Berrie 307

department: Department of Dermatology

institute: Columbia University

description:
Gene expression data from dermal papilla cells at p5
DP14

hyb_protocol: Following fragmentation, 15ug cRNA was hybridized onto U133 Plus 2.0 genechips from Affymetrix.  The Affymetrix GeneChip Hybridization Oven 640, and the GeneChip Fluidics Station 450 were used for hybridization and chip processing.

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

data_processing: Data was analyzed using GeneSpring 12.0 software.  Data was RMA normalized, baseline transformed (baseline to median of all samples), and log2 transformed for analysis within GeneSpring.  We used a one way ANOVA, coupled with a Benjamini-Hochberg multiple testing correction to perform paired comparisons between cells at different stages in culture respective to intact papilla.  Other analytical software was also employed.  We used iPAGE (RMA normalized values used here), and GEDI (RMA normalized, baseline and log2 transformed values used) to identify pathways and metagenes with interesting changes in gene expression.

source_name: Cultured dermal papilla cells-passage 5

label_protocol: The Affymetrix two-cycle amplification kit was used to generate biotin labelled cRNA.  Two rounds of amplification were performed, following the manufacturers instructions.

growth_protocol: Intact papillae were isolated from occipital scalp skin from 3 male donors undergoing hair transplantation procedures.  27G needles were used for microdissection. For culture, isolated papillae were adhered in 35mm dishes, at which point they collapsed, and cells migrate out from the papillae forming an explant (passage 0).  Spheroids containing 3000 cells were established from cells cultured at passage 3, using hanging drop culture.

extract_protocol: Cells and tissues were collected in RLT buffer containing BME.  Total RNA was isolated using the mRNA micro Kit from Qiagen.

treatment_protocol: Cells were cultured in dMEM containing 10% FBS.  No antibiotics were used during cell culture.  Cells were passaged using Trypsin-EDTA.  Cells were fed every four days, and when RNA was collected, it was done so 72 hours post feeding cells that were 70% confluent.  For spheroids, RNA was collected 48 hours after hanging drop cultures were started.

tag: donor id

tag: tissue origin

value: Occipital Scalp

tag: tissue/cell type

value: Cultured dermal papilla cells

tag: passage


title: Dermal papilla cells-cultured, passage 5-donor D5

description:
Gene expression data from dermal papilla cells at p5
DP13


title: Dermal papilla cells-cultured, passage 1-donor D5

description:
Gene expression data from dermal papilla cells at p1
DP7

source_name: Cultured dermal papilla cells-passage 1


title: Dermal papilla cells-cultured, passage 3-donor D7

description:
Gene expression data from dermal papilla cells at p3
DP12

source_name: Cultured dermal papilla cells-passage 3


title: Scalp dermal papillae-intact tissue-donor D5

description:
Gene expression data from intact scalp dermal papillae
DP1

source_name: Intact dermal papilla tissue

value: Intact dermal papilla tissue


title: Dermal papilla cells-cultured, passage 3-donor D5

description:
Gene expression data from dermal papilla cells at p3
DP10


title: Dermal papilla cells-cultured, passage 5-donor D7

description:
Gene expression data from dermal papilla cells at p5
DP15


title: Dermal papilla cells-spheroid culture-donor D6

description:
Gene expression data from dermal papilla spheroids
DP17

source_name: Cultured cell dermal papilla spheroids-passage 3

value: Cultured cell dermal papilla spheroids


title: Dermal papilla cells-spheroid culture-donor D7

description:
Gene expression data from dermal papilla spheroids
DP18


title: Dermal papilla cells-cultured, passage 0-donor D5

description:
Gene expression data from dermal papilla cells at p0
DP4

source_name: Cultured dermal papilla cells-passage 0


title: Scalp dermal papillae-intact tissue-donor D7

description:
Gene expression data from intact scalp dermal papillae
DP3


title: Dermal papilla cells-spheroid culture-donor D5

description:
Gene expression data from dermal papilla spheroids
DP16


title: Scalp dermal papillae-intact tissue-donor D6

description:
Gene expression data from intact scalp dermal papillae
DP2


title: Dermal papilla cells-cultured, passage 1-donor D7

description:
Gene expression data from dermal papilla cells at p1
DP9


title: Dermal papilla cells-cultured, passage 0-donor D6

description:
Gene expression data from dermal papilla cells at p0
DP5


title: Dermal papilla cells-cultured, passage 0-donor D7

description:
Gene expression data from dermal papilla cells at p0
DP6


title: Dermal papilla cells-cultured, passage 1-donor D6

description:
Gene expression data from dermal papilla cells at p1
DP8


title: Colony_Q-W_24hvs.REF

city: Lausanne

first: Yannick

last: Wurm

address: Biophore

department: Ecology and Evolution

country: Switzerland

institute: University of Lausanne

description: Colony_Q-W_24hvs.REF Microarray batch: G

hyb_protocol: Hybridization buffer (3x SSC, 0.18% SDS, 200 ng/μl yeast tRNA, 200 ng/µl polyA DNA; final concentration) was added to samples; samples were denatured, applied to microarrays, and hybridized overnight at 64°C. After hybridization, slides were washed sequential.

scan_protocol: Scanner: Agilent Technologies microarray scanner. Image quantification GenePix 5.1

data_processing:
Median signal and background intensities for each cDNA probe were extracted from scanned microarray images using Axon Genepix Pro 6.0. The limma 2.16 package (Smyth 2004) in R 2.8.1 (The R Development Core Team 2007) was used for Normexp background correction, Print-tip Loess normalization within arrays, and Aquantile normalization between arrays (Smyth & Speed 2003). The arrayQualityMetrics package (Kauffmann et al. 2009) and custom R scripts were used for quality control. We determined during this step that a 384-well plate containing four 96-well sub plates, namely ABE ABF, ABG and ABH, was upside down when printing the G series, so the gene positions in the .GPRs for the "G" arrays are incorrect for 384 positions (those that end in "ABE", "ABF", "ABG" or "ABH"). This was corrected by reversing the order of the values on each of the sub-plates prior to analysis in R with the following code ("RG" represents all raw data):

clonesFromABEtoABH = substr(RG$genes$ID, 8,10) %in% c("ABE", "ABF", "ABG", "ABH")
gBatchChips = unlist(strsplit(RG$targets$FileName[RG$targets$Batch=="G"], ".gpr"))
for (gChip in gBatchChips) {
RG$R[clonesFromABEtoABH, gChip] = rev(RG$R[clonesFromABEtoABH, gChip])
RG$G[clonesFromABEtoABH, gChip] = rev(RG$G[clonesFromABEtoABH, gChip])
}
rm(gBatchChips, gChip, clonesFromABEtoABH)

We constructed a design matrix incorporating effects for each of the 21 timepoints for males, 20 timepoints for queens, and 19 timepoints for workers, as well as effects for replicate (confounded with colony of origin) and microarray batch (the large number of hybridizations required splitting the experiment across two microarray batches). The linear model applied to each gene may thus be represented as 'expression = caste_timepoint+replicate+microarray_batch'. The limma package was used for fitting of the model and computation of moderated t-statistics using empirical Bayes shrinkage for five sets of contrasts. A first set of contrasts determined gene expression differences between all pairs of castes at the first and last timepoint (three contrasts at T0, three at Tlast). Three additional sets of contrasts, one for each caste, determined gene expression differences between neighboring timepoints (respectively 20, 19 and 18 contrasts for males, queens and workers). P-values for differential expression were globally adjusted within each of these first four sets of contrasts for 0.1% False Discovery Rate (FDR; Benjamini Hochberg 1995). A final set of contrasts was used to combine information from replicates into single gene expression level estimates for each caste and timepoint relative to reference RNA.

