title: healthy control NA ascending colon P8


title: healthy control NA ascending colon P36

status: Public on Sep 05 2014

type: RNA

city: London

first: Professor Anthony

middle: W

last: Segal

address: Rayne Building, 5 University Street

department: Division of Medicine

country: United Kingdom

institute: Centre for Molecular Medicine

hyb_protocol: 750 ng of biotin-labelled cRNA (150 ng/μl) was hybridised to Illumina HumanHT-12v4 beadarrays (Illumina, CA, USA) for 16 hours at 58°C.

scan_protocol: Following hybridisation, beadarrays were washed and stained with streptavidin-Cy3 (GE Healthcare, UK), scanned using the Beadarray reader, and processed using Genome Studio software (Illumina).

data_processing: Expression data for Illumina HumanHT-12v4 beadarrays was normalised after Log2 transformation within Genome Studio (Illumina) using cubic spline normalisation followed by ComBat normalisation for chip effects in R.

label: Biotin, Cy3

molecule: total RNA

organism: Homo sapiens

source_name: Ascol

extract_protocol: Biopsies (~25 mg) were lysed in a 300 µl RNeasy Fibrous Tissue kit (Qiagen, Hilden, Germany) RLT buffer and 0.14 M β-mercaptoethanol (β-ME) (Sigma-Aldrich, St. Louis, USA), and then homogenised by centrifugation at 10,000 g through a Qiashredder column (Qiagen). Protein was removed by incubation for 10 minutes at 55°C with 10 µl Proteinase K (20 mg/ml) (>600 mAU/ml) (Qiagen).  Total RNA was extracted on RNeasy Mini spin columns and DNA was removed with RNase free DNase digestion (Qiagen). Samples were included in the microarray experiment if they had an optical density ratio reading of 1.8-2.0 OD260/OD280 and >1.8 OD260/OD230 as well as a RNA concentration of greater than 50 ng/μl.  For each biopsy sample, 500 ng of total RNA was amplified and purified using the Illumina TotalPrep-96 RNA Amplification kit (Ambion®, Life Technologies™, CA, USA).

tag: biopsy

value: Pinch biopsy

tag: gender

value: F

tag: disease state

value: healthy control

tag: phenotype

tag: tissue

value: ascending colon


title: AERD012

type: genomic

city: Bucheon-si

first: Seung-Woo

last: Shin

state: Gyeonggi-do

address: 1174 Jung-dong, Wonmi-gu

department: Genome research Center for Allergy and Respiratory Diseases

country: South Korea

institute: Soon Chun Hyang University hospital

description: Genomic DNA extracted from breast tumors was genotyped using HumanExome v1.1 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from AERD and ATA subjects was genotyped using Infinium HumanExome Genotyping BeadChips (Illumina).  We used the GenomeStudio (V2011.1) software and GT module (V1.9.4) with default parameter. Genotype values: AA,AB,BB,or NC (no call). Processed data were filtered such that processed data files contain data only for ~52K polymorphic SNPs. Processed data are available on the series record in the tar archive: All-reduced-AsthmaExome_969_processed.tar.gz. Raw data is available in the IDAT files. Raw data are also available on the series record in the tar archive: All-reduced-AsthmaExome_969_matrix_signal.tar.gz All-reduced-AsthmaExome_969_matrix_signal.tar.gz

molecule: genomic DNA

source_name: ATA

label_protocol: 250ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

value: Female

value: Blood

value: ATA


title: ulcerative colitis Pancolitis ascending colon P56

label_protocol: 750 ng of biotin-labelled cRNA (150 ng/μl) was hybridised to Illumina HumanHT-12v4 beadarrays (Illumina, CA, USA) for 16 hours at 58°C.

value: ulcerative colitis

value: Pancolitis


title: AERD019

source_name: NC

value: Male


title: AERD010


title: AERD009


title: ulcerative colitis Left ascending colon P34

value: M

value: Left


title: AERD007


title: AERD008


title: AERD005


title: AERD006


title: AERD004


title: AERD002


title: AERD003


title: Crohn's disease Ileocolonic ascending colon P2

value: Crohn's disease

value: Ileocolonic


title: AERD001


title: ulcerative colitis Pancolitis ascending colon P23


title: ulcerative colitis Left ascending colon P26


title: Crohn's disease Ileocolonic ascending colon P20


title: ulcerative colitis Pancolitis ascending colon P33


title: AERD011


title: ulcerative colitis Left ascending colon P62


title: AERD081


title: Crohn's disease Colonic ascending colon P30

value: Colonic


title: ulcerative colitis Proctitis descending colon P59

source_name: Descol

value: Proctitis

value: descending colon


title: ctrl_MPH

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: RNA pool from MPH-treated LCLs generated from unaffected controls

hyb_protocol: 200µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C to GeneChip Human Genome U133 Plus 2.0 arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0001.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed in the R v3.0.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

label: biotin

label_protocol: 100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: LCLs were generated from the EDTA-blood of ADHD patients and unaffected controls according to the Leucosep-protocol (Greiner Bio-One) Ficoll-Paque PLUS and transformed with Eppstein-Barr virus (EBV). LCLs were cultured in RPMI1640 medium (Gibco) supplemented with 15% fetal bovine serum (FBS) and 2 mM L-glutamine at 37 °C and 5% CO2.

extract_protocol: Total RNA was isolated with the RNeasy Protect Cell kit (Qiagen) according to the  manufacturer's protocol.

treatment_protocol: For MPH treatment, LCL culture medium was supplemented with 30 ng/µl MPH, corresponding to the maximum recommended concentration in human blood.

tag: affection

value: unaffected

tag: treatment

value: MPH

value: EBV-transformed lymphoblastoid cell lines

tag: pool size

value: LCLs from 6 unaffected controls


title: healthy control NA descending colon P41

value: Pinch biopsy

value: healthy control


title: healthy control NA descending colon P17


title: ctrl_untreat

description: RNA pool from untreated LCLs generated from unaffected controls

value: untreated


title: KLF5_siRNA_YCC3_3

city: Singapore

first: Niantao

last: Deng

state: Singapore

address: Center for Computational Biology, level 6, 8 College Road

country: Singapore

institute: Duke NUS Graduate Medical School

hyb_protocol: Following fragmentation, 12.5ug of cRNA were hybridized on the Affymetrix Human Genome U133 plus Genechips (HG-U133 Plus 2.0, Affymetrix) for 16hr at 45oC.

scan_protocol: GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) and scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using R/bioconductor affy package

label_protocol: Biotinylated cRNA were prepared according the Attymetrix protocol from 250ng of total RNA (GeneChip® 3’ IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: YCC3 cell lines were grown in MEM/10%FBS/ 1X NEAA/ 1X L-glutamine/ Pen-strep. AGS and KATOIII cell lines grown in RPMI 1640/10%FBS/ 1X NEAA/ 1X L-glutamine/ Pen-strep. They are cultured at 37 °C with 5% CO2.

extract_protocol: Total RNA was extracted, DNAse treated, and purified using a RNAeasy Mini Kit (Qiagen). Reverse transcription to obtain cDNAs were performed using SuperScript III Kits (Life Technologies).

tag: cell line

tag: cell type

value: gastric cancer


title: Crohn's disease Ileal descending colon P44

value: Ileal


title: ADHD_untreat

description: RNA pool from untreated LCLs generated from ADHD patients

value: ADHD

value: LCLs from 7 ADHD patients


title: KLF5_siRNA_KatoIII_2

value: KATOIII


title: KLF5_siRNA_KatoIII_1


title: KLF5_siRNA_KatoIII_3


title: KLF5_siRNA_YCC3_2


title: GATA6_siRNA_YCC3_3


title: KLF5_siRNA_AGS_3

value: AGS


title: healthy control NA descending colon P18

value: M


title: KLF5_siRNA_AGS_1


title: healthy control NA descending colon P19


title: KLF5_siRNA_YCC3_1


title: KLF5_siRNA_AGS_2


title: healthy control NA descending colon P40


title: healthy control NA descending colon P51

value: F


title: GATA6_siRNA_YCC3_2


title: GATA6_siRNA_YCC3_1


title: healthy control NA descending colon P38


title: ADHD_MPH

description: RNA pool from MPH-treated LCLs generated from ADHD patients


title: GATA6_siRNA_KatoIII_3


title: healthy control NA descending colon P50


title: ulcerative colitis Left descending colon P34

value: ulcerative colitis

value: Left


title: GATA6_siRNA_AGS_2


title: GATA6_siRNA_AGS_3


title: GATA6_siRNA_KatoIII_1


title: ulcerative colitis Left descending colon P48

value: descending colon


title: GATA4_siRNA_YCC3_2


title: GATA6_siRNA_KatoIII_2


title: healthy control NA descending colon P63


title: GATA4_siRNA_YCC3_3


title: GATA6_siRNA_AGS_1


title: ulcerative colitis Pancolitis descending colon P56

value: Pancolitis


title: GATA4_siRNA_KatoIII_3


title: GATA4_siRNA_AGS_2


title: GATA4_siRNA_YCC3_1


title: GATA4_siRNA_KatoIII_2


title: ulcerative colitis Pancolitis descending colon P4


title: ulcerative colitis Pancolitis descending colon P22


title: GATA4_siRNA_KatoIII_1


title: healthy control NA descending colon P9


title: NT_siRNA_YCC3_3


title: GATA4_siRNA_AGS_1


title: NT_siRNA_YCC3_2


title: GATA4_siRNA_AGS_3


title: healthy control NA descending colon P28


title: NT_siRNA_AGS_3


title: NT_siRNA_YCC3_1


title: Crohn's disease Ileal descending colon P32

value: Crohn's disease


title: healthy control NA descending colon P37


title: NT_siRNA_AGS_1


title: NT_siRNA_KatoIII_2


title: NT_siRNA_KatoIII_3


title: NT_siRNA_AGS_2


title: ulcerative colitis Pancolitis descending colon P15


title: NT_siRNA_KatoIII_1


title: healthy control NA descending colon P27


title: healthy control NA ascending colon P28

value: ascending colon


title: gastric tumor GC-990286T

first: Zhengdeng

last: Lei

address: 8 College Road

institute: Duke-NUS graduate medical school

description: gene expression data from gastric tumor GC-990286T

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000 7G.

data_processing: The data were RMA normalized with R (v.2.12.0) package affy.

source_name: gastric tumor GC-990286T

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 to 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

extract_protocol: Total RNA was extracted from primary tumors using RNeasy mini spin columns (Qiagen) according to the instructions of the manufacturer.

