title: precervical anterior vaginal wall (non POP site)_sample22

status: Public on Jul 31 2015

type: RNA

city: Amsterdam

first: Manon

middle: Heleen

last: Kerkhof

state: Noord Holland

address: de Boelelaan 1118

department: Obstetrics & Gynaecology

country: Netherlands

institute: VU University Medical Centre

description:
Raw data file:
US22502676_251485056640_S01_GE2-v5_95_Feb07_1_3.txt
22_cervix

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent Scan protocol

data_processing: All analyses of the gene expression microarray data were done within the R statistical software, using the Limma-package.  Preprocessing of the gene expression data comprised of RMA background correction, loess within-array normalization and A-quantile between-array normalization.  The moderated t-test implemented in Limma, employing empirical Bayes estimation of the variance, is used to evaluate the difference in gene expression between the two groups. The multiplicity problem (many genes are tested) is address by application of the Benjamini-Hochberg procedure to raw p-values which controls the FDR (False Discovery Rate).

molecule: total RNA

organism: Homo sapiens

source_name: precervical anterior vaginal wall

label_protocol: 200 ng total RNA per sample was used as input for amplification and labeled with the Low Input Quick Amp Labeling kit (Agilent Technologies, Palo Alto, CA, USA), including control spikes according to the manufacturer’s guidelines

extract_protocol: The snap frozen tissues were de-epitheliased and total RNA was extracted with the Trizol reagent according to the manufacturere's protocol

tag: individual

tag: tissue

value: precervical anterior vaginal wall


title: precervical anterior vaginal wall (non POP site)_sample9

description:
Raw data file:
US22502676_251485056634_S01_GE2-v5_95_Feb07_1_1.txt
9_cervix


title: precervical anterior vaginal wall (non POP site)_sample8

description:
Raw data file:
US22502676_251485056640_S01_GE2-v5_95_Feb07_1_4.txt
8_cervix


title: precervical anterior vaginal wall (non POP site)_sample10

description:
Raw data file:
US22502676_251485056634_S01_GE2-v5_95_Feb07_1_2.txt
10_cervix


title: precervical anterior vaginal wall (non POP site)_sample25

description:
Raw data file:
US22502676_251485056640_S01_GE2-v5_95_Feb07_1_1.txt
25_cervix


title: precervical anterior vaginal wall (non POP site)_sample6

description:
Raw data file:
US22502676_251485056640_S01_GE2-v5_95_Feb07_1_2.txt
6_cervix


title: precervical anterior vaginal wall (non POP site)_sample3

description:
Raw data file:
US22502676_251485056634_S01_GE2-v5_95_Feb07_1_4.txt
3_cervix


title: anterior vaginal wall (POP site)_sample24

description:
Raw data file:
US22502676_251485056639_S01_GE2-v5_95_Feb07_1_4.txt
24_vaginavoorwand

source_name: anterior vaginal wall

value: anterior vaginal wall


title: anterior vaginal wall (POP site)_sample25

description:
Raw data file:
US22502676_251485056640_S01_GE2-v5_95_Feb07_1_1.txt
25_vaginavoorwand


title: precervical anterior vaginal wall (non POP site)_sample1

description:
Raw data file:
US22502676_251485056639_S01_GE2-v5_95_Feb07_1_1.txt
1_cervix


title: precervical anterior vaginal wall (non POP site)_sample24

description:
Raw data file:
US22502676_251485056639_S01_GE2-v5_95_Feb07_1_4.txt
24_cervix


title: anterior vaginal wall (POP site)_sample7

description:
Raw data file:
US22502676_251485056639_S01_GE2-v5_95_Feb07_1_3.txt
7_vaginavoorwand


title: anterior vaginal wall (POP site)_sample9

description:
Raw data file:
US22502676_251485056634_S01_GE2-v5_95_Feb07_1_1.txt
9_vaginavoorwand


title: anterior vaginal wall (POP site)_sample4

description:
Raw data file:
US22502676_251485056639_S01_GE2-v5_95_Feb07_1_2.txt
4_vaginavoorwand


title: anterior vaginal wall (POP site)_sample22

description:
Raw data file:
US22502676_251485056640_S01_GE2-v5_95_Feb07_1_3.txt
22_vaginavoorwand


title: precervical anterior vaginal wall (non POP site)_sample4

description:
Raw data file:
US22502676_251485056639_S01_GE2-v5_95_Feb07_1_2.txt
4_cervix


title: precervical anterior vaginal wall (non POP site)_sample7

description:
Raw data file:
US22502676_251485056639_S01_GE2-v5_95_Feb07_1_3.txt
7_cervix


title: precervical anterior vaginal wall (non POP site)_sample2

description:
Raw data file:
US22502676_251485056634_S01_GE2-v5_95_Feb07_1_3.txt
2_cervix


title: anterior vaginal wall (POP site)_sample10

description:
Raw data file:
US22502676_251485056634_S01_GE2-v5_95_Feb07_1_2.txt
10_vaginavoorwand


title: anterior vaginal wall (POP site)_sample1

description:
Raw data file:
US22502676_251485056639_S01_GE2-v5_95_Feb07_1_1.txt
1_vaginavoorwand


title: Cells expressing mutant H1069Q, biological rep1

city: Napoli

first: Giancarlo

last: Chesi

address: via Castellino 111

country: Italy

institute: Tigem

description:
Gene expression data from cells infected with adenovirus expressing H1069Q -GFP.
Cell line derived from the liver tissue of a Caucasian American male.

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133A 2.0.

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

label: biotin

source_name: human liver carcinoma cell line, ATP7B H1069Q mutant

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

growth_protocol: The cells were grown for 72 hours at 37°C in 5% CO2.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: The cells, after 24 hour of plating, were infected with adenovirus. The cells infected were grown for 48 hours. After the treatment, the cells were scraped with a lysis buffer (Qiagen).

tag: cell line

tag: cell type

value: hepatocellular carcinoma cell line

tag: overexpression

value: ATP7B H1069Q


title: Cells expressing mutant H1069Q, biological rep2


title: anterior vaginal wall (POP site)_sample3

description:
Raw data file:
US22502676_251485056634_S01_GE2-v5_95_Feb07_1_4.txt
3_vaginavoorwand


title: anterior vaginal wall (POP site)_sample2

description:
Raw data file:
US22502676_251485056634_S01_GE2-v5_95_Feb07_1_3.txt
2_vaginavoorwand


title: anterior vaginal wall (POP site)_sample8

description:
Raw data file:
US22502676_251485056640_S01_GE2-v5_95_Feb07_1_4.txt
8_vaginavoorwand


title: anterior vaginal wall (POP site)_sample6

description:
Raw data file:
US22502676_251485056640_S01_GE2-v5_95_Feb07_1_2.txt
6_vaginavoorwand


title: Cells expressing ATP7B wt, biological rep1

description:
Gene expression data from cells infected with adenovirus expressing ATP7B wt -GFP.
Cell line derived from the liver tissue of a Caucasian American male.

source_name: human liver carcinoma cell line, ATP7B wt

value: ATP7B wt


title: Cells expressing ATP7B wt, biological rep2


title: Kidney_FAO_Myf_12months_uRBP>1000mg/L

city: São Paulo

first: Hatylas

last: Azevedo

state: Sao Paulo

address: Doutor Arnaldo Avenue, 455

department: Pediatrics

country: Brazil

institute: University of São Paulo

description:
FAO 15.01.08
Gene expression of kidney cells from patient FAO, submitted to mycophenolate treatment, 12 months post transplant.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F-014850) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 Feb07 and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Kidney cells, Patient FAO, Mycophenolate, 12 months after transplant, uRBP > 1000 mg/L

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen). RNA concentration and purity were determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Total RNA was extracted from these samples at 0 and 12 months after transplant using Trizol reagent (Life Technologies, USA) and purified using RNeasy Spin Columns (Qiagen, USA). RNA quantity was determined using a Nanovue spectrophotometer (GE Healthcare, USA). The RNA quality was performed using a 2100 Bioanalyzer with an RNA 6000 Nano kit and Ladder (Agilent Technologies, USA), according to the manufacturer's instructions.

treatment_protocol: Renal transplanted patients with good (serum creatinine <1.5 mg/dL) and stable (for at least 3 months) clinical conditions were followed-up for 12 months after transplantation. They were screened for PTD during the early post-transplant period and 33 patients with elevated uRBP (urinary retinol-binding protein) levels were selected for further investigation. These patients were randomly divided for immunosuppressive intervention with either Azathioprine (AZA) or Mycophenolate mofetil (MYF) and submitted to renal allograft biopsies.

value: kidney

tag: immunosuppression treatment

value: Mycophenolate mofetil

tag: urbp level

tag: time after transplantation

value: 12 months

tag: patient

value: FAO


title: Kidney_VM_Aza_12months_uRBP<1000mg/L

description:
VM 26
Gene expression of kidney cells from patient VM, submitted to azathioprine treatment, 12 months post transplant.

source_name: Kidney cells, Patient VM, Azathioprine, 12 months after transplant, uRBP < 1000 mg/L

value: Azathioprine

value: VM


title: Kidney_MAGF_Myf_0months_uRBP>1000mg/L

description:
MAGF 21.09.05
Gene expression of kidney cells from patient MAGF, submitted to mycophenolate treatment, 0 months post transplant.

source_name: Kidney cells, Patient MAGF, Mycophenolate, 0 months after transplant, uRBP > 1000 mg/L

value: 0 months

value: MAGF


title: Kidney_MAGF_Myf_12months_uRBP<1000mg/L

description:
MAGF 09.10.07
Gene expression of kidney cells from patient MAGF, submitted to mycophenolate treatment, 12 months post transplant.

source_name: Kidney cells, Patient MAGF, Mycophenolate, 12 months after transplant, uRBP < 1000 mg/L


title: Kidney_NNSX_Myf_12months_uRBP<1000mg/L

description:
NNSX 06.19.07
Gene expression of kidney cells from patient NNSX, submitted to mycophenolate treatment, 12 months post transplant.

source_name: Kidney cells, Patient NNSX, Mycophenolate, 12 months after transplant, uRBP < 1000 mg/L

value: NNSX


title: Kidney_CSSM_Myf_12months_uRBP<1000mg/L

description:
CSSM 02.10.07
Gene expression of kidney cells from patient CSSM, submitted to mycophenolate treatment, 12 months post transplant.

source_name: Kidney cells, Patient CSSM, Mycophenolate, 12 months after transplant, uRBP < 1000 mg/L

value: CSSM


title: Kidney_RT_Aza_12months_uRBP>1000mg/L

description:
RT 08.17.05
Gene expression of kidney cells from patient RT, submitted to azathioprine treatment, 12 months post transplant.

source_name: Kidney cells, Patient RT, Azathioprine, 12 months after transplant, uRBP > 1000 mg/L

value: RT


title: Kidney_NPS_Myf_12months_uRBP<1000mg/L

description:
NPS 07.20.05
Gene expression of kidney cells from patient NPS, submitted to mycophenolate treatment, 12 months post transplant.

source_name: Kidney cells, Patient NPS, Mycophenolate, 12 months after transplant, uRBP < 1000 mg/L

value: NPS


title: Kidney_MTO_Aza_12months_uRBP>1000mg/L

description:
MTO 14.09.06
Gene expression of kidney cells from patient MTO, submitted to azathioprine treatment, 12 months post transplant.

source_name: Kidney cells, Patient MTO, Azathioprine, 12 months after transplant, uRBP > 1000 mg/L

value: MTO


title: Kidney_MAA_Myf_0months_uRBP>1000mg/L

description:
MAA 29.01.06
Gene expression of kidney cells from patient MAA, submitted to mycophenolate treatment, 0 months post transplant.