organism: Solenopsis invicta

label_protocol: Total RNA was amplified using the Ambion Message Amp II kit. Amplified RNA plus Alien spike control RNAs (Stratagene) were labeled using the indirect aa-dUTP labeling method. Reverse transcription primers: random 9mers.

growth_protocol: 12 monogyne S. invicta fire ant colonies were collected from a single population around Athens GA, USA. All colonies were returned to the laboratory and reared for two month under standard conditions (Jouvenaz et al., 1977). Four colonies produced many males, four colonies produced many queens, and four colonies produced only workers. There is genetic variability between colonies, however it is moderate because only few queens founded the North American S. invicta population when they were introduced from South America in the 1930s (Ross et al., 1993; Ross and Shoemaker, 2008).

extract_protocol: Samples were ground using 500 mg of 1.4 mm ceramic beads (Quackenbush) and a Fastprep bead shaker. Tissue was then homogenized in Trizol (invitrogen) and RNA extracted using the manufacturer's recommended protocol. Caste could not be visually determined unambiguously for male- and queen-destined brood within the first days of voiding the meconium. In this case DNA was extracted from the organic hase of the Trizol extraction, and sex was determined based on heterozygosity at six microsatellite markers (male ants are haploid, queens are diploid). Subsequently, extracted RNA was pooled to obtain for each replicate, caste and time point a single pool of either 10 workers, 4 queens, or 4 males.

treatment_protocol: Three castes: Worker, queen & male; four colonies used for each caste (12 colonies total). To synchronize development, colony queens were isolated for eight hours in small boxes with ten adult workers. Larvae reaching the L4 stage were visually inspected either every hour (for hour timepoints) or every eight hours (for day timepoints); developing individuals that had voided their meconium were isolated with adult workers until collection. After 0h, 3h, 6h, 12h, 18h, 24h, 36h and 48h (hour timepoints) and once every 24hours until eclosion (day timepoints),  a group of five workers, a single male or a single queen were placed in 2ml screwcap tubes and immediately flash-frozen in liquid nitrogen. Eclosion occured after 15 days for male, 14 days for queen and 12 days for worker larvae. Only media workers, approximately 2mm long were retained.

tag: caste

value: Worker

tag: colony

value: Q

tag: timepoint

value: 24 hours

tag: biomaterial

value: pooled mRNA from 10 developing workers

source_name: REF

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Dermal papilla cells-cultured, passage 3-donor D6

description:
Gene expression data from dermal papilla cells at p3
DP11

value: male


title: Colony_Q-W_10vs.W_11

description: Colony_Q-W_10vs.W_11 Microarray batch: I

value: 10 days

value: 11 days


title: Colony_Q-W_3hvs.REF

description: Colony_Q-W_3hvs.REF Microarray batch: I

value: 3 hours


title: MCF7_AGO2-IP_1

description:
4763734046_D
Replicate 1 of 3.

