title: A431 expressing empty vector, -Tet

status: Public on Jun 30 2015

type: RNA

city: Washington

first: Rosenthal

middle: S

last: Dean

state: DC

address: 3900 Reservoir Rd., NW

department: Biochemistry and Molecular & Cellular Biology

country: USA

institute: Georgetown University

description: SCC cell line stably transfected with empty vector

hyb_protocol: 15ng of fragmented cDNA was hybridized on Affymetrix HG-U133A chip for 16 hours at 45◦C and washed and stained using GeneChip® Hybridization, wash and stain kit based on the manufacturer's instructions.

scan_protocol: Scanning was performed using Affymetrix GeneChip Scanner 7G based on the manufacturer's instructions.

data_processing: Data normalization and analysis was performed using dChip and MetaCore software, respectively.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Patient-derived tumor cells

label_protocol: Biotinylated cDNA was made using Affymetrix 3' IVT expressing kit according to the manufacturer's instructions from 300ng of total RNA.

growth_protocol: Cells were cultured in DMEM/10% Tet-free FBS/1% Pen/Strep until 90% confluency before induction.

extract_protocol: Total RNA from each sample was extracted using Trizol reagent based on the manufacturer's instructions.

treatment_protocol: Induced samples were treated with 1ug/ml of tetracycline and uninduced samples were not treated.

tag: cell line

tag: cell type

value: squamous carcinoma cells

tag: transfectant

value: empty vector


title: rAd_1bis_vac_dc_mouse_2

city: Paris

first: Nicolas

last: Dérian

address: Bâtiment CERVI, 83 bvd de l'Hôpital

country: France

institute: UPMC

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_1bis.txt
T00345302

hyb_protocol: CodeLink Expression Assay protocol

scan_protocol: GenePix Personal 4100A scanner

data_processing: Raw data extraction were performed using GenePix Pro 6.0. Normalization and log2 transformation were performed on R software. Probes with wrong detection in all samples of a comparison were removed.

label: biotin

organism: Mus musculus

source_name: Sorted dendritic cells from spleen

label_protocol: CodeLink Expression Assay protocol

growth_protocol: Fresh sorted dendritic cells from spleen using CD11c+-conjugated MACS magnetic beads (Miltenyi Biotec)

extract_protocol: Total RNA extraction using Nucleospin RNAII (Macherey Nagel)

treatment_protocol: Incubation for 20 minutes at 4°C, cells were washed and passed over a MACS column. Positively selected cells were suspended in appropriate buffer.

tag: tissue

value: dendritic cells

tag: strain


title: A431 expressing Id3 construct, +Tet

description: SCC cell line stably transfected with Id3 construct

value: Id3 construct


title: Fsh1C_101810

city: Kansas City

first: Kaiyu

last: Kubota

state: KS

address: 3901 Rainbow Blvd

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

description:
Grhl3_041911_(Rat230_2)
Gene expression data from differentiated Rcho1 trophoblast stem cells expressing Fosl1 shRNA

hyb_protocol: RNA samples hybridized to Affymetrix U133 2.0 DNA microarray chip using GeneChip Hybridization Oven 640 (Affymetrix). Washing was performed using GeneChip fluidics station 450 (Affymatrix).

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

data_processing: The data were normalized to internal controls using the MAS 5 algorithm in the Expression Console (Affymetrix).

organism: Rattus norvegicus

source_name: Rcho1 trophoblast stem cells, differentiated, expressing Fosl1 shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: Cells were grown in RPMI media supplemented with 20% FBS, 1 mM sodium pyruvate, 50 uM 2-mercaptoethanol and penicillin-streptomycin and then differentiated for 8 days in NCTC media supplemented with 1% HS, 1 mM sodium pyruvate, 10 mM HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, 38 mM sodium bicarbonate, 50 uM 2-mercaptoethanol and penicillin-streptomycin

extract_protocol: Trizol extraction of total RNA (manufactured protocol)

treatment_protocol: Cells were lentivirally transduced with control or Fosl1 shRNA

value: Choriocarcinoma cell line

tag: cell subtype

tag: genotype/variation

value: expressing Fosl1 shRNA


title: Xoo BXO43 rep3

city: Hyderabad

first: Ramesh

middle: V.

last: Sonti

state: Andhra Pradesh

address: Uppal Road

department: Plant Microbe Interactions

country: India

institute: Centre for cellular and molecular biology (CCMB)

description: Gene expression data from rice leaf treated with Xoo BXO43

hyb_protocol: The hybridization of fragmented and labeled aRNA with the rice GeneChip array (Affymetrix, California, U. S. A.)  was done according to the manufacturer’s protocol at 45˚C for 16 hours in Hybridization Oven 640. The GeneChips were later washed and stained using Affymetrix GeneChip Fluidics station 450 according to the manufacturer’s protocol.

scan_protocol: The stained GeneChips were later scanned using the Affymetrix GeneChip Scanner 450 to obtain the DAT file which contains the optical image of the hybridized chip in TIFF format

data_processing: The DAT file  was then processed using the Affymetrix Genechip Command Console (GCOS) to obtain the CEL files which contain the light intensity information corresponding to each probe location in the GeneChip. CEL files are further processed along with the CDF (Chip description file) to obtain the TXT file which contains the intensity values of each probeset. The data were normalized using probe intensity logarithmic error (PLIER) algorithm.

organism: Oryza sativa

source_name: Rice leaf midvein 15 h after treatment with Xoo BXO43

label_protocol: 250 ng of RNA was used as the starting material in cDNA preparation. First strand cDNA synthesis was done using the components of GeneChip IVT express kit (Affymetrix, California, U. S. A.) using the manufacturer’s protocol. 30 µl of in vitro transcription (IVT) master mix containing IVT biotin labeled uridine trinucleotide, IVT labeling buffer and IVT enzyme mix was mixed thoroughly with 30 μl of double stranded cDNA sample and incubated at 40˚C for 4 hours to obtain antisense RNA (aRNA).

growth_protocol: Rice seeds were germinated in petriplates containing moist bloting paper. Seedlings were later planted to pots containing soil. One week old seedlings were transplanted to a field. 30 days old rice plants were transferred to pots and kept in temperature and humidity controlled green house conditions for 10 days prior to the experimental treatments.

extract_protocol: RNA was isolated using the Trizol (Life technologies, California, U. S. A) reagent using the manufactures protocol. Treated mid vein tissue was isolated, flash freezed using liquid nitrogen and was used for sample preparation.

treatment_protocol: Leaves from plants in a single pot were injected with 200 micro liter of either milliQ water or cultures of Xoo strains (BXO1003, BXO1002 or BXO43) grown upto 0.8 OD measured at 600nm. For each treatment, injections were performed into the mid veins of 5 leaves. 15 h after injection, 4 cm long portions of mid veins were cut out from below the point of injection and snap freezed in liquid nitrogen. One biological replicate constituted each such pot with the treated leaves.

tag: treatment

value: Xoo BXO43 (wild type)

value: Midvein of rice leaf


title: ScrA_101810

description:
Scr1_041911_(Rat230_2)
Gene expression data from differentiated Rcho1 trophoblast stem cells expressing control shRNA

source_name: Rcho1 trophoblast stem cells, differentiated, expressing control shRNA

value: expressing control shRNA


title: Fsh1A_101810

description:
Grhl1_041911_(Rat230_2)
Gene expression data from differentiated Rcho1 trophoblast stem cells expressing Fosl1 shRNA


title: Xoo BXO43 rep2


title: A431 expressing Id3 construct, -Tet


title: rAd_3bis_vac_dc_mouse_3

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_3bis.txt
T00345310


title: Fsh1B_101810

description:
Grhl2_041911_(Rat230_2)
Gene expression data from differentiated Rcho1 trophoblast stem cells expressing Fosl1 shRNA


title: A431 expressing empty vector, +Tet


title: ScrB_101810

description:
Scr2_041911_(Rat230_2)
Gene expression data from differentiated Rcho1 trophoblast stem cells expressing control shRNA


title: Xoo BXO1002 rep3

description: Gene expression data from rice leaf treated with Xoo BXO1002

source_name: Rice leaf midvein 15 h after treatment with Xoo BXO1002

value: Xoo BXO1002 (EPS-)


title: Xoo BXO43 rep1


title: ScrC_101810

description:
Scr3_041911_(Rat230_2)
Gene expression data from differentiated Rcho1 trophoblast stem cells expressing control shRNA


title: Xoo BXO1003 rep3

description: Gene expression data from rice leaf treated with Xoo BXO1003

source_name: Rice leaf midvein 15 h after treatment with Xoo BXO1003

value: Xoo BXO1003 (LPS-, EPS-)


title: Xoo BXO1002 rep2


title: MilliQ rep3

description: Gene expression data from rice leaf treated with MilliQ

source_name: Rice leaf midvein 15 h after treatment with milliQ

value: MilliQ


title: Xoo BXO1003 rep2


title: Xoo BXO1003 rep1


title: rAd_1bis_vac_dc_mouse_1

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_1bis.txt
T00345301


title: Xoo BXO1002 rep1


title: Xoo LPS rep3

description: Gene expression data from rice leaf treated with lipopolysaccharide isolated from Xanthomonas oryzae pv. oryzae

hyb_protocol: The hybridization of fragmented and labeled aRNA with the rice GeneChip array (Affymetrix, California, U. S. A.)  was done according to the manufacturer’s protocol at 45˚C for 16 hours in an Affymetrix Hybridization Oven 640. The GeneChips were later washed and stained using the Affymetrix GeneChip Fluidics station 450 according to the manufacturer’s protocol.

data_processing: The DAT file  was then processed using the Affymetrix Genechip Command Console (GCOS) to obtain the CEL files which contain the light intensity information corresponding to each probe location in the GeneChip. CEL files were further processed along with the CDF (Chip description file) to obtain the TXT file which contains the intensity values of each probeset. The data were normalized using the probe intensity logarithmic error (PLIER) algorithm.

source_name: Rice leaf midvein 15 h after treatment with Xoo LPS

growth_protocol: Rice seeds were germinated in petriplates containing moist bloting paper. Seedlings were later transferd to soil in pots. One week old seedlings were transplanted to a field. 30 days old rice plants were again transferred to pots and kept in green house conditions for 10 days prior to the experimental treatments.