value: gastric adenocarcinoma


title: ulcerative colitis Pancolitis descending colon P55

value: Pinch biopsy


title: gastric tumor GC-990436T

description: gene expression data from gastric tumor GC-990436T

source_name: gastric tumor GC-990436T


title: ulcerative colitis Pancolitis descending colon P16


title: gastric tumor GC-990488T

description: gene expression data from gastric tumor GC-990488T

source_name: gastric tumor GC-990488T


title: gastric tumor GC-990231T

description: gene expression data from gastric tumor GC-990231T

source_name: gastric tumor GC-990231T


title: gastric tumor GC-990428T

description: gene expression data from gastric tumor GC-990428T

source_name: gastric tumor GC-990428T


title: gastric tumor GC-990247T

description: gene expression data from gastric tumor GC-990247T

source_name: gastric tumor GC-990247T


title: ulcerative colitis Left descending colon P62


title: gastric tumor GC-990070T

description: gene expression data from gastric tumor GC-990070T

source_name: gastric tumor GC-990070T


title: gastric tumor GC-990020T

description: gene expression data from gastric tumor GC-990020T

source_name: gastric tumor GC-990020T


title: gastric tumor GC-980437T

description: gene expression data from gastric tumor GC-980437T

source_name: gastric tumor GC-980437T


title: gastric tumor GC-990187T

description: gene expression data from gastric tumor GC-990187T

source_name: gastric tumor GC-990187T


title: gastric tumor GC-980184T

description: gene expression data from gastric tumor GC-980184T

source_name: gastric tumor GC-980184T


title: ulcerative colitis Left descending colon P14


title: gastric tumor GC-980151T

description: gene expression data from gastric tumor GC-980151T

source_name: gastric tumor GC-980151T


title: gastric tumor GC-980255T

description: gene expression data from gastric tumor GC-980255T

source_name: gastric tumor GC-980255T


title: ulcerative colitis Pancolitis descending colon P25


title: gastric tumor GC-980324T

description: gene expression data from gastric tumor GC-980324T

source_name: gastric tumor GC-980324T


title: ulcerative colitis Pancolitis descending colon P33


title: receptive endometrium at day 7 of estrous cycle after in vivo embryo produce transfer pool2

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: miRNA expression data from endometrium

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Bos taurus

source_name: endometrium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: breed

value: Simmental

value: heifers

tag: time

value: day 7

tag: type of transfer

value: in vivo

tag: receptive

value: yes


title: gastric tumor GC-980161T

description: gene expression data from gastric tumor GC-980161T

source_name: gastric tumor GC-980161T


title: gastric tumor GC-980447T

description: gene expression data from gastric tumor GC-980447T

source_name: gastric tumor GC-980447T


title: gastric tumor GC-980024T

description: gene expression data from gastric tumor GC-980024T

source_name: gastric tumor GC-980024T


title: healthy control NA descending colon P36

source_name: Descol

value: healthy control


title: receptive endometrium at day 7 of estrous cycle after in vivo embryo produce transfer pool3

description: miRNA expression data from endometrium


title: gastric tumor GC-970032T

description: gene expression data from gastric tumor GC-970032T

source_name: gastric tumor GC-970032T


title: Crohn's disease Ileocolonic descending colon P12

value: Ileocolonic


title: gastric tumor GC-96141474T

description: gene expression data from gastric tumor GC-96141474T

source_name: gastric tumor GC-96141474T


title: receptive endometrium at day 3 of estrous cycle after in vivo embryo produce transfer pool3

description: miRNA expression data from endometrium

value: day 3


title: gastric tumor GC-9432729T

description: gene expression data from gastric tumor GC-9432729T

source_name: gastric tumor GC-9432729T


title: receptive endometrium at day 3 of estrous cycle after in vivo embryo produce transfer pool1

description: miRNA expression data from endometrium


title: receptive endometrium at day 3 of estrous cycle after in vivo embryo produce transfer pool2

description: miRNA expression data from endometrium


title: gastric tumor GC-980029T

description: gene expression data from gastric tumor GC-980029T

source_name: gastric tumor GC-980029T


title: Crohn's disease Ileal descending colon P1

value: M

value: Ileal


title: gastric tumor GC-90929219T

description: gene expression data from gastric tumor GC-90929219T

source_name: gastric tumor GC-90929219T


title: U373-MG

description: Gene expression profile of U373-MG glioblastoma cell line

hyb_protocol: 200µl hybridization mix prepared from labeled cRNA fragments was hybridized to oligonucleotide arrays for 16h at 45°C. Microarrays were washed and stained using the Affymetrix GeneTitan instrument with the Hyb-Wash-Scan setup option.

scan_protocol: The microarray plate was scanned with the GeneAtlas Scanner.

source_name: tumor cell culture

label_protocol: 100ng of total RNA were amplified and labeled with the HT 3' IVT Express Kit (Affymetrix); all steps were performed according to the manufacturer's protocol.

growth_protocol: Gliobastoma cell lines were cultured in the indicated growth medium supplemented with 10% fetal calf serum, 100 units/ml penicillin, 100 µg/ml streptomycin and 2 mM L-glutamine at 37°C.

extract_protocol: Total RNA was isolated with RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

value: glioblastoma

tag: p53 status

value: mutated

tag: pten status

tag: invasive behavior

value: invasive

tag: growth medium

value: Minimum Essential Medium


title: healthy control NA descending colon P8

tag: biopsy

tag: gender

value: F

value: descending colon


title: Crohn's disease Ileal descending colon P31

value: Pinch biopsy

tag: disease state

value: Crohn's disease

tag: phenotype


title: receptive endometrium at day 7 of estrous cycle after in vivo embryo produce transfer pool1

description: miRNA expression data from endometrium

value: Simmental

value: heifers


title: SNB19

description: Gene expression profile of SNB19 glioblastoma cell line

tag: tissue

value: Dulbecco's Modified Eagle Medium


title: healthy control NA descending colon P29


title: gastric tumor GC-74765340T

description: gene expression data from gastric tumor GC-74765340T

source_name: gastric tumor GC-74765340T

value: gastric adenocarcinoma


title: non receptive endometrium at day 7 of estrous cycle after in vivo embryo produce transfer pool2

description: miRNA expression data from endometrium

value: day 7

value: in vivo

value: no


title: non receptive endometrium at day 7 of estrous cycle after in vivo embryo produce transfer pool3

description: miRNA expression data from endometrium


title: non receptive endometrium at day 3 of estrous cycle after in vivo embryo produce transfer pool3

description: miRNA expression data from endometrium

value: day 3


title: GaMG

description: Gene expression profile of GaMG glioblastoma cell line

value: GaMG

value: wild type

value: Non-invasive


title: U87-MG

description: Gene expression profile of U87-MG glioblastoma cell line

value: glioblastoma

value: mutated


title: gastric tumor GC-73499299T

description: gene expression data from gastric tumor GC-73499299T

source_name: gastric tumor GC-73499299T


title: gastric tumor GC-73813499T

description: gene expression data from gastric tumor GC-73813499T

source_name: gastric tumor GC-73813499T


title: gastric tumor GC-80903789T

description: gene expression data from gastric tumor GC-80903789T

source_name: gastric tumor GC-80903789T


title: non receptive endometrium at day 7 of estrous cycle after in vivo embryo produce transfer pool1

description: miRNA expression data from endometrium


title: ulcerative colitis Pancolitis descending colon P23

value: M

value: ulcerative colitis

value: Pancolitis


title: ulcerative colitis Left descending colon P6

value: Pinch biopsy

value: Left

value: descending colon


title: healthy control NA descending colon P11

value: healthy control


title: ulcerative colitis Left descending colon P61


title: ulcerative colitis Pancolitis descending colon P24


title: non receptive endometrium at day 3 of estrous cycle after in vivo embryo produce transfer pool2

description: miRNA expression data from endometrium

value: Simmental

value: heifers


title: gastric tumor GC-73499279T

description: gene expression data from gastric tumor GC-73499279T

source_name: gastric tumor GC-73499279T

value: gastric adenocarcinoma


title: non receptive endometrium at day 3 of estrous cycle after in vivo embryo produce transfer pool1

description: miRNA expression data from endometrium

value: in vivo

value: no


title: DK-MG

description: Gene expression profile of DK-MG glioblastoma cell line

value: DK-MG

value: Dulbecco's Modified Eagle Medium


title: ulcerative colitis Left descending colon P26


title: gastric tumor GC-54119380T

description: gene expression data from gastric tumor GC-54119380T

source_name: gastric tumor GC-54119380T


title: Crohn's disease Ileal descending colon P3

value: F

value: Crohn's disease

value: Ileal


title: receptive endometrium at day 7 of estrous cycle after in vitro embryo produce transfer pool2

description: miRNA expression data from endometrium

source_name: endometrium

value: day 7

value: in vitro

value: yes


title: receptive endometrium at day 7 of estrous cycle after in vitro embryo produce transfer pool1

description: miRNA expression data from endometrium


title: gastric tumor GC-55761861T

description: gene expression data from gastric tumor GC-55761861T

source_name: gastric tumor GC-55761861T


title: Crohn's disease Ileocolonic descending colon P2

value: Pinch biopsy

value: M

value: Ileocolonic


title: receptive endometrium at day 7 of estrous cycle after in vitro embryo produce transfer pool3

description: miRNA expression data from endometrium


title: Crohn's disease Ileocolonic descending colon P20

value: descending colon


title: gastric tumor GC-63540193T

description: gene expression data from gastric tumor GC-63540193T

source_name: gastric tumor GC-63540193T


title: ulcerative colitis Left descending colon P60

value: ulcerative colitis

value: Left


title: receptive endometrium at day 3 of estrous cycle after in vitro embryo produce transfer pool1

description: miRNA expression data from endometrium

value: Simmental

value: heifers

value: day 3


title: receptive endometrium at day 3 of estrous cycle after in vitro embryo produce transfer pool3

description: miRNA expression data from endometrium


title: non receptive endometrium at day 7 of estrous cycle after in vitro embryo produce transfer pool3

description: miRNA expression data from endometrium

value: no


title: gastric tumor GC-42761681T

description: gene expression data from gastric tumor GC-42761681T

source_name: gastric tumor GC-42761681T

value: gastric adenocarcinoma


title: gastric tumor GC-37357120T

description: gene expression data from gastric tumor GC-37357120T

source_name: gastric tumor GC-37357120T


title: gastric tumor GC-21080055T

description: gene expression data from gastric tumor GC-21080055T

source_name: gastric tumor GC-21080055T


title: ulcerative colitis Proctitis rectum P59

source_name: R

value: F

value: Proctitis

value: rectum


title: Crohn's disease Ileal descending colon P13

source_name: Descol

value: Crohn's disease

value: Ileal


title: gastric tumor GC-20021031T

description: gene expression data from gastric tumor GC-20021031T

source_name: gastric tumor GC-20021031T


title: gastric tumor GC-20021007T

description: gene expression data from gastric tumor GC-20021007T

source_name: gastric tumor GC-20021007T


title: non receptive endometrium at day 7 of estrous cycle after in vitro embryo produce transfer pool1