source_name: Kidney cells, Patient MAA, Mycophenolate, 0 months after transplant, uRBP > 1000 mg/L

value: MAA


title: Kidney_EAC_Aza_12months_uRBP<1000mg/L

description:
EAC 18.09.07
Gene expression of kidney cells from patient EAC, submitted to azathioprine treatment, 12 months post transplant.

source_name: Kidney cells, Patient EAC, Azathioprine, 12 months after transplant, uRBP < 1000 mg/L

value: EAC


title: Kidney_MTO_Aza_0months_uRBP>1000mg/L

description:
MTO 05.09.05
Gene expression of kidney cells from patient MTO, submitted to azathioprine treatment, 0 months post transplant.

source_name: Kidney cells, Patient MTO, Azathioprine, 0 months after transplant, uRBP > 1000 mg/L


title: Kidney_IGL_Aza_12months_uRBP>1000mg/L

description:
IGL 02.08.08
Gene expression of kidney cells from patient IGL, submitted to azathioprine treatment, 12 months post transplant.

source_name: Kidney cells, Patient IGL, Azathioprine, 12 months after transplant, uRBP > 1000 mg/L

value: IGL


title: Kidney_DP_Aza_12months_uRBP>1000mg/L

description:
DP 11.12.07
Gene expression of kidney cells from patient DP, submitted to azathioprine treatment, 12 months post transplant.

source_name: Kidney cells, Patient DP, Azathioprine, 12 months after transplant, uRBP > 1000 mg/L

value: DP


title: Kidney_IGL_Aza_0months_uRBP>1000mg/L

description:
IGL 01.16.07
Gene expression of kidney cells from patient IGL, submitted to azathioprine treatment, 0 months post transplant.

source_name: Kidney cells, Patient IGL, Azathioprine, 0 months after transplant, uRBP > 1000 mg/L

value: kidney


title: Kidney_ADO_Aza_12months_uRBP>1000mg/L

description:
ADO 24.07.07
Gene expression of kidney cells from patient ADO, submitted to azathioprine treatment, 12 months post transplant.

source_name: Kidney cells, Patient ADO, Azathioprine, 12 months after transplant, uRBP > 1000 mg/L

value: ADO


title: Kidney_CSSM_Myf_0months_uRBP>1000mg/L

description:
CSSM 31.05.06
Gene expression of kidney cells from patient CSSM, submitted to mycophenolate treatment, 0 months post transplant.

source_name: Kidney cells, Patient CSSM, Mycophenolate, 0 months after transplant, uRBP > 1000 mg/L

value: Mycophenolate mofetil


title: Kidney_FAO_Myf_0months_uRBP>1000mg/L

description:
FAO 23.02.06
Gene expression of kidney cells from patient FAO, submitted to mycophenolate treatment, 0 months post transplant.

source_name: Kidney cells, Patient FAO, Mycophenolate, 0 months after transplant, uRBP > 1000 mg/L

value: FAO


title: Kidney_CJS_Myf_0months_uRBP>1000mg/L

description:
CJS 10.18.05
Gene expression of kidney cells from patient CJS, submitted to mycophenolate treatment, 0 months post transplant.

source_name: Kidney cells, Patient CJS, Mycophenolate, 0 months after transplant, uRBP > 1000 mg/L

value: CJS


title: Kidney_MICF_Myf_12months_uRBP<1000mg/L

description:
MICF 24.05.06
Gene expression of kidney cells from patient MICF, submitted to mycophenolate treatment, 12 months post transplant.

source_name: Kidney cells, Patient MICF, Mycophenolate, 12 months after transplant, uRBP < 1000 mg/L

value: 12 months

value: MICF


title: Kidney_VM_Aza_0months_uRBP<1000mg/L

description:
VM 25
Gene expression of kidney cells from patient VM, submitted to azathioprine treatment, 0 months post transplant.

source_name: Kidney cells, Patient VM, Azathioprine, 0 months after transplant, uRBP < 1000 mg/L

value: Azathioprine

value: 0 months

value: VM


title: Kidney_MFM_Aza_0months_uRBP<1000mg/L

description:
MFM 12.07.05
Gene expression of kidney cells from patient MFM, submitted to azathioprine treatment, 0 months post transplant.

source_name: Kidney cells, Patient MFM, Azathioprine, 0 months after transplant, uRBP < 1000 mg/L

value: MFM


title: Kidney_MICF_Myf_0months_uRBP>1000mg/L

description:
MICF 04.05.05
Gene expression of kidney cells from patient MICF, submitted to mycophenolate treatment, 0 months post transplant.

source_name: Kidney cells, Patient MICF, Mycophenolate, 0 months after transplant, uRBP > 1000 mg/L


title: Kidney_ADO_Aza_0months_uRBP>1000mg/L

description:
ADO 02.02.06
Gene expression of kidney cells from patient ADO, submitted to azathioprine treatment, 0 months post transplant.

source_name: Kidney cells, Patient ADO, Azathioprine, 0 months after transplant, uRBP > 1000 mg/L


title: Data lame 289 area4

city: Quebec

first: Annie

last: Girard

state: Quebec

address: 2440, boul. Hochelaga

department: Sciences animales

country: Canada

institute: Université Laval

hyb_protocol: Samples were prepared with Gene Expression Hybridization Kit (Agilent, Santa Clara, CA) then hybridized onto Agilent-manufactured EmbryoGENE bovine microarray slides, using Agilent hybridization chambers.

scan_protocol: Microarray slides were read by the Tecan’s PowerScanner with the Autogain procedure on each individual array.

data_processing: Images were processed with Array-Pro Analyzer 6.4 (Media Cybernetics, Rockville, MD) and the FlexArray software (1.6.1) was used based on the limma Bioconductor package. Background subtraction was followed by loess within-array and quantile between-arrays normalization. The expression data were then fit to a linear model to estimate fold-changes and an empirical Bayes procedure was used to produce associated p-values.

organism: Bos taurus

source_name: BHBH

label_protocol: 825 ng of total RNA from each pool was labelled with ULS Fluorescent Labelling Kit for Agilent arrays (Kreatech Inc., Durham, NC).

growth_protocol: Dominant follicles were collected by aspiration on day 60 postpartum, 42hrs after a single PG injection.

extract_protocol:
Total RNA was extracted using PicoPure RNA Isolation kit (Life Technologies Inc., Burlington, ON).
Samples were pooled into four pools per group (3 animals per pool, for a total of 12 cows per group). Linear amplification was done using RiboAmp HSPlus RNA Amplification Kit (Life Technologies Inc., Burlington, ON) .

treatment_protocol: Animals were classified into two groups based on their beta-hydroxybutyrate (BHB) blood profiles : mild negative energy balance (BHB low = BHBL) or severe negative energy balance (BHB High = BHBH).

tag: breed (cattle)

value: holstein

tag: follicular size

value: > 9 mm

tag: cell collection method

value: aspiration

tag: status of negative energy balance

value: Severe

value: granulosa

source_name: BHBL

value: Mild


title: Data lame 288 area3


title: Data lame 288 area2


title: Data lame 288 area4


title: Kidney_EAC_Aza_0months_uRBP<1000mg/L

description:
EAC 23.02.06
Gene expression of kidney cells from patient EAC, submitted to azathioprine treatment, 0 months post transplant.

source_name: Kidney cells, Patient EAC, Azathioprine, 0 months after transplant, uRBP < 1000 mg/L

value: kidney

value: EAC


title: DEN T4

city: Valencia

first: Angela

middle: L.

last: Riffo-Campos

state: Valencia

address: Avda. Blasco Ibáñes, 17

department: Department of Biochemistry and Molecular Biology

country: Spain

institute: University of Valencia, and INCLIVA

description: Gene expression

hyb_protocol: The labeled cRNA was hybridized to the microarray according to the manufacturer's protocol.

scan_protocol: The arrays were washed, and scanned on an Agilent G2565CA microarray scanner at 100% PMT and 3 m resolution.

data_processing: The intensity data was extracted using the Feature Extraction Software (Agilent).

organism: Mus musculus

source_name: Mice developing DEN-induced hepatocellular carcinoma

label_protocol: 100 ng of total RNA were labeled using LowInputQuick Amp Labeling kit (Agilent 5190-2305) following manufacturer instructions. Briefly: mRNA was reverse transcribed in the presence of T7-oligo-dT primer to produce cDNA, which was transcribed in vitro with T7 RNA polymerase in the presence of Cy3-CTP to produce labeled cRNA.

growth_protocol: Ten week-old CD1 male mice were obtained from the animal facilities of the University of Valencia, and fed ad libitum with standard diet.

extract_protocol: RNA was extracted using the TRIZOL method (Chomczynski and Sacchi, 1987)

treatment_protocol: Hydrodynamic gene delivery (HGD) was performed as described by Liu et al. {Liu, Song, et al. 1999 #16551}, using 50 μg of plasmid DNA.

tag: strain

value: Liver

tag: gender

value: male

tag: age

value: ten week-old

tag: treatment

value: DEN-induced hepatocellular carcinoma


title: DEN T5

description: Gene expression


title: DEN T2

description: Gene expression


title: DEN T3

description: Gene expression


title: Data lame 289 area2


title: Kidney_DP_Aza_0months_uRBP<1000mg/L

description:
DP 22.09.06
Gene expression of kidney cells from patient DP, submitted to azathioprine treatment, 0 months post transplant.

source_name: Kidney cells, Patient DP, Azathioprine, 0 months after transplant, uRBP < 1000 mg/L

value: DP


title: Gas1 G5

description: Gene expression

source_name: Mice developing DEN-induced hepatocellular carcinoma, subsequent transfection with Gas1


title: Data lame 288 area1.2


title: Gas1 G1

description: Gene expression

value: DEN-induced hepatocellular carcinoma, subsequent transfection with Gas1


title: Gas1 G3

description: Gene expression


title: Control C1

description: Gene expression

source_name: control

value: control


title: DEN T1

description: Gene expression


title: Gas1 G4

description: Gene expression


title: Kidney_ASB_Aza_0months_uRBP>1000mg/L

description:
ASB 04.24.06
Gene expression of kidney cells from patient ASB, submitted to azathioprine treatment, 0 months post transplant.