extract_protocol: RNA was isolated using the TrizolTM (Life technologies, California, U. S. A) reagent using the manufacturer's protocol. Mid veinal tissues of rice leaves were isolated, frozen in liquid nitrogen and subsequently used for sample preparation.

treatment_protocol: Leaves from plants in a single pot were either injected with 200 micro liter Xoo LPS (100 µg/ml) or 200 µl control solution. For each treatment, injections were performed into the mid veins of 5 leaves. 15 h after injection, 4 cm long portions of mid vein was cut out from below the point of injection and snap freezed in liquid nitrogen. Each such pot constituted one biological replicate.

value: LPS extracted from Xoo BXO43


title: rAd_3bis_vac_dc_mouse_2

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_3bis.txt
T00345309


title: rAd_3bis_vac_dc_mouse_1

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_3bis.txt
T00345306


title: rAd_1bis_vac_dc_mouse_3

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_1bis.txt
T00345314


title: PBS_inj_dc_mouse_2_13

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_rAd_1bis.txt,GSE66930_normData_dc_rAd_3bis.txt
T00345320


title: rAd_3_vac_dc_mouse_3

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_3.txt
T00302438


title: rAd_3_vac_dc_mouse_1

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_3.txt
T00302436


title: PBS_inj_dc_mouse_1_13

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_rAd_1bis.txt,GSE66930_normData_dc_rAd_3bis.txt
T00345304


title: PBS_inj_dc_mouse_3_13

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_rAd_1bis.txt,GSE66930_normData_dc_rAd_3bis.txt
T00345321


title: rAd_1_vac_dc_mouse_3

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_1.txt
T00302423


title: rAd_3_vac_dc_mouse_2

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_3.txt
T00302437


title: PBS_inj_dc_mouse_2_12

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_rAd_1.txt,GSE66930_normData_dc_rAd_3.txt
T00302429


title: rAd_2bis_vac_dc_mouse_3

description:
Adnovirus
processed data file: GSE66930_normData_dc_rAd_2bis.txt
T00345278


title: MilliQ rep2


title: Buffer rep2

description: Gene expression data from rice leaf treated with buffer

source_name: Rice leaf midvein 15 h after treatment with buffer

value: Buffer


title: rAd_1_vac_dc_mouse_2

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_1.txt
T00302421


title: rAd_2bis_vac_dc_mouse_2

description:
Adnovirus
processed data file: GSE66930_normData_dc_rAd_2bis.txt
T00345277


title: MilliQ rep1

description: Gene expression data from rice leaf treated with MilliQ


title: rAd_1_vac_dc_mouse_1

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_1.txt
T00302420


title: Xoo LPS rep2

description: Gene expression data from rice leaf treated with lipopolysaccharide isolated from Xanthomonas oryzae pv. oryzae


title: Xoo LPS rep1


title: root +gln, biological rep 1

city: Taipei

first: Ming-Hsiun

last: Hsieh

address: 128 Academia Road, Section 2

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression data from rice roots with gln treatment for 0.5 hour

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The Affymetrix CEL data were generated from GCOS and normalized using RMA algorithm in Genespring 11.5 software. Baselines were transformed to median of control samples. Expression value of probeset that >100 was defined as present. Unpaired t-test was performed to examine the reproducibility of the data sets. Probesets with P-value <0.05 and at least two-fold change between control and treatment groups were selected into the final list.

organism: Oryza sativa Japonica Group

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rice (Oryza sativa L. ssp. Japonica cv. TNG67) seeds were germinated in continuous dark at 30°C for 3 days and then transferred to hydroponic solution (Yoshida et al., 1976) without NH4NO3 (-N) and grown under controlled conditions (30°C, 12-h photoperiod, 200 µmol photons m-2 s-1, 70% relative humidity) for 2 weeks.

extract_protocol: Total RNA from –N and + Gln-treated roots was extracted using a phenol extraction protocol.

treatment_protocol: 17-day-old rice seedlings grown in –N hydroponic solution were transferred to -N or +2.5 mM Gln solution for 30 min.

tag: variety

value: root

tag: growth stage

value: 17 day-old seedling


title: Buffer rep1


title: root +gln, biological rep 2

source_name: rice roots with gln treatment for 0.5 hour


title: Lipase/Esterase A treated leaves, biological replicate3 (120min_RMA)

description:
Raw data file: 120 min Lipase-3.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 120 min after infiltration

hyb_protocol: The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rice Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450

scan_protocol: The gene chips were scanned on an Affymetrix Scanner 3000

data_processing: The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to GeneSpring 12.6 - GX - PA  (Agilent Technology) for further analysis. The PLIER 16 and RMA algorithms were used for data normalization

source_name: two weeks old

label_protocol: 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)

growth_protocol: TN-1 rice seeds were germinated in petri plates containing moistened filter paper. Three days old seedlings were transferred to plastic pots containing soil and were grown for 10 days in a green house. Two days before the actual treatment, the pots containing the rice seedlings were transferred to a growth chamber (28oC; 80% relative humidity with 12/12h light/dark cycle)

extract_protocol: 20-30 leaf pieces covering the infiltrated zone from each of the treatments were harvested 30 min. and 120 min. after infiltration and subjected to total RNA isolation using Trizol (Invitrogen)

treatment_protocol: 30-40μl of either Lipase/Esterase A (500μg/ml) purified from the culture supernatant of wild type Xoo or 10mM potassium phosphate buffer (pH 6.0) were infiltrated to the adaxial surfaces of rice leaves with a 1ml hypodermal syringe without the needle (as described in Jha et al. 2007; MPMI vol 20, pp 31-40)

tag: cultivar

value: bacterial blight susceptible rice cultivar (Taichung Native-1; TN-1)

tag: age

value: two weeks old rice seedlings

value: leaves

tag: agent

value: Lipase/Esterase A

tag: time

value: 120 min


title: Lipase/Esterase A treated leaves, biological replicate1 (120min_RMA)

description:
Raw data file: 120 min Lipase-1.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 120 minafter infiltration


title: Buffer treated leaves, biological replicate1 (120min_RMA)

description:
Raw data file: 120 min Buffer-1.CEL
Expression profile of buffer treated rice leaves,120 min after infiltration

value: control


title: Buffer treated leaves, biological replicate3 (120min_RMA)

description:
Raw data file: 120 min Buffer-3.CEL
Expression profile of buffer treated rice leaves, 120 minafter infiltration


title: PBS_inj_dc_mouse_3_12

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_rAd_1.txt,GSE66930_normData_dc_rAd_3.txt
T00302435

value: dendritic cells


title: Buffer rep3


title: Lipase/Esterase A treated leaves, biological replicate2 (120min_RMA)

description:
Raw data file: 120 min Lipase-2.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 120 min after infiltration


title: PBS_inj_dc_mouse_1_12

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_rAd_1.txt,GSE66930_normData_dc_rAd_3.txt
T00302428


title: Lipase/Esterase A treated leaves, biological replicate1 (30min_RMA)

description:
Raw data file: 30 min Lipase-1.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 30 min after infiltration

value: 30 min


title: PBS_inj_dc_mouse_2_11

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_MVA_2bis.txt,GSE66930_normData_dc_rAd_2bis.txt
T00345275


title: rAd_2bis_vac_dc_mouse_1

description:
Adnovirus
processed data file: GSE66930_normData_dc_rAd_2bis.txt
T00345276


title: rAd_2_vac_dc_mouse_4

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_2.txt
T00345327


title: MVA_2bis_vac_dc_mouse_3

description:
Vaccinia virus
processed data file: GSE66930_normData_dc_MVA_2bis.txt
T00345280


title: MVA_2bis_vac_dc_mouse_2

description:
Vaccinia virus
processed data file: GSE66930_normData_dc_MVA_2bis.txt
T00342919


title: rAd_2_vac_dc_mouse_3

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_2.txt
T00345325


title: PBS_inj_dc_mouse_1_11

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_MVA_2bis.txt,GSE66930_normData_dc_rAd_2bis.txt
T00342920


title: PBS_inj_dc_mouse_3_11

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_MVA_2bis.txt,GSE66930_normData_dc_rAd_2bis.txt
T00345279


title: rAd_2_vac_dc_mouse_2

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_2.txt
T00345324


title: MVA_2_vac_dc_mouse_4

description:
Vaccinia virus
processed data file: GSE66930_normData_dc_MVA_2.txt
T00345334


title: rAd_2_vac_dc_mouse_1

description:
Adenovirus
processed data file: GSE66930_normData_dc_rAd_2.txt
T00345323


title: MVA_2bis_vac_dc_mouse_1

description:
Vaccinia virus
processed data file: GSE66930_normData_dc_MVA_2bis.txt
T00342918


title: MVA_2_vac_dc_mouse_3

description:
Vaccinia virus
processed data file: GSE66930_normData_dc_MVA_2.txt
T00345333


title: PBS_inj_dc_mouse_3_10

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_MVA_2.txt,GSE66930_normData_dc_rAd_2.txt
T00345340


title: Buffer treated leaves, biological replicate1 (30min_RMA)

description:
Raw data file: 30 min Buffer-1.CEL
Expression profile of buffer treated rice leaves, 30 minafter infiltration


title: Lipase/Esterase A treated leaves, biological replicate1 (120min_PLIER16)

description:
Raw data file: 120 min Lipase-1.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 120 minafter infiltration


title: Lipase/Esterase A treated leaves, biological replicate3 (30min_RMA)

description:
Raw data file: 30 min Lipase-3.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 30 min after infiltration


title: Lipase/Esterase A treated leaves, biological replicate3 (120min_PLIER16)

description:
Raw data file: 120 min Lipase-3.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 120 min after infiltration


title: Buffer treated leaves, biological replicate2 (120min_RMA)

description:
Raw data file: 120 min Buffer-2.CEL
Expression profile of buffer treated rice leaves, 120 min after infiltration


title: Buffer treated leaves, biological replicate3 (120min_PLIER16)

description:
Raw data file: 120 min Buffer-3.CEL
Expression profile of buffer treated rice leaves, 120 minafter infiltration


title: Lipase/Esterase A treated leaves, biological replicate2 (120min_PLIER16)

description:
Raw data file: 120 min Lipase-2.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 120 min after infiltration


title: Buffer treated leaves, biological replicate2 (120min_PLIER16)


title: PBS_inj_dc_mouse_1_10

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_MVA_2.txt,GSE66930_normData_dc_rAd_2.txt
T00345338


title: Buffer treated leaves, biological replicate2 (30min_RMA)