source_name: MCF7, AGO2-IP

tag: cell type

value: luminal breast cancer cells

tag: chip antibody

value: anti-human Ago2

value: Clone 2E12-1C9

value: Abnova


title: Colony_Q-W_6vs.W_7

description: Colony_Q-W_6vs.W_7 Microarray batch: I

value: 6 days

value: 7 days


title: Colony_Q-W_3vs.W_5

description: Colony_Q-W_3vs.W_5 Microarray batch: G

value: Worker

value: 3 days

value: 5 days


title: Colony_Q-W_10vs.REF

description: Colony_Q-W_10vs.REF Microarray batch: G

value: Q

value: pooled mRNA from 10 developing workers


title: Colony_Q-W_12hvs.W_18h

description: Colony_Q-W_12hvs.W_18h Microarray batch: G

value: 12 hours

value: 18 hours


title: Colony_Q-W_5vs.W_6

description: Colony_Q-W_5vs.W_6 Microarray batch: G


title: Colony_Q-W_0hvs.W_3h

description: Colony_Q-W_0hvs.W_3h Microarray batch: G

value: 0 hours


title: Colony_Q-W_36hvs.W_48h

description: Colony_Q-W_36hvs.W_48h Microarray batch: G

value: 36 hours

value: 48 hours


title: Colony_Q-W_24hvs.W_36h

description: Colony_Q-W_24hvs.W_36h Microarray batch: G

value: 24 hours


title: Colony_Q-W_10vs.W_12

description: Colony_Q-W_10vs.W_12 Microarray batch: G

value: 10 days

value: 12 days


title: Colony_Q-W_8vs.W_9

description: Colony_Q-W_8vs.W_9 Microarray batch: G

value: 8 days

value: 9 days


title: Colony_N-W_0hvs.REF

description: Colony_N-W_0hvs.REF Microarray batch: I

value: N

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_Q-W_48hvs.W_3

description: Colony_Q-W_48hvs.W_3 Microarray batch: G

value: Worker

value: 3 days


title: Colony_Q-W_3hvs.W_6h

description: Colony_Q-W_3hvs.W_6h Microarray batch: G

value: Q

value: 3 hours

value: pooled mRNA from 10 developing workers

value: 6 hours


title: Colony_Q-W_12vs.W_0h

description: Colony_Q-W_12vs.W_0h Microarray batch: G

value: 0 hours


title: Colony_Q-W_9vs.W_10

description: Colony_Q-W_9vs.W_10 Microarray batch: I


title: Colony_Q-W_3vs.REF

description: Colony_Q-W_3vs.REF Microarray batch: G


title: Colony_N-W_5vs.REF

description: Colony_N-W_5vs.REF Microarray batch: I

value: 5 days


title: Colony_Q-W_6hvs.W_12h

description: Colony_Q-W_6hvs.W_12h Microarray batch: G

value: 12 hours


title: Colony_N-W_3vs.REF

description: Colony_N-W_3vs.REF Microarray batch: G


title: Colony_N-W_24hvs.REF

description: Colony_N-W_24hvs.REF Microarray batch: G

value: 24 hours


title: Colony_N-W_6vs.W_7

description: Colony_N-W_6vs.W_7 Microarray batch: G

value: 6 days

value: 7 days


title: Colony_N-W_10vs.REF

description: Colony_N-W_10vs.REF Microarray batch: G

value: 10 days


title: Colony_N-W_7vs.W_8

description: Colony_N-W_7vs.W_8 Microarray batch: G

value: N

value: 8 days


title: Colony_N-W_9vs.W_10

description: Colony_N-W_9vs.W_10 Microarray batch: I

value: 9 days


title: Colony_N-W_24hvs.W_36h

description: Colony_N-W_24hvs.W_36h Microarray batch: G

value: 36 hours


title: Colony_N-W_13vs.W_0h

description: Colony_N-W_13vs.W_0h Microarray batch: G

value: Worker

value: 13 days


title: Colony_N-W_3hvs.W_6h

description: Colony_N-W_3hvs.W_6h Microarray batch: G


title: Colony_N-W_48hvs.W_3

description: Colony_N-W_48hvs.W_3 Microarray batch: G

value: 48 hours

value: 3 days


title: Colony_N-W_6hvs.W_12h

description: Colony_N-W_6hvs.W_12h Microarray batch: G

value: pooled mRNA from 10 developing workers


title: Colony_N-W_3vs.W_4

description: Colony_N-W_3vs.W_4 Microarray batch: G

value: 4 days


title: Colony_N-W_18hvs.W_24h

description: Colony_N-W_18hvs.W_24h Microarray batch: G

value: 18 hours


title: Colony_N-W_12hvs.W_18h

description: Colony_N-W_12hvs.W_18h Microarray batch: G


title: Colony_N-W_5vs.W_6

description: Colony_N-W_5vs.W_6 Microarray batch: G

value: 5 days


title: Colony_N-W_10vs.W_11

description: Colony_N-W_10vs.W_11 Microarray batch: G

value: 11 days


title: Colony_N-W_11vs.W_12

description: Colony_N-W_11vs.W_12 Microarray batch: G

value: 12 days


title: Colony_N-W_0hvs.W_3h

description: Colony_N-W_0hvs.W_3h Microarray batch: G

value: 0 hours

value: 3 hours


title: Colony_N-W_4vs.W_5

description: Colony_N-W_4vs.W_5 Microarray batch: G


title: Colony_N-W_36hvs.W_48h

description: Colony_N-W_36hvs.W_48h Microarray batch: G


title: Colony_N-W_12vs.W_13

description: Colony_N-W_12vs.W_13 Microarray batch: G


title: PCN_conrtol shRNA_rep2

city: Nagoya

first: Shinsuke

last: Ishigaki

address: 65 Tsurumai-cho, Showa-ku

department: Department of Neurology

institute: Nagoya University School of Medicine

hyb_protocol: Samples were hybridized with GeneChip mouse exon 1.0 ST Arrays (Affymetrix) and scanned accoding to the manufacture's protocol.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip 3000 7G

data_processing:
The data were background corrected and normalized using the robust multiarray average (RMA) procedure implemented in the Affymetrix Expression Console software [probe group file: MoEx-1_0-st-v1.r2.pgf; meta-probeset file: MoEx-1_0-st-v1.r2.dtl.mm9.full.ps]
affymetrix-algorithm-name = rma-exon-full : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.28061

source_name: primary cortical neurons, control shRNA

label_protocol: 100ng of total RNA were used to generate labeled cDNA. Biotinylated DNA probes were prepared using Affymetrix WT Expression kit for Affymetrix Whole Transcript Sense Expression arrays and Affymetrix geneChip WT Terminal Labeling kit according to the manufacture's protocol.

growth_protocol: Mouse fetal brain was taken from C57BL/6 mouse embryos at E15. After removing meninges cortical tissue was dissociated into a single-cell suspension by Sumilon dissociation solution (Sumitomo Bakelite, Tokyo Japan). Cells were plated at a density of 1.5 x 106 cells in a 60 mm-well culture plate with the medium containing 0.5x Sumilon nerve-culture medium (Sumitomo Bakelite), 0.5x Neurobasal medium, 1% FBS, 0.5x B27 supplements (Invitrogen), 0.5x Glutamax, 5 µg/ml of BDNF, 5 µg/ml of CNTF, and 0.5% Pen-Strep. A day after plating (day 2), neurons were supplemented with 10 ng/µl of AraC and incubated overnight.

extract_protocol: Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) followed by DnaseI (Qiagen) treatment.

treatment_protocol: On day 5, neurons were infected with 2 x 1010 copies/well (1.5 x 107 copies/µl) of lentivirus expressing shRNA against mouse Tdp-43 (shTdp-43-1 or shTdp-43-2) or control (shCont). After 4 hr of infection, the virus media was removed. Neurons were then cultured for 6 additional days, and were harvested on day 11 followed by RNA extraction and cDNA synthesis.