source_name: Kidney cells, Patient ASB, Azathioprine, 0 months after transplant, uRBP > 1000 mg/L

value: Azathioprine

value: 0 months

value: ASB


title: Control C2

description: Gene expression


title: Gas1 G2

description: Gene expression


title: Gas1 G6

description: Gene expression


title: Data lame 289 area3

value: holstein

value: > 9 mm


title: Control C4

description: Gene expression


title: Control C3

description: Gene expression


title: serum miRNA from non-drinking control subject replicate 6

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

country: USA

institute: SUNY Upstate Medical Univ

description: miRNA expression data from the peripheral blood serum

hyb_protocol: Affymetrix EukGE-WS2v4 Protocol

scan_protocol: Standard Affymetrix Genechip 7G Scanner

data_processing: RMA

source_name: Peripheral blood serum

label_protocol: Affymetrix standard 1 cycle

extract_protocol: Qiagen total RNA

tag: broad diagnosis

value: non-drinking control

tag: narrow diagnosis

tag: age (years)

tag: Sex

value: Female


title: serum miRNA from alcohol use disorder subject replicate 12

value: alcohol use disorder

value: alcohol dependence


title: serum miRNA from non-drinking control subject replicate 1

value: Male


title: serum miRNA from non-drinking control subject replicate 5


title: serum miRNA from alcohol use disorder subject replicate 13


title: serum miRNA from alcohol use disorder subject replicate 14


title: serum miRNA from non-drinking control subject replicate 10


title: serum miRNA from alcohol use disorder subject replicate 19


title: serum miRNA from alcohol use disorder subject replicate 16


title: serum miRNA from alcohol use disorder subject replicate 15


title: serum miRNA from non-drinking control subject replicate 8


title: serum miRNA from non-drinking control subject replicate 2


title: serum miRNA from alcohol use disorder subject replicate 18


title: serum miRNA from alcohol use disorder subject replicate 7


title: serum miRNA from alcohol use disorder subject replicate 20


title: serum miRNA from alcohol use disorder subject replicate 11


title: serum miRNA from non-drinking control subject replicate 3


title: serum miRNA from alcohol use disorder subject replicate 4

value: alcohol abuse


title: serum miRNA from alcohol use disorder subject replicate 5


title: serum miRNA from non-drinking control subject replicate 4


title: serum miRNA from alcohol use disorder subject replicate 6


title: serum miRNA from alcohol use disorder subject replicate 3


title: serum miRNA from non-drinking control subject replicate 9


title: serum miRNA from alcohol use disorder subject replicate 8


title: serum miRNA from non-drinking control subject replicate 7


title: serum miRNA from alcohol use disorder subject replicate 2


title: serum miRNA from alcohol use disorder subject replicate 1


title: serum miRNA from alcohol use disorder subject replicate 10


title: SKOV3_Low attachment+FP001 11days_3

city: Shiraoka

first: Ayako

last: Otani

state: Saitama

address: 1470 Shiraoka

department: Medical Materials group

country: Japan

institute: Nissan Chemical Industries

description: Gene expression data from SKOV3 cells cultured in 3D condition.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

source_name: SKOV3 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: SKOV3 cells were cultured in McCoy's 5A medium supplemented with 15% FBS.

extract_protocol: Extraction of total RNA was performed with Quiagen RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: SKOV3 cells were cultured for 11 days in attachment or low-attachment 96 well plates with 15 % FBS/McCoy's 5A medium supplemented with FP001 (0.015 w/v%) or Milli-Q water.

tag: cell line

value: SKOV3 cells

value: 3D culture


title: A549_Attachment+FP001 5days_1

description: Gene expression data from A549 cells which were isolated from cultured A549 cells.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: A549 cells

growth_protocol: Non-small lung cancer cells A549 were cultured in DMEM supplemented with 10% FBS.

treatment_protocol: A549 cells were cultured for 5 days in attachment 96 well plate with 10 % FBS/DMEM supplemented with FP001 (0.015 w/v%) or Milli-Q water. For attachment+FP001 sample, cells were seeded on attachment plate and we changed normal medium to FP001 containing medium after 12h.

tag: medium

value: normal attachment plate with FP001


title: SKOV3_Attachment 11days_1

description: Gene expression data from SKOV3 cells cultured in 2D condition. (Control)

value: 2D culture


title: A549_Attachment+FP001 5days_3


title: SKOV3_Low attachment+FP001 11days_1


title: 689_dev.meta

city: Milan

first: Francesca

last: D'Aiuto

address: Via Amadeo, 42

department: Department of Experimental Oncology and Molecular Medicine

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: Clinical Breast Cancer Specimen from patient developing distant metastasis

hyb_protocol: Biotinylated cRNA sample were hybridazed onto Illumina miRNA BeadChip according to the standard Illumina protocol.

scan_protocol: The Illumina BeadArray Reader was used for scanning the arrays and the Illumina BeadScan software was used for image acquisition and recovery of primary signals.

data_processing: Raw data were generated using the Illumina BeadStudio 3.8 software and analyzed with R/Bioconductor. After quality control and log2 transformation, the Robust Spline Normalization was applied. Only probes targeting validated human miRNAs were selected. Experimental batch effects were eliminated by treating normalized expression data with the Combat method.

source_name: Clinical Breast Cancer Specimen

label_protocol: 600 ng of total RNA were amplified using Illumina Human_v2 MicroRNA expression profiling kit based on DASL (cDNA-mediated Annealing, Selection, Extension, and Ligation) assay according to manufacturer’s recommendations (Illumina Inc., San Diego, CA, USA) and labeled with biotin.

growth_protocol: Tissue samples collected at time of surgery were stored at -80°C until RNA extraction.

extract_protocol: Tissue was pulverized using a Mikrodismembrator (Braun Biotech International , Germany). Total RNA was extracted with the Trizol reagent (Invitrogen, Carlsbad, CA) according to manufacture instructions.

tag: dfs (months)

tag: histotype

value: CDI


title: A549_Low attachment+FP001 5days_1

source_name: A549 cells_low-attachment plate with FP001-containing medium

treatment_protocol: A549 cells were cultured for 5 days in attachment or low-attachment 96 well plate with 10 % FBS/DMEM supplemented with FP001 (0.015 w/v%) or Milli-Q water.


title: A549_Attachment 5days_3

source_name: A549 cells_normal attachment plate with normal medium


title: 691_dev.meta


title: A549_Low attachment+FP001 5days_3


title: A549_Low attachment 5days_2

source_name: A549 cells_low-attachment plate with normal medium


title: SKOV3_Attachment 11days_3


title: SKOV3_Low attachment+FP001 11days_2


title: 690_dev.meta


title: 694_dev.meta


title: 692_dev.meta


title: 693_dev.meta


title: A549_Low attachment 5days_1


title: SKOV3_Attachment 11days_2


title: A549_Low attachment 5days_3


title: A549_Low attachment+FP001 5days_2


title: 687_dev.meta

value: CLI


title: 688_dev.meta


title: A549_Attachment+FP001 5days_2


title: A549_Attachment 5days_1


title: 686_dev.meta


title: A549_Attachment 5days_2


title: 684_dev.meta


title: 685_dev.meta


title: 682_dev.meta


title: 662_dev.meta


title: 663_dev.meta


title: 676_dev.meta

value: CDI+CLI


title: 681_dev.meta


title: 677_dev.meta


title: 659_dev.meta


title: 680_dev.meta


title: 661_dev.meta


title: 660_dev.meta


title: 670_dev.meta


title: 668_dev.meta


title: 671_dev.meta


title: 667_dev.meta


title: 675_dev.meta


title: 673_dev.meta


title: 672_dev.meta


title: 674_dev.meta


title: 656_dev.meta


title: 655_dev.meta


title: 651_dev.meta


title: 654_dev.meta


title: 653_dev.meta


title: 652_dev.meta


title: 678_dev.meta


title: 650_dev.meta


title: 649_dev.meta


title: 646_dev.meta


title: Data lame 289 area1

value: aspiration

value: Severe

tag: cell type

value: granulosa

value: Mild


title: 647_dev.meta


title: 640_dev.meta


title: 648_dev.meta


title: 630_dev.meta


title: 639_dev.meta


title: 644_dev.meta


title: 635_dev.meta


title: 637_dev.meta


title: 638_dev.meta


title: 645_dev.meta


title: 618_dev.meta


title: 624_dev.meta


title: 622_dev.meta


title: 620_dev.meta


title: 611_dev.meta


title: 617_dev.meta


title: 629_dev.meta


title: 614_dev.meta


title: 471_disease.free

description: Clinical Breast Cancer Specimen from disease free patient


title: 477_disease.free

value: other


title: 610_dev.meta


title: 463_disease.free


title: 455_disease.free


title: 612_dev.meta


title: 450_disease.free


title: 445_disease.free


title: serum miRNA from alcohol use disorder subject replicate 9

value: Female


title: 425_disease.free


title: 430_disease.free


title: 418_disease.free


title: 419_disease.free


title: 408_disease.free


title: 415_disease.free


title: 416_disease.free


title: 398_disease.free


title: 387_disease.free


title: 383_disease.free


title: 340_disease.free


title: 334_disease.free


title: 350_disease.free


title: 400_disease.free


title: 344_disease.free


title: 330_disease.free


title: 361_disease.free


title: 346_disease.free


title: 352_disease.free


title: 318_disease.free


title: 312_disease.free


title: 327_disease.free


title: 295_disease.free


title: 303_disease.free


title: serum miRNA from alcohol use disorder subject replicate 17

value: alcohol use disorder


title: 310_disease.free


title: 276_disease.free


title: 271_disease.free


title: 268_disease.free


title: 230_disease.free


title: 232_disease.free


title: 254_disease.free


title: 260_disease.free


title: 264_disease.free


title: 237_disease.free


title: 250_disease.free


title: 227_disease.free


title: 225_disease.free


title: 224_disease.free


title: b-catenin knockout (BKO) wounded skin

city: San Francisco

first: Yuko

last: Oda

state: CA

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

description: low calcium diet

hyb_protocol: Standard Illumina hybridization protocol done by UCLA neuroscience genomics core

scan_protocol: Standard Illumina scanning protocol

data_processing: data were normalized by using quantile method in Genome studio V2011.1

label: Biotin

source_name: skin

label_protocol: Standard Illumina hybridization protocol cDNA labeled by Biotin and detected by Cy3-streptoavidin

growth_protocol: b-catenin is removed from keratin 14 (K14) expressing keratinocytes by using Crelox strategy

extract_protocol: Total RNA was isolated from wounded or non wounded skin by using combination of Stat60 method and RNAeasy RNA purification kit (Qiagen).

treatment_protocol: b-catenin KO mice and their littermate control mice received two full-thickness wounds with a 6-mm biopsy punch on the back skin at 3 month of age.  The wounded skin was excised by using 8-mm biopsy punch after 3 days of wound preparation.

tag: genotype

value: b-catenin fl/fl Cre K14 driven

tag: tissue

value: skin

value: 3 months


title: VDR knockout (KO) wounded skin

description: low calcium diet

growth_protocol: VDR is removed from keratin 14 (K14) expressing keratinocytes by using Crelox stragety

treatment_protocol: VDR KO mice and their littermate control mice received two full-thickness wounds with a 6-mm biopsy punch on the back skin at 3 month of age.  The wounded skin was excised by using 8-mm biopsy punch after 3 days of wound preparation.

tag: time after wounding

value: VDR fl/fl K14 driven Cre


title: VDR knockout (KO) keratinocytes

description: low calcium diet

source_name: keratinocyte

growth_protocol: VDR is removed from keratin 14 (K14) expressing keratinocytes by using Crelox stragety and maintained in low calcium diet to suppress compensation pathways

extract_protocol: Total RNA was isolated from keratinocytes using Pico Pure RNA purification kit (ABI).

treatment_protocol: Keratinocytes were isolated from the skin accoding to the method previously described (Section 3.3 Nowarks JA Fuchs E Mol Biol. 2009 ; 482: 215–232). Briefly, excised skin was incubated with 0.25% trypsin and epidermis was separated from dermis. Keratinocytes were then isolated from the epidermis.

value: 3 month

value: keratinocyte


title: 215_disease.free


title: 214_disease.free


title: 223_disease.free


title: VDR Control (CON) wounded skin

description: low calcium diet

value: VDR fl/fl   3month


title: 191_disease.free

value: CDI


title: 198_disease.free


title: 207_disease.free


title: 213_disease.free


title: 205_disease.free


title: 193_disease.free


title: 203_disease.free


title: Epidermis, separated from littermate control (CON) skin

description: combined triplicates of CON epidermis

source_name: Skin, epidermis separated from dermis by diapase treatment of the back skin

growth_protocol: Both Vitamin D receptor (VDR) and Calcium sensing receptor (CaSR) are removed from keratin 14 (K14) expressing keratinocytes by using Crelox strategy.