description:
Raw data file: 30 min Buffer-2.CEL
Expression profile of buffer treated rice leaves, 30 min after infiltration


title: Buffer treated leaves, biological replicate3 (30min_RMA)

description:
Raw data file: 30 min Buffer-3.CEL
Expression profile of buffer treated rice leaves, 30 minafter infiltration


title: MVA_1_vac_dc_mouse_3

description:
Vaccinia virus
processed data file: GSE66930_normData_dc_MVA_1.txt
T00346421


title: MVA_2_vac_dc_mouse_1

description:
Vaccinia virus
processed data file: GSE66930_normData_dc_MVA_2.txt
T00345328


title: Buffer treated leaves, biological replicate1 (120min_PLIER16)

description:
Raw data file: 120 min Buffer-1.CEL
Expression profile of buffer treated rice leaves,120 min after infiltration


title: Lipase/Esterase A treated leaves, biological replicate3 (30min_PLIER16)


title: Lipase/Esterase A treated leaves, biological replicate1 (30min_PLIER16)

description:
Raw data file: 30 min Lipase-1.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 30 min after infiltration


title: Lipase/Esterase A treated leaves, biological replicate2 (30min_PLIER16)

description:
Raw data file: 30 min Lipase-2.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 30 min after infiltration


title: PBS_inj_dc_mouse_4_10

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_MVA_2.txt,GSE66930_normData_dc_rAd_2.txt
T00345341


title: Lipase/Esterase A treated leaves, biological replicate2 (30min_RMA)


title: Buffer treated leaves, biological replicate1 (30min_PLIER16)


title: PBS_inj_dc_mouse_2_10

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_MVA_2.txt,GSE66930_normData_dc_rAd_2.txt
T00345339


title: MVA_2_vac_dc_mouse_2

description:
Vaccinia virus
processed data file: GSE66930_normData_dc_MVA_2.txt
T00345329


title: MVA_1_vac_dc_mouse_4

description:
Vaccinia virus
processed data file: GSE66930_normData_dc_MVA_1.txt
T00346423


title: PBS_inj_dc_mouse_3_9

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_MVA_1.txt
T00346425


title: MVA_1_vac_dc_mouse_1

description:
Vaccinia virus
processed data file: GSE66930_normData_dc_MVA_1.txt
T00346418


title: PBS_inj_dc_mouse_2_9

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_MVA_1.txt
T00346424


title: MVA_1_vac_dc_mouse_2

description:
Vaccinia virus
processed data file: GSE66930_normData_dc_MVA_1.txt
T00346419


title: PBS_inj_dc_mouse_1_9

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_MVA_1.txt
T00346417


title: PBS_inj_dc_mouse_4_9

description:
100 µL of phosphate buffered saline solution
processed data file: GSE66930_normData_dc_MVA_1.txt
T00346434


title: MPY_2_vac_dc_mouse_3

description:
processed data file: GSE66930_normData_dc_MPY_2.txt
T00342923

value: Murine polyomavirus


title: Buffer treated leaves, biological replicate3 (30min_PLIER16)

description:
Raw data file: 30 min Buffer-3.CEL
Expression profile of buffer treated rice leaves, 30 minafter infiltration


title: 6 h stress Dagad deshi 7-day-old seedling, Biological replicate 1

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

institute: University of Delhi South Campus

description: Gene expression data of 6 h stressed 7-day-old Dagad deshi seedling

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 h at 450C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300.

data_processing: First-order analysis was performed using Affymetrix Gene Chip Operating (GCOS) software 1.2.1. Normalization of data and differential expression analysis was done using ArrayAssist ver 5.5  (Stratagene, CA, USA).

organism: Oryza sativa Indica Group

source_name: 7-day-old seedling

label_protocol: Biotinylated aRNA were prepared according to the revised 3' IVT Affymetrix protocol from 500ng total RNA.

growth_protocol: Seeds of each variety were surface sterilized with 70% ethanol followed by 0.1 % HgCl2 with repeated rinses with Mili-Q water, and were allowed to imbibe in water for 16 h. The seedlings were grown hydroponically for seven days on rice growth medium (RGM), pH 4.8.

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

treatment_protocol: The seven-day-old seedings of each variety were subjected to drought stress by placing them on 3 mm Whatmann sheets for 3 h and 6 h at 28±1oC, respectively. Control tissues were maintained on RGM for 6 h at 28±1oC.

value: Dagad deshi

tag: stress

value: drought stress

value: seedling


title: 6 h stress Dagad deshi 7-day-old seedling, Biological replicate 2


title: 6 h stress IR20 7-day-old seedling, Biological replicate 1

description: Gene expression data of 6 h stressed 7-day-old IR20 seedling


title: MPY_2_vac_dc_mouse_1

description:
processed data file: GSE66930_normData_dc_MPY_2.txt
T00342915


title: PBS_inj_dc_mouse_1_8

description:
processed data file: GSE66930_normData_dc_MPY_2.txt,GSE66930_normData_dc_MPY_3bis.txt
T00342917

value: 100 µL of phosphate buffered saline solution


title: MPY_3bis_vac_dc_mouse_3

description:
processed data file: GSE66930_normData_dc_MPY_3bis.txt
T00342925


title: MPY_3bis_vac_dc_mouse_2

description:
processed data file: GSE66930_normData_dc_MPY_3bis.txt
T00342924


title: 6 h stress IR20 7-day-old seedling, Biological replicate 2


title: MPY_3bis_vac_dc_mouse_1

description:
processed data file: GSE66930_normData_dc_MPY_3bis.txt
T00342916


title: 6 h stress IR20 7-day-old seedling, Biological replicate 3


title: Buffer treated leaves, biological replicate2 (30min_PLIER16)

description:
Raw data file: 30 min Buffer-2.CEL
Expression profile of buffer treated rice leaves, 30 min after infiltration


title: 6 h stress Dagad deshi 7-day-old seedling, Biological replicate 3


title: 3 h stress Dagad deshi 7-day-old seedling, Biological replicate 2

description: Gene expression data of 3 h drought stressed 7-day-old Dagad deshi seedling


title: Control IR20 7-day-old seedling, Biological replicate 2

description: Gene expression data of control unstressed 7-day-old IR20 seedling

value: control unstressed


title: MPY_2_vac_dc_mouse_2

description:
processed data file: GSE66930_normData_dc_MPY_2.txt
T00342922


title: 3 h stress IR20 7-day-old seedling, Biological replicate 1

description: Gene expression data of 3 h drought stressed 7-day-old IR20 seedling


title: 3 h stress IR20 7-day-old seedling, Biological replicate 3


title: Control IR20 7-day-old seedling, Biological replicate 3


title: Control Dagad deshi 7-day old-seedling, Biological replicate 3

description: Gene expression data of control unstressed 7-day-old Dagad deshi seedling


title: Control Dagad deshi 7-day-old seedling, Biological replicate 1


title: PBS_inj_dc_mouse_3_8

description:
processed data file: GSE66930_normData_dc_MPY_2.txt,GSE66930_normData_dc_MPY_3bis.txt
T00342927


title: 3 h stress Dagad deshi 7-day-old seedling, Biological replicate 3


title: MPY_3_vac_dc_mouse_3

description:
processed data file: GSE66930_normData_dc_MPY_3.txt
T00340218

value: Murine polyomavirus VLP


title: PBS_inj_dc_mouse_2_8

description:
processed data file: GSE66930_normData_dc_MPY_2.txt,GSE66930_normData_dc_MPY_3bis.txt
T00342921


title: MPY_3_vac_dc_mouse_2

description:
processed data file: GSE66930_normData_dc_MPY_3.txt
T00340217


title: MPY_3_vac_dc_mouse_1

description:
processed data file: GSE66930_normData_dc_MPY_3.txt
T00340215


title: Control IR20 7-day-old seedling, Biological replicate 1


title: MPY_1_vac_dc_mouse_2

description:
processed data file: GSE66930_normData_dc_MPY_1.txt
T00340212


title: 3 h stress IR20 7-day-old seedling, Biological replicate 2


title: MPY_1_vac_dc_mouse_1

description:
processed data file: GSE66930_normData_dc_MPY_1.txt
T00340204


title: MPT_1_vac_dc_mouse_3

description:
processed data file: GSE66930_normData_dc_MPT_1.txt
T00340211

value: Murine pneumotropic virus VLP


title: MPY_1_vac_dc_mouse_3

description:
processed data file: GSE66930_normData_dc_MPY_1.txt
T00340213


title: MPT_1_vac_dc_mouse_2

description:
processed data file: GSE66930_normData_dc_MPT_1.txt
T00340210


title: MPT_1_vac_dc_mouse_1

description:
processed data file: GSE66930_normData_dc_MPT_1.txt
T00340203


title: PBS_inj_dc_mouse_2_7

description:
processed data file: GSE66930_normData_dc_MPT_1.txt,GSE66930_normData_dc_MPY_1.txt,GSE66930_normData_dc_MPY_3.txt
T00340214


title: G6L3  144h+d

city: London

first: Kathy

last: Niakan

address: Mill Hill

country: United Kingdom

institute: The Francis Crick Institute

description: Gata6 line3 144 hours following doxycycline treatment replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R. The raw expression values were first log2 transformed and then quantile normalized. Batch effects were corrected using empirical Bayes methods. Coefficient of variation (CV) was calculated for each probe across all samples according to the normalized values. Normalized data summarized by gene symbol are available on the series record in the file "Normalized_data.txt".

source_name: Embryonic stem cell 144h Gata6 induction

label_protocol: Biotinylated cRNA were prepared with the TotalPrep 96 RNA amplification kit

growth_protocol: KSR+LIF media: 78% Advanced DMEM/F12, 20% Knockout serum replacer, 2mM L-glutamine; 0.1mM B-mercaptoethanol, 1% penicillin/streptomycin, 10ng/mL LIF

extract_protocol: RNA was extracted with TRI Reagent (Sigma), followed by clean-up and DNase I treatment (Ambion) in accordance with the manufacturer's instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Induction of mES cells was performed in pluripotency maintenance media (KSR+LIF) using doxycycline at a final concentration of 1 μg/mL

value: Embryonic stem cell

value: 144 hours doxycyline-mediated Gata6 induction


title: S7L1  144h+d

description: Sox7 line1 144 hours following doxycycline treatment replicate 1

source_name: Embryonic stem cell 144h Sox7 induction

value: 144 hours doxycyline-mediated Sox7 induction


title: S7L3  144h+d

description: Sox7 line3 144 hours following doxycycline treatment replicate 3


title: OA chondrocyte 1 (OA1)

city: Stanford

first: Nidhi

last: Bhutani

state: California

address: 300 Pasteur Drive, R164 Edwards Bldg

department: Orthopaedic Surgery

institute: Stanford University

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
Data were processed using dChip software. Background correction was applied and normalization to the median array intensity was performed, gene level expression were summarized from the corrected intensities.
Probe group file: HuGene-1_0-st-v1.r3.cdf
Meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: OA chondrocytes

label_protocol: Ambion WT Expression kit was used to generate ssDNA performed using Affymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: Human chondrocytes were isolated from patients undergoing TKR (OA samples) or ACL revisions (normal samples). Additional normal samples were obtained commercially. Cells were expanded for two passages in standard chondrocyte growth medium, before RNA extraction.