tag: strain

tag: developmental stage

value: embryo

value: primary cortical neurons

tag: genotype/variation

value: control


title: PCN_conrtol shRNA_rep3


title: Colony_P-W_24hvs.REF

description: Colony_P-W_24hvs.REF Microarray batch: I

value: P

value: 24 hours

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_N-W_8vs.W_9

description: Colony_N-W_8vs.W_9 Microarray batch: G

value: Worker

value: N

value: 8 days

value: 9 days


title: PCN_shRNA Cugbp1_rep2

source_name: primary cortical neurons, shRNA Cugbp1

value: Cugbp1 knockdown


title: Colony_P-W_10vs.W_11

description: Colony_P-W_10vs.W_11 Microarray batch: G

value: 10 days

value: pooled mRNA from 10 developing workers

value: 11 days


title: Colony_P-W_11vs.W_12

description: Colony_P-W_11vs.W_12 Microarray batch: G

value: 12 days


title: Colony_P-W_5vs.REF

description: Colony_P-W_5vs.REF Microarray batch: G

value: 5 days


title: Colony_P-W_0hvs.REF

description: Colony_P-W_0hvs.REF Microarray batch: I

value: 0 hours


title: Colony_P-W_4vs.W_5

description: Colony_P-W_4vs.W_5 Microarray batch: G

value: 4 days


title: Colony_P-W_12hvs.W_18h

description: Colony_P-W_12hvs.W_18h Microarray batch: I

value: P

value: 12 hours

value: 18 hours


title: Colony_P-W_12vs.W_13

description: Colony_P-W_12vs.W_13 Microarray batch: I

value: 13 days


title: Colony_P-W_7vs.W_8

description: Colony_P-W_7vs.W_8 Microarray batch: G

value: 7 days


title: Colony_P-W_9vs.W_10

description: Colony_P-W_9vs.W_10 Microarray batch: G

value: Worker


title: Colony_P-W_6vs.W_7

description: Colony_P-W_6vs.W_7 Microarray batch: G

value: 6 days


title: Colony_P-W_8vs.W_9

description: Colony_P-W_8vs.W_9 Microarray batch: I

value: 8 days


title: Colony_P-W_6hvs.W_12h

description: Colony_P-W_6hvs.W_12h Microarray batch: I

value: 6 hours


title: PCN_shRNA Cugbp1_rep3

value: embryo

value: primary cortical neurons

value: Cugbp1 knockdown


title: Colony_P-W_3vs.W_4

description: Colony_P-W_3vs.W_4 Microarray batch: G

value: 3 days

value: pooled mRNA from 10 developing workers


title: Colony_P-W_13vs.W_0h

description: Colony_P-W_13vs.W_0h Microarray batch: G


title: Colony_P-W_48hvs.W_3

description: Colony_P-W_48hvs.W_3 Microarray batch: G

value: 48 hours


title: Colony_P-W_36hvs.W_48h

description: Colony_P-W_36hvs.W_48h Microarray batch: G

value: 36 hours


title: Colony_S-W_9vs.REF

description: Colony_S-W_9vs.REF Microarray batch: G

value: S

value: 9 days

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_P-W_5vs.W_6

description: Colony_P-W_5vs.W_6 Microarray batch: G

value: P

value: 5 days


title: Colony_P-W_24hvs.W_36h

description: Colony_P-W_24hvs.W_36h Microarray batch: G

value: Worker

value: 24 hours


title: Colony_P-W_3hvs.W_6h

description: Colony_P-W_3hvs.W_6h Microarray batch: G

value: 3 hours

value: 6 hours


title: Colony_P-W_6hvs.W_18h

description: Colony_P-W_6hvs.W_18h Microarray batch: I

value: 18 hours


title: Colony_P-W_18hvs.W_24h

description: Colony_P-W_18hvs.W_24h Microarray batch: G


title: Colony_Q-W_18hvs.W_24h

description: Colony_Q-W_18hvs.W_24h Microarray batch: G

value: Q


title: Colony_S-W_5vs.REF

description: Colony_S-W_5vs.REF Microarray batch: G


title: Colony_S-W_9vs.W_11

description: Colony_S-W_9vs.W_11 Microarray batch: I

value: 11 days


title: Colony_S-W_24hvs.REF

description: Colony_S-W_24hvs.REF Microarray batch: I

value: pooled mRNA from 10 developing workers


title: Colony_P-W_0hvs.W_3h

description: Colony_P-W_0hvs.W_3h Microarray batch: G

value: 0 hours


title: Colony_S-W_8vs.W_9

description: Colony_S-W_8vs.W_9 Microarray batch: G

value: 8 days


title: Colony_S-W_0hvs.REF

description: Colony_S-W_0hvs.REF Microarray batch: G

value: S


title: Colony_S-W_11vs.W_0h

description: Colony_S-W_11vs.W_0h Microarray batch: I


title: Colony_S-W_3vs.W_5

description: Colony_S-W_3vs.W_5 Microarray batch: I

value: 3 days


title: Colony_S-W_36hvs.W_48h

description: Colony_S-W_36hvs.W_48h Microarray batch: G

value: 36 hours

value: 48 hours


title: Colony_S-W_6vs.W_8

description: Colony_S-W_6vs.W_8 Microarray batch: G

value: 6 days


title: Colony_S-W_12hvs.W_18h

description: Colony_S-W_12hvs.W_18h Microarray batch: G

value: 12 hours


title: Colony_S-W_3hvs.W_6h

description: Colony_S-W_3hvs.W_6h Microarray batch: G


title: Colony_S-W_48hvs.W_3

description: Colony_S-W_48hvs.W_3 Microarray batch: G


title: Colony_H-Q_5vs.REF

description: Colony_H-Q_5vs.REF Microarray batch: I

value: Queen

value: H

value: 5 days

value: pooled mRNA from 4 developing queens

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_S-W_0hvs.W_3h

description: Colony_S-W_0hvs.W_3h Microarray batch: G

value: Worker

value: 3 hours


title: Colony_S-W_6hvs.W_12h

description: Colony_S-W_6hvs.W_12h Microarray batch: I

value: 6 hours

value: pooled mRNA from 10 developing workers


title: Colony_H-Q_0hvs.REF

description: Colony_H-Q_0hvs.REF Microarray batch: G

value: 0 hours


title: Colony_H-Q_11vs.Q_12

description: Colony_H-Q_11vs.Q_12 Microarray batch: I

value: 11 days

value: 12 days


title: Colony_H-Q_13vs.Q_14

description: Colony_H-Q_13vs.Q_14 Microarray batch: G

value: 13 days

value: 14 days


title: Colony_S-W_24hvs.W_36h

description: Colony_S-W_24hvs.W_36h Microarray batch: G

value: S

value: 24 hours

value: 36 hours


title: Colony_H-Q_12vs.Q_13

description: Colony_H-Q_12vs.Q_13 Microarray batch: G

value: Queen

value: H


title: Colony_S-W_5vs.W_6

description: Colony_S-W_5vs.W_6 Microarray batch: G

value: 5 days

value: 6 days


title: Colony_H-Q_8vs.Q_9

description: Colony_H-Q_8vs.Q_9 Microarray batch: G

value: 8 days

value: pooled mRNA from 4 developing queens

value: 9 days


title: Colony_S-W_18hvs.W_24h

description: Colony_S-W_18hvs.W_24h Microarray batch: G

value: Worker

value: 18 hours


title: Colony_H-Q_6vs.Q_7

description: Colony_H-Q_6vs.Q_7 Microarray batch: G

value: 7 days


title: Colony_H-Q_14vs.Q_0h

description: Colony_H-Q_14vs.Q_0h Microarray batch: I

value: 0 hours


title: GFI1_wildtype, rep3

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description:
SAM9259613
Mouse wildtype ILC2 cells.

hyb_protocol: cRNA was hybridized on Agilent-026655 Whole Mouse Genome Microarray 4x44K.

scan_protocol: Chips were scanned using the Agilent Surescan Microarray Scanner.

data_processing: The data were processed with Agilent Feature Extraction software, version 10.7.3.1, using default settings, including linear and Lowess normalization.

source_name: ILC2 cells, wildtype

label_protocol: Biotinylated cRNA were prepared according to the standard Agilent protocol.

growth_protocol: Cells were isolated from either wild-type or GFi1 KO mice. Purified ILC2s were cultured for 6 days in RPMI 1640, 10% FBS, Gln, P/S, 2ME, IL-2 (50ng/ml), IL-7 (10ng/ml), and IL-25 (50ng/ml).

extract_protocol: RNeasy Mini Kit (Qiagen).

tag: genotype

value: wildtype

extract_protocol: Stratagene Universal Mouse Reference RNA (catalog number 740100).

tag: sample type

value: reference


title: Colony_H-Q_24hvs.REF

description: Colony_H-Q_24hvs.REF Microarray batch: G

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_H-Q_7vs.Q_8

description: Colony_H-Q_7vs.Q_8 Microarray batch: G


title: Colony_H-Q_3vs.Q_4

description: Colony_H-Q_3vs.Q_4 Microarray batch: G

value: 3 days

value: 4 days


title: Colony_H-Q_10vs.Q_11

description: Colony_H-Q_10vs.Q_11 Microarray batch: G

value: Queen

value: H

value: 10 days

value: 11 days


title: GFI1_wildtype, rep4

description:
SAM9259614
Mouse wildtype ILC2 cells.

source_name: Stratagene Universal Mouse Reference RNA


title: Colony_H-Q_10vs.REF

description: Colony_H-Q_10vs.REF Microarray batch: I

value: pooled mRNA from 4 developing queens


title: GFI1_knockout, rep3

description:
SAM9259615
Mouse GFi1 knockout ILC2 cells.

source_name: ILC2 cells, Gfi1 KO

value: Gfi1 knockout


title: GFI1_knockout, rep2

description:
SAM9259612
Mouse GFi1 knockout ILC2 cells.


title: Colony_H-Q_4vs.Q_5

description: Colony_H-Q_4vs.Q_5 Microarray batch: I

value: 5 days


title: Colony_H-Q_9vs.Q_10

description: Colony_H-Q_9vs.Q_10 Microarray batch: G

value: 9 days


title: Colony_H-Q_5vs.Q_6

description: Colony_H-Q_5vs.Q_6 Microarray batch: G

value: 6 days


title: Colony_H-Q_3hvs.Q_6h

description: Colony_H-Q_3hvs.Q_6h Microarray batch: G

value: 3 hours

value: 6 hours


title: Colony_H-Q_36hvs.Q_48h

description: Colony_H-Q_36hvs.Q_48h Microarray batch: I

value: 36 hours

value: 48 hours


title: Colony_H-Q_12hvs.Q_18h

description: Colony_H-Q_12hvs.Q_18h Microarray batch: G

value: 12 hours

value: 18 hours


title: Colony_L-Q_13vs.REF

description: Colony_L-Q_13vs.REF Microarray batch: I

value: L

value: 13 days

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: GFI1_knockout, rep1

description:
SAM9259611
Mouse GFi1 knockout ILC2 cells.

value: reference


title: GFI1_wildtype, rep1

description:
SAM9259609
Mouse wildtype ILC2 cells.

value: wildtype


title: Colony_L-Q_11vs.Q_12

description: Colony_L-Q_11vs.Q_12 Microarray batch: G

value: Queen

value: 11 days

value: pooled mRNA from 4 developing queens

value: 12 days


title: Colony_P-W_10vs.REF

description: Colony_P-W_10vs.REF Microarray batch: G

value: Worker

value: P

value: 10 days

value: pooled mRNA from 10 developing workers


title: GFI1_wildtype, rep2

description:
SAM9259610
Mouse wildtype ILC2 cells.