extract_protocol: RNA was extracted with Stat60 reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: K14Cre VDR/CaSR double knockout mice and their littermate control mice at P5 were sacrificed. The genotypes were determined by extracting tail DNA by using PCR. The back skin was excised from mice and treated with dispase. The epidermis was separated from dermis. RNA was extracted from epidermis of each mice. The gene expression for specific genes were evaluated by reverse transcription and QPCR to confirm that the variation of gene expression is small within the group. The RNA was combined from 3 mice for CON and VDR KO group.

value: VDR  fl/fl CaSR fl/fl


title: Epidermis, separated from CaSR knockout (KO) skin

description: combined triplicates of KO epidermis

growth_protocol: CaSR (CaSR) is removed from keratin 14 (K14) expressing keratinocytes by using Crelox stragety

treatment_protocol: K14CreCaSR KO mice and their littermate control mice at P5 were sacrified. The genotypes were determined by extacting tail DNA by using PCR. The back skin was excised from mice and treated with dispase. The epidermis was separated from dermis. RNA was extracted from epidermis of each mice. The gene expression for specific genes were evaluated by reverse transcription and QPCR to confirm that the variation of gene expression is small within the group. The RNA was combined from 3 mice for CON and VDR KO group.

value: CaSR fl/fl Cre K14 driven


title: BKO_Control (CON) wounded skin

description: low calcium diet

value: b-catenin fl/fl


title: Epidermis, separated from CaSR littermate control (CON) skin

description: combined triplicates of CON epidermis

value: CaSR fl/fl CON


title: 158_disease.free


title: 148_disease.free


title: 184_disease.free


title: 147_disease.free


title: 144_disease.free


title: Epidermis, separated from double knockout of VDR/CaSR (DKO) skin

description: combined triplicates of DKO epidermis

value: VDR  fl/fl CaSR fl/fl Cre K14 driven


title: Control (CON) keratinocytes

description: low calcium diet

value: VDR fl/fl


title: 141_disease.free


title: 98_disease.free

value: other


title: 137_disease.free


title: Epidermis, separated from VDR littermate control (CON) skin

description: combined triplicates of CON epidermis

growth_protocol: Vitamin D receptor (VDR) is removed from keratin 14 (K14) expressing keratinocytes by using Crelox stragety

treatment_protocol: K14CreVDR KO mice and their littermate control mice at P5 were sacrified. The genotypes were determined by extacting tail DNA by using PCR. The back skin was excised from mice and treated with dispase. The epidermis was separated from dermis. RNA was extracted from epidermis of each mice. The gene expression for specific genes were evaluated by reverse transcription and QPCR to confirm that the variation of gene expression is small within the group. The RNA was combined from 3 mice for CON and VDR KO group.


title: Epidermis, separated from VDR knockout (KO) skin

description: combined triplicates of VDR KO epidermis

value: VDR fl/fl Cre K14 driven


title: PR200_12 [miRNA]

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

hyb_protocol: The labeled miRNAs were hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 55 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner G2505C with the Scan Control software (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 019118_D_F_20100604) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hormone-refractory prostate cancer cell lines, 200 nM Paclitaxel resistant PC3

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 0.1 ug RNA using the Agilent miRNA Complete Labeling and Hybridization Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA containing miRNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).

value: male

value: prostate cancer

tag: cell line background

value: 200 nM Paclitaxel resistant PC3 cells

tag: paclitaxel resistance


title: AI-2 treated Cy3 vs. untreated Cy5 rep8

city: Dallas

first: Palmy

middle: R

last: Jesudhasan

state: TX

department: Microbiology

institute: University of Texas Southwestern Medical Center

description: The slides were prehybridized following PFGRC's SOP # M007.

hyb_protocol: The labeled mixtures were further purified using a QIAquick PCR purification kit (Qiagen). Equal amounts of labeled cDNA from the treatment and control were used to hybridize on S. Typhimurium LT2 genome microarrays (version 2), obtained from JCVI (formerly, TIGR, Rockville, MD) and provided by the Pathogen Functional Genome Resource Center (PFGRC). These arrays were amplicon arrays with 6780 ORF each, with 2 replicate spots per ORF. The labeled cDNA was applied to the above arrays. Hybridization was carried out overnight at 42°C in a water bath using Corning hybridization chamber. The pre- and post-hybridization was carried out using the the PFGRC SOP #M008.

scan_protocol: The slides were washed and scanned using a GenePix 4100A scanner (Axon Instruments Inc., Union City, CA) at 532 nm (Cy3 channel) and 635 nm (Cy5 channel), and the images were stored for further analysis.

data_processing: The signal intensity of each gene was globally normalized using LOWESS within the R statistics package. The normalized data was analyzed using commercial SAS 9.1.3 program (SAS Institute Inc. Cary, NC).

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella Typhimurium

label_protocol: Total RNA (5 µg) was used to synthesize cDNA using a random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and aminoallyl-deoxyuridine triphosphate mix) was then incubated overnight with Superscript III reverse transcriptase (Invitrogen) at 42°C. Residual RNA was removed by alkaline treatment followed by neutralization, and the cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNA was labeled with Cy-5 mono-Reactive Dye (GE Health Care).

growth_protocol: Fresh Salmonella Typhimurium was allowed to grow in the presence of 10% PBS for 3 hours.

extract_protocol: Total RNA was isolated from the cultures using an RNeasy mini kit (QIAGEN, Inc., Valencia, CA) according to the manufacturer's protocol. RNAprotect bacteria reagent (QIAGEN, Inc., Valencia, CA) was added to the cultures to stabilize RNA before isolation. The RNase-free DNase set (QIAGEN, Inc., Valencia, CA) was used for on-column DNase digestion to remove residual genomic DNA. The quantity and quality of RNA was examined using ND-1000 spectrophotometer (NanoDrop® Technologies, Wilmington, DE) and bioanalyser 2100 (Agilent Technologies, Santa Clara, CA) respectively.

treatment_protocol: Salmonella Typhimurium with 10% PBS (control).

tag: sample type

value: pj002 (luxs::cat), luxS mutant of this strain of S. Typhimurium (Accession # 87-26254) poultry isolate obtained from the National Veterinary Service Laboratory, Ames, Iowa.

value: 10% PBS (control)

value: luxS mutant

label_protocol: Total RNA (5 µg) was used to synthesize cDNA using a random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and aminoallyl-deoxyuridine triphosphate mix) was then incubated overnight with Superscript III reverse transcriptase (Invitrogen) at 42°C. Residual RNA was removed by alkaline treatment followed by neutralization, and the cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNA was labeled with Cy-3 mono-Reactive Dye (GE Health Care).

growth_protocol: Fresh Salmonella Typhimurium was allowed to grow in the presence of 10% (25 mM) in vitro synthesized AI-2 for 3 hours.

treatment_protocol: Salmonella Typhimurium treated with 25 mM in vitro synthesized AI-2 (Treatment).


title: TAMU_Wcfs_Salmonella enterica Serovar Typhimurium_4.3K_v 2.0_5

hyb_protocol: The labeled mixtures were further purified using a QIAquick PCR purification kit (Qiagen). Equal amounts of labeled cDNA from the treatment and control were used to hybridize on S. Typhimurium LT2 genome microarrays (version 2), obtained from JCVI (formerly, TIGR, Rockville, MD) and provided by the Pathogen Functional Genome Resource Center (PFGRC). These arrays were amplicon arrays with 6780 ORF each, with 2 replicate spots per ORF. The labeled cDNA was applied to the arrays. Hybridization was carried out overnight at 42°C in a water bath using Corning hybridization chamber. The pre- and post-hybridization was carried out using the the PFGRC SOP #M008.

source_name: PBS

growth_protocol: Fresh Salmonella Typhimurium was allowed to grow in the presence of Salmonella Typhimurium luxS mutant cell free supernatant (PBS) for 3 hours.

extract_protocol: Total RNA was isolated from the cultures using an RNeasy mini kit (QIAGEN, Inc., Valencia, CA) according to the manufacturer's protocol. RNAprotect bacteria reagent (QIAGEN, Inc., Valencia, CA) was added to the cultures to stabilize RNA before isolation. The RNase-free DNase set (QIAGEN, Inc., Valencia, CA) was used for on-column DNase digestion to remove residual genomic DNA. The quantity and quality of RNA was examined using ND-1000 spectrophotometer (NanoDropÂ® Technologies, Wilmington, DE) and bioanalyser 2100 (Agilent Technologies, Santa Clara, CA) respectively.

treatment_protocol: Salmonella Typhimurium with 10%  of luxS mutant cell free supernatant (control)

tag: strain

source_name: wild type cell free supernatant (wCFS)

growth_protocol: Fresh Salmonella Typhimurium was allowed to grow in the presence of 10% of Salmonella Typhimurium wild type cell free supernatant (wCFS) that has AI-2 for 3 hours.

treatment_protocol: Salmonella Typhimurium treated with 10% of Salmonella Typhimurium wild type cell free supernatant (wCFS) that has AI-2 for 3 hours (Treatment)


title: PR200_3 [miRNA]

tag: gender


title: TAMU_Wcfs_Salmonella enterica Serovar Typhimurium_4.3K_v 2.0_1


title: PR200_3

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.


title: TAMU_Wcfs_Salmonella enterica Serovar Typhimurium_4.3K_v 2.0_3


title: PR200_11 [miRNA]


title: AI-2 treated Cy5 vs. untreated Cy3 rep3

tag: treatment

value: 25 mM in vitro synthesized AI-2 (Treatment)

growth_protocol: Fresh Salmonella Typhimurium was allowed to grow in the presence of 10% PBS for 3 hours

extract_protocol: Total RNA was isolated from the cultures using an RNeasy mini kit (QIAGEN, Inc., Valencia, CA) according to the manufacturer's protocol. RNAprotect bacteria reagent (QIAGEN, Inc., Valencia, CA) was added to the cultures to stabilize RNA before isolation. The RNase-free DNase set (QIAGEN, Inc., Valencia, CA) was used for on-column DNase digestion to remove residual genomic DNA. The quantity and quality of RNA was examined using ND-1000 spectrophotometer (NanoDrop® Technologies, Wilmington, DE) and bioanalyser 2100 (Agilent Technologies, Santa Clara, CA) respectively

treatment_protocol: Salmonella Typhimurium with 10% PBS (control)


title: PR70_11

source_name: hormone-refractory prostate cancer cell lines, 70 nM Paclitaxel resistant PC3

value: 70 nM Paclitaxel resistant PC3 cells

value: 70 nM


title: PR200_11


title: AI-2 treated Cy5 vs. untreated Cy3 rep1

growth_protocol: Fresh Salmonella Typhimurium was allowed to grow in the presence of 10% (25 mM) in vitro synthesized AI-2 for 3 hours

treatment_protocol: Salmonella Typhimurium treated with 25 mM in vitro synthesized AI-2 (Treatment)


title: TAMU_Wcfs_Salmonella enterica Serovar Typhimurium_4.3K_v 2.0_4


title: PR70_3


title: MCF7_EtOH1 [8118927043_J]

city: Houston

first: Nicholes

last: Candelaria

state: Texas

address: 3605 Cullen Boulevard SERC (Building 545), Rm 3023

department: Cellular and Molecular Biology

institute: University of Houston

description: Ethanol-treated replicate 1

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Array data were normalized and analyzed using R program, lumi and limma packages.

label_protocol: cRNA were prepared and labeled with Cy3 dye using Illumina TotalPrep-96RNA Amplification Kit and Illumina Whole-Genome Gene Expression Direct Hybridisation Kit

extract_protocol: RNA was extracted using EZNA Total RNA Kit I, from Omega

treatment_protocol: MCF-7 breast cancer cells starved of estrogen in 5% charcoal filtered FBS were treated to either a 0.1% ethanol concentration or left untreated.