extract_protocol: QIAGEN RNeasy.

tag: donor disease status

value: osteoarthritis

value: chondrocytes


title: OA chondrocyte 2 (OA2)


title: G6L2  144h+d

description: Gata6 line2 144 hours following doxycycline treatment replicate 2


title: PBS_inj_dc_mouse_1_7

description:
processed data file: GSE66930_normData_dc_MPT_1.txt,GSE66930_normData_dc_MPY_1.txt,GSE66930_normData_dc_MPY_3.txt
T00340208


title: G6L1  144h+d

description: Gata6 line1 144 hours following doxycycline treatment replicate 1


title: G6L3  96h+d

description: Gata6 line3 96 hours following doxycycline treatment replicate 3

source_name: Embryonic stem cell 96h Gata6 induction

value: 96 hours doxycyline-mediated Gata6 induction


title: MLV_2_vac_dc_mouse_4

description:
processed data file: GSE66930_normData_dc_MLV_2.txt
T00346387

value: Moloney murine leukemia retrovirus VLP


title: Normal chondrocyte 5 (N5)

source_name: Normal chondrocytes

value: normal


title: Normal chondrocyte 4 (N4)


title: G6L2 96h+d

description: Gata6 line2 96 hours following doxycycline treatment replicate 2


title: Normal chondrocyte 3 (N3)


title: Normal chondrocyte 1 (N1)


title: MLV_2_vac_dc_mouse_2

description:
processed data file: GSE66930_normData_dc_MLV_2.txt
T00346385

source_name: Sorted dendritic cells from spleen

value: dendritic cells


title: G6L3 48h+d

description: Gata6 line3 48 hours following doxycycline treatment replicate 3

source_name: Embryonic stem cell 48h Gata6 induction

value: 48 hours doxycyline-mediated Gata6 induction


title: S7L2  144h+d

description: Sox7 line2 144 hours following doxycycline treatment replicate 2


title: MLV_2_vac_dc_mouse_1

description:
processed data file: GSE66930_normData_dc_MLV_2.txt
T00346384


title: PBS_inj_dc_mouse_4_6

description:
processed data file: GSE66930_normData_dc_MLV_2.txt
T00346383


title: G6L1 96h+d

description: Gata6 line1 96 hours following doxycycline treatment replicate 1


title: Control Dagad deshi 7-day-old seedling, Biological replicate 2

description: Gene expression data of control unstressed 7-day-old Dagad deshi seedling

value: Dagad deshi

value: control


title: Normal chondrocyte 2 (N2)


title: G6L2 48h+d

description: Gata6 line2 48 hours following doxycycline treatment replicate 2


title: PBS_inj_dc_mouse_3_6

description:
processed data file: GSE66930_normData_dc_MLV_2.txt
T00346379


title: PBS_inj_dc_mouse_3_7

description:
processed data file: GSE66930_normData_dc_MPT_1.txt,GSE66930_normData_dc_MPY_1.txt,GSE66930_normData_dc_MPY_3.txt
T00340216


title: G6L1 48h+d

description: Gata6 line1 48 hours following doxycycline treatment replicate 1


title: G6L2 36h+d

description: Gata6 line2 36 hours following doxycycline treatment replicate 2

source_name: Embryonic stem cell 36h Gata6 induction

value: 36 hours doxycyline-mediated Gata6 induction


title: PBS_inj_dc_mouse_1_6

description:
processed data file: GSE66930_normData_dc_MLV_2.txt
T00346377

value: 100 µL of phosphate buffered saline solution


title: PBS_inj_dc_mouse_2_6

description:
processed data file: GSE66930_normData_dc_MLV_2.txt
T00346378


title: G6L1 36h+d

description: Gata6 line1 36 hours following doxycycline treatment replicate 1


title: MLV_1_vac_dc_mouse_3

description:
T00339435
processed data file: GSE66930_normData_MLV_1.txt


title: MLV_1_vac_dc_mouse_2

description:
T00339434
processed data file: GSE66930_normData_MLV_1.txt


title: MLV_2_vac_dc_mouse_3

description:
processed data file: GSE66930_normData_dc_MLV_2.txt
T00346386


title: G6L3 24h+d

description: Gata6 line3 24 hours following doxycycline treatment replicate 3

source_name: Embryonic stem cell 24h Gata6 induction

value: 24 hours doxycyline-mediated Gata6 induction


title: G6L2 24h+d

description: Gata6 line2 24 hours following doxycycline treatment replicate 2


title: PBS_inj_dc_mouse_3_5

description:
T00339436
processed data file: GSE66930_normData_MLV_1.txt


title: MLV_1_vac_dc_mouse_1

description:
T00339433
processed data file: GSE66930_normData_MLV_1.txt


title: G6L1 24h+d

description: Gata6 line1 24 hours following doxycycline treatment replicate 1


title: PBS_inj_dc_mouse_2_5

description:
T00339431
processed data file: GSE66930_normData_MLV_1.txt


title: PBS_inj_dc_mouse_1_5

description:
T00339423
processed data file: GSE66930_normData_MLV_1.txt


title: G6L2  12h+d

description: Gata6 line2 12 hours following doxycycline treatment replicate 2

source_name: Embryonic stem cell 12h Gata6 induction

value: 12 hours doxycyline-mediated Gata6 induction


title: BCG_3_vac_dc_mouse_3

description:
T00345274
processed data file: GSE66930_normData_BCG_3.txt.gz

value: BCG bacteria-based vector-plaforms


title: G6L3 12h+d

description: Gata6 line3 12 hours following doxycycline treatment replicate 3

value: Embryonic stem cell


title: G6L1  12h+d

description: Gata6 line1 12 hours following doxycycline treatment replicate 1


title: eXEN1

description: Embryo-derived XEN GFP replicate 1

source_name: Extraembryonic endoderm stem cell

value: Extraembryonic endoderm stem cell

value: Uninduced control


title: BCG_3_vac_dc_mouse_2

description:
T00345267
processed data file: GSE66930_normData_BCG_3.txt.gz


title: mESC4

description: Gata6 line 3 no doxycycline control 4

source_name: Embryonic stem cell


title: BCG_2_vac_dc_mouse_3

description:
T00345270
processed data file: GSE66930_normData_BCG_2.txt.gz


title: BCG_2_vac_dc_mouse_2

description:
T00345266
processed data file: GSE66930_normData_BCG_2.txt.gz


title: BCG_3_vac_dc_mouse_1

description:
T00345261
processed data file: GSE66930_normData_BCG_3.txt.gz


title: G6L3 36h+d

description: Gata6 line3 36 hours following doxycycline treatment replicate 3


title: BCG_2_vac_dc_mouse_1

description:
T00345251
processed data file: GSE66930_normData_BCG_2.txt.gz


title: mESC3

description: mESC control replicate 3


title: mESC1

description: mESC control replicate 1


title: BCG_1_vac_dc_mouse_2

description:
T00345268
processed data file: GSE66930_normData_BCG_1.txt.gz


title: mESC2

description: mESC control replicate 2


title: BCG_1_vac_dc_mouse_1

description:
T00345262
processed data file: GSE66930_normData_BCG_1.txt.gz


title: PBS_inj_dc_mouse_3_4

description:
T00345269
processed data file: GSE66930_normData_BCG_1.txt.gz, GSE66930_normData_BCG_2.txt.gz, GSE66930_normData_BCG_3.txt.gz


title: PBS_inj_dc_mouse_2_4

description:
T00345265
processed data file: GSE66930_normData_BCG_1.txt.gz, GSE66930_normData_BCG_2.txt.gz, GSE66930_normData_BCG_3.txt.gz


title: PBS_inj_dc_mouse_1_4

description:
T00345250
processed data file: GSE66930_normData_BCG_1.txt.gz, GSE66930_normData_BCG_2.txt.gz, GSE66930_normData_BCG_3.txt.gz


title: AP205_3_vac_dc_mouse_3

description:
processed data file: GSE66930_normData_AP205_3.txt
T00340231

value: AP205 bacteriophage based VLP


title: AP205_3_vac_dc_mouse_1

description:
processed data file: GSE66930_normData_AP205_3.txt
T00340225


title: eXEN2

description: Embryo-derive XEN YFP replicate 2


title: PBS_inj_dc_mouse_3_3

description:
processed data file: GSE66930_normData_AP205_3.txt
T00340227


title: PBS_inj_dc_mouse_2_3

description:
processed data file: GSE66930_normData_AP205_3.txt
T00340226


title: AP205_1bis_vac_mouse_3

description:
T00346391
processed data file: GSE66930_normData_AP205_1bis.txt


title: BCG_1_vac_dc_mouse_3

description:
T00345273
processed data file: GSE66930_normData_BCG_1.txt.gz


title: PBS_inj_dc_mouse_1_3

description:
processed data file: GSE66930_normData_AP205_3.txt
T00340219


title: AP205_1bis_vac_mouse_2

description:
T00346390
processed data file: GSE66930_normData_AP205_1bis.txt


title: AP205_1bis_vac_mouse_1

description:
T00346393
processed data file: GSE66930_normData_AP205_1bis.txt


title: PBS_inj_dc_mouse_4_2

description:
T00346396
processed data file: GSE66930_normData_AP205_1bis.txt


title: TAC DKO_6

city: Bad Krozingen

first: Thomas

middle: G

last: Nuehrenberg

state: Baden-Württemberg

address: Südring 15

department: Klinik für Kardiologie II

country: Germany

institute: Universitäts-Herzzentrum Freiburg • Bad Krozingen

data_processing: For data analysis, Illumina GenomeStudio V2010.3 was used (pFDR < 0.05, fold change > 1.5).

source_name: cardiac ventricle

label_protocol: mRNA isolation and preparation of cRNA were conducted as indicated by the manufacturer (Epicentre TargetAmp™-Nano Labeling Kit, Biozym Scientific, Hessisch Oldendorf, Germany).