title: Colony_L-Q_10vs.REF

description: Colony_L-Q_10vs.REF Microarray batch: G


title: Colony_L-Q_13vs.Q_14

description: Colony_L-Q_13vs.Q_14 Microarray batch: G

value: 14 days


title: Colony_H-Q_0hvs.Q_3h

description: Colony_H-Q_0hvs.Q_3h Microarray batch: G

value: H

value: 0 hours

value: 3 hours


title: Colony_L-Q_3vs.Q_4

description: Colony_L-Q_3vs.Q_4 Microarray batch: G

value: L

value: 3 days

value: 4 days


title: Colony_L-Q_5vs.REF

description: Colony_L-Q_5vs.REF Microarray batch: I

value: 5 days

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_H-Q_18hvs.Q_24h

description: Colony_H-Q_18hvs.Q_24h Microarray batch: G

value: Queen

value: 18 hours

value: pooled mRNA from 4 developing queens

value: 24 hours


title: Colony_H-Q_24hvs.Q_36h

description: Colony_H-Q_24hvs.Q_36h Microarray batch: G

value: 36 hours


title: Colony_L-Q_9vs.Q_10

description: Colony_L-Q_9vs.Q_10 Microarray batch: G

value: 9 days

value: 10 days


title: Colony_H-Q_6hvs.Q_12h

description: Colony_H-Q_6hvs.Q_12h Microarray batch: G

value: H

value: 6 hours

value: 12 hours


title: Colony_L-Q_4vs.Q_5

description: Colony_L-Q_4vs.Q_5 Microarray batch: G

value: L


title: Colony_L-Q_10vs.Q_11

description: Colony_L-Q_10vs.Q_11 Microarray batch: G

value: 11 days


title: Colony_L-Q_5vs.Q_6

description: Colony_L-Q_5vs.Q_6 Microarray batch: G

value: 6 days


title: Colony_L-Q_12vs.Q_13

description: Colony_L-Q_12vs.Q_13 Microarray batch: G

value: 12 days

value: 13 days


title: Colony_L-Q_7vs.Q_8

description: Colony_L-Q_7vs.Q_8 Microarray batch: G

value: 7 days

value: 8 days


title: Colony_B-Q_10vs.REF

description: Colony_B-Q_10vs.REF Microarray batch: G

value: Queen

value: B

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_B-Q_24hvs.REF

description: Colony_B-Q_24hvs.REF Microarray batch: G

value: 24 hours

value: pooled mRNA from 4 developing queens


title: Colony_L-Q_8vs.Q_9

description: Colony_L-Q_8vs.Q_9 Microarray batch: G

value: 9 days


title: Colony_L-Q_14vs.Q_3

description: Colony_L-Q_14vs.Q_3 Microarray batch: G

value: 14 days

value: 3 days


title: Colony_B-Q_0hvs.REF

description: Colony_B-Q_0hvs.REF Microarray batch: G

value: 0 hours


title: Colony_B-Q_5vs.REF

description: Colony_B-Q_5vs.REF Microarray batch: G

value: 5 days


title: Colony_B-Q_3hvs.Q_6h

description: Colony_B-Q_3hvs.Q_6h Microarray batch: G

value: 3 hours

value: 6 hours


title: Colony_B-Q_6hvs.Q_12h

description: Colony_B-Q_6hvs.Q_12h Microarray batch: G

value: 12 hours


title: Colony_B-Q_6vs.Q_7

description: Colony_B-Q_6vs.Q_7 Microarray batch: G

value: 6 days

value: 7 days


title: Colony_B-Q_11vs.Q_12

description: Colony_B-Q_11vs.Q_12 Microarray batch: G

value: Queen

value: 11 days

value: 12 days


title: Colony_B-Q_7vs.Q_8

description: Colony_B-Q_7vs.Q_8 Microarray batch: G

value: B

value: 8 days


title: Colony_B-Q_24hvs.Q_36h

description: Colony_B-Q_24hvs.Q_36h Microarray batch: G

value: 24 hours

value: 36 hours


title: Colony_B-Q_4vs.Q_5

description: Colony_B-Q_4vs.Q_5 Microarray batch: G

value: 4 days

value: pooled mRNA from 4 developing queens


title: Colony_B-Q_14vs.Q_15

description: Colony_B-Q_14vs.Q_15 Microarray batch: G

value: 14 days

value: 15 days


title: Colony_B-Q_13vs.Q_14

description: Colony_B-Q_13vs.Q_14 Microarray batch: G

value: 13 days


title: Colony_B-Q_0hvs.Q_3h

description: Colony_B-Q_0hvs.Q_3h Microarray batch: G

value: 0 hours

value: 3 hours


title: Colony_B-Q_5vs.Q_6

description: Colony_B-Q_5vs.Q_6 Microarray batch: G

value: 5 days


title: Colony_B-Q_48hvs.Q_3

description: Colony_B-Q_48hvs.Q_3 Microarray batch: G

value: 48 hours

value: 3 days


title: Colony_B-Q_3vs.Q_4

description: Colony_B-Q_3vs.Q_4 Microarray batch: G

value: Queen


title: Colony_E-Q_24hvs.REF

description: Colony_E-Q_24hvs.REF Microarray batch: I

value: E

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_B-Q_12vs.Q_13

description: Colony_B-Q_12vs.Q_13 Microarray batch: G

value: B

value: 12 days


title: Colony_B-Q_10vs.Q_11

description: Colony_B-Q_10vs.Q_11 Microarray batch: G

value: 10 days

value: 11 days


title: Colony_B-Q_36hvs.Q_48h

description: Colony_B-Q_36hvs.Q_48h Microarray batch: G

value: 36 hours

value: pooled mRNA from 4 developing queens


title: Colony_B-Q_18hvs.Q_24h

description: Colony_B-Q_18hvs.Q_24h Microarray batch: G

value: 18 hours

value: 24 hours


title: Colony_B-Q_8vs.Q_9

description: Colony_B-Q_8vs.Q_9 Microarray batch: G

value: 8 days

value: 9 days


title: Colony_E-Q_5vs.REF

description: Colony_E-Q_5vs.REF Microarray batch: G

value: 5 days


title: Colony_B-Q_15vs.Q_0h

description: Colony_B-Q_15vs.Q_0h Microarray batch: G

value: 15 days

value: 0 hours


title: Colony_B-Q_9vs.Q_10

description: Colony_B-Q_9vs.Q_10 Microarray batch: G

value: Queen


title: Colony_E-Q_4vs.Q_5

description: Colony_E-Q_4vs.Q_5 Microarray batch: I

value: E

value: 4 days


title: Colony_E-Q_48hvs.Q_3

description: Colony_E-Q_48hvs.Q_3 Microarray batch: G

value: 48 hours

value: 3 days


title: Colony_E-Q_24hvs.Q_36h

description: Colony_E-Q_24hvs.Q_36h Microarray batch: G


title: Colony_E-Q_36hvs.Q_48h

description: Colony_E-Q_36hvs.Q_48h Microarray batch: G


title: Colony_E-Q_0hvs.REF