value: breast cancer cells

tag: er status

value: ER+

tag: treated with

value: 0.1% Ethanol


title: AI-2 treated Cy3 vs. untreated Cy5 rep7


title: AI-2 treated Cy5 vs. untreated Cy3 rep5


title: AI-2 treated Cy3 vs. untreated Cy5 rep4


title: TAMU_Wcfs_Salmonella enterica Serovar Typhimurium_4.3K_v 2.0_2


title: MCF7_EtOH3 [8118927043_L]

description: Ethanol-treated replicate 3


title: PR200_2


title: PR70_2


title: PR20_11

source_name: hormone-refractory prostate cancer cell lines, 20 nM Paclitaxel resistant PC3

value: 20 nM Paclitaxel resistant PC3 cells

value: 20 nM


title: MCF7_EtOH2 [8118927043_K]

description: Ethanol-treated replicate 2


title: AI-2 treated Cy3 vs. untreated Cy5 rep6


title: AI-2 treated Cy3 vs. untreated Cy5 rep2


title: 152_disease.free

tag: age

value: CDI


title: PR200_2 [miRNA]

tag: cell line


title: 128_disease.free


title: PR70_2 [miRNA]


title: PR70_11 [miRNA]


title: PR20_12 [miRNA]


title: PR70_3 [miRNA]


title: PC3_2 [miRNA]

source_name: hormone-refractory prostate cancer cell lines, PC3

value: Paclitaxel sensitive PC3 cells

value: sensitive


title: PR20_11 [miRNA]

value: male


title: PC3_11 [miRNA]

value: prostate cancer


title: 12.CEL

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

description: gi/cdf

hyb_protocol: Biotin-labeled cRNA samples (15 μg) were randomly fragmented for 35 min at 94°C in fragmentation buffer (Affymetrix). Biotinylated cRNA samples were mixed in 250 μL of Hybridization Mix (Affymetrix; 900720) containing Hybridization Controls and Control Oligonucleotide B2 (Affymetrix; 900454). Samples were hybridized onto Affymetrix AGRONOMICS1 Arabidopsis tiling arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 using the FS450_0004 protocol.

scan_protocol: An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled targets.

data_processing: LOG2 RMA normalisation

organism: Arabidopsis thaliana

source_name: Seedlings

label_protocol: Total RNA samples (150 ng) were reverse transcribed into double-stranded cDNA and then in vitro transcribed in the presence of biotin-labeled nucleotides using the GeneChip 3′ IVT Express kit (Affymetrix; 901229) including poly(A) controls as recommended by the manufacturer. The quality and quantity of the biotinylated cRNA were determined using a NanoDrop ND 1000 and Bioanalyzer 2100.

extract_protocol: RNA was prepared using RNeasy columns (Quiagen) and DNA removed with DNA-free reagents (Ambion) following manufacturer’s instructions. The quality of the isolated RNA was assessed with a Nanochip on the Bioanalyzer 2100 (Agilent).

value: gi-100 cdf1-R cdf2-1 cdf3-1 cdf5-1 quintuple mutant


title: PR20_2 [miRNA]


title: PR20_3 [miRNA]


title: PR20_3


title: PC3_11


title: PR20_2


title: PC3_3


title: MCF7_Control3 [8118927043_I]

description: Untreated replicate 3

value: none (untreated control)


title: TNFα-treated SND1 (IP) HepG2 replicate 3

type: genomic

city: Leioa

first: Enara

last: Arretxe

address: Sarriena

department: Phisiology

institute: University of the Basque Country

description: Biological replicate 3 of 3. Control HepG2 cells untreated

hyb_protocol: 5 µg of IP and Input samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the the Agilent protocol, using the Stabilization and Druing solution and ozone-barrier slide covers, in order to avoid the ozone-mediated CY5 degradation

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and Lowess normalization. The filtering strategy was for P(Xbar)<0.05, and P(x)<0.1, and the log ratios of the Normalized Ratio Distributions are Log2.

molecule: genomic DNA

source_name: HepG2 hepatoma cells TNFα-treated

label_protocol: 5 µg of immunoprecipitated chromatin were labeld with Cy5 and 5 µg input were labeled with Cy3 following Agilent Genomic DNA Enzymatic Labeling kit's instructions.

growth_protocol: 70% confluent-HepG2 cells were non-treated or treated with TNFα (50ng/ml) for 24 hours, then fixed with 1% formaldehyde and harvested.

extract_protocol: The crhomatin was extracted and sonicated. The sonicated chromatin was immunoprecipitated with the especific anti-SND1 antibody. The whole chromatin fraction was used as the input.

tag: antibody

source_name: HepG2 hepatoma cells


title: PC3_3 [miRNA]


title: PC3_5 [miRNA]


title: MCF7_Control2 [8118927043_H]

description: Untreated replicate 2


title: 11.CEL

description: gi/cdf


title: MCF7_Control1 [8118927043_G]

description: Untreated replicate 1


title: TNFα-treated SND1 (IP) HepG2 replicate 2

description: Biological replicate 2 of 3. Control HepG2 cells untreated


title: TNFα-treated SND1 (IP) HepG2 replicate 1

description: Biological replicate 1 of 3. Control HepG2 cells untreated


title: Control SND1 (IP) HepG2 replicate 3


title: Control SND1 (IP) HepG2 replicate 2


title: 7.CEL

description: cdf

value: cdf1-R cdf2-1 cdf3-1 cdf5-1 quadruple mutant


title: 6v.CEL

description: gi


title: PC3_2


title: Vehicle d2.5

city: St. Louis

first: Jason

last: Mills

state: Mo

address: Department of Medicine - GI

institute: Washington University in St. Louis

hyb_protocol: Total RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays according to manufacturers instructions

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner

data_processing: Microarray data were analyzed using Partek Genomic Suite v6.6 (Partek Inc., St Louis, MO). Microarray CEL files were imported into Partek and normalized using RMA.

source_name: Gastric Corpus Epithelium

label_protocol: Total RNA extracted and pooled from 3  dissections and mice was  amplirifed, labeled, and fragmented (by Arctureus RiboAmp HS kit followed by the RNA Amplification and Labeling Kit from Enzo Life Sciences)

growth_protocol: All experiments involving animals were performed according to protocols approved by the Washington University School of Medicine Animal Studies Committee. Mice were maintained in a specified-pathogen-free barrier facility under a 12 hour light cycle. Wild type C57BL/6, BALB/c and FVB/N mice were purchased from The Jackson Laboratory. Mice were 6 weeks old at time of treatment.

extract_protocol: Total RNA was extracted, purified by RNEasy Mini Kit, and RNA integrity verified on Agilent Bioanalyzer

treatment_protocol: Tamoxifen (5mg/20g body weight) was injected intraperitoneally for one or three days to induce SPEM and mice were dissected at 12 hours, 2.5 days, and 4.5 days after treatment. Tamoxifen was dissolved in a vehicle of 10% ethanol and 90% sunflower seed oil (Sigma)

value: WT

tag: agent

value: Vehicle

tag: time point

value: 2.5 days


title: 5.CEL

description: gi


title: 4.CEL

description: gi


title: Tamoxifen 12h

value: Tamoxifen

value: 12 hours


title: dnMPL_GFP neg_1

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

description:
SAMPLE 4
Gene expression data from GFP-negative LSK cells from dnMPL transplanted mice

hyb_protocol: amplified, fragmented, biotin labeled aRNA was hybridized for 18 hr at 45C on Affymetrix GeneChip Mouse 430 2.0. Chips were washed and stained in the Affymetrix Fluidics Station 450 according to manufacturers instructions

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA (Robust Multichip Average; Bioconductor)

source_name: GFP- LSK cells from C57Bl/6 mice 8 wks after Tx with dnMPL transduced LSK cells

label_protocol: RNA was reverse transcribed, amplified and labelled using the Nugen Ovation Pico and Encore biotin kits (Nugen Technologies, AC Bemmel, Netherlands).

growth_protocol: transgene positive and negative Lin-Sca1+cKit+ (LSK) cells were isolated from dnMpl and control transplanted mice by fluorescent activated cell sorting. For each sample, BM of 2-5 mice were pooled.

extract_protocol: RNeasy Micro Kit (Qiagen GmbH, Hilden, Germany)

treatment_protocol: Transduction with retroviral supernatants 48h after isolation; transplantation into syngenic mice. FACS-isolation  8 weeks after transplantation

tag: strain background

tag: transplanted with

value: dnMPL transduced LSK cells

tag: cell type

value: GFP negative Lin-Sca1+cKit+ (LSK) cells


title: 10.CEL

description: gi/cdf

tag: genotype


title: dnMPL_GFP pos_3

description:
SAMPLE 9
Gene expression data from GFP-positive LSK cells from dnMPL transplanted mice

source_name: GFP+ LSK cells from C57Bl/6 mice 8 wks after Tx with dnMPL transduced LSK cells

value: GFP positive Lin-Sca1+cKit+ (LSK) cells


title: dnMPL_GFP pos_1

description:
SAMPLE 7
Gene expression data from GFP-positive LSK cells from dnMPL transplanted mice


title: 9.CEL

description: cdf


title: Tamoxifen d2.5


title: 8.CEL

description: cdf


title: 3.CEL


title: ctrl_3

description:
SAMPLE 3
Gene expression data from control LSK cells

source_name: LSK cells from C57Bl/6 mice 8 wks after Tx with wild type LSK cells

value: wild type LSK cells

value: Lin-Sca1+cKit+ (LSK) cells


title: dnMPL_GFP neg_3

description:
SAMPLE 6
Gene expression data from GFP-negative LSK cells from dnMPL transplanted mice


title: Control SND1 (IP) HepG2 replicate 1


title: dnMPL_GFP pos_2

description:
SAMPLE 8
Gene expression data from GFP-positive LSK cells from dnMPL transplanted mice


title: 2.CEL


title: 1.CEL


title: Tamoxifen d4.5

value: 4.5 days


title: dnMPL_GFP neg_2

description:
SAMPLE 5
Gene expression data from GFP-negative LSK cells from dnMPL transplanted mice


title: ctrl_1

description:
SAMPLE 1
Gene expression data from control LSK cells


title: Whole brain of neonatal male mice treated with vehicle control

city: Kumamoto

first: Yutaka

last: Nakachi

address: 1-1-1 Honjo, Chuo-ku

department: Faculty of Life Sciences

institute: Kumamoto University

description: Gene expression data from pooled RNA obtained from whole brains obtained from six neonatal male mice treated with vehicle control by intraperitoneal injection.

hyb_protocol: Labeled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was preformed as described elsewhere (Irizarry et al, Nucleic Acids Res 31, e15, 2003), using Affymetrix GeneArray Scanner 3000 7G with GCOS software.

data_processing: The intensity data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al. Nucleic Acids Res 31(4): e15, 2003) via R/Bioconductor affy 1.28.1 package using default analysis settings.

source_name: neonatal male mice brains, vehicle control injection

label_protocol: Biotinylated cRNA were prepared using the GeneChip 3'IVT Express Kit (Affymetrix).

growth_protocol: Healthy grown neonatal C57BL/6 mice were used.