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol for fibrous tissue.

treatment_protocol: To establish left ventricular pressure overload for 4 weeks, 10-12 week old male mice were anaesthetized with 2% (vol) isoflurane in oxygen and underwent transverse aortic constriction (TAC). After partial thoracotomy limited to the upper 2 ribs, a 7.0 silk suture was pulled tightly around both the aortic arch distal to the brachiocephalic trunk and a 27-G hypodermic needle in order to constrict the transverse aorta in a defined way as described previously [16]. 14-16 week-old mice were weighed, sacrificed and heart and lung tissues were removed and dissected for assessment of ventricular and lung weight, respectively.

value: cardiac ventricle

value: TAC

tag: genotype

value: double-knockout

tag: gender

value: male


title: AP205_3_vac_dc_mouse_2

description:
processed data file: GSE66930_normData_AP205_3.txt
T00340230

value: dendritic cells


title: PBS_inj_dc_mouse_2_2

description:
T00346389
processed data file: GSE66930_normData_AP205_1bis.txt


title: TAC CTL_6


title: TAC CTL_5


title: TAC DKO_4


title: PBS_inj_dc_mouse_3_2

description:
T00346395
processed data file: GSE66930_normData_AP205_1bis.txt


title: AP205_1_vac_dc_mouse_2

description:
T00302433
processed data file: GSE66930_normData_dc_AP205_1.txt.gz

value: AP205 bacteriophage


title: TAC DKO_5


title: AP205_1_vac_dc_mouse_1

description:
T00302430
processed data file: GSE66930_normData_dc_AP205_1.txt.gz


title: TAC DKO_2


title: TAC DKO_3


title: TAC CTL_2


title: TAC CTL_3


title: TAC CTL_4


title: AP205_1_vac_dc_mouse_3

description:
T00302434
processed data file: GSE66930_normData_dc_AP205_1.txt.gz


title: PBS_inj_dc_mouse_3

description:
T00302454
processed data file: GSE66930_normData_dc_AP205_1.txt.gz


title: TAC DKO_1


title: Sham DKO_2

value: Sham


title: TAC CTL_1

value: control


title: PBS_inj_dc_mouse_1

description:
T00278888
processed data file: GSE66930_normData_dc_AP205_1.txt.gz


title: Sham DKO_4


title: PBS_inj_dc_mouse_2

description:
T00278889
processed data file: GSE66930_normData_dc_AP205_1.txt.gz


title: Sham CTL_4


title: Sham CTL_1


title: Sham DKO_1


title: Sham DKO_3


title: Sham CTL_3


title: Sham CTL_2


title: ZT54

city: ShangHai

first: Haifang

last: Wang

address: NO 320, Yueyang Road

department: functional genomics group

country: China

institute: PICB

hyb_protocol: Same as above. The entire reaction was hybridized to the array for 20 hours at 55°C.

scan_protocol: Microarray results were extracted using Agilent Microarray Scanner (Agilent)

data_processing: The miRNA signals and errors on miRNA microarray were obtained from gTotalGeneSignal and gTotalGeneError respectively in the output files of Agilent Feature Extraction software (v9.5.3.1), subsequently analyzed by Gene-Spring GX 7.3.1 software (Agilent).

source_name: liver total RNA, ZT54

label_protocol: Labeling and hybridization of total RNA were performed according to the manufacturer’s protocol with no modification.

growth_protocol: Adults mice were housed under 1 12-h light/12-h dark regimen

extract_protocol: Total RNA from each tissue sample was extracted using TRizol (Invitrogen) according to the manufacturer's instructions. Total RNA quality was assessed by Bioanalyzer 2100 (Agilent). Total RNA of each time point were mixed in the equal amount into one pooled sample.

treatment_protocol: Food and water available ad libitum.

value: liver


title: ZT58

source_name: liver total RNA, ZT58


title: ZT62

source_name: liver total RNA, ZT62


title: ZT50

source_name: liver total RNA, ZT50


title: PBS_inj_48_spleen_mouse_3

description:
Control_group
processed data file: GSE66797_normData_spleen_rAd_48h.txt.gz

scan_protocol: Illumina BeadArray 500GX Reader

data_processing: The data were extracted using BeadStudio without modification, normalized with quantile with limma package from R, log2 transformed and filtered for probes with bad detection p-values in all samples within a comparison.

source_name: Whole delicerated spleen

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

growth_protocol: Fresh whole spleen cells

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

treatment_protocol: Whole spleen deliceration  were stored at -80°C in trizol solution

value: spleen

value: 100 µL of phosphate buffered saline solution

tag: time point


title: PBS_inj_48_spleen_mouse_5


title: PBS_inj_dc_mouse_1_2

description:
T00346388
processed data file: GSE66930_normData_AP205_1bis.txt


title: PBS_inj_48_spleen_mouse_4


title: ZT46

source_name: liver total RNA, ZT46


title: 3 h stress Dagad deshi 7-day-old seedling, Biological replicate 1

description: Gene expression data of 3 h drought stressed 7-day-old Dagad deshi seedling

source_name: 7-day-old seedling

value: Dagad deshi

value: drought stress

value: seedling


title: ZT30

source_name: liver total RNA, ZT30


title: ZT34

source_name: liver total RNA, ZT34


title: Adeno_1_vac_48_spleen_mouse_5

description:
Adnovirus
processed data file: GSE66797_normData_spleen_rAd_48h.txt.gz

value: Adnovirus


title: ZT38

source_name: liver total RNA, ZT38


title: ZT18

source_name: liver total RNA, ZT18


title: PBS_inj_48_spleen_mouse_2


title: Adeno_1_vac_72_spleen_mouse_4

description:
Adnovirus
processed data file: GSE66797_normData_spleen_rAd_72h.txt.gz


title: ZT42

source_name: liver total RNA, ZT42


title: Adeno_1_vac_72_spleen_mouse_3


title: PBS_inj_48_spleen_mouse_1


title: Adeno_1_vac_72_spleen_mouse_1


title: PBS_inj_6_spleen_mouse_5

description:
Control_group
processed data file: GSE66797_normData_spleen_rAd_6h.txt.gz


title: ZT26

source_name: liver total RNA, ZT26


title: PBS_inj_6_spleen_mouse_6


title: PBS_inj_6_spleen_mouse_4


title: Adeno_1_vac_72_spleen_mouse_2


title: Adeno_1_vac_48_spleen_mouse_3


title: Adeno_1_vac_48_spleen_mouse_4


title: RPMI8226

type: genomic

city: Atlanta

first: Jeanne

last: Kowalski

address: 1365-B Clifton Rd. NE.

department: Winship Cancer Institute

institute: Emory University

description: SNP-CN data from RPMI8226 multiple myeloma cell line

hyb_protocol: Standard illumina protocol for HumanOmni1-Quad Beadchip

data_processing: Genomic DNA extracted was genotyped using Illumina's BeadStudio software. The data was processed using Illumina's GenomeStudio software. Copy Number Variation (CNV) detection was performed using algorithm with default settings in Partek software (v6.6, Partek Inc.). Data was normalized against the HapMaP reference population. The allelic signal intensities and genotypes were generated using GenomeStudio.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: RPMI8226 human myeloma cell line

growth_protocol: The cell lines were grown in for 2 weeks. Subcultured 24 hours before harvest for DNA extraction

tag: cell line

tag: cancer type

value: multiple myeloma


title: MM.1S

description: SNP-CN data from MM.1S multiple myeloma cell line

scan_protocol: Standard illumina protocol for HumanOmni1-Quad Beadchip

source_name: MM.1S human myeloma cell line


title: KMS11

description: SNP-CN data from KMS11 multiple myeloma cell line

source_name: KMS11 human myeloma cell line

label_protocol: Standard illumina protocol for HumanOmni1-Quad Beadchip


title: adult Whole Cortex Input rep2

city: New York

first: Awni

last: Mousa

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description: Gene expression data from Cortex Input of BAC transgenic mice expressing EGFP-L10

hyb_protocol: Following fragmentation,20 ug of cRNA were hybridizied to Genechip Mouse Genome 430 2.0 microarrays (Affymetrix, Santa Clara, CA). GeneChips were washed and stained in the Affymetrix GeneChip Scanner 3000 7G System.

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

data_processing: The data were analyzed with the Affymetrix software suite provided by the affy R-package (version 1.40.0) using default analysis settings. The normalized data tables can be found on the series record and contain the log base 2 scale RMA normalized signal intensity.

source_name: Cortex

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's instructions (Affymetrix, Santa Clara, CA)

growth_protocol: Animals were raised at 78oC in 12h light:12h dark conditions with food and water provided ad libitum. All experimental animals were adults between 8-10 weeks old.

extract_protocol: Polysomes from cortices of bacTRAP transgenic mice were immunoprecipitated with anti-EGFP antibodies bound to Protein L conjugated Streptavidin My-One Dynabeads. Bound RNA was extracted and purified using Absolutely NanoPrep RNA purification kit (Stratagene, La Jolla, CA). 15 ng of RNA was amplified with Genechip Expression 3' Amplification 2-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

tag: tissue

value: Cerebral cortex

tag: transgene

value: adults (8-10 weeks old)


title: adult Whole Cortex Input rep3


title: adult Whole Cortex Input rep4


title: adult Whole Cortex Input rep1


title: adult OLIG2 bacTRAP mouse, biological rep3

description: Gene expression data from BAC transgenic mice expressing EGFP-L10 under the control of OLIG2 gene driver

source_name: OLIG2 bacTRAP


title: Adeno_1_vac_48_spleen_mouse_2

tag: strain


title: ZT22

source_name: liver total RNA, ZT22


title: PBS_inj_72_spleen_mouse_5

description:
Control_group
processed data file: GSE66797_normData_spleen_rAd_72h.txt.gz

tag: treatment


title: miR-125a (+/-) MPD

city: Suita

first: Naoya

last: Tatsumi

state: Osaka

address: 1-7 Yamada-Oka

department: Functional Diagnostic Science

country: Japan

institute: Osaka University Graduate School of Medicine

description: miR-125a (+/-) MPD

hyb_protocol: The biotin-labeled aRNA was fragmented to uniform size and added to a bioarrays.