description: miRNA expression data from endometrium

value: day 7

value: in vitro


title: non receptive endometrium at day 7 of estrous cycle after in vitro embryo produce transfer pool2

description: miRNA expression data from endometrium


title: healthy control NA rectum P57

value: Pinch biopsy

value: healthy control


title: receptive endometrium at day 3 of estrous cycle after in vitro embryo produce transfer pool2

description: miRNA expression data from endometrium

value: yes


title: ulcerative colitis Pancolitis descending colon P35

value: ulcerative colitis

value: Pancolitis

value: descending colon


title: ulcerative colitis Pancolitis rectum P56


title: healthy control NA rectum P58


title: gastric tumor GC-20020756T

description: gene expression data from gastric tumor GC-20020756T

source_name: gastric tumor GC-20020756T


title: gastric tumor GC-20020700T

description: gene expression data from gastric tumor GC-20020700T

source_name: gastric tumor GC-20020700T


title: non receptive endometrium at day 3 of estrous cycle after in vitro embryo produce transfer pool3

description: miRNA expression data from endometrium

value: Simmental

value: heifers


title: ulcerative colitis Pancolitis rectum P55

value: M


title: ulcerative colitis Proctitis rectum P54


title: gastric tumor GC-20020457T

description: gene expression data from gastric tumor GC-20020457T

source_name: gastric tumor GC-20020457T

value: gastric adenocarcinoma


title: gastric tumor GC-2001098T

description: gene expression data from gastric tumor GC-2001098T

source_name: gastric tumor GC-2001098T


title: gastric tumor GC-20020447T

description: gene expression data from gastric tumor GC-20020447T

source_name: gastric tumor GC-20020447T


title: healthy control NA rectum P52

value: F


title: gastric tumor GC-20020563T

description: gene expression data from gastric tumor GC-20020563T

source_name: gastric tumor GC-20020563T


title: 1737

city: Kelvin Grove

first: Joanne

last: Voisey

state: Queensland

address: 60 Musk Ave

department: IHBI

country: Australia

institute: Queensland University of Technology

description: genomic DNA from frontal cortex

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: standard Illumina scan settings

data_processing: GenomeStudio v2011.1 with Methylation module 1.9.0 softward

label: cy3, cy5

source_name: frontal cortex

label_protocol: Standard Illumina protocol

extract_protocol: genomic DNA was extracted using the Roche MagNa Pure Compact

tag: disease status (1=control, 2=scz patient)

tag: age

tag: pmi (hours)

tag: sample well

tag: sentrix id

tag: sentrix position


title: non receptive endometrium at day 3 of estrous cycle after in vitro embryo produce transfer pool2

description: miRNA expression data from endometrium

source_name: endometrium

tag: breed

tag: time

value: day 3

tag: type of transfer

value: no


title: healthy control NA rectum P51

value: rectum


title: healthy control NA rectum P47


title: healthy control NA rectum P50


title: gastric tumor GC-2000616T

description: gene expression data from gastric tumor GC-2000616T

source_name: gastric tumor GC-2000616T


title: Crohn's disease Colonic rectum P45

value: Crohn's disease

value: Colonic


title: healthy control NA rectum P49


title: gastric tumor GC-2001094T

description: gene expression data from gastric tumor GC-2001094T

source_name: gastric tumor GC-2001094T


title: gastric tumor GC-2001271T

description: gene expression data from gastric tumor GC-2001271T

source_name: gastric tumor GC-2001271T


title: gastric tumor GC-2000762T

description: gene expression data from gastric tumor GC-2000762T

source_name: gastric tumor GC-2000762T


title: ulcerative colitis Left rectum P48

value: Left


title: gastric tumor GC-2000763T

description: gene expression data from gastric tumor GC-2000763T

source_name: gastric tumor GC-2000763T


title: Crohn's disease Ileal rectum P44

source_name: R

value: Pinch biopsy

value: Ileal


title: gastric tumor GC-2000734T

description: gene expression data from gastric tumor GC-2000734T

source_name: gastric tumor GC-2000734T


title: gastric tumor GC-2000710T

description: gene expression data from gastric tumor GC-2000710T

source_name: gastric tumor GC-2000710T


title: Crohn's disease Ileal rectum P46


title: healthy control NA rectum P43

value: healthy control


title: gastric tumor GC-2001140T

description: gene expression data from gastric tumor GC-2001140T

source_name: gastric tumor GC-2001140T


title: healthy control NA rectum P53


title: healthy control NA rectum P41


title: gastric tumor GC-20020159T

description: gene expression data from gastric tumor GC-20020159T

source_name: gastric tumor GC-20020159T


title: gastric tumor GC-2000563T

description: gene expression data from gastric tumor GC-2000563T

source_name: gastric tumor GC-2000563T


title: healthy control NA rectum P39


title: healthy control NA rectum P40


title: non receptive endometrium at day 3 of estrous cycle after in vitro embryo produce transfer pool1

description: miRNA expression data from endometrium

value: in vitro

tag: receptive


title: gastric tumor GC-2000510T

description: gene expression data from gastric tumor GC-2000510T

source_name: gastric tumor GC-2000510T


title: healthy control NA rectum P42


title: Lymphoblastoid cell line_Individual 3-3_cycle 0_hybridization_batch_1

city: Philadelphia

first: Minal

last: Caliskan

state: PA

address: 415 Curie Blvd., Room 540

department: Genetics

country: USA

institute: University of Pennsylvania

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data across four hybridization batches are included in the file named Matrix non-normalized_batch 1, Matrix non-normalized_batch 2, Matrix non-normalized_batch 3, Matrix non-normalized_batch 4. Among all probes targeted, 24,314 probes passed our probe quality control check (probes that mapped to unique Ensembl gene IDs and probes that did not contain any HapMap SNPs with minor allele frequency > 0.01 in the CEU population). We performed our analyses in 12,972 of the 24,314 probes that were detected as expressed (probes with a detection P value < 0.05 in at least 25% of the 187 samples). Log2-transformed and rank-invariant normalized (using scripts developed in-house by Russell Bainer)  probe intensity data are included in data tables.

label: Biotin

source_name: Lymphoblastoid cell line

label_protocol: Standard Illumina label protocol

growth_protocol: A unit of blood was obtained from six unrelated healthy individuals of Caucasian ethnicity by Research Blood Components, LLC. Unpurified buffy coats were prepared from whole blood and shipped to the University of Chicago. At the University of Chicago, peripheral blood mononuclear cells were isolated by further processing of the unpurified buffy coats using ficoll-hypaque protocol. CD20+ B cells are isolated from peripheral blood mononuclear cells using magnetic anti-CD20 mAb-coated microbeads (MACs, Miltenyi Biotec, CA, USA). LCLs are established by EBV-mediated transformation, using the protocol provided by Coriell Cell Repositories.

extract_protocol: Total RNA was extracted using the Rneasy Plus Mini Kit

value: Female

tag: hybridization batch

tag: cell type

value: Lymphoblastoid cell line


title: gastric tumor GC-2000038T

description: gene expression data from gastric tumor GC-2000038T

source_name: gastric tumor GC-2000038T


title: gastric tumor GC-2000137T

description: gene expression data from gastric tumor GC-2000137T

source_name: gastric tumor GC-2000137T


title: gastric tumor GC-2000344T

description: gene expression data from gastric tumor GC-2000344T

source_name: gastric tumor GC-2000344T


title: healthy control NA rectum P38

tag: biopsy


title: healthy control NA rectum P37

tag: gender


title: Lymphoblastoid cell line_Individual 6-6_cycle 0_hybridization_batch_1

value: Male


title: healthy control NA rectum P36

tag: disease state


title: ulcerative colitis Pancolitis rectum P35

value: ulcerative colitis

tag: phenotype

value: Pancolitis


title: B cell_Individual 5_hybridization_batch_1

source_name: B cell

value: B cell


title: B cell_Individual 2_hybridization_batch_1


title: Lymphoblastoid cell line_Individual 4-4_cycle 0_hybridization_batch_1


title: Crohn's disease Ileal rectum P32

value: F

tag: tissue


title: 665

description: genomic DNA from frontal cortex

source_name: frontal cortex

tag: disease status (1=control, 2=scz patient)

value: MM


title: Crohn's disease Colonic rectum P30

value: M


title: Lymphoblastoid cell line_Individual 2-4_cycle 0_hybridization_batch_1


title: 683

description: genomic DNA from frontal cortex

tag: age


title: Lymphoblastoid cell line_Individual 5-4_cycle 0_hybridization_batch_1


title: 707

description: genomic DNA from frontal cortex

tag: pmi (hours)