description: Colony_E-Q_0hvs.REF Microarray batch: I

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_E-Q_9vs.Q_10

description: Colony_E-Q_9vs.Q_10 Microarray batch: G

value: 10 days


title: Colony_E-Q_10vs.Q_11

description: Colony_E-Q_10vs.Q_11 Microarray batch: G

value: pooled mRNA from 4 developing queens

value: 11 days


title: Colony_E-Q_12hvs.Q_18h

description: Colony_E-Q_12hvs.Q_18h Microarray batch: G

value: 12 hours

value: 18 hours


title: Colony_E-Q_12vs.Q_13

description: Colony_E-Q_12vs.Q_13 Microarray batch: G

value: 12 days

value: 13 days


title: Colony_E-Q_18hvs.Q_24h

description: Colony_E-Q_18hvs.Q_24h Microarray batch: G

value: 24 hours


title: Colony_E-Q_11vs.Q_12

description: Colony_E-Q_11vs.Q_12 Microarray batch: G


title: Colony_E-Q_8vs.Q_9

description: Colony_E-Q_8vs.Q_9 Microarray batch: G

value: 8 days

value: 9 days


title: Colony_G-M_24hvs.REF

description: Colony_G-M_24hvs.REF Microarray batch: I

value: Male

value: G

value: pooled mRNA from 4 developing males


title: Colony_E-Q_14vs.Q_0h

description: Colony_E-Q_14vs.Q_0h Microarray batch: G

value: Queen

value: E

value: 14 days

value: 0 hours


title: Colony_E-Q_0hvs.Q_3h

description: Colony_E-Q_0hvs.Q_3h Microarray batch: G

value: 3 hours


title: Colony_G-M_0hvs.REF

description: Colony_G-M_0hvs.REF Microarray batch: G

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_E-Q_6vs.Q_7

description: Colony_E-Q_6vs.Q_7 Microarray batch: G

value: 6 days

value: pooled mRNA from 4 developing queens

value: 7 days


title: Colony_E-Q_5vs.Q_6

description: Colony_E-Q_5vs.Q_6 Microarray batch: G

value: 5 days


title: Colony_E-Q_3hvs.Q_6h

description: Colony_E-Q_3hvs.Q_6h Microarray batch: G

value: 6 hours


title: Colony_E-Q_6hvs.Q_12h

description: Colony_E-Q_6hvs.Q_12h Microarray batch: G

value: 12 hours


title: Colony_E-Q_7vs.Q_8

description: Colony_E-Q_7vs.Q_8 Microarray batch: G

value: 8 days


title: Colony_E-Q_13vs.Q_14

description: Colony_E-Q_13vs.Q_14 Microarray batch: G

value: 13 days


title: Colony_G-M_15vs.M_0h

description: Colony_G-M_15vs.M_0h Microarray batch: I

value: Male

value: G

value: 15 days

value: pooled mRNA from 4 developing males


title: Colony_G-M_13vs.M_14

description: Colony_G-M_13vs.M_14 Microarray batch: G

value: 14 days


title: Colony_G-M_14vs.M_15

description: Colony_G-M_14vs.M_15 Microarray batch: G


title: Colony_G-M_5vs.REF

description: Colony_G-M_5vs.REF Microarray batch: G


title: Colony_G-M_12vs.M_13

description: Colony_G-M_12vs.M_13 Microarray batch: G

value: 12 days


title: Colony_G-M_9vs.M_10

description: Colony_G-M_9vs.M_10 Microarray batch: G

value: 9 days

value: 10 days


title: Colony_G-M_11vs.M_12

description: Colony_G-M_11vs.M_12 Microarray batch: G

value: 11 days


title: Colony_H-Q_48hvs.Q_3

description: Colony_H-Q_48hvs.Q_3 Microarray batch: G

value: Queen

value: H

value: 48 hours

value: 3 days


title: Colony_G-M_8vs.M_9

description: Colony_G-M_8vs.M_9 Microarray batch: G


title: Colony_G-M_10vs.REF

description: Colony_G-M_10vs.REF Microarray batch: I

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_G-M_7vs.M_8

description: Colony_G-M_7vs.M_8 Microarray batch: G

value: 7 days

value: 8 days


title: Colony_G-M_6vs.M_7

description: Colony_G-M_6vs.M_7 Microarray batch: G

value: Male

value: G

value: 6 days


title: Colony_G-M_10vs.M_11

description: Colony_G-M_10vs.M_11 Microarray batch: G

value: pooled mRNA from 4 developing males


title: Colony_G-M_5vs.M_6

description: Colony_G-M_5vs.M_6 Microarray batch: I

value: 5 days


title: Colony_G-M_12hvs.M_18h

description: Colony_G-M_12hvs.M_18h Microarray batch: G

value: 12 hours

value: 18 hours


title: Colony_G-M_3vs.M_4

description: Colony_G-M_3vs.M_4 Microarray batch: G

value: 4 days


title: Colony_G-M_4vs.M_5

description: Colony_G-M_4vs.M_5 Microarray batch: G


title: Colony_G-M_3hvs.M_6h

description: Colony_G-M_3hvs.M_6h Microarray batch: G

value: 3 hours

value: 6 hours


title: Colony_G-M_48hvs.M_3

description: Colony_G-M_48hvs.M_3 Microarray batch: G

value: 48 hours


title: Colony_K-M_0hvs.REF

description: Colony_K-M_0hvs.REF Microarray batch: I

value: K

value: 0 hours


title: Colony_G-M_6hvs.M_12h

description: Colony_G-M_6hvs.M_12h Microarray batch: G


title: Colony_K-M_24hvs.REF

description: Colony_K-M_24hvs.REF Microarray batch: G

value: 24 hours

value: Mixed

value: not available


title: Colony_G-M_24hvs.M_36h

description: Colony_G-M_24hvs.M_36h Microarray batch: G

value: 36 hours


title: Colony_G-M_36hvs.M_48h

description: Colony_G-M_36hvs.M_48h Microarray batch: G

value: Male


title: Colony_G-M_18hvs.M_24h

description: Colony_G-M_18hvs.M_24h Microarray batch: G

value: G


title: Colony_K-M_13vs.M_14

description: Colony_K-M_13vs.M_14 Microarray batch: G

value: 13 days

value: 14 days


title: Colony_K-M_4vs.M_5

description: Colony_K-M_4vs.M_5 Microarray batch: I

value: pooled mRNA from 4 developing males

value: 5 days


title: Colony_G-M_0hvs.M_3h

description: Colony_G-M_0hvs.M_3h Microarray batch: G


title: Colony_K-M_10vs.M_11

description: Colony_K-M_10vs.M_11 Microarray batch: G

value: 10 days

value: 11 days


title: Colony_K-M_36hvs.M_48h

description: Colony_K-M_36hvs.M_48h Microarray batch: G