scan_protocol: The bioarrays were washed, exposed to Cy5-streptavidin and scanned using GenePix 4000B laser scanner (Molecular Devices, Sunnyvale, CA).

data_processing: The scanned image information was converted into spot intensity values using CodeLink™ Expression Analysis software v5.0 (Applied Microarrays, Tempe, AZ) and normalized by quantile method.

source_name: HSC

label_protocol: Biotinylated aRNA was synthesized with two round amplification steps via TargetAmpTM2-round Aminoallyl-aRNA Amplification Kit (Illumia, Inc) and Biotin-X-X-NHS kit (Illumina, Inc).

extract_protocol: Total RNA was extracted from the FACS-sorted Lin-Sca1+cKit+Flt3- hematopoietic stem cells from BM of miR-125a (+/+) and miR-125a (+/-) MPD mice with TRIZOL (Invitrogen).

tag: genotype/variation


title: Adeno_1_vac_6_spleen_mouse_4

description:
Adnovirus
processed data file: GSE66797_normData_spleen_rAd_6h.txt.gz


title: PBS_inj_72_spleen_mouse_3


title: Adeno_1_vac_6_spleen_mouse_1


title: Adeno_1_vac_6_spleen_mouse_5


title: Adeno_1_vac_6_spleen_mouse_3


title: Adeno_1_vac_6_spleen_mouse_2


title: adult OLIG2 bacTRAP mouse, biological rep2


title: PBS_inj_6_spleen_mouse_3


title: miR-125a (+/+) control

description: miR-125a (+/+) control

value: miR-125a (+/+) control


title: PBS_inj_6_spleen_mouse_2


title: adult OLIG2 bacTRAP mouse, biological rep1


title: adult ALDH1L1 bacTRAP mouse, biological rep3

description: Gene expression data from BAC transgenic mice expressing EGFP-L10 under the control of ALDH1L1 gene driver

source_name: ALDH1L1 bacTRAP


title: adult ALDH1L1 bacTRAP mouse, biological rep2


title: PBS_inj_72_spleen_mouse_4

source_name: Whole delicerated spleen


title: Adeno_1_vac_48_spleen_mouse_1


title: PBS_inj_72_spleen_mouse_1


title: PBS_inj_72_spleen_mouse_2


title: adult ALDH1L1 bacTRAP mouse, biological rep1


title: rAd_1_vac_spleen_mouse_5

description:
Adenovirus
processed data file: GSE66797_normData_spleen_rAd_1.txt.gz

value: Adenovirus


title: PBS_inj_6_spleen_mouse_1


title: adult NEK7 bacTRAP mouse, biological rep3

description: Gene expression data from BAC transgenic mice expressing EGFP-L10 under the control of NEK7 gene driver

source_name: NEK7 bacTRAP


title: adult NEK7 bacTRAP mouse, biological rep2


title: adult DLX1 bacTRAP mouse, biological rep3

description: Gene expression data from BAC transgenic mice expressing EGFP-L10 under the control of DLX1 gene driver

source_name: DLX1 bacTRAP


title: adult NEK7 bacTRAP mouse, biological rep1


title: adult DLX1 bacTRAP mouse, biological rep2


title: adult NTSR1 bacTRAP mouse, biological rep2

description: Gene expression data from BAC transgenic mice expressing EGFP-L10 under the control of NTSR1 gene driver

source_name: NTSR1 bacTRAP


title: adult NTSR1 bacTRAP mouse, biological rep3


title: rAd_1_vac_spleen_mouse_3


title: adult DLX1 bacTRAP mouse, biological rep1


title: adult NTSR1 bacTRAP mouse, biological rep1


title: adult S100A10 bacTRAP mouse, biological rep2

description: Gene expression data from BAC transgenic mice expressing EGFP-L10 under the control of S100A10 gene driver

source_name: S100A10 bacTRAP


title: adult S100A10 bacTRAP mouse, biological rep1


title: adult S100A10 bacTRAP mouse, biological rep3


title: AP205_1_vac_spleen_mouse_3

description:
AP205 bacteriophage based VLP
processed data file: GSE66797_normData_spleen_AP205_1.txt.gz

value: AP205 bacteriophage based VLP


title: PBS_inj_spleen_mouse_1_2

description:
Control_group
processed data file: GSE66797_normData_spleen_rAd_1.txt.gz


title: adult GLT25D2 bacTRAP mouse, biological rep2

description: Gene expression data from BAC transgenic mice expressing EGFP-L10 under the control of GLT25D2 gene driver

source_name: GLT25D2 bacTRAP


title: adult GLT25D2 bacTRAP mouse, biological rep1


title: PBS_inj_spleen_mouse_4_2


title: PBS_inj_spleen_mouse_2_2


title: adult NTF3 bacTRAP mouse, biological rep3

description: Gene expression data from BAC transgenic mice expressing EGFP-L10 under the control of Ntf3 gene driver

source_name: NTF3 bacTRAP


title: adult NTF3 bacTRAP mouse, biological rep2


title: rAd_1_vac_spleen_mouse_1


title: rAd_1_vac_spleen_mouse_4


title: AP205_1_vac_spleen_mouse_2


title: MVA_1_vac_spleen_mouse_5

description:
Vaccinia virus
processed data file: GSE66797_normData_spleen_MVA_1.txt.gz

value: Vaccinia virus


title: AP205_1_vac_spleen_mouse_4


title: PBS_inj_spleen_mouse_3_2


title: adult NTF3 bacTRAP mouse, biological rep1


title: rAd_1_vac_spleen_mouse_2


title: AP205_1_vac_spleen_mouse_1


title: MVA_1_vac_spleen_mouse_2


title: MLV_1_vac_spleen_mouse_4

description:
Moloney murine leukemia retrovirus VLP
processed data file: GSE66797_normData_spleen_MLV_1.txt.gz

value: Moloney murine leukemia retrovirus VLP


title: MVA_1_vac_spleen_mouse_1


title: PBS_inj_spleen_mouse_5_2


title: MVA_1_vac_spleen_mouse_4


title: MVA_1_vac_spleen_mouse_3


title: MLV_1_vac_spleen_mouse_3


title: MLV_1_vac_spleen_mouse_1


title: MPT_1_vac_spleen_mouse_2

description:
Murine pneumotrophic virus VLP
processed data file: GSE66797_normData_spleen_MPT_1.txt.gz

value: Murine pneumotrophic virus VLP


title: PRDM2 KD S48 2

city: Bad nauheim

first: Sirisha

last: Cheedipudi

state: Hessen

department: cardiac origin cell lines

institute: Max-planck institue for heart and lung research

description:
G0 arrested myoblasts of C2C12 PRDM2sh stable pool Biological replicate 2
Expression profile of PRDM2 shRNA transfected quiescent C2C12 myobalsts

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray GeneChipsoftware (GCOS), normalised using PLIER algorthim

source_name: C2C12 transfected with PRDM2 shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Grown in Dulbecco's modified Eagle medium supplemented with 20% Fetal calf serum

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

treatment_protocol: Synchronized cells in G0 for 48hrs in methyl cellulose suspension medium with 20% Fetal calf serum

value: transfected with PRDM2 shRNA


title: MLV_1_vac_spleen_mouse_2


title: PRDM2 KD S48 1

description:
G0 arrested myoblasts of C2C12 PRDM2sh stable pool Biological replicate 1
Expression profile of PRDM2 shRNA transfected quiescent C2C12 myobalsts


title: GFP S48 1

description:
G0 arrested myoblasts of C2C12 GFPsh control stable pool Biological replicate 1
Expression profile of control GFPshRNA transfected quiescent C2C12 myobalsts

source_name: C2C12 transfected with control GFPshRNA

value: transfected with control GFPshRNA


title: GFP S48 3

description:
G0 arrested myoblasts of C2C12 GFPsh control stable pool Biological replicate 3
Expression profile of control GFPshRNA transfected quiescent C2C12 myobalsts


title: MPT_1_vac_spleen_mouse_1

value: spleen


title: MPT_1_vac_spleen_mouse_3


title: PBS_inj_spleen_mouse_5

description:
Control_group
processed data file: GSE66797_normData_spleen_AP205_1.txt.gz, GSE66797_normData_spleen_MLV_1.txt.gz, GSE66797_normData_spleen_MPT_1.txt.gz, GSE66797_normData_spleen_MVA_1.txt.gz

value: 100 µL of phosphate buffered saline solution


title: PRDM2 KD D28 3

description:
C2C12 PRDM2 sh myoblasts grown in differentiating conditions Biological replicate 3
Expression profile of PRDM2 shRNA transfected 28hrs differentiated C2C12 myobalsts

growth_protocol: Grown in Dulbecco's modified Eagle medium supplemented with 2% horse serum for 28hrs

treatment_protocol: Differentiated myoblasts for 28hrs in reduced serum conditions


title: PRDM2 KD D28 1

description:
C2C12 PRDM2 sh myoblasts grown in differentiating conditions Biological replicate 1
Expression profile of PRDM2 shRNA transfected 28hrs differentiated C2C12 myobalsts


title: GFP D28 2

description:
C2C12 GFPsh control myoblasts grown in differentiating conditions Biological replicate 2
Expression profile of control GFPshRNA transfected 28hrs differentiated C2C12 myobalsts


title: Qb_5_vac_pbmc_mouse_3

description:
Bacteriophage based VLP
processed data file: GSE66797_normData_PBMC_Qb_5.txt.gz

source_name: PBMC

value: PBMC

value: Bacteriophage based VLP


title: PBS_inj_spleen_mouse_2


title: embryonic ovary Wnt4 KO male_E14.5-1

city: Oulu

first: Florence

last: Naillat

address: Aapistie 5A

country: Finland

institute: Oulu University

description: Gene expression data from embryonic gonad

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Expression Set 430_2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GenChip Scanner 3000.

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 500.

source_name: embryonic testis at E14.5 biological rep1

growth_protocol: Embryonic gonad were dissected and frozen immediately until PCR genotyping was carried out.