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

treatment_protocol: We prepared neonatal mice (C57BL/6J) injected intraperitoneally with TP (1mg in 20uL sesame oil per mice) and vehicle control (sesame oil only 20uL per mice) at postnatal 2 day (at the period of mice brain sex differentiation) and obtained mRNA from these mice whole brain at postnatal 6day.

value: Male

tag: tissue

value: Whole brain

value: vehicle control injection


title: Whole brain of neonatal female mice treated with testosterone propionate, replica of 01_Female_TPplus

description: Gene expression data from pooled RNA obtained from whole brains obtained from six neonatal female mice treated with testosterone propionate by intraperitoneal injection, replica of 01

source_name: neonatal female mice brains, testosterone propionate injection, replica

value: Female

value: testosterone propionate injection


title: Whole brain of neonatal female mice treated with vehicle control

description: Gene expression data from pooled RNA obtained from whole brains obtained from six neonatal female mice treated with vehicle control by intraperitoneal injection.

source_name: neonatal female mice brains, vehicle control injection


title: Participant 43: V7

status: Public on Jul 30 2015

city: Seattle

first: John

middle: D

last: Potter

state: WA

address: 1100 Fairview Ave N

department: Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

description: gene level summarization of .CEL file; exported from GCOS

hyb_protocol: Following fragmentation, 15ug of biotin labeled cRNA was hybridized overnight to the Affymetrix U133+2.0 Genechip arrays.GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: For 3' expression analysis, GCOS expression analysis algorithm (GCOS) and the cell intensity file (.cel) was used to compute a single-array expression analysis. To account for potential systematic variation in microarray experiments, data were normalized by the Robust Multi-array Analysis with correction for GC content of the oligo (GC-RMA) and the gene (probe-set) expression level were log2-transformed. The original normalized dataset file became corrupted. The normalized dataset posted here was re-created on July 8, 2015, using the original CEL files and the updated gcrma (version 2.40.0) R package. R version 3.2.1 (2015-06-18) was used with default function settings (as was done for generation of the original expression data). Many of the genes represented by the 54675 probe sets on the array are not expressed or the expression levels are relatively constant across treatments or tissue types. Hence the probes for those genes were removed from the analysis. We required estimated intensities to be above 100 fluorescence units in at least 25% of the samples, and the interquartile range (IQR) across the samples on the log base 2 scale to be at least 0.6. We started this nonspecific filtering first across all two treatments and two tissue types after removing the probe sets for control genes. We then repeated the same criteria within each tissue type and across treatments; and within each treatment and across tissue types.

source_name: Participant 43, epithelial tissue after treatment a

label_protocol: cRNA was synthesized from 100ng of total RNA and biotin-labeled using the GeneChip Two-cycle cDNA synthesis labeling protocol (Affymetrix, Inc., Santa Clara, California)

extract_protocol: At each sigmoidoscopy, biopsies of normal-appearing mucosa from the distal sigmoid colon were obtained. Within 1 min of removal from the colon,  biopsies were transferred to a Hank’s buffer containing 20mM EDTA and 40mM dithiotreitol at 4°C and were held on ice for 10-15 mins.  The epithelial cells were separated from the stromal layer by vortexing. Both cell fractions were collected by centrifugation. Both fractions were frozen and stored in liquid nitrogen until RNA extraction.  Each participant's epithelial and stromal samples were processed at the same time. Total RNA was extracted using RNeasy extraction kits (Qiagen, Valencia, California) and treated with DNAse I according to the manufacturer’s protocol.

value: colon epthelial

tag: Sex

value: female

tag: ugt1a6 genotype

tag: treatment type

value: a


title: Participant 44: W4

source_name: Participant 44, stromal tissue after treatment a

value: colon stromal

value: male


title: ctrl_2

description:
SAMPLE 2
Gene expression data from control LSK cells


title: Participant 43: V5

source_name: Participant 43, epithelial tissue after treatment b

value: b


title: Whole brain of neonatal male mice treated with testosterone propionate

description: Gene expression data from pooled RNA obtained from whole brains obtained from six neonatal male mice treated with testosterone propionate by intraperitoneal injection.

source_name: neonatal male mice brains, testosterone propionate injection

tag: gender

tag: strain


title: Participant 42: V1

source_name: Participant 42, epithelial tissue after treatment a


title: PTX-DC

city: shanghai

first: haiyan

last: zhou

address: No.320Yueyang Road

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology

description: gene expression data from BMDCs stimulated with PTX

hyb_protocol: Following fragmentation, 12.5ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430_2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.Eukaryotic Target Hybridization,Lot no.900720, is used for the experiment.

scan_protocol: the chips were scanned withthe affymetrix genechip 7G plus, and GCOS v1.0 is used for the image processing.

data_processing: genespring 10.0, is used for automatic normalizing the chip data and analysis the fold change.

source_name: BMDCs stimulated with PTX

label_protocol: start with 3μg total RNA, and Biotinylated cRNA were prepared according to the standard Affymetrix protocol, in which, One-Cycle Eukaryotic Target Labeling Assay(Lot no. 900493) is used in the experiment.

growth_protocol: Femal C57BL6 is grow in SPF condition until 6 weeks. Dendritic cells were generated from bone marrow cells.Cells were cultured in medium supplemented with 20 ng/ml of murine rGM-CSF. Nonadherent cells were removed carefully, and fresh medium was added every 2 days. On day 7, nonadherent cells that were released spontaneously from proliferating cell clusters were collected.

treatment_protocol: DCs were incubated with either PBS, LPS (1 µg/mL) or PTX (100 ng/mL)  for 24 h.

value: bone marrow dendritic cell

tag: treatment

value: PTX


title: Whole brain of neonatal female mice treated with testosterone propionate

description: Gene expression data from pooled RNA obtained from whole brains obtained from six neonatal female mice treated with testosterone propionate by intraperitoneal injection.

source_name: neonatal female mice brains, testosterone propionate injection


title: Participant 43: V6

source_name: Participant 43, stromal tissue after treatment b


title: Participant 44: W3

source_name: Participant 44, epithelial tissue after treatment a


title: Participant 42: V2

source_name: Participant 42, stromal tissue after treatment a


title: Whole brain of neonatal female mice treated with vehicle control, replica of 02_Female_TPminus

description: Gene expression data from pooled RNA obtained from whole brains obtained from six neonatal female mice treated with vehicle control by intraperitoneal injection, replica of 02

source_name: neonatal female mice brains, vehicle control injection, replica


title: Participant 44: W2

source_name: Participant 44, stromal tissue after treatment b


title: Participant 42: V3

source_name: Participant 42, epithelial tissue after treatment b


title: PBS-DC

description: gene expression data from BMDCs stimulated with PBS

source_name: BMDCs stimulated with PBS

value: PBS


title: Participant 44: W1

source_name: Participant 44, epithelial tissue after treatment b


title: Participant 42: V4

source_name: Participant 42, stromal tissue after treatment b


title: Participant 41: U5

source_name: Participant 41, epithelial tissue after treatment a


title: PR70_12 [miRNA]

source_name: hormone-refractory prostate cancer cell lines, 70 nM Paclitaxel resistant PC3

value: prostate cancer

tag: cell line background

value: 70 nM Paclitaxel resistant PC3 cells

tag: paclitaxel resistance

value: 70 nM


title: HCC4006ER

city: Tampa

first: Takeshi

last: Yoshida

state: FL

address: 12902 Magnolia Dr

department: Experimental Therapeutics

institute: H.Lee Moffitt Cancer Center

description: Gene expression data from HCC4006ER cells

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C to the Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scaner.

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

source_name: HCC4006ER cells

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

growth_protocol: HCC4006 and HCC4006ER cells were incubated in RPMI medium with 10% FBS for 48 hours at ~80-90% of cell confluence.

extract_protocol: Isolation of total RNA was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

treatment_protocol: No additional treatment was done.