title: Lymphoblastoid cell line_Individual 1-2_cycle 0_hybridization_batch_1


title: ulcerative colitis Left rectum P34

value: rectum


title: Crohn's disease Ileal rectum P31

value: Crohn's disease


title: healthy control NA rectum P28


title: ulcerative colitis Pancolitis rectum P33


title: 677

description: genomic DNA from frontal cortex

tag: sample well


title: healthy control NA rectum P29


title: Lymphoblastoid cell line_Individual 6-4_cycle 0_hybridization_batch_1


title: 615

description: genomic DNA from frontal cortex

tag: sentrix id


title: Lymphoblastoid cell line_Individual 3-1_cycle 0_hybridization_batch_1


title: Lymphoblastoid cell line_Individual 4-3_cycle 0_hybridization_batch_1


title: 2464

description: genomic DNA from frontal cortex

tag: sentrix position


title: 320

description: genomic DNA from frontal cortex


title: Lymphoblastoid cell line_Individual 4-6_cycle 0_hybridization_batch_1


title: 336

description: genomic DNA from frontal cortex


title: Lymphoblastoid cell line_Individual 6-3_cycle 0_hybridization_batch_1


title: healthy control NA rectum P27


title: ulcerative colitis Pancolitis rectum P22


title: ulcerative colitis Pancolitis rectum P25


title: ulcerative colitis Pancolitis rectum P24


title: 2586

description: genomic DNA from frontal cortex


title: 2583

description: genomic DNA from frontal cortex


title: Lymphoblastoid cell line_Individual 2-5_cycle 0_hybridization_batch_1


title: Lymphoblastoid cell line_Individual 5-2_cycle 0_hybridization_batch_1


title: gastric tumor GC-2000525T

description: gene expression data from gastric tumor GC-2000525T

source_name: gastric tumor GC-2000525T

value: gastric adenocarcinoma


title: Crohn's disease Colonic rectum P21

value: Colonic


title: B cell_Individual 1_hybridization_batch_1


title: ulcerative colitis Pancolitis rectum P23

value: Pinch biopsy


title: 885

description: genomic DNA from frontal cortex


title: 925

description: genomic DNA from frontal cortex


title: Crohn's disease Ileocolonic rectum P20

value: Ileocolonic


title: 1651

description: genomic DNA from frontal cortex


title: 2785

description: genomic DNA from frontal cortex


title: 2211

description: genomic DNA from frontal cortex


title: Lymphoblastoid cell line_Individual 6-5_cycle 0_hybridization_batch_1


title: Lymphoblastoid cell line_Individual 5-5_cycle 0_hybridization_batch_1


title: Lymphoblastoid cell line_Individual 3-4_cycle 0_hybridization_batch_1


title: Lymphoblastoid cell line_Individual 6-1_cycle 0_hybridization_batch_1


title: Lymphoblastoid cell line_Individual 4-7_cycle 0_hybridization_batch_1


title: ulcerative colitis Pancolitis rectum P16


title: ulcerative colitis Pancolitis rectum P15


title: healthy control NA rectum P17

value: healthy control


title: healthy control NA rectum P18


title: ulcerative colitis Left rectum P14

value: Left


title: healthy control NA rectum P19


title: Lymphoblastoid cell line_Individual 1-4_cycle 0_hybridization_batch_1


title: 1671

description: genomic DNA from frontal cortex


title: Lymphoblastoid cell line_Individual 5-1_cycle 0_hybridization_batch_1


title: 549

description: genomic DNA from frontal cortex


title: 3436

description: genomic DNA from frontal cortex


title: Crohn's disease Ileal rectum P13

value: Ileal


title: 3739

description: genomic DNA from frontal cortex


title: ulcerative colitis Left rectum P26


title: 532

description: genomic DNA from frontal cortex


title: B cell_Individual 4_hybridization_batch_1

value: Female


title: healthy control NA rectum P10


title: K_Free, rep_3

city: Moscow

first: Sergei

last: Orlov

address: 1/b.12 Leninskie Gory

country: Russia

institute: Moscow State Univeristy

description: gene expression data from aortic smooth muscle cells

hyb_protocol: 2.5 µg of fragmented and labeled ss-DNA were hybridized onto the chip for 16 hr at 45°C. The chips were washed and stained in the GeneChip® Fluidics Station 450, using the fluidic protocol FS450_0007.

scan_protocol: Rat Gene 1.0 ST arrays were scanned using the GeneChip® Scanner 3000 7G. The software used for image processing was AGCC version 3.2.

data_processing: Partek Genomics Suite (Partek, St. Louis, Missouri) was used for data analysis. The data were normalized by Robust Multichip Average (RMA) algorithm with adjustment for GC content, which uses background adjustment, quantile normalization and summarization.

organism: Rattus norvegicus

source_name: K_Free, rep_3

label_protocol: The Fragmented Single-Stranded DNA was labeled by TdT with the Affymetrix® DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Rat aortic smooth muscle cells (RASMC), purchased from Lonza (Walkersville, MD, USA), were grown at 37oC in a CO2 incubator in Dulbecco’s modified Eagle medium (DMEM, Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, 100 g/ml streptomycin, and subjected to less than 10 passages. To establish quiescence, the cells were incubated for 24 hr in media in which FBS concentration was reduced to 0.2%.

extract_protocol: Total RNA was extracted from cells grown in 6-well plates with TRIzol® reagent (Invitrogen) and purified with RNeasy® MinElute cleanup kit (Qiagen, Valencia, CA, USA), following the manufacturers’ protocols.

treatment_protocol: Quiescent cells were washed with K+-free DMEM (Sp-DMEM; Invitrogen) and incubated for 6 hr at 37oC in a humidified atmosphere with 5% CO2/balance air in control DMEM, K+-free DMEM and DMEM containing 3 mM ouabain.

value: aortic smooth muscle cells

tag: protocol

value: K+-free DMEM


title: 509

description: genomic DNA from frontal cortex


title: healthy control NA rectum P11


title: K_Free, rep_2

source_name: K_Free, rep_2


title: skeletal muscle tissue from healthy individual 2

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Normalized average beta value. The methylation level of each of the >  480,000 CpG sites was calculated using the GenomeStudio Methylation Module 1.9.0 (Illumina). Normalization was performed using Normalization to Internal Controls and Background Subtraction options implemented in the Methylation Module 1.9.0.

label: Cy3 and Cy5

source_name: skeletal muscle

label_protocol: Standard Illumina labelling protocol

growth_protocol: Human primary skeletal muscle myoblasts (CC-2580, Lonza) were cultured with in SkGM-2 medium (CC-3245, Lonza). Differentiation into myotubes was stimulated by switching the culture medium to DMEM-F12 (SH30023.01, Thermo scientific) supplemented with 2% horse serum (H1138, Sigma Aldrich) when cells reached about 50% confluencet (day 1). Medium was replaced every other day, and changed to SkGM-2 medium at day 8. SkGM-2 medium was replaced every other day until day 15. Cells were collected on days 1, day3, day8, and day15 for subsequent analyses. Human normal skeletal muscle tissues from two individuals were obtained from Tissue Solutions (SK052009, SKm1;, SKM102210A, SKm2). Human mesenchymal stem cells (hHMSCs, PT-2501, Lonza) were grown in DMEM (SH30022.01, Thermo Scientific) supplemented with 10% fetal bovinene  serum (SH30070.03, Thermo Scientific). All cell lines and human tissues were derived from male individuals.

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

value: male

tag: health status

value: healthy


title: Lymphoblastoid cell line_Individual 2-1_cycle 0_hybridization_batch_1

value: Lymphoblastoid cell line


title: Lymphoblastoid cell line_Individual 6-2_cycle 0_hybridization_batch_1

value: Male


title: K_Free, rep_1

source_name: K_Free, rep_1


title: 3754

description: genomic DNA from frontal cortex

value: F


title: healthy control NA rectum P8

source_name: R

value: rectum


title: healthy control NA rectum P9

value: M


title: Ouabain, rep_3

source_name: Ouabain, rep_3

value: DMEM containing 3 mM ouabain


title: Crohn's disease Ileocolonic rectum P12

value: Crohn's disease


title: ulcerative colitis Left rectum P7

value: Pinch biopsy

value: ulcerative colitis


title: myoblasts 3 days after myogenic stimuli

source_name: myoblasts


title: myoblasts 8 days after myogenic stimuli


title: myoblasts 15 days after myogenic stimuli


title: ulcerative colitis Left rectum P6


title: human mesenchymal stem cells

source_name: mesenchymal stem cells


title: 3788

description: genomic DNA from frontal cortex


title: Lymphoblastoid cell line_Individual 3-5_cycle 0_hybridization_batch_1


title: Ouabain, rep_1

source_name: Ouabain, rep_1


title: ulcerative colitis Pancolitis rectum P4

value: Pancolitis


title: Lymphoblastoid cell line_Individual 2-3_cycle 0_hybridization_batch_1


title: Control, rep_1

source_name: Control, rep_1

value: control DMEM


title: Lymphoblastoid cell line_Individual 5-8_cycle 0_hybridization_batch_1

source_name: Lymphoblastoid cell line


title: B cell_Individual 3_hybridization_batch_1

value: B cell


title: Lymphoblastoid cell line_Individual 5-7_cycle 0_hybridization_batch_1


title: Crohn's disease Ileal rectum P3

value: Ileal


title: Control, rep_2

source_name: Control, rep_2

value: aortic smooth muscle cells


title: Lymphoblastoid cell line_Individual 4-8_cycle 0_hybridization_batch_1

value: Female


title: Lymphoblastoid cell line_Individual 2-2_cycle 0_hybridization_batch_1


title: Crohn's disease Ileocolonic rectum P2

value: Ileocolonic


title: Ouabain, rep_2

source_name: Ouabain, rep_2


title: Lymphoblastoid cell line_Individual 3-6_cycle 0_hybridization_batch_1


title: ga1-3 SCL3OE replicate 2

city: Seoul

first: Eun Kyung

last: Yoon

address: 120 Neungdong-ro Gwangjin-gu

institute: KonKuk University

description: ga1 SCL3OE-2

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45°C on Affymetrix ATH1 GeneChip® Arabidopsis Genome Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Microarray Suite version 5.0 (MAS 5.0) algorithm implemented in Affymetrix Expression Console software (version1.1) was used to normalize the raw data. To reduce noise for the significance analysis, probe sets that were called Present by the MAS5 detection call in 100% of the samples were selected.  Highly expressed genes that showed over 1.5-fold difference between the signal values of control and test samples were selected for further study.

organism: Arabidopsis thaliana

source_name: ga1 muant and SCL3 overexpression

label_protocol: Biotinylated cDNA were prepared from 300  ng total RNA (GeneChip® 3’ IVT Express Kit User Manual P/N 702646 Rev. 1, Affymetrix), according to the standard Affymetrix ATH1 microarray instructions.

growth_protocol: plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C

extract_protocol: RNeasy plant mini kit (Qiagen), according to manufacturer's instructions

tag: genotype/variation

value: ga1 muant and SCL3 overexpression

value: whole root


title: ga1-3 scl3-1 replicate 3

description: ga1 scl3-3

source_name: ga1 scl3 double mutant

value: ga1 scl3 double mutant


title: ga1-3 SCL3OE replicate 1

description: ga1 SCL3OE-1


title: tNGFR CD34+CD38-

city: Groningen

first: Hein

last: Schepers

state: Groningen

address: Hanzeplein 1

department: Internal Medicine

country: Netherlands

institute: University Medical Center Groningen

description:
6898376049_B
tNGFR CD34+CD38-

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: Illumina i-Scan reader

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

source_name: CB derived CD34+CD38-

label_protocol: Standard Illumina hybridization protocol

growth_protocol: CB CD34+ cells were isolated by Miltenyi miniMACS column. Cells were prestimulated in HPGM with 100 ng/ml KITL, FLT3L and TPO for 12 hrs. Cells were transduced with control or CITED2 overexpression lentivectors, or shRNA CITED2 lentivectors, in three rounds over 48 hrs. Transduced cells were sorted after which RNA was isolated for Illumina beadhchip arrays HT12 v4