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

value: embryonic gonad

value: Wnt4 knock-out

value: Embryonic day 14.5


title: GFP S48 2

description:
G0 arrested myoblasts of C2C12 GFPsh control stable pool Biological replicate 2
Expression profile of control GFPshRNA transfected quiescent C2C12 myobalsts


title: GFP D28 3

description:
C2C12 GFPsh control myoblasts grown in differentiating conditions Biological replicate 3
Expression profile of control GFPshRNA transfected 28hrs differentiated C2C12 myobalsts


title: PRDM2 KD D28 2

description:
C2C12 PRDM2 sh myoblasts grown in differentiating conditions Biological replicate 2
Expression profile of PRDM2 shRNA transfected 28hrs differentiated C2C12 myobalsts


title: GFP D28 1

description:
C2C12 GFPsh control myoblasts grown in differentiating conditions Biological replicate 1
Expression profile of control GFPshRNA transfected 28hrs differentiated C2C12 myobalsts


title: PBS_inj_spleen_mouse_1


title: PBS_inj_spleen_mouse_4


title: Qb_5_vac_pbmc_mouse_2


title: embryonic ovary Wnt4 KO male_E14.5-2

source_name: embryonic testis at E14.5 biological rep2


title: PBS_inj_spleen_mouse_7


title: PBS_inj_spleen_mouse_3


title: PBS_inj_spleen_mouse_6


title: Qb_5_vac_pbmc_mouse_1


title: Qb_4_vac_pbmc_mouse_3

description:
Bacteriophage based VLP
processed data file: GSE66797_normData_PBMC_Qb_4.txt.gz


title: embryonic ovary WT male_E14.5-2

value: wild type


title: Qb_4_vac_pbmc_mouse_2


title: embryonic ovary WT male_E14.5-1


title: embryonic ovary Wnt4 KO female_E14.5-2

source_name: embryonic ovary at E14.5 biological rep2


title: Qb_3_vac_pbmc_mouse_3

description:
Bacteriophage based VLP
processed data file: GSE66797_normData_PBMC_Qb_3.txt.gz


title: embryonic ovary Wnt4 KO female_E12.5-2

source_name: embryonic ovary at E12.5 biological rep2

value: Embryonic day 12.5


title: embryonic ovary Wnt4 KO female_E12.5-1

source_name: embryonic ovary at E12.5 biological rep1


title: Qb_4_vac_pbmc_mouse_1


title: embryonic ovary WT female_E14.5-2


title: Qb_3_vac_pbmc_mouse_2


title: Qb_2_vac_pbmc_mouse_1

description:
Bacteriophage based VLP
processed data file: GSE66797_normData_PBMC_Qb_2.txt.gz


title: Qb_3_vac_pbmc_mouse_1


title: embryonic ovary WT female_E14.5-1

source_name: embryonic ovary at E14.5 biological rep1


title: embryonic ovary WT male_E12.5-2

source_name: embryonic testis at E12.5 biological rep2


title: embryonic ovary Wnt4 KO male_E12.5-2


title: embryonic ovary Wnt4 KO male_E12.5-1

source_name: embryonic testis at E12.5 biological rep1


title: Qb_1_vac_pbmc_mouse_1

description:
Bacteriophage based VLP
processed data file: GSE66797_normData_PBMC_Qb_1.txt.gz


title: Qb_2_vac_pbmc_mouse_2


title: Qb_2_vac_pbmc_mouse_4


title: embryonic ovary Wnt4 KO female_E14.5-1


title: Qb_1_vac_pbmc_mouse_2


title: Qb_1_vac_pbmc_mouse_4


title: embryonic ovary WT female_E12.5-2


title: embryonic ovary WT male_E12.5-1


title: Qb_1_vac_pbmc_mouse_3


title: embryonic ovary WT female_E12.5-1


title: PBS_inj_pbmc_mouse_3_2

description:
Control_group
processed data file: GSE66797_normData_PBMC_Qb_1.txt.gz, GSE66797_normData_PBMC_Qb_2.txt.gz, GSE66797_normData_PBMC_Qb_3.txt.gz, GSE66797_normData_PBMC_Qb_4.txt.gz, GSE66797_normData_PBMC_Qb_5.txt.gz


title: PBS_inj_pbmc_mouse_2_2


title: Qb_2_vac_pbmc_mouse_3


title: Qb_1_vac_pbmc_mouse_5


title: PRDM2 KD S48 3

description:
G0 arrested myoblasts of C2C12 PRDM2sh stable pool Biological replicate 3
Expression profile of PRDM2 shRNA transfected quiescent C2C12 myobalsts


title: AP205_1_vac_pbmc_mouse_2

description:
AP205 bacteriophage based VLP
processed data file: GSE66799_normData_PBMC_AP205_1.txt.gz


title: AP205_1_vac_pbmc_mouse_1


title: MVA_1_vac_pbmc_mouse_3

description:
Vaccinia virus
processed data file: GSE66799_normData_PBMC_MVA_1.txt.gz


title: RNA_MIN6_AdmiR7b

city: Rehovot

first: Jean

last: Hausser

address: Herzl St.

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw data (CEL files) from the Affymetrix scanner were loaded into R using the the R software (www.R-project.org) with the BioConductor affy package [Gentleman et al., Genome Biology 2004]. Probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm [Wu et al., Journal of the American Statistical Association 2004]. Per gene log2 fold change were obtained through the following procedure. Probe sets for which more than half of the probes (i.e. 6 probes) mapped ambiguously (more than 1 match) to the genome were discarded, as were probe sets that mapped to multiple genes. We then collected all remaining probe sets matching a given gene, and averaged their log2 fold changes to obtain an expression change per gene. For the MIN6 over-expression data, we considered all genes for which at least one probeset was called present in either the GFP expression control or both the miR-7a and miR-7b overexpression experiments as expressed. Only these genes were retained for further analyses. In the KO experiment, we considered all genes for which at least one probeset was called present in either the WT or the KO as expressed.

molecule: polyA RNA

source_name: MIN6 cells, AdmiR7b infected

label_protocol: standard Affymetrix protocol

growth_protocol: MIN6 cells were maintained in DMEM medium as described in Poy et al., Nature 2004.

extract_protocol: Trizol

treatment_protocol: MIN6 adenoviral infections were performed at a MOI of 250 for 48hrs in DMEM medium containing 4.5 g/l glucose, Glutamax, 2% FBS, and 5.5 µM 2-mercaptoethanol.

value: AdmiR7b infection


title: RNA_MIN6_AdGFP

source_name: MIN6 cells, AdGFP infected

value: AdGFP infection


title: PBS_inj_pbmc_mouse_1_2


title: Wt_CD4+ helper T cell

city: Obu

first: Yoshinori

last: Naoe

state: Aichi

address: 35 Gengo Morioka

department: Department of mechanism of aging

institute: National Institute for Longevity and Gerontology

description: Gene expression in CD4SP

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_F_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Wt_CD4 T

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

extract_protocol: RNA was prepared using the RNAeasy column purification (QIAGEN, Valencia, CA)

treatment_protocol: The splenocytes were isolated by cell sorting.

tag: cell type

value: CD4+helper T cell

tag: cell

value: Splenocyte


title: RNA_MIN6_AdmiR7a_rep2

source_name: MIN6 cells, AdmiR7a infected

value: AdmiR7a infection


title: MLV_1_vac_pbmc_mouse_1

description:
Moloney murine leukemia retrovirus VLP
processed data file: GSE66799_normData_PBMC_MLV_1.txt.gz

value: Moloney murine leukemia retrovirus VLP


title: Wt_CD8+ cytotoxic T cell

description: Gene expression in CD8SP

source_name: Wt_CD8 T

value: CD8+ cytotoxic T cell


title: α-amanitin treatment_replicate 4_with dyeswap

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

description:
Raw data file: α-amanitin assay_rep4.txt
α-amanitin treated cells_Cy3
Untreated cells_Cy5
Raw data file: α-amanitin assay_rep4_swap.txt
Untreated cells_Cy3
α-amanitin treated cells_Cy5
Replicate 4 of 4. α-amanitin treated cells  vs. untreated control cells.
Replicate 4 of 4 (dye-swap). α-amanitin treated cells  vs. untreated control cells.

hyb_protocol: Agilent Gene Expression Hybridization Kit were used and samples were applied to microarrays enclosed in Agilent  Microarray Hybridization Chamber. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent High-Resolution Microarray scanner . Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing:
Filtering was performed prior to normalization and statistical analysis.
Agilent Feature Extraction Software (version 9.5) was used for background subtraction (BGSubSignal was used). Averages of dye swap ratios were used. 13,130 probes with expression significantly greater than the corresponding background (2-sided t-test, flag ‘IsPosAndSignif’) in at least six of the eight control sample replicates were defined as expressed and further analyzed.

label: Cy3, Cy5

source_name: α-amanitin treated cells

label_protocol: 200 ng of DNAse-treated total RNA aliquots were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit following manufacturer's instructions

growth_protocol: HeLa cells were grown in culture medium according to ATCC recomendations

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

value: HeLa (ATCC CCL-2)

value: α-amanitin

source_name: Untreated cells

value: control


title: MVA_1_vac_pbmc_mouse_2

city: Paris

first: Nicolas

last: Dérian

institute: UPMC

value: PBMC

value: Vaccinia virus


title: RNA_Islets_miR7a2WT

source_name: Pancreatic islets, WT

value: Pancreatic islets

value: WT

tag: genetic background


title: MVA_1_vac_pbmc_mouse_1

source_name: PBMC


title: MVA_1_vac_pbmc_mouse_4


title: MPT_1_vac_pbmc_mouse_2

description:
Murine pneumotropic virus VLP
processed data file: GSE66799_normData_PBMC_MPT_1.txt.gz

value: Murine pneumotropic virus VLP


title: RNA_MIN6_AdmiR7a_rep1


title: MPT_1_vac_pbmc_mouse_4


title: RNA_Islets_miR7a2KO

source_name: Pancreatic islets, miR7a2 KO

value: miR-7a2 KO


title: AP205_1_vac_pbmc_mouse_3

value: AP205 bacteriophage based VLP


title: MPT_1_vac_pbmc_mouse_3


title: α-amanitin treatment_replicate 3_with dyeswap

description:
Raw data file: α-amanitin assay_rep3.txt
α-amanitin treated cells_Cy3
Untreated cells_Cy5
Raw data file: α-amanitin assay_rep3_swap.txt
Untreated cells_Cy3
α-amanitin treated cells_Cy5
Replicate 3 of 4. α-amanitin treated cells  vs. untreated control cells.
Replicate 3 of 4 (dye-swap). α-amanitin treated cells  vs. untreated control cells.