title: Colony_K-M_12vs.M_13

description: Colony_K-M_12vs.M_13 Microarray batch: G

value: 12 days


title: Colony_K-M_3vs.M_4

description: Colony_K-M_3vs.M_4 Microarray batch: G

value: 3 days

value: 4 days


title: Colony_K-M_5vs.M_6

description: Colony_K-M_5vs.M_6 Microarray batch: G

value: K

value: 6 days


title: Colony_K-M_11vs.M_12

description: Colony_K-M_11vs.M_12 Microarray batch: I


title: Colony_K-M_9vs.M_10

description: Colony_K-M_9vs.M_10 Microarray batch: G

value: 9 days


title: Colony_K-M_7vs.M_8

description: Colony_K-M_7vs.M_8 Microarray batch: G

value: 7 days

value: 8 days


title: Colony_K-M_10vs.REF

description: Colony_K-M_10vs.REF Microarray batch: G

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_K-M_5vs.REF

description: Colony_K-M_5vs.REF Microarray batch: G

value: Male


title: Colony_K-M_18hvs.M_24h

description: Colony_K-M_18hvs.M_24h Microarray batch: G

value: 18 hours

value: 24 hours


title: Colony_K-M_48hvs.M_3

description: Colony_K-M_48hvs.M_3 Microarray batch: G

value: 48 hours

value: pooled mRNA from 4 developing males


title: Colony_E-Q_10vs.REF

description: Colony_E-Q_10vs.REF Microarray batch: G

value: Queen

value: E

value: 10 days

value: pooled mRNA from 4 developing queens


title: Colony_K-M_0hvs.M_3h

description: Colony_K-M_0hvs.M_3h Microarray batch: G

value: K

value: 0 hours

value: 3 hours


title: Colony_K-M_24hvs.M_36h

description: Colony_K-M_24hvs.M_36h Microarray batch: G

value: 36 hours


title: Colony_A-M_0hvs.REF

description: Colony_A-M_0hvs.REF Microarray batch: G

value: A


title: Colony_K-M_6vs.M_7

description: Colony_K-M_6vs.M_7 Microarray batch: G

value: 6 days

value: 7 days


title: Colony_K-M_8vs.M_9

description: Colony_K-M_8vs.M_9 Microarray batch: G

value: 8 days

value: 9 days


title: Colony_A-M_24hvs.REF

description: Colony_A-M_24hvs.REF Microarray batch: G

value: Male

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_K-M_14vs.M_15

description: Colony_K-M_14vs.M_15 Microarray batch: G

value: 14 days

value: pooled mRNA from 4 developing males

value: 15 days


title: Colony_K-M_15vs.M_0h

description: Colony_K-M_15vs.M_0h Microarray batch: G


title: Colony_A-M_5vs.REF

description: Colony_A-M_5vs.REF Microarray batch: G

value: 5 days


title: Colony_K-M_3hvs.M_18h

description: Colony_K-M_3hvs.M_18h Microarray batch: G

value: K

value: 18 hours


title: Preterm proband blood spot at 18 years age 32

type: genomic

city: NEDLANDS

first: David

last: Martino

state: Western Australia

address: Perth Childrens Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute

hyb_protocol: Contained within the Illumina Infinium HumanMethylation450 BeadChips protocol

scan_protocol: HiScan - iScan Control Software

data_processing: Probes were excluded that failed in one or more samples based on a detection p-value of >0.01; One term birth sample with mean detection p-value >0.05 was excluded from analysis (Sample name: 48); The data were pre-processed using the Illumina method (bg.correct = FALSE, normalize = controls) and subset-quantile within-array normalization (SWAN) was performed. Probes targeting CpG dinucleotides containing a known SNP and HM450 control probes were excluded from analyses

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PTB_6-18 years blood spot

growth_protocol: Dried blood spots were stored at room temperature

extract_protocol: Six to ten 3 mm punches of dried blood spots obtained were placed in a 1.5 ml tube with 100 μl water and a Tungsten Carbide Bead (3mm; cat#69997, [QIAGEN, Victoria, Australia]). Samples were macerated with a TissueLyser II (time: 5x30 secs, frequency: 30 Hz, Qiagen). Beads were removed and samples were further processed using the QIAamp DNA Mini Kit according to manufacturer’s instructions, with the following modifications. The macerated sample was incubated with 190 μl extraction buffer (ATL) for 10 minutes at 85oC for 10 minutes. Supernatant was collected and the ATL extraction of the homogenate was repeated twice. The resulting extract was pooled and further processed by Proteinase K digestion (60 μl, 10 mg/ml at 56oC for 1 hour), incubated with 600 μl buffer AL for 10 minutes at 70oC and 600 μl 100% ethanol was added. After mixing by inversion, samples were loaded onto a single QIAamp column by repeat centrifugation. Following washes, DNA was collected by incubating with 100 μl buffer AE for 10 minutes twice and once with 50 μl buffer AE for 10 minutes. The combined eluates were placed in a Speedvac at 45oC for 8 hours. The dry pellet was resuspended in 40 μl TE and quantified by spectrophotometry (Nanodrop, Wilmington, DE, USA). DNA samples (1 μg) were bisulphite converted using the MethylEasy Xceed bisulphite conversion kit (Human Genetic Signatures, North Ryde, Australia), according to the manufacturer’s instructions.

tag: pre-delivery

value: No labour

tag: onset of delivery

value: Iatrogenic

tag: type of delivery

value: Cesarean section


title: Colony_A-M_10vs.REF

description: Colony_A-M_10vs.REF Microarray batch: G

value: A

value: 10 days


title: Genomic DNA from Preterm infant blood spot 44

source_name: PTB_12-Birth Blood Spot

label_protocol: Contained within the Illumina Infinium HumanMethylation450 BeadChips protocol