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

tag: transducer

value: tNGFR


title: Lymphoblastoid cell line_Individual 1-3_cycle 0_hybridization_batch_1

value: Male

tag: hybridization batch

value: Lymphoblastoid cell line


title: myoblasts before myogenic stimuli

value: male

value: healthy


title: ulcerative colitis Left rectum P5

value: Pinch biopsy

value: F

value: Left

value: rectum


title: B cell_Individual 6_hybridization_batch_1

source_name: B cell

tag: cell type

value: B cell


title: ga1-3 scl3-1 replicate 1

description: ga1 scl3-1


title: CITED2 CD34+CD38-

description:
6898376049_D
CITED2 CD34+CD38-


title: ga1-3 scl3-1 replicate 2

description: ga1 scl3-2


title: shCITED2 CD34+CD38+

description:
6898376049_K
shCITED2 CD34+CD38+

source_name: CB derived CD34+CD38+


title: Lymphoblastoid cell line_Individual 3-7_cycle 0_hybridization_batch_1


title: Crohn's disease Ileal rectum P1

tag: biopsy

value: M

value: Crohn's disease

value: Ileal


title: Lymphoblastoid cell line_Individual 1-8_cycle 0_hybridization_batch_1

tag: gender


title: skeletal muscle tissue from healthy individual 1


title: Lymphoblastoid cell line_Individual 2-6_cycle 0_hybridization_batch_1

value: Female


title: Lymphoblastoid cell line_Individual 4-1_cycle 0_hybridization_batch_1


title: shSCR CD34+CD38+

description:
6898376049_G
shSCR CD34+CD38+

value: shSCR


title: shCITED CD34+CD38-

description:
6898376049_I
shCITED CD34+CD38-


title: ga1-3 replicate 2

source_name: ga1 mutant

value: ga1 mutant

value: whole root


title: ga1-3 replicate 3


title: Lymphoblastoid cell line_Individual 1-5_cycle 0_hybridization_batch_1


title: ga1-3 replicate 1


title: shSCR CD34+CD38-

description:
6898376049_E
shSCR CD34+CD38-


title: SG200∆hxt1 24hpi rep2

status: Public on Sep 04 2014

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

description: Gene expression data from cells growing on the plant surface 24 hour post inoculation

scan_protocol: Affymetrix GSC3000

data_processing: Affymetrix Micro Array Suite 5.0

organism: Mycosarcoma maydis

source_name: Ustilago maydis 24 hours post inoculation

label_protocol: Affymetrix GeneChip® 3.’ IVT Express Kit

growth_protocol: Growth of cells, plant infections, cell harvest and RNA extraction is described in Doehlemann G et al. 2008. Establishment of compatibility in the Ustilago maydis/maize pathosystem. Journal of Plant Physiology 165(1): 29-40.

tag: genotype

tag: sample type

value: cells collected from plant surface


title: SG200∆hxt1 hxt1(R164K):eGFP 24hpi rep3

extract_protocol: Growth of cells, plant infections, cell harvest and RNA extraction is described in Doehlemann G et al. 2008. Establishment of compatibility in the Ustilago maydis/maize pathosystem. Journal of Plant Physiology 165(1): 29-40.

value: SG200∆hxt1 hxt1(R164K):eGFP


title: SG200 24hpi rep2


title: SG200∆hxt1 hxt1(R164K):eGFP 24hpi rep2


title: SG200∆hxt1 hxt1(R164K):eGFP 24hpi rep1


title: SG200∆hxt1 24hpi rep3


title: SG200 24hpi rep3


title: SG200 24hpi rep1


title: SG200∆hxt1 24hpi rep1


title: Egg_High quality_10-somite stage_rep2

city: Oslo

first: Knut Erik

last: Tollefsen

address: Gaustadallèen 21

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

description: Basal gene expression, egg larvae of high quality

hyb_protocol: Totally 600 ng of Cy3-labeled, linearly amplified cRNA was fragmented and hybridized to 8x60k microarrays and rotationally (10 rpm) incubated at 65 ºC for 17 h.

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (Dye channel: G (green), scan region: Agilent HD (61 × 21.6 mm), Scan resolution: 3 µm, Tiff file dynamic range: 20 bit, Green PMI gain: 100%).

data_processing: The microarray scan images (raw signal intensity) were extracted using Agilent Feature Extraction software v7.2. Raw data were normalization (quantile), filtered to be within the 20-100% percentile of intensity values and non-uniform outliers were excluded using GeneSpring GX v10.0.2 (Agilent Technologies). All data were filtered for missing values, replaced by row mean imputation and a cut-off of ≥0.5 applied to all data to remove features close to the mean low intensity threshold across arays. Differential gene expression analysis were performed by Limma with Benjamini-Hochberg FDR correction by Babelomics 4.3 (see http://babelomics.bioinfo.cipf.es/) and  a 2-fold cut-off imposed prior to additional analysis.

organism: Hippoglossus hippoglossus

source_name: Egg_10-somite stage

label_protocol: Cyanine 3-CTP (Cy3) labeled cRNA was made from 200 ng total RNA using Agilent Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, California, USA). The cRNA dye incorporation and yiled were checked using Agilent Bioanalyzer (Agilent Technologies)

growth_protocol: Developing embryos at the 8-cell stage, 8 h post fertilisation (hpf, 8C); germ ring stage (GR), 82 hpf; 10-somite stage (10SS) 142 hpf; and hatched larvae (HT), 340 hpf, were collected from eight females (30-40 kg) at a commercial Atlantic halibut farm (Risørfisk AS, Risør, Norway). All oocytes were fertilized in vitro with pooled sperm from two random males (15-20 kg) being at the peak of reproductive season. Eggs were incubated in large scale 280 L incubators (salinity 34 ± 1 ‰ and temperature 6.3 ± 0.1 ºC). Eggs were sampled at different developmetnal stages by snap-freezing in liquid nitrogen.

extract_protocol: Total RNA was extracted from frozen eggs using the Tri reagent method (sigma-Aldrich, St.Louis, Mo, USA) using QIAazol (Qiagen, Nydalen, Sweden) according to the manufacturer’s instructions. The RNA quality (purity and yield) was controlled by photometric analyses (260/230 > 1.8, 260/280>1.5, yield >200 ng/μL) using Nanodrop® spectrophotometer (ND-1000, Nanodrop Technologies, Wilminton, Delaware, USA) and RNA integrity (RIN>9.0) inspected by Bioanalyzer gelelectrophoresis with RNA 6000 Nano chips (Agilent technologies, Santa Clara, California, USA) according to the manufacturer’s instructions.

tag: developmental stage

value: 10-somite stage


title: Hatched embryo_High quality_Rep1

source_name: Hatched embryo

value: Hatched embryo


title: Hatched embryo_High quality_Rep2


title: Egg_High quality_10-somite stage_rep3


title: Egg_High quality_Germ ring stage_rep3

source_name: Egg_Germ ring stage

value: Germ ring stage


title: Hatched embryo_High quality_Rep3


title: Egg_High quality_10-somite stage_rep1


title: FAE KO1

city: Toyama

first: yukihiro

last: furusawa

address: Kurokawa

institute: Toyama Prefectural University

description: Untreated

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

scan_protocol: GeneChips were scanned using the  Scanner

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 arbitrarily set to 100.

organism: Mus musculus

source_name: follicle associated epithelium (FAE) of small intestine

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

extract_protocol: QIAGEN Rneasy mini kit

tag: strain

value: depleted of RBP-J


title: Egg_Low quality_8-cell embryo_rep3

description: Basal gene expression, egg larvae of Low quality

source_name: Egg_8-cell embryo

value: 8-cell embryo


title: FAE KO2

description: Untreated


title: Egg_Low quality_8-cell embryo_rep2


title: Egg_High quality_8-cell embryo_rep2


title: Egg_High quality_8-cell embryo_rep3


title: FAE WT

description: Untreated

value: wild type RBP-J


title: Egg_High quality_8-cell embryo_rep1


title: Egg_High quality_Germ ring stage_rep2


title: Egg_Low quality_8-cell embryo_rep1


title: Sham_Control_7d_5

city: Louisville

first: Nigel

middle: G. F.

last: Cooper

state: KY

address: 500 S Preston St.

department: Anatomical Science and Neurobiology

institute: University of Louisville

hyb_protocol: The dried RNA sample was re-suspended in 18μl of DNase/RNase-free water and then hybridized to Agilent rat miRNA microarrays (8x15K feature with 350 miRNA, CA G4472A) with hybridization buffer at 550C for 20 hours. After hybridization, the microarray slides were washed with Agilent gene expression wash buffer kit (Agilent, 5188-5327): buffer 1 at room temperature for 5min; and buffer 2 at 370C for 5min.

scan_protocol: The microarray slides were scanned with the aid of an Agilent microarray scanner (G2565BA) with a setting for one-color using the green channel and 5um resolution. The one-color microarray images (.tif) were extracted with the aid of Feature Extraction software (v 9.5.1, Agilent).

data_processing: The raw data files with total 350 miRNAs extracted from Agilent Feature extraction software were further processed and analyzed by GeneSpring GX10.0 software. The raw data were at first normalized with the following conditions and then filtered by the flag using GeneSpring GX10.0 software. The normalization included log2 transformation, per chip normalization to 75% quantile and  dropped per gene normalization to median. Filtered on the flag included miRNAs where at least 100 percent of samples in any 1 out of 15 conditions have flags in Present or Marginal. We retained the 219 normalized miRNAs for the further statistical analysis.

label_protocol: 100ng total RNA was used to generate fluorescent miRNA with the aid of  Calf Intestine Alkaline Phosphatase (CIP) kit (GE Healthcare, Ca E2250Y), T4 RNA Ligase kit (GE Healthcare, CA E2050Y), Agilent’s miRNA Labeling Reagent and Hybridization kit provided with the Cyanine 3-pCP (Agilent, Wilmington De 5190-0408). Briefly, the RNA was treated with CIP (16U/uL) and denatured with 100% DMSO.  The dephosphorylated RNA was ligated to pCP-Cy3 by T4-RNA Ligase. The labeled RNA was purified with the Micro Bio-Spin 6 Column (Bio-Rad, CA 732-6221). The desalted labeled RNA was dried down using a Speed-vac.

growth_protocol: Long Evan’s hooded male rats (Harlan, Indianapolis, IN) weighing 250 to 300g were used. All animals were housed on a 12-hour light– dark cycle with food and water. The treatment and care of all animals used in this study were approved by the University of Louisville Institutional Animal Care and Use Committee (IACUC) and were performed in accordance with the ARVO Statement for the Use and Care of Animals in Ophthalmic and Vision Research.

extract_protocol: Retinas were homogenized in lysis/binding buffer (Ambion, Inc.) using a motorized rotor-stator homogenizer. Total RNA was isolated using mirVana™ miRNA Isolation Kit (Ambion, Inc, Austin TX). The quality of the RNA was checked with the aid of the spectrophotometer (NanoDrop Technologies, Wilmington, DE). The RNA integrity numbers (RIN) for all samples were greater than 8.

treatment_protocol: To induce ischemia, rats were first anesthetized with sodium pentobarbital (50 mg/kg, i.p.). Tetracaine hydrochloride 0.5% and tropicamide 1% ophthalmic drops were administered to provide local anesthesia and mydriasis, respectively. For induction of high intra-ocular pressure (IOP) the anterior chamber of one eye was cannulated with a 30 gauge needle attached to an elevated 1L sterile saline reservoir. High IOP of 110 mmHg was maintained for 60 min.  Reperfusion proceeded for the 5 time points: 0h, 2h, 24h, 48h and 7 days after which animals were euthanized and tissues were collected. The same procedures were administered to rats receiving sham surgeries except that high IOP was not induced.  IOP was measured in mmHg at 15, 30 and 60min using a TonoLab tonometer device (Colonial Medical Supply, Franconia, NH). Retinas were dissected from each eye, flash frozen in liquid nitrogen, and stored in -80°C for subsequent use.

value: Long Evan’s hooded rat

value: male

tag: sample group

value: Sham control

tag: time point

value: 7d after sham surgery

tag: tissue

value: whole retina


title: Egg_High quality_Germ ring stage_rep1


title: ErbB4-/- Mouse Liver Tissue Replicate 2

city: Suzhou

first: Jianming

last: Li

address: 199 Renai Road

country: China

institute: Soochow University

description:
Full ErbB4 mutant mice were rescued from embryonic lethality by transgenic ErbB4 overexpression in the heart (ErbB4-/-HER4heart). ErbB4-/-HER4heart mice were backcrossed to C57BL/6J mice for >15 generations.
Full ErbB4 mutant mice were rescued from embryonic lethality by transgenic ErbB4 overexpression in the heart (ErbB4-/-HER4heart). ErbB4-/-HER4heart mice were backcrossed to C57BL/6J mice for >15 generations.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00‐0331‐220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00‐0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00‐00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: The Student’s t-test were used to detect gene expression differences of the two groups.

source_name: ErbB4-/- mouse liver tissue

label_protocol: Total RNA were amplified, labeled and purified by using Affymetrix WT Amplication Kit(Cat#902224， Affymetrix, Santa Clara, CA, US) and GeneChip WT Terminal Labeling Kit(Cat#900671, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: All mice were maintained under a 12/12 h light/dark cycle and received food ad libit um.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: The mouse was injected with a single dose of DEN on postnatal day 14, and were dissected after 32 weeks.

tag: treatment

value: The mouse was injected with a single dose of DEN on postnatal day 14, and were dissected after 36 weeks.

value: liver


title: Sham_Control_7d_6


title: Normal_brain_5

city: shanghai

first: Yong

last: Yan

address: 415# of Fengyang street

department: neurosurgery

institute: changzheng hospital

description: long noncoding RNA expression in normal brain tissue 5

hyb_protocol: Hybridization Procedure: 1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:  For 1*244K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.5ug  10X Blocking Agent 50ul  Nuclease-free water ×ul  25X Fragmentation Buffer 10ul  Total volume 250ul    For 2*105K array Amount  cyanine 3-labeled, linearly amplified cRNA 1. 5ug  10X Blocking Agent 25ul  Nuclease-free water ×ul  25X Fragmentation Buffer 5ul  Total volume 125ul    For 4*44K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.65ug  10X Blocking Agent 11ul  Nuclease-free water ×ul  25X Fragmentation Buffer 2.2ul  Total volume 55ul    For 8*15K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul    For 8*60K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul      4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  Volumes per hybridization   Components 1*244K 2*105K 4*44K 8*15K 8*60k  cRNA from Fragmentation Mix 250ul 125ul 55ul 25ul 25ul  2* GEx Hybridization Buffer HI-RPM 250ul 125ul 55ul 25ul 25ul    7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  Volumes per hybridization   Components 1*244K 2*105K 4*44K 8*15K 8*60K  Volume Prepared 500ul 250ul 110ul 50ul 50ul  Hybridization Sample Volume 490ul 245ul 100ul 40ul 40ul    12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.

scan_protocol: Scanning Procedure: 1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Extract data using Agilent Feature Extraction Software  Software:  Agilent Feature Extraction    Procedure:  1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.

source_name: normal brain

label_protocol: Purify the labeled/amplified RNA and labeled cRNA QC 1. Add 20 uL of nuclease-free water to your cRNA sample, for a total volume of 100 uL. 2. Add 350 uL of Buffer RLT and mix well by pipetting. 3. Add 250 uL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge. 4. Transfer the 700 uL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube. 5. Transfer the RNeasy column to a new collection tube and add 500 uL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube. 6. Add another 500 uL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube. 7. Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report "Labeling Efficiency-QC") directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm. 8. Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column. 9. Take 1.5 ul of each sample to determine the yield and specific activity by using the NanoDrop ND-1000( Passed-please see report "Labeling Efficiency-QC"). - From the main menu, choose MicroArray Measurement. Go to the Sample Type pull-down menu and select DNA-50. - Blank the instrument with 1.5 uL of 1x labeling solution. - Use 1.5 uL of purified labeled genomic DNA for quantitation. Measure the absorbance at A260nm (DNA), A550nm (cyanine 3). - The specific activity (pmol dyes per ug genomic DNA) of the labeled genomic DNA can be obtained by the following calculation: (Concentration of Cy3) Specific Activity = pmol Cy3 per ug cRNA (Concentration of cRNA) * 1000 * If the yield is <1.65 ug and the specific activity is <9.0 pmol Cy3 per ug cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

growth_protocol: Prepare the tissue RNA Sample 1. Homogenization - Cryopulverization of tissue using the Biopulverizer - Place the BioPulverizer in a shallow container and cool thoroughly with either liquid nitrogen. - Place prefrozen tissue in the well of the mortar. - Remove the mortar from the shallow container, place it on the lab bench and pulverize the tissue with one or two blows to the pestle with a hammer (models 59012MS). - Empty the powdered contents for subsequent homogenization or extraction procedures. b) Homogenization using the Mini-Bead-Beater-16 - Fill the 2 ml screw-cap microtube one-half full with 1.0mm beads. Then add TRIzol and tissue, being sure to fill the microtube almost to the top. Exclude as much air from the microtube as possible. Use screw-cap microtubes with integral o-ring seals in order to eliminate aerosol formation during the homogenization. Be sure there are no beads on the threads of the microtubes when screwing down the cap.  - Insert 1 to 16 microtubes into the holder. Distribute them symmetrically as you would do with a centrifuge. Screw in the black plastic chamber cap until it is in contact with the tops of the microtube caps. Tighten the lid by hand so the vials are firmly held in place. Do not overtighten. - Set the timer depending on the type of sample. Start the machine. 2. Phase Separation Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000  g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization. 3. RNA Precipitation Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000  g for 10 minutes at 4°C.  4. RNA Wash Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500  g for 5 minutes at 4°C. 5. Redissolving the RNA At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

extract_protocol: Prepare labeling reaction:1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.   2. Add 1.2 μL of T7 Promoter Primer.   3. Use nuclease-free water to bring the total reaction volume to 11.5 μL.  4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5. Place the reactions on ice and incubate for 5 minutes.  6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.   Volume(ul) per reaction  5×First Strand Buffer 4  0.1M DTT 2  10mM dNTP mix 1  MMLV-RT 1  RNaseOut 0.5  Total volume 8.5  7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.  8. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9. Incubate samples at 40°C in a circulating water bath for 2 hours.  10. Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11. Move samples to ice. Incubate for 5 minutes.  12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.   Volume(ul) per reaction  Nuclease-free water 15.3  4X Transcription Buffer 20  0.1 M DTT 6  NTP mix 8  50% PEG 6.4  RNaseOUT 0.5  Inorganic pyrophosphatase 0.6  T7 RNA Polymerase 0.8  Cyanine-3-CTP 2.4  Total volume 60  14. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.  15. Incubate samples in a circulating water bath at 40°C for 2 hours.

treatment_protocol: Total RNA Clean-up and RNA QC: 1. Mix the following in a microcentrifuge tube:  Redissolved RNA ≤85ul  10×Reaction buffer 10ul  Baseline-ZERO DNase 5ul  RNase-free water X ul  Total volume 100ul  2. Incubate at 37°C for 30 minutes.  3. Add 350 μl Buffer RLT, and mix well.  4. Add 250 μl ethanol (96–100%) to the diluted RNA, and mix well by pipetting. Do not centrifuge. Proceed immediately to step 5.  5. Transfer the sample (700 μl) to an RNeasy Mini spin column placed in a 2 ml collection tube. Close the lid gently, and centrifuge for 15 s at ≥8000 x g (≥10,000 rpm). Discard the flow-through.  6. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 15 s at≥8000 x g (≥10,000 rpm) to wash the spin column membrane. Discard the flow-through.  7. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 2 min at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane.  8. Place the RNeasy spin column in a new 2 ml collection tube, and discard the old collection tube with the flow-through. Close the lid gently, and centrifuge at full speed for 1 min.  9. Place the RNeasy spin column in a new 1.5 ml collection tube. Add appropriate RNase-free water (please see report ”RNA-QC”) directly to the spin column membrane. Close the lid gently, and centrifuge for 1 min at ≥8000 x g (≥10,000 rpm) to elute the RNA.  10. RNA quantification and quality control(Passed-please see report ”RNA-QC”).

tag: age


title: Lymphoblastoid cell line_Individual 1-6_cycle 0_hybridization_batch_1

source_name: Lymphoblastoid cell line

value: Male

value: Lymphoblastoid cell line


title: ErbB4-/- Mouse Liver Tissue Replicate 3

value: The mouse was injected with a single dose of DEN on postnatal day 14, and were dissected after 37 weeks.


title: ga1-3 SCL3OE replicate 3

description: ga1 SCL3OE-3

value: ga1 muant and SCL3 overexpression

value: whole root


title: Sham_Control_7d_4


title: Sham_Control_7d_3


title: Sham_Control_7d_2


title: Sham_Control_48h_5

value: 48hr after sham surgery


title: Sham_Control_48h_6


title: Sham_Control_48h_4


title: Sham_Control_24h_6

value: 24hr after sham surgery


title: Sham_Control_48h_1


title: Sham_Control_24h_5


title: Sham_Control_24h_3


title: Sham_Control_48h_2


title: Sham_Control_24h_4


title: Sham_Control_48h_3


title: Sham_Control_24h_2


title: Control Mouse liver Tissue Replicate 2

description:
C57BL/6J mice
none

source_name: Control mouse liver tissue

value: The mouse was injected with a single dose of DEN on postnatal day 14, and were dissected after 33 weeks.

value: wild type


title: Sham_Control_7d_1


title: Control Mouse liver Tissue Replicate 3

description:
C57BL/6J mice
none

value: The mouse was injected with a single dose of DEN on postnatal day 14, and were dissected after 34 weeks.


title: Sham_Control_24h_1

value: Long Evan’s hooded rat


title: Control Mouse liver Tissue Replicate 1

description:
C57BL/6J mice
none

value: The mouse was injected with a single dose of DEN on postnatal day 14, and were dissected after 32 weeks.


title: Control, rep_3

source_name: Control, rep_3

value: aortic smooth muscle cells

tag: protocol

value: control DMEM


title: Blood_DNA_ED8-8

city: Uppsala

first: Joakim

last: Klar

state: SVERIGE

address: Box 815

country: Sweden

institute: Uppsala University

description:
Hybridized to 250K_Nsp
PA024 ED8-8

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Data were processed from .CEL files into genotype calls using Genotyping Console; Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Salt precipitation from peripheral blood

value: blood

tag: diagnosis

value: anhidrosis


title: Sham_Control_2h_6

value: male

value: Sham control

value: 2hr after sham surgery

value: whole retina


title: ErbB4-/- Mouse Liver Tissue Replicate 1

value: The mouse was injected with a single dose of DEN on postnatal day 14, and were dissected after 35 weeks.

value: liver


title: Sham_Control_2h_4


title: Sham_Control_2h_2


title: Sham_Control_2h_3


title: Sham_Control_2h_5


title: Blood_DNA_ED8-7

description:
Hybridized to 250K_Nsp
PA024 ED8-7


title: Blood_DNA_ED8-1

description:
Hybridized to 250K_Nsp
PA024 ED8-1


title: Sham_Control_0h_5

value: 0hr after sham surgery


title: Ischemia_Reperfusion_7d_6

source_name: Retina_Experimental sample_7d

value: Ischemia reperfusion

value: 7d post-ischemia


title: Ischemia_Reperfusion_7d_5


title: Ischemia_Reperfusion_7d_2


title: Sham_Control_0h_3


title: Sham_Control_0h_1


title: Sham_Control_0h_2


title: Ischemia_Reperfusion_7d_4


title: Ischemia_Reperfusion_7d_1


title: Ischemia_Reperfusion_48h_6

source_name: Retina_Experimental sample_48h

value: 48hr post-ischemia


title: Ischemia_Reperfusion_7d_3


title: Sham_Control_0h_4


title: Sham_Control_2h_1


title: Ischemia_Reperfusion_48h_2


title: Ischemia_Reperfusion_48h_3


title: Ischemia_Reperfusion_48h_5


title: Ischemia_Reperfusion_48h_4


title: Ischemia_Reperfusion_48h_1


title: Ischemia_Reperfusion_24h_5

source_name: Retina_Experimental sample_24h

value: 24hr post-ischemia


title: Ischemia_Reperfusion_24h_6

value: Long Evan’s hooded rat


title: Sham_Control_0h_6


title: Ischemia_Reperfusion_24h_3


title: Ischemia_Reperfusion_24h_4


title: Ischemia_Reperfusion_2h_6

source_name: Retina_Experimental sample_2h

value: 2hr post-ischemia


title: Ischemia_Reperfusion_24h_1


title: Ischemia_Reperfusion_2h_5


title: Blood_DNA_ED8-2

description:
Hybridized to 250K_Nsp
PA024 ED8-2


title: Ischemia_Reperfusion_2h_4


title: Ischemia_Reperfusion_2h_3


title: Ischemia_Reperfusion_0h_1

source_name: Retina_Experimental sample_0h

value: 0hr post-ischemia


title: Ischemia_Reperfusion_2h_2


title: Ischemia_Reperfusion_0h_2


title: Ischemia_Reperfusion_0h_6


title: Ischemia_Reperfusion_0h_3


title: Ischemia_Reperfusion_0h_4


title: Ischemia_Reperfusion_2h_1


title: Ischemia_Reperfusion_24h_2


title: T47D ABT888

city: Boston

first: Kristin

last: Krukenberg

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

description: SAMPLE 8

scan_protocol: Standard Illumina scan protocol

data_processing: Data was processed and normalized using the Illumina GenomeStudio software.

source_name: T47D ABT888

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit from Ambion

growth_protocol: Cells were grown in RPMI + 10% FBS at 37C and 5% C02.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit following the manufacturer's protocol.

treatment_protocol: Cells were treated with 10uM ABT-888 or vehicle control (DMSO) for 48 hours.

value: breast

tag: cell line

value: epithelial

tag: tumor type

value: ductal carcinoma

tag: agent


title: T47D

description: SAMPLE 7

tag: cell type

value: control


title: Embryo exposed to Morphine, biological rep5

city: Salamanca

first: Raquel

middle: E.

last: Rodriguez

state: Salamanca

address: C/ Pintor Fernando Gallego, 1

country: Spain

institute: Institute of Neurosciences of Castilla y León

hyb_protocol: Following fragmentation, cRNA were hybridized to GeneChip® Zebrafish Genome Array (Affymetrix). Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

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

data_processing: The RMA (Robust Multi-array Analysis) algorithm was used for background correction and normalization of fluorescent hybridization signals of the microarrays, both at internal (intra-microarrays) and comparative (inter-microarrays) levels. We used Bioconductor and R as computational tools (www.bioconductor.org), to apply RMA to the data set of 12 microarray hybridizations including six different biological replicas corresponding to each of the different experimental groups under study (Control and Morphine).  After quantitation of expression level of each probe set in all microarrays analyzed, the SAM algorithm was used to identify probe sets displaying significant differential expression when comparing the treat samples to it controls, using a False Discovery Rate (FDR) of 10% or less as significant.

organism: Danio rerio

source_name: Embryo at 5 hpf exposed to Morphine at collected at 24 hpf

label_protocol: Microarray analysis was performed in the Cancer Research Center (CIC) of Salamanca according to standard procedures. Label protocol was performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA).

growth_protocol: Adult zebrafish (wild-type AB strain) were raised in a cycle of 14 h light: 10 h dark at 26ºC in a multi-tank system at our Fish Facilities at the Institute of Neuroscience of Castile & Leon, University of Salamanca. Embryos obtained from natural fertilization were selected at 24 hpf using a Discovery V8 stereomicroscope (Carl Zeiss, Germany), after which fish were raised at 28.5ºC and maintained in dishes containing sterile E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl, 0.33 mM MgSO4) in distilled water.

extract_protocol: Total RNA was purified using TRIZOL (Gibco BRL, Gaithersburg, MD, USA) following further RNA purification using an RNeasy Mini Kit for RNA clean-up (Qiagen Sicences, Maryland, USA). RNA quantification and quality was then assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), to test the integrity of the 18S and 28S rRNA bands, and samples with an RNA integrity number (RIN) > 8.0 were used.

treatment_protocol: Embryos of the appropriate stage, according to development in hpf according to Kimmel et al. (1995), were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL). In the case of embryos at 5 hpf exposed to 10 nM morphine and collected at 24 hpf (covering the complete embryogenesis). Morphine was administered to the embryos in their water environment, i.e., diluted in E3 embryonic medium. The exposition to begun at the stage of 5 hpf (end of blastula) is continuous, in order to study the chronic effects of the exposure to drug.

tag: genotype/variation

value: wild-type AB strain


title: Ischemia_Reperfusion_0h_5

tag: gender

value: male


title: ZR7530 ABT888

description: SAMPLE 6


title: MCF7 ABT888

description: SAMPLE 2

source_name: MCF7 ABT888

value: adenocarcinoma


title: SKBR3

description: SAMPLE 9


title: Olaparib 1uM

description: biological replicate 1

source_name: MCF7 cells_Olaparib_1uM

treatment_protocol: Cells were treated with compound or vehicle control (DMSO) for 6 hours.

tag: tumour type


title: ABT888 1uM

description: biological replicate 1

source_name: MCF7 cells_ABT888_1uM


title: Hs578T

description: SAMPLE 11

value: carcinoma


title: KPL-1

description: SAMPLE 3


title: ABT888 5uM

description: biological replicate 1

source_name: MCF7 cells_ABT888_5uM


title: Olaparib 500nM

description: biological replicate 1

source_name: MCF7 cells_Olaparib_500nM


title: ZR7530

description: SAMPLE 5


title: KPL-1 ABT888

description: SAMPLE 4

source_name: KPL-1 ABT888


title: Embryo exposed to Morphine, biological rep3

value: 5 hpf exposed to Morphine at collected at 24 hpf


title: MCF7

description: SAMPLE 1


title: SKBR3 ABT888

description: SAMPLE 10

source_name: SKBR3 ABT888


title: Olaparib 100nM

description: biological replicate 1

source_name: MCF7 cells_Olaparib_100nM


title: Hs578T ABT888

description: SAMPLE 12

source_name: Hs578T ABT888


title: Embryo exposed to Morphine, biological rep6


title: Embryo exposed to Morphine, biological rep2


title: Control embryo, biological rep6

source_name: Control embryo


title: Embryo exposed to Morphine, biological rep4


title: Embryo exposed to Morphine, biological rep1


title: PJ34 10uM

description: biological replicate 1

source_name: MCF7 cells_PJ34_10uM


title: ABT888 250nM

description: biological replicate 1

source_name: MCF7 cells_ABT888_250nM


title: PJ34 1uM

description: biological replicate 1

source_name: MCF7 cells_PJ34_1uM


title: Control embryo, biological rep5


title: Control embryo, biological rep3


title: DMSO rep 3

description: biological replicate 3

source_name: MCF7 cells_DMSO


title: PJ34 500nM

description: biological replicate 1

source_name: MCF7 cells_PJ34_500nM


title: Control embryo, biological rep2


title: DMSO rep 2

description: biological replicate 2


title: Control embryo, biological rep4


title: DMSO rep 1

description: biological replicate 1


title: TC32 YK-4-279-Selected-CP

city: Houston

first: Joseph

middle: A.

last: Ludwig

state: Texas

department: Sarcoma Medical Oncology

institute: UT-MD-Anderson Cancer Center

description: Resistant Ewing Sarcoma Cell line to YK-4-279 (Treated)

hyb_protocol: Amplified and biotinylated cRNAs were hybridized onto Affymetrix GeneChip Human Genome U133A 2.0 cartridge arrays, Washed, and Stained with kit following manufacturer’s instructions.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000 and the initial raw data were extracted using Affymetrix GeneChip Command Console-Expression software.

data_processing: The statistical analyses of scanned data were processed using default setting on GeneSpring GX 12.1 software (Agilent) by performing one-way ANOVA followed by Tukey’s test to compare each pair of group in order to borrow strength from more samples to estimate the between-group variance

source_name: TC32 YK-4-279-Resistant-CP

label_protocol: Amplification and labeling were performed using Affymetrix’s GeneChip GeneChip®3’ IVT Express Kit following manufacturer’s instructions.

growth_protocol: TC32 and TC71 ES YK acquired resistant clones (YK-4-279 Selected) were obtained from the corresponding parental cell lines by maintaining them within an escalating small molecule concentration YK-4-279 (up to 3 μM) for 7 months.