tag: cell line

value: NSCLC

tag: mutation

value: EGFR Ex19 del

tag: resistance

value: erlotinib resistant

tag: phenotype

value: EMT


title: LPS-DC

description: gene expression data from BMDCs stimulated with LPS

source_name: BMDCs stimulated with LPS

value: LPS


title: Participant 43: V8

source_name: Participant 43, stromal tissue after treatment a


title: Participant 41: U8

source_name: Participant 41, stromal tissue after treatment b


title: Participant 41: U6

source_name: Participant 41, stromal tissue after treatment a


title: Participant 40: U2

source_name: Participant 40, stromal tissue after treatment b


title: Participant 40: U3

source_name: Participant 40, epithelial tissue after treatment a

value: colon epthelial


title: HCC4006

description: Gene expression data from HCC4006 cells

source_name: HCC4006 cells

value: erlotinib sensitive

value: wildtype


title: Participant 39: T5

source_name: Participant 39, epithelial tissue after treatment b

value: female


title: Participant 39: T8

source_name: Participant 39, stromal tissue after treatment a

value: colon stromal

value: a


title: Participant 38: T2

source_name: Participant 38, stromal tissue after treatment b

value: b


title: Participant 38: T4

source_name: Participant 38, stromal tissue after treatment a


title: Participant 37: S8

source_name: Participant 37, stromal tissue after treatment a


title: Participant 36: S3

source_name: Participant 36, epithelial tissue after treatment a


title: Participant 40: U4

source_name: Participant 40, stromal tissue after treatment a


title: Participant 36: S1

source_name: Participant 36, epithelial tissue after treatment b


title: Participant 38: T1

source_name: Participant 38, epithelial tissue after treatment b


title: Participant 36: S4

source_name: Participant 36, stromal tissue after treatment a


title: Participant 39: T7

source_name: Participant 39, epithelial tissue after treatment a


title: Participant 41: U7

source_name: Participant 41, epithelial tissue after treatment b


title: Participant 35: R6

source_name: Participant 35, stromal tissue after treatment a

value: male


title: Participant 35: R7

source_name: Participant 35, epithelial tissue after treatment b


title: Participant 38: T3

source_name: Participant 38, epithelial tissue after treatment a


title: Participant 35: R8

source_name: Participant 35, stromal tissue after treatment b


title: Participant 40: U1

source_name: Participant 40, epithelial tissue after treatment b


title: Participant 37: S6

source_name: Participant 37, stromal tissue after treatment b


title: Participant 34: R4

source_name: Participant 34, stromal tissue after treatment b


title: Participant 34: R3

source_name: Participant 34, epithelial tissue after treatment b


title: Participant 37: S5

source_name: Participant 37, epithelial tissue after treatment b


title: Participant 34: R2

source_name: Participant 34, stromal tissue after treatment a


title: Participant 36: S2

source_name: Participant 36, stromal tissue after treatment b


title: Participant 35: R5

source_name: Participant 35, epithelial tissue after treatment a


title: Participant 33: Q8

source_name: Participant 33, stromal tissue after treatment b


title: Participant 34: R1

source_name: Participant 34, epithelial tissue after treatment a


title: Participant 33: Q7

source_name: Participant 33, epithelial tissue after treatment b


title: Participant 33: Q6

source_name: Participant 33, stromal tissue after treatment a


title: Participant 33: Q5

source_name: Participant 33, epithelial tissue after treatment a


title: Participant 32: Q1

source_name: Participant 32, epithelial tissue after treatment a


title: Participant 30: P4

source_name: Participant 30, stromal tissue after treatment a


title: Participant 30: P1

source_name: Participant 30, epithelial tissue after treatment b


title: Participant 32: Q2

source_name: Participant 32, stromal tissue after treatment a


title: Participant 39: T6

source_name: Participant 39, stromal tissue after treatment b


title: Participant 30: P3

source_name: Participant 30, epithelial tissue after treatment a


title: Participant 30: P2

source_name: Participant 30, stromal tissue after treatment b


title: Participant 32: Q4

source_name: Participant 32, stromal tissue after treatment b


title: Participant 29: O6

source_name: Participant 29, stromal tissue after treatment a


title: Participant 29: O5

source_name: Participant 29, epithelial tissue after treatment a


title: Participant 31: P6

source_name: Participant 31, stromal tissue after treatment b


title: Participant 31: P7

source_name: Participant 31, epithelial tissue after treatment a


title: Participant 31: P8

source_name: Participant 31, stromal tissue after treatment a


title: Participant 29: O8

source_name: Participant 29, stromal tissue after treatment b


title: Participant 31: P5

source_name: Participant 31, epithelial tissue after treatment b


title: Participant 29: O7

source_name: Participant 29, epithelial tissue after treatment b


title: Participant 28: O4

source_name: Participant 28, stromal tissue after treatment a


title: Participant 28: O1

source_name: Participant 28, epithelial tissue after treatment b


title: Participant 27: N8

source_name: Participant 27, stromal tissue after treatment a


title: Participant 28: O2

source_name: Participant 28, stromal tissue after treatment b


title: Participant 37: S7

source_name: Participant 37, epithelial tissue after treatment a


title: Participant 28: O3

source_name: Participant 28, epithelial tissue after treatment a


title: Participant 26: N4

source_name: Participant 26, stromal tissue after treatment b


title: Participant 23: L8

source_name: Participant 23, stromal tissue after treatment b


title: Participant 23: L6

source_name: Participant 23, stromal tissue after treatment a


title: Participant 24: M3

source_name: Participant 24, epithelial tissue after treatment b


title: Participant 24: M2

source_name: Participant 24, stromal tissue after treatment a


title: Participant 25: M7

source_name: Participant 25, epithelial tissue after treatment a


title: Participant 27: N7

source_name: Participant 27, epithelial tissue after treatment a


title: Participant 22: L4

source_name: Participant 22, stromal tissue after treatment a


title: Participant 25: M5

source_name: Participant 25, epithelial tissue after treatment b


title: Participant 27: N5

source_name: Participant 27, epithelial tissue after treatment b


title: Participant 24: M1

source_name: Participant 24, epithelial tissue after treatment a


title: Participant 27: N6

source_name: Participant 27, stromal tissue after treatment b


title: Participant 26: N2

source_name: Participant 26, stromal tissue after treatment a


title: Participant 22: L1

source_name: Participant 22, epithelial tissue after treatment b


title: Participant 23: L7

source_name: Participant 23, epithelial tissue after treatment b


title: Participant 25: M8

source_name: Participant 25, stromal tissue after treatment a


title: Participant 23: L5

source_name: Participant 23, epithelial tissue after treatment a


title: Participant 26: N3

source_name: Participant 26, epithelial tissue after treatment b


title: Participant 25: M6

source_name: Participant 25, stromal tissue after treatment b


title: Participant 22: L3

source_name: Participant 22, epithelial tissue after treatment a


title: Participant 26: N1

source_name: Participant 26, epithelial tissue after treatment a


title: Participant 22: L2

source_name: Participant 22, stromal tissue after treatment b


title: Participant 24: M4

source_name: Participant 24, stromal tissue after treatment b


title: Participant 21: K8

source_name: Participant 21, stromal tissue after treatment a


title: Participant 32: Q3

source_name: Participant 32, epithelial tissue after treatment b


title: Participant 20: K2

source_name: Participant 20, stromal tissue after treatment b


title: Participant 21: K6

source_name: Participant 21, stromal tissue after treatment b


title: Participant 20: K3

source_name: Participant 20, epithelial tissue after treatment a


title: Participant 20: K4

source_name: Participant 20, stromal tissue after treatment a


title: Participant 19: J8

source_name: Participant 19, stromal tissue after treatment a


title: Participant 18: J1

source_name: Participant 18, epithelial tissue after treatment a


title: Participant 19: J5

source_name: Participant 19, epithelial tissue after treatment b


title: Participant 18: J2

source_name: Participant 18, stromal tissue after treatment a


title: Participant 20: K1

source_name: Participant 20, epithelial tissue after treatment b


title: Participant 18: J4

source_name: Participant 18, stromal tissue after treatment b


title: Participant 21: K7

source_name: Participant 21, epithelial tissue after treatment a


title: Participant 19: J7

source_name: Participant 19, epithelial tissue after treatment a


title: Participant 17: I4

source_name: Participant 17, stromal tissue after treatment b


title: Participant 17: I2

source_name: Participant 17, stromal tissue after treatment a


title: Participant 18: J3

source_name: Participant 18, epithelial tissue after treatment b


title: Participant 16: H8

source_name: Participant 16, stromal tissue after treatment b


title: Participant 17: I3

source_name: Participant 17, epithelial tissue after treatment b


title: Participant 19: J6

source_name: Participant 19, stromal tissue after treatment b


title: Cecum_SAHC.AC_pod2_rep2

city: Chicago

middle: C

last: Alverdy

state: IL

address: 5841 South Maryland Avenue

department: Surgery

institute: University of Chicago

data_processing: The data were normalized using quantile normalization with Illumina Beadstudio software by the University of Chicago Genomics Core (900 E. 57th Street, Room # 1230C, Chicago, IL 60637). Functional analysis of differentially expressed genes using Ingenuity pathway analysis and DAVID software.

source_name: Cecum, SAHC + AC

label_protocol: Standard Illumina labeling protocol

growth_protocol: Four pathogen community consisting of Candida albicans, Enterococcus faecalis, multi-drug resistant Klebsiella oxytoca, and multi-drug resistant Serratia marcescens was isolated from the stool of a critically ill patient who was exposed to numerous antibiotics over the course of his sepsis. Each pathogen were grown overnight on TSB agar. Colonies were suspended in liquid TSB medium for 1hr and then adjusted to a final OD600 of 0.2. All four pathogens were then combined together in equal volumes. Bacterial suspension was centrifuged at 6,000 rpm for 10min, the excess TSB removed and the remaining pellet was re-suspended in the same volume of 10% glycerol. The resulting microbial suspension was used for cecal injections.

extract_protocol: The cecum, left lobe of the liver, and spleen were isolated from mice and stored in RNAprotect cell reagent (Qiagen, 76526). RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen, 74134). In order to maximize the yield of RNA extraction, chloroform extraction technique was utilized on the liver samples.