tag: agent


title: PBS_inj_pbmc_mouse_4

description:
Control_group
processed data file: GSE66799_normData_PBMC_AP205_1.txt.gz, GSE66799_normData_PBMC_MLV_1.txt.gz, GSE66799_normData_PBMC_MPT_1.txt.gz, GSE66799_normData_PBMC_MVA_1.txt.gz

value: 100 µL of phosphate buffered saline solution


title: α-amanitin treatment_replicate 1_with dyeswap

description:
Raw data file: α-amanitin assay_rep1.txt
α-amanitin treated cells_Cy3
Untreated cells_Cy5
Raw data file: α-amanitin assay_rep1_swap.txt
Untreated cells_Cy3
α-amanitin treated cells_Cy5
Replicate 1 of 4. α-amanitin treated cells  vs. untreated control cells.
Replicate 1 of 4 (dye-swap). α-amanitin treated cells  vs. untreated control cells.


title: MLV_1_vac_pbmc_mouse_3


title: PBS_inj_pbmc_mouse_1


title: Cell fractionation_replicate 1_with dyeswap

description:
Raw data file: Cell fractionation assay_rep1.txt
Nuclear fraction_Cy3
Cytoplasmic fraction_Cy5
Raw data file: Cell fractionation assay_rep1_swap.txt
Cytoplasmic fraction_Cy3
Nuclear fraction_Cy5
Replicate 1 of 2. nuclear fraction  vs. cytoplasmic fraction.
Replicate 1 of 2 (dye-swap). nuclear fraction  vs. cytoplasmic fraction.

data_processing:
Filtering was performed prior to normalization and statistical analysis.
Agilent Feature Extraction Software (version 9.5) was used for background subtraction (BGSubSignal was used). Averages of dye swap ratios were used. 11,657 probes with signals detected at significantly greater levels than the corresponding background (2-sided t-test, flag “IsPosAndSignif”) in at least one of two replicates of nuclear or cytoplasmic samples and whose replicate nucleus/cytoplasm ratios were concordant (same direction of increased/decreased expression) were defined as expressed and further analyzed.

source_name: Nuclear fraction

label_protocol: 500 ng of DNAse-treated total RNA aliquots were amplified and labeled using Agilent Quick Amp Labeling Kit following manufacturer's instructions

tag: fraction

value: nucleus

source_name: Cytoplasmic fraction

value: cytoplasm


title: α-amanitin treatment_replicate 2_with dyeswap

description:
Raw data file: α-amanitin assay_rep2.txt
α-amanitin treated cells_Cy3
Untreated cells_Cy5
Raw data file: α-amanitin assay_rep2_swap.txt
Untreated cells_Cy3
α-amanitin treated cells_Cy5
Replicate 2 of 4. α-amanitin treated cells  vs. untreated control cells.
Replicate 2 of 4 (dye-swap). α-amanitin treated cells  vs. untreated control cells.


title: Cell fractionation_replicate 2_with dyeswap

description:
Raw data file: Cell fractionation assay_rep2.txt
Cytoplasmic fraction_Cy3
Nuclear fraction_Cy5
Raw data file: Cell fractionation assay_rep2_swap.txt
Nuclear fraction_Cy3
Cytoplasmic fraction_Cy5
Replicate 2 of 2. nuclear fraction  vs. cytoplasmic fraction.
Replicate 2 of 2 (dye-swap). nuclear fraction  vs. cytoplasmic fraction.


title: MLV_1_vac_pbmc_mouse_2


title: LV_2_vac_dc_mouse_5

description:
Lentivirus
processed data file: GSE66797_normData_dc_LV_2.txt.gz

source_name: sorted dendritic cells

value: dendritic cells

value: Lentivirus vector-plaform


title: PBS_inj_pbmc_mouse_3


title: MPT_1_vac_pbmc_mouse_1


title: LV_2_vac_dc_mouse_4


title: PBS_inj_pbmc_mouse_2


title: TAP/5'-exo treatment_replicate 4_with dyeswap

description:
Raw data file: TAP_5'-exo assay_rep4.txt
TAP-/5'-exo+ treated cells_Cy3
TAP+/5'-exo+ treated cells_Cy5
Raw data file: TAP_5'-exo assay_rep4_swap.txt
TAP+/5'-exo+ treated cells_Cy3
TAP-/5'-exo+ treated cells_Cy5
Replicate 4 of 4. TAP+/5'-exo+  vs. TAP-/5'-exo+  treated RNA samples.
Replicate 4 of 4 (dye-swap). TAP+/5'-exo+  vs. TAP-/5'-exo+  treated RNA samples.

data_processing:
Filtering was performed prior to normalization and statistical analysis.
Agilent Feature Extraction Software (version 9.5) was used for background subtraction (BGSubSignal was used). Averages of dye swap ratios were used. 14,262 probes with expression significantly greater  than the corresponding background ( 2-sided t-test, flag ‘IsPosAndSignif’) in at least three of the four TAP-/5'-exo+ sample replicates were defined as expressed and further analyzed. The filtered data was normalized by the average intensity of 320 control probes that reports the signals from labeled targets generated from Agilent's synthetic spiked-in mRNAs.

source_name: TAP-/5'-exo+ treated cells

label_protocol: 200 ng of DNAse-treated  total RNA aliquots were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit following manufacturer's instructions

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. HeLa total RNA (10µg) was treated with terminator 5’-phosphate-dependent exonuclease (5’-exo, 1 unit; Epicentre Biotechnologies). Samples were treated with 5’-exo for 2h at 30°C without (TAP-/5’-exo+) or with pre-treatment with tobacco acid pyrophosphatase (TAP, 10 units; Epicentre Biotechnologies) (TAP+/5’ -exo+) for 1h at 37°C, according to the manufacturer’s protocol.

source_name: TAP+/5'-exo+ treated cells


title: LV_2_vac_dc_mouse_2


title: LV_2_vac_dc_mouse_3


title: LV_1_vac_dc_mouse_5

description:
Lentivirus
processed data file: GSE66797_normData_dc_LV_1.txt.gz


title: TAP/5'-exo treatment_replicate 3_with dyeswap

description:
Raw data file: TAP_5'-exo assay_rep3.txt
TAP-/5'-exo+ treated cells_Cy3
TAP+/5'-exo+ treated cells_Cy5
Raw data file: TAP_5'-exo assay_rep3_swap.txt
TAP+/5'-exo+ treated cells_Cy3
TAP-/5'-exo+ treated cells_Cy5
Replicate 3 of 4. TAP+/5'-exo+  vs. TAP-/5'-exo+  treated RNA samples.
Replicate 3 of 4 (dye-swap). TAP+/5'-exo+  vs. TAP-/5'-exo+  treated RNA samples.


title: LV_2_vac_dc_mouse_1


title: TAP/5'-exo treatment_replicate 2_with dyeswap

description:
Raw data file: TAP_5'-exo assay_rep2.txt
TAP+/5'-exo+ treated cells_Cy3
TAP-/5'-exo+ treated cells_Cy5
Raw data file: TAP_5'-exo assay_rep2_swap.txt
TAP-/5'-exo+ treated cells_Cy3
TAP+/5'-exo+ treated cells_Cy5
Replicate 2 of 4. TAP+/5'-exo+  vs. TAP-/5'-exo+  treated RNA samples.
Replicate 2 of 4 (dye-swap). TAP+/5'-exo+  vs. TAP-/5'-exo+  treated RNA samples.


title: LV_1_vac_dc_mouse_2


title: TAP/5'-exo treatment_replicate 1_with dyeswap

description:
Raw data file: TAP_5'-exo assay_rep1.txt
TAP+/5'-exo+ treated cells_Cy3
TAP-/5'-exo+ treated cells_Cy5
Raw data file: TAP_5'-exo assay_rep1_swap.txt
TAP-/5'-exo+ treated cells_Cy3
TAP+/5'-exo+ treated cells_Cy5
Replicate 1 of 4. TAP+/5'-exo+  vs. TAP-/5'-exo+  treated RNA samples.
Replicate 1 of 4 (dye-swap). TAP+/5'-exo+  vs. TAP-/5'-exo+  treated RNA samples.


title: LV_1_vac_dc_mouse_3


title: LV_1_vac_dc_mouse_4


title: actinomycin D treatment_8h_rep4

description: replicate 4 of 4. actinomycin D treated cells - 8h vs. untreated control cells.

data_processing:
Filtering was performed prior to normalization and statistical analysis.
Agilent Feature Extraction Software (version 9.5) was used for background subtraction (BGSubSignal was used). 5,874 probes with significant expression in the reference sample as determined by a 2-sided t-test (IsPosAndSignif flag in Feature Extraction output) and signal at least two-fold greater than the background measurement in at least three of the four replicates of each time-point treatment were further analyzed. The time-course expression data set was normalized by the expression level that was measured prior to treatment (0h), which was set to 1 (log2 = 0).

source_name: actinomycin D treated cells - 8h

label_protocol: 200 ng of total RNA were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit following manufacturer's instructions

value: actinomycin D

tag: time

source_name: pooled samples treated with DMSO vehicle (control)

tag: control composition

value: pooled samples, untreated


title: PBS_inj_dc_mouse_5

description:
Control_group
processed data file: GSE66797_normData_dc_LV_1.txt.gz and GSE66797_normData_dc_LV_2.txt.gz

value: 100 µL of phosphate buffered saline solution (PBS)


title: PBS_inj_dc_mouse_4


title: PBS_inj_dc_mouse_3


title: PBS_inj_dc_mouse_2


title: Heart WT E13.5 5

first: Matt

last: Burney

address: 30 Guilford Street

department: Developmental Biology of Birth Defects

institute: University College London Institute of Child Health

hyb_protocol: Performed on GeneChip Fluidics Station 450 using standard manufacturers protocols

scan_protocol: Scanned using Affymetrix GeneChip Scanner using standard manufacturers protocols

data_processing: Normalised by RMA algorith using Affy R package (Bioconductor) and LIMMA

source_name: Heart E13.5 WT

label_protocol: cDNA was generated from total RNA using the Ambion WT Expression Kit, which was then fragmented and labelled using Affymetrix GeneChip WT Terminal Labeling kit

growth_protocol: Embryos taken at E11.5 and E13.5 from heterozygous Chd7fl/+;Mesp1-Cre crossed with Chd7