extract_protocol: Total RNA was extracted from the cell lines using the Qiagen miRNeasy Mini kit. RNA quality was assessed to have an RNA integrity number before amplification and labeling

treatment_protocol: The adherently growing Ewing's Sarcoma cells were cultivated for 24 h before adding YK-4-279 (3 μM) for up to 72 hours

value: Ewing Sarcoma

tag: phenotype

value: Resistant to YK-4-279


title: TC32 YK-4-279-Selected-C1

source_name: TC32 YK-4-279-Resistant-C1


title: TC71 YK-4-279-Selected-C4A

source_name: TC71 YK-4-279-Resistant-C4A


title: LPS WT

city: Chicago

first: Sin Yi

last: Kong

state: IL

address: 300 E Chicago

department: pathology

institute: Northwestern University

description:
RNA pooled from 3 mice
DF 7

hyb_protocol: standard Illumina hybridization protocol performed by University of Chicago Genomics core facility

scan_protocol: standard Illumina scanning protocol performed by University of Chicago Genomics core facility

data_processing: data was background substracted quantile normalized with Genomestudio performed by University of Chicago genomics core facility

source_name: LPS WT

label_protocol: biotin labeled cRNA performed by University of Chicago Genomics core facility

growth_protocol: primary B cells were isolated from mouse spleens and cultured in RPMI supplemented with 10% FBS and 1% pen/strep for 4 hours

extract_protocol: RNA was isolated using Qiagen Rneasy mini kit, and DNAse I treated per manufacturer's instructions

treatment_protocol: B cells were either cultured in media, or activated with anti-IgM, anti-CD40 or LPS for 4 hours

value: splenic B cells

value: LPS


title: unstim WT

description:
RNA pooled from 3 mice
DF 1

source_name: unstim WT

value: media


title: anti-IgM KO

description:
RNA pooled from 3 mice
DF 4

source_name: anti-IgM KO

value: anti-IgM


title: TC32 YK-4-279-Selected-C4

source_name: TC32 YK-4-279-Resistant-C4


title: TC71 YK-4-279-Selected-C5

source_name: TC71 YK-4-279-Resistant-C5


title: LPS KO

description:
RNA pooled from 3 mice
DF 8

source_name: LPS KO


title: Control embryo, biological rep1


title: TC71 YK-4-279-Selected-C3

source_name: TC71 YK-4-279-Resistant-C3


title: TC71 Parental-YK-4-279-72hrs-Rep1

description: Sensitive Ewing Sarcoma Cell line to YK-4-279 (Treated For 72 h)

source_name: TC71 Ewing Sarcoma Cell line YK-4-279 treated for 72 h

value: Sensitive to YK-4-279


title: TC71 Parental-YK-4-279-72hrs-Rep3


title: anti-CD40 KO

description:
RNA pooled from 3 mice
DF 6

source_name: anti-CD40 KO


title: anti-CD40 WT

description:
RNA pooled from 3 mice
DF 5

source_name: anti-CD40 WT


title: wdr-5  null mutant gonads sample 3

city: Lyon

first: Valerie

middle: J

last: Robert

address: 46 Allee d'Italie

department: LBMC

country: France

institute: ENS Lyon

hyb_protocol: Cy3 labelled RNA was fragmented 30 minutes at 60°C. On completionof the fragmentation reaction the same volume of 2X Agilent hybridization buffer was added to the fragmentation mixtureand hybridized to Agilent C.elegans (V2) Gene Expression Microarray 4x44K for 17h at 65°C in a rotating Agilent hybridization oven. After hybridization Microarray was washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediatly after washing on the Agilent Microarray Scanner, using one color setting for 4x44K array slides.

data_processing: Microarray normalization and analysis were performed with Bioconductor tools (http://www.bioconductor.org) and custom scripts using R statistical programming language.

organism: Caenorhabditis elegans

source_name: dissected gonads from young adults

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the OneColor Microarray Based Gene Expession analysis-Low input QuickAmp Labeling (Agilent Technologies) according to the manufacturer's intructions.

growth_protocol: Freshly outcrossed animals grown at 20°C were dissected at the young adult stage.

extract_protocol: Total RNA from C.elegans gonads was isolated using PicoPure® RNA Isolation Kit (Applied Biosystems®) following the manufacturer's recommendations. RNA was quantified using a Qubit® fluorometric quantification (Life technologies) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: genotype

value: wdr-5 null

value: hermaphrodite

value: gonad

tag: developmental stage

value: young adult


title: anti-IgM WT

description:
RNA pooled from 3 mice
DF 3

source_name: anti-IgM WT

tag: strain


title: TC71 Parental-YK-4-279-72hrs-Rep2


title: unstim KO

description:
RNA pooled from 3 mice
DF 2

source_name: unstim KO


title: TC32 Parental-YK-4-279-72hrs-Rep1

source_name: TC32 Ewing Sarcoma Cell line YK-4-279 treated for 72 h


title: wdr-5  null mutant gonads sample 1


title: TC32 Parental-YK-4-279-72hrs-Rep3


title: TC71 Parental-Rep2

description: Sensitive Ewing Sarcoma Cell line to YK-4-279 (Untreated)

source_name: TC71 Ewing Sarcoma Cell line


title: set-2  null mutant gonads sample 2

value: set-2 null


title: set-2  null mutant gonads sample 1


title: TC71 Parental-Rep3


title: wdr-5  null mutant gonads sample 2


title: set-2  null mutant gonads sample 3


title: TC71 Parental-Rep1


title: TC32 Parental-YK-4-279-72hrs-Rep2


title: TC32 Parental-Rep1

source_name: TC32 Ewing Sarcoma Cell line


title: ash-2 loss of function gonads sample 3

value: ash-2 null


title: WT gonads sample 3

value: wildtype


title: TC32 Parental-Rep3


title: TC32 Parental-Rep2


title: ash-2 null mutant gonads sample 2


title: WT gonads sample 2


title: WT gonads sample 1


title: ash-2 null mutant gonads sample 1


title: saliva_lowstress_biorep24

city: Menlo Park

first: Aaron

last: Wacholder

state: CA

address: 333 Ravenswood Ave

department: Molecular Genetics Program

institute: SRI International

hyb_protocol: The biotin-dscDNA was hybridized for 18h at 47C to Affymetrix® Whole-Transcript Expression Arrays. Washing and Staining were done with the GeneChip(R) Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner and Affymetrix GeneChip Command Console Version 3.0.

data_processing: Probe data was generated using the RMA function in the Oligo R package from Bioconductor.

source_name: whole saliva, low chronic stress exposure

label_protocol: Fragmented dscDNA samples were end-labeled with terminal deoxynucleotidyl transferase and an Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.

extract_protocol: RNA was extracted using the Genotek Expression Analysis Self-Collection Kit according to the manufacturer's protocol.

value: whole saliva

value: male

tag: race

value: white

tag: smoking status

value: current

tag: chronic stress level

value: low


title: saliva_highstress_biorep23

source_name: whole saliva, high chronic stress exposure

tag: tissue

value: female

tag: age

value: never

value: high


title: saliva_highstress_biorep24

value: former


title: CAM explants infected with wild type B. abortus 2308: Replicate 4

city: Belo Horizonte

first: Alex

middle: FIORINI

last: Carvalho

state: MG

address: Avenida Antonio Carlos 6627

department: DMVP

country: Brazil

institute: UFMG

description:
Biological replicate 4 of 4. Chorioallantoic membrane explant culture (CAM) infected-wild type B. abortus 2308
Sample W9

hyb_protocol: 825 ng of Cy3-labelled cRNA and 825 ng of Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5/ug cRNA) were mixed and fragmented at 60°C for 30 minutes in a reaction volume of 50 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ull of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Bovine Oligo Microarrays design ID 023647 - GPL11648 (4x44K ) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C  GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: bovine trophoblastic cells [test]

label_protocol: Labeled cRNA was prepared from 0.5 ug RNA using the Two-Color Quick amp Iabelink 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.

growth_protocol: Seven intact pregnant bovine uteruses at the final third of gestation were obtained at local slaughterhouses. All fetuses were serologically negative for Brucella spp. by using the Acidified Antigen Buffered test with fetal amniotic fluid. Prior to obtaining the CAM, the perimetrium was thoroughly decontaminated with iodinated alcohol, the uterus was then opened and CAM removed and placed in sterile medium containing antibiotics. Snapwell plates were used for culturing CAM explants. Sterile rings and detachable supports were positioned over the intercotyledonary portion of the CAM explants. Excess tissue was removed from CAM explants, which were placed in 6 well culture plates containing supplemented sterile culture medium and incubated at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: The trophoblastic surface of the CAM explants was inoculated with 2.0 x 107 CFU, in a multiplicity of infection of approximately 1000 (MOI 1000:1). CAM explants were inoculated in triplicates with wild type, ΔvirB2, or ΔbtpB B. abortus 2308. Plates were incubated at 37°C with 5% CO2 for 4 h, the medium was then replaced with medium supplemented with 50 µg gentamicin/mL (Invitrogen, São Paulo, Brazil) to inactivate extracellular bacteria. Plates were maintained at 37°C with an atmosphere containing 5% CO2 for 1 h followed by washing three times with with PBS (phosphate buffered saline - pH 7.4) to eliminate the antibiotic. Uninfected CAM controls were inoculated with sterile medium and kept under the same conditions

tag: source tissue

value: trophoblastic cells

tag: infection

value: wild type B. abortus 2308

tag: infection time

value: 4 hours

source_name: bovine trophoblastic cells [reference]

value: Non-infected

tag: sample type

value: reference


title: CAM explants infected with DbtpB B. abortus: Replicate 4

description:
Biological replicate 4 of 4. Chorioallantoic membrane explant culture (CAM) infected-DbtpB B. abortus 2308
Sample 109

value: intact pregnant bovine uteruses at the final third of gestation

tag: cell type

value: DbtpB B. abortus 2308


title: CAM explants infected with DvirB2 B. abortus: Replicate 4

description:
Biological replicate 4 of 4. Chorioallantoic membrane explant culture (CAM) infected-DvirB2 B. abortus 2308
Sample V9

value: DvirB2 B. abortus 2308


title: saliva_lowstress_biorep23

value: whole saliva


title: saliva_lowstress_biorep21

value: male


title: saliva_lowstress_biorep22

value: white


title: CAM explants infected with DbtpB B. abortus: Replicate 3

description:
Biological replicate 3 of 4. Chorioallantoic membrane explant culture (CAM) infected-DbtpB B. abortus 2308
Sample 106


title: saliva_highstress_biorep22


title: saliva_lowstress_biorep18


title: saliva_lowstress_biorep20


title: saliva_lowstress_biorep19


title: CAM explants infected with wild type B. abortus 2308: Replicate 3

description:
Biological replicate 3 of 4. Chorioallantoic membrane explant culture (CAM) infected-wild type B. abortus 2308
Sample W6


title: Control CAM explants without infection: Replicate 4

description:
Biological replicate 4 of 4. Control Chorioallantoic membrane explant culture (CAM), non-infected
Sample C9

value: control


title: saliva_highstress_biorep21

value: current


title: saliva_lowstress_biorep17

value: female

value: low


title: Control CAM explants without infection: Replicate 3

description:
Biological replicate 3 of 4. Control Chorioallantoic membrane explant culture (CAM), non-infected
Sample C6


title: CAM explants infected with DbtpB B. abortus: Replicate 2

description:
Biological replicate 2 of 4. Chorioallantoic membrane explant culture (CAM) infected-DbtpB B. abortus 2308
Sample 105