value: Labour

value: Spontaneous

value: Vaginal

tag: gender


title: Preterm proband blood spot at 18 years age 37

source_name: PTB_10-18 years blood spot

value: Male


title: Colony_A-M_18hvs.M_24h

description: Colony_A-M_18hvs.M_24h Microarray batch: I

value: 24 hours


title: Term proband blood spot at 18 years age 39

description: Term proband blood spot at 18 years age

source_name: Term_11-18 years blood spot


title: Preterm infant blood spot 38

description: Preterm infant blood spot

source_name: PTB_11-Birth Blood Spot

value: Female


title: Colony_A-M_15vs.M_0h

description: Colony_A-M_15vs.M_0h Microarray batch: G

value: 0 hours


title: Term infant blood spot 31

description: Term infant blood spot

source_name: Term_7-Birth Blood Spot


title: Preterm infant blood spot 33

description: Preterm infant blood spot

source_name: PTB_8-Birth Blood Spot


title: Preterm proband blood spot at 18 years age 41

source_name: PTB_11-18 years blood spot


title: Preterm proband blood spot at 18 years age 34

source_name: PTB_8-18 years blood spot


title: Preterm proband blood spot at 18 years age 43

source_name: PTB_12-18 years blood spot


title: Term proband blood spot at 18 years age 30

description: Term proband blood spot at 18 years age

source_name: Term_8-18 years blood spot


title: Preterm infant blood spot 35

description: Preterm infant blood spot

source_name: PTB_7-Birth Blood Spot


title: Term infant blood spot 42

description: Term infant blood spot

source_name: Term_11-Birth Blood Spot


title: Colony_A-M_6vs.M_7

description: Colony_A-M_6vs.M_7 Microarray batch: G

value: 6 days

value: pooled mRNA from 4 developing males

value: 7 days


title: Preterm infant blood spot 28

description: Preterm infant blood spot

source_name: PTB_6-Birth Blood Spot


title: Colony_A-M_12vs.M_13

description: Colony_A-M_12vs.M_13 Microarray batch: G

value: 12 days

value: 13 days


title: Colony_A-M_9vs.M_10

description: Colony_A-M_9vs.M_10 Microarray batch: G

value: 9 days


title: Term proband blood spot at 18 years age 47

description: Term proband blood spot at 18 years age

source_name: Term_10-18 years blood spot


title: Preterm proband blood spot at 18 years age 26

source_name: PTB_7-18 years blood spot


title: Term proband blood spot at 18 years age 29

description: Term proband blood spot at 18 years age

source_name: Term_7-18 years blood spot


title: Colony_A-M_48hvs.M_3

description: Colony_A-M_48hvs.M_3 Microarray batch: G

value: 48 hours

value: 3 days


title: Term proband blood spot at 18 years age 45

description: Term proband blood spot at 18 years age

source_name: Term_12-18 years blood spot


title: Genomic DNA from Preterm infant blood spot 46

source_name: PTB_10-Birth Blood Spot


title: Term infant blood spot 40

description: Term infant blood spot

source_name: Term_10-Birth Blood Spot


title: Term infant blood spot 27

description: Term infant blood spot

source_name: Term_8-Birth Blood Spot


title: Term infant blood spot 25

description: Term infant blood spot

source_name: Term_6-Birth Blood Spot


title: Term proband blood spot at 18 years age 36

description: Term proband blood spot at 18 years age

source_name: Term_6-18 years blood spot


title: Term proband blood spot at 18 years age 24

description: Term proband blood spot at 18 years age

source_name: Term_5-18 years blood spot

value: Cesarean section


title: Term infant blood spot 19

description: Term infant blood spot

source_name: Term_5-Birth Blood Spot


title: Colony_A-M_5vs.M_6

description: Colony_A-M_5vs.M_6 Microarray batch: G

value: A

value: 5 days


title: Preterm proband blood spot at 18 years age 22

source_name: PTB_4-18 years blood spot

value: No labour

value: Iatrogenic


title: Preterm infant blood spot 21

description: Preterm infant blood spot

source_name: PTB_3-Birth Blood Spot

value: Labour

value: Spontaneous

value: Vaginal

value: Male


title: Term infant blood spot 23

description: Term infant blood spot

source_name: Term_4-Birth Blood Spot


title: Term proband blood spot at 18 years age 18

description: Term proband blood spot at 18 years age

source_name: Term_4-18 years blood spot


title: Colony_A-M_11vs.M_12

description: Colony_A-M_11vs.M_12 Microarray batch: G

value: 11 days


title: Colony_A-M_12hvs.M_18h

description: Colony_A-M_12hvs.M_18h Microarray batch: G

value: 12 hours

value: pooled mRNA from 4 developing males

value: 18 hours


title: Term proband blood spot at 18 years age 15

description: Term proband blood spot at 18 years age

source_name: Term_3-18 years blood spot

value: Female


title: Preterm infant blood spot 16

description: Preterm infant blood spot

source_name: PTB_4-Birth Blood Spot


title: Colony_A-M_4vs.M_5

description: Colony_A-M_4vs.M_5 Microarray batch: G

value: 4 days


title: Preterm infant blood spot 14

description: Preterm infant blood spot

source_name: PTB_5-Birth Blood Spot


title: Colony_A-M_8vs.M_9

description: Colony_A-M_8vs.M_9 Microarray batch: G

value: 8 days

value: 9 days


title: Colony_A-M_36hvs.M_48h

description: Colony_A-M_36hvs.M_48h Microarray batch: G

value: 36 hours

value: 48 hours


title: Preterm proband blood spot at 18 years age 12

source_name: PTB_2-18 years blood spot


title: Colony_A-M_7vs.M_8

description: Colony_A-M_7vs.M_8 Microarray batch: G

value: A

value: 7 days


title: Colony_A-M_0hvs.M_3h

description: Colony_A-M_0hvs.M_3h Microarray batch: G

value: 0 hours

value: 3 hours


title: Term infant blood spot 8

description: Term infant blood spot

source_name: Term_2-Birth Blood Spot

value: No labour

value: Iatrogenic

value: Cesarean section


title: Preterm proband blood spot at 18 years age 20

source_name: PTB_5-18 years blood spot

value: Male


title: Colony_A-M_6hvs.M_12h

description: Colony_A-M_6hvs.M_12h Microarray batch: G

value: 6 hours

value: 12 hours


title: Colony_A-M_14vs.M_15

description: Colony_A-M_14vs.M_15 Microarray batch: G

value: 14 days

value: pooled mRNA from 4 developing males

value: 15 days


title: Preterm proband blood spot at 18 years age 17

source_name: PTB_3-18 years blood spot

value: Labour

value: Spontaneous

value: Vaginal


title: Preterm proband blood spot at 18 years age 6

source_name: PTB_1-18 years blood spot


title: Preterm proband blood spot at 18 years age 2

source_name: PTB_9-18 years blood spot

value: Female


title: Term infant blood spot 11

description: Term infant blood spot

source_name: Term_1-Birth Blood Spot


title: Term proband blood spot at 18 years age 9

description: Term proband blood spot at 18 years age

source_name: Term_1-18 years blood spot


title: Term proband blood spot at 18 years age 3

description: Term proband blood spot at 18 years age

source_name: Term_2-18 years blood spot


title: Preterm infant blood spot 1

description: Preterm infant blood spot

source_name: PTB_1-Birth Blood Spot


title: Preterm infant blood spot 5

description: Preterm infant blood spot

source_name: PTB_2-Birth Blood Spot


title: Preterm infant blood spot 10

description: Preterm infant blood spot

source_name: PTB_9-Birth Blood Spot


title: Colony_A-M_24hvs.M_36h

description: Colony_A-M_24hvs.M_36h Microarray batch: G

value: A

value: 24 hours

value: 36 hours


title: Term infant blood spot 13

description: Term infant blood spot

source_name: Term_3-Birth Blood Spot


title: Colony_A-M_3hvs.M_6h

description: Colony_A-M_3hvs.M_6h Microarray batch: G

value: 3 hours


title: Colony_A-M_3vs.M_4

description: Colony_A-M_3vs.M_4 Microarray batch: G

value: 3 days

value: 4 days


title: Colony_D-M_6vs.REF

description: Colony_D-M_6vs.REF Microarray batch: I

value: D

value: 6 days

source_name: REF

value: Mixed

value: not available

value: mix of all castes and stages from many colonies


title: Colony_D-M_3vs.REF

description: Colony_D-M_3vs.REF Microarray batch: I

value: Male

value: pooled mRNA from 4 developing males


title: Technical_Control [UnMet_Ctrl_B]

city: Singapore

first: Weng Khong

last: Lim

state: Singapore

address: 11 Hospital Drive

department: Department of Medical Sciences

country: Singapore

institute: National Cancer Centre Singapore

description: Methylation profiling on IDH1/2 wild-type and mutant CCA tumors

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation540 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using recommended Illumina scanner settings

data_processing: GenomeStudio software was used to analyze raw Illumina BeadChip data and generate summary files containing average beta avalues.

label_protocol: According to manufacturer's protocol

extract_protocol: Genomic DNA was extracted from cells using Qiagen Blood and Cell Culture DNA kit (Qiagen, CA)

tag: tissue type

tag: idh1/2 mutation status

value: WildType

tag: cca-type (ov or non-ov)


title: Term infant blood spot 4

description: Term infant blood spot

source_name: Term_9-Birth Blood Spot

value: No labour

value: Spontaneous

value: Cesarean section


title: Term proband blood spot at 18 years age 7

description: Term proband blood spot at 18 years age

source_name: Term_9-18 years blood spot


title: CCA_Tumor_Sample [W040T]

value: CCA Tumor

value: OV


title: CCA_Tumor_Sample [Y020T]


title: Colony_D-M_24hvs.REF

description: Colony_D-M_24hvs.REF Microarray batch: I

tag: caste

tag: colony

value: 24 hours


title: Colony_D-M_0hvs.REF

description: Colony_D-M_0hvs.REF Microarray batch: I

tag: timepoint

value: 0 hours

tag: biomaterial


title: CCA_Tumor_Sample [B085T]


title: CCA_Tumor_Sample [Y002T]


title: Colony_A-M_10vs.M_11

description: Colony_A-M_10vs.M_11 Microarray batch: G

value: A

value: 10 days

value: 11 days


title: Colony_D-M_6hvs.M_12h

description: Colony_D-M_6hvs.M_12h Microarray batch: I

value: D

value: 6 hours

value: 12 hours


title: CCA_Tumor_Sample [B099T]


title: Colony_D-M_4vs.M_6

description: Colony_D-M_4vs.M_6 Microarray batch: I

value: 4 days

value: 6 days


title: CCA_Tumor_Sample [T026T]


title: CCA_Tumor_Sample [2000861T]

value: Non-OV


title: CCA_Tumor_Sample [R104T]

value: WildType


title: CCA_Tumor_Sample [21914187T]

value: Mutant


title: CCA_Tumor_Sample [72600277T]


title: CCA_Tumor_Sample [2000123T]


title: CCA_Tumor_Sample [W012T]


title: Technical_Control [UnmetControl_B]


title: CCA_Tumor_Sample [Z639T]


title: CCA_Tumor_Sample [00990196T]