tag: organ

value: Cecum

value: SAHC + AC

tag: pod

tag: status

value: Septic

tag: mouse


title: Liver_SAHC.FMT_pod7_rep3

source_name: Liver, SAHC + FMT

value: Liver

value: SAHC + FMT

value: Healthy


title: Cecum_None_pod0_rep3

source_name: Cecum, non-treated Control


title: Participant 21: K5

source_name: Participant 21, epithelial tissue after treatment b

tag: tissue


title: Cecum_SAHC.AC_pod7_rep4


title: Cecum_SAHC.FMT_pod2_rep3

source_name: Cecum, SAHC + FMT


title: Spleen_SAHC.AC_pod2_rep3

source_name: Spleen, SAHC + AC

value: Spleen


title: Liver_None_pod0_rep3

source_name: Liver, non-treated Control


title: Participant 16: H7

source_name: Participant 16, epithelial tissue after treatment b

tag: Sex


title: Participant 16: H6

source_name: Participant 16, stromal tissue after treatment a

tag: ugt1a6 genotype


title: Participant 17: I1

source_name: Participant 17, epithelial tissue after treatment a

tag: treatment type


title: Cecum_None_pod0_rep4

value: N4 C


title: Liver_SAHC.FMT_pod2_rep3


title: Participant 15: H4

source_name: Participant 15, stromal tissue after treatment a


title: Cecum_SAHC.FMT_pod7_rep3


title: Liver_SAHC.FMT_pod7_rep2


title: Spleen_SAHC.FMT_pod7_rep3

source_name: Spleen, SAHC + FMT


title: Participant 16: H5

source_name: Participant 16, epithelial tissue after treatment a


title: Cecum_SAHC_pod1_rep3

source_name: Cecum, SAHC

value: SAHC

value: Sick


title: Participant 15: H1

source_name: Participant 15, epithelial tissue after treatment b

value: colon epthelial


title: Participant 14: G8

source_name: Participant 14, stromal tissue after treatment b


title: Liver_SAHC_pod1_rep3

source_name: Liver, SAHC


title: Cecum_SAHC_pod1_rep2


title: Participant 15: H2

source_name: Participant 15, stromal tissue after treatment b


title: Participant 14: G6

source_name: Participant 14, stromal tissue after treatment a


title: Participant 15: H3

source_name: Participant 15, epithelial tissue after treatment a


title: Spleen_SAHC.AC_pod7_rep2


title: Participant 14: G7

source_name: Participant 14, epithelial tissue after treatment b


title: Spleen_SAHC.AC_pod7_rep1


title: Participant 13: G4

source_name: Participant 13, stromal tissue after treatment a


title: Spleen_SAHC.AC_pod2_rep2

source_name: Spleen, SAHC + AC


title: Spleen_None_pod0_rep3

source_name: Spleen, non-treated Control


title: Participant 14: G5

source_name: Participant 14, epithelial tissue after treatment a


title: Liver_SAHC.AC_pod7_rep3

source_name: Liver, SAHC + AC


title: Liver_None_pod0_rep2

source_name: Liver, non-treated Control


title: Participant 13: G2

source_name: Participant 13, stromal tissue after treatment b


title: Cecum_SAHC.FMT_pod2_rep1

source_name: Cecum, SAHC + FMT


title: Participant 13: G3

source_name: Participant 13, epithelial tissue after treatment a


title: Participant 12: F6

source_name: Participant 12, stromal tissue after treatment a


title: Cecum_SAHC.FMT_pod2_rep2


title: Participant 12: F8

source_name: Participant 12, stromal tissue after treatment b


title: Spleen_SAHC.AC_pod2_rep1


title: Participant 13: G1

source_name: Participant 13, epithelial tissue after treatment b


title: Participant 11: F4

source_name: Participant 11, stromal tissue after treatment b


title: Participant 12: F5

source_name: Participant 12, epithelial tissue after treatment a


title: Liver_SAHC.AC_pod7_rep2


title: Spleen_None_pod0_rep2


title: Participant 12: F7

source_name: Participant 12, epithelial tissue after treatment b


title: Participant 11: F2

source_name: Participant 11, stromal tissue after treatment a


title: Participant 11: F1

source_name: Participant 11, epithelial tissue after treatment a


title: Participant 11: F3

source_name: Participant 11, epithelial tissue after treatment b


title: Participant 10: E7

source_name: Participant 10, epithelial tissue after treatment a


title: Spleen_SAHC_pod1_rep3

source_name: Spleen, SAHC


title: Spleen_SAHC.FMT_pod2_rep3

source_name: Spleen, SAHC + FMT


title: Participant 10: E8

source_name: Participant 10, stromal tissue after treatment a


title: Liver_SAHC.AC_pod7_rep1

source_name: Liver, SAHC + AC


title: Liver_SAHC.AC_pod2_rep3


title: Participant 10: E6

source_name: Participant 10, stromal tissue after treatment b


title: Liver_SAHC.FMT_pod2_rep2

source_name: Liver, SAHC + FMT


title: Spleen_SAHC_pod1_rep2


title: Cecum_SAHC.FMT_pod7_rep2

source_name: Cecum, SAHC + FMT


title: Liver_SAHC.FMT_pod7_rep1


title: Cecum_SAHC.AC_pod2_rep1

source_name: Cecum, SAHC + AC


title: Participant 10: E5

source_name: Participant 10, epithelial tissue after treatment b


title: Cecum_SAHC.AC_pod7_rep2


title: Cecum_SAHC_pod1_rep1

source_name: Cecum, SAHC


title: Spleen_SAHC.FMT_pod7_rep2


title: Liver_SAHC_pod1_rep2

source_name: Liver, SAHC


title: Cecum_SAHC.FMT_pod7_rep1


title: Spleen_None_pod0_rep1

source_name: Spleen, non-treated Control


title: Cecum_SAHC.AC_pod7_rep3


title: Liver_SAHC_pod1_rep1


title: Participant 8: D7

source_name: Participant 8, epithelial tissue after treatment a


title: Participant 7: D4

source_name: Participant 7, stromal tissue after treatment b


title: Participant 9: E2

source_name: Participant 9, stromal tissue after treatment b


title: Liver_SAHC.FMT_pod2_rep1


title: Participant 8: D8

source_name: Participant 8, stromal tissue after treatment a


title: Participant 9: E3

source_name: Participant 9, epithelial tissue after treatment a


title: Participant 8: D5

source_name: Participant 8, epithelial tissue after treatment b


title: Participant 9: E1

source_name: Participant 9, epithelial tissue after treatment b


title: Participant 9: E4

source_name: Participant 9, stromal tissue after treatment a


title: Participant 7: D1

source_name: Participant 7, epithelial tissue after treatment a


title: Participant 7: D3

source_name: Participant 7, epithelial tissue after treatment b


title: Participant 8: D6

source_name: Participant 8, stromal tissue after treatment b


title: Liver_SAHC.AC_pod2_rep2

source_name: Liver, SAHC + AC


title: Cecum_SAHC.AC_pod7_rep1

source_name: Cecum, SAHC + AC


title: Participant 6: C8

source_name: Participant 6, stromal tissue after treatment a


title: Spleen_SAHC.FMT_pod2_rep2

source_name: Spleen, SAHC + FMT


title: Liver_SAHC.AC_pod2_rep1


title: Participant 6: C6

source_name: Participant 6, stromal tissue after treatment b


title: Participant 7: D2

source_name: Participant 7, stromal tissue after treatment a


title: Liver_None_pod0_rep1

source_name: Liver, non-treated Control


title: Participant 5: C4

source_name: Participant 5, stromal tissue after treatment b


title: Spleen_SAHC.FMT_pod7_rep1


title: Spleen_SAHC_pod1_rep1

source_name: Spleen, SAHC


title: Participant 5: C3

source_name: Participant 5, epithelial tissue after treatment b


title: Participant 4: B7

source_name: Participant 4, epithelial tissue after treatment b


title: Spleen_SAHC.FMT_pod2_rep1


title: Participant 3: B4

source_name: Participant 3, stromal tissue after treatment a


title: Participant 4: B6

source_name: Participant 4, stromal tissue after treatment a


title: Participant 6: C5

source_name: Participant 6, epithelial tissue after treatment b


title: Cecum_None_pod0_rep1

source_name: Cecum, non-treated Control


title: Cecum_None_pod0_rep2


title: Participant 5: C1

source_name: Participant 5, epithelial tissue after treatment a


title: NG2C_C

city: New York

first: Daochun

last: Sun

state: New York

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

description: NG2-creERTM Control Biological Replicate 3

data_processing: The data were normalized using nqec method by beadarray package in R

source_name: brain

label_protocol: Standard Illumina label protocol

extract_protocol: Tissue were flash frozen in liquid nitrogen and RNA extracted using Qiagen Lipid Tissue RNeasy Mini Kit and performed according to manufacturer’s instructions.

tag: genotype/variation

value: NG2creERTM driven control


title: Participant 4: B8

source_name: Participant 4, stromal tissue after treatment b


title: Participant 5: C2

source_name: Participant 5, stromal tissue after treatment a

value: female


title: NstC_C

description: Nestin-creERT2 Control Biological Replicate 3

value: Nestin-creERT2 driven control


title: NstT_C

description: Nestin-creERT2 Independent Tumor Tissue 3

value: Nestin-creERT2 driven tumor


title: Participant 3: B3

source_name: Participant 3, epithelial tissue after treatment a

value: a


title: Participant 6: C7

source_name: Participant 6, epithelial tissue after treatment a


title: Participant 4: B5

source_name: Participant 4, epithelial tissue after treatment a

value: male


title: NG2C_A

description: NG2-creERTM Control Biological Replicate 1


title: NG2C_B

description: NG2-creERTM Control Biological Replicate 2


title: NG2T_D

description: NG2-creERTM Independent Tumor Tissue 3

value: NG2creERTM driven tumor


title: NstC_B

description: Nestin-creERT2 Control Biological Replicate 2


title: Participant 2: A6

source_name: Participant 2, stromal tissue after treatment b

value: colon stromal

value: b


title: Participant 3: B2

source_name: Participant 3, stromal tissue after treatment b


title: NG2T_A

description: NG2-creERTM Independent Tumor Tissue 4


title: NG2T_B

description: NG2-creERTM Independent Tumor Tissue 1


title: Participant 1: A4

source_name: Participant 1, stromal tissue after treatment a


title: Participant 2: A8

source_name: Participant 2, stromal tissue after treatment a


title: Participant 3: B1

source_name: Participant 3, epithelial tissue after treatment b


title: NG2T_C

description: NG2-creERTM Independent Tumor Tissue 2


title: NstT_B

description: Nestin-creERT2 Independent Tumor Tissue 2


title: NstT_A

description: Nestin-creERT2 Independent Tumor Tissue 1


title: Participant 2: A5

description: gene level summarization of .CEL file; exported from GCOS

source_name: Participant 2, epithelial tissue after treatment b


title: NstC_A

description: Nestin-creERT2 Control Biological Replicate 1


title: Participant 1: A3

source_name: Participant 1, epithelial tissue after treatment a


title: Participant 1: A1

source_name: Participant 1, epithelial tissue after treatment b


title: Participant 2: A7

source_name: Participant 2, epithelial tissue after treatment a


title: Participant 1: A2

source_name: Participant 1, stromal tissue after treatment b


title: ASCL1TU_G

description: Independent Tumor Tissue 9

data_processing: The data were normalized using nqec with beadarray package in R

value: Tumor Tissue


title: ASCL1TU_E

description: Independent Tumor Tissue 7


title: ASCL1TU_H

description: Independent Tumor Tissue 10


title: ASCL1TU_C

description: Independent Tumor Tissue 5


title: ASCL1TU_D

description: Independent Tumor Tissue 6


title: ASCL1VC_C

description: Biological Replicate 3

value: Ventrol Brain Control Tissue


title: ASCL1TU_F

description: Independent Tumor Tissue 8


title: 959M

city: Gdansk

first: Arkadiusz

last: Piotrowski

address: Hallera 107

department: Biology and Pharmaceutical Botany

country: Poland

institute: Medical University of Gdansk

description: Comparative Genomic Hybridization of tissues from breast cancer patients

hyb_protocol: Sample labeling, hybridization, washing and two-color scanning was performed according to Nimblegen’s protocol with modification as previously described (Ronowicz et al. 2012, Anal Biochem. 426:91-3, PMID: 22504026).

data_processing: Microarray data were extracted with DEVA software v1.2 CGH, including spatial correction (LOESS) and qspline fit normalization, in order to compensate for differences in signal between the two dyes (Workman et al., 2002, Genome Biol 3(9):research0048, PMID: 12225587).

source_name: lymph node metastasis

extract_protocol: DNA from solid tissues was isolated using standard phenol – chloroform extraction method (Sambrook, J., Russell, D.W., 2001, Molecular Cloning: A Laboratory Manual, Volume 1st of 3, 6.4-6.12, Cold Spring Harbor Laboratory Press, ISBN 9780879695774) with modifications. DNA from blood samples was isolated by QIAamp DNA Blood Kit according to manufacturer’s protocol (QIAamp DNA Blood Midi Kit, QIAGEN, Hilden, Germany, #5118).

tag: gender

source_name: uninvolved glandular tissue


title: ASCL1VC_B

description: Biological Replicate 2

source_name: brain


title: ASCL1TU_A

description: Independent Tumor Tissue 2


title: ASCL1TU_B

description: Independent Tumor Tissue 3


title: ASCL1VC_A

description: Biological Replicate 1


title: 963H

scan_protocol: Sample labeling, hybridization, washing and two-color scanning was performed according to Nimblegen’s protocol with modification as previously described (Ronowicz et al. 2012, Anal Biochem. 426:91-3, PMID: 22504026).

source_name: peripheral blood leukocytes


title: ASCL1DC_E

description: Biological Replicate 5

value: Dorsal Brain Control Tissue


title: ASCL1DC_C

description: Biological Replicate 3


title: 1431M

label_protocol: Sample labeling, hybridization, washing and two-color scanning was performed according to Nimblegen’s protocol with modification as previously described (Ronowicz et al. 2012, Anal Biochem. 426:91-3, PMID: 22504026).


title: 2512H


title: 643H

source_name: genomic DNA from a pool of female individuals (Promega)


title: 641T

source_name: primary tumor


title: ASCL1DC_A

description: Biological Replicate 1


title: 1254M


title: ASCL1DC_D

description: Biological Replicate 4


title: 652H


title: 1431H


title: 911T


title: 652M


title: 989H


title: 954T


title: 989T


title: ASCL1DC_B

description: Biological Replicate 2


title: 910H


title: 999H


title: 632T


title: 954M


title: 2652T


title: 632H


title: 968T


title: 963M


title: shSOX17 D10 rep1

city: London

first: Michael

middle: D.

last: Schneider

address: Du Cane Road

department: Imperial Centre for Translational and Experimental Medicine

country: United Kingdom

institute: Imperial College London

description: Gene expression data from mouse ES cells containing shRNA against Sox17 at day 10 of differentiation.

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol by the Baylor College of Medicine Microarray Facility, using Affymetrix Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GeneArray 2500 Scanner.

data_processing: The data were analysed with the R/Bioconductor platform (version 3.0.2). The expression signal values were generated using the Frozen-RMA (fRMA) pre-processing algorithm [PMID:20097884].

source_name: mESCs, Sox17-shRNA, day 10

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol by the Baylor College of Medicine Microarray Facility (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse embryonic stem cells (AB2.2) were differentiated in vitro by embryoid body formation with hanging droplet technique [PMID:8155574]

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and RNeasy reagents (Qiagen) according to the manufacturers' instructions.

treatment_protocol: ESCs were transduced with lentiviral vectors coexpressing enhanced green fluorescent protein (eGFP) with shRNA against Sox17, or against firefly luciferase. Transduced cells were flow-sorted based on GFP fluorescence, grown as embryoid bodies, and transferred to tissue culture plates after 4.5 days [PMID:17360443]. Expression profiling was performed after further culture for up to 10 days.

tag: transduction

value: Sox17 shRNA

tag: differentiation

value: day 10


title: shSOX17 D10 rep2


title: 909M


title: 632M


title: 640H


title: shSOX17 D8 rep1

description: Gene expression data from mouse ES cells containing shRNA against Sox17 at day 8 of differentiation.

source_name: mESCs, Sox17-shRNA, day 8

value: day 8


title: 916T


title: 910M


title: 608M


title: 600M


title: 2652M


title: 902H


title: 1409M


title: 933H


title: shSOX17 D6 rep2

description: Gene expression data from mouse ES cells containing shRNA against Sox17 at day 6 of differentiation.

source_name: mESCs, Sox17-shRNA, day 6

value: day 6


title: 917H


title: 957T


title: 946T


title: shSOX17 D6 rep1


title: 949T


title: 001M


title: shSOX17 D8 rep2


title: 1254T


title: 900H


title: shSOX17 D5 rep1

description: Gene expression data from mouse ES cells containing shRNA against Sox17 at day 5 of differentiation.

source_name: mESCs, Sox17-shRNA, day 5

value: day 5


title: 1254H


title: shSOX17 D5 rep2


title: self2-self2


title: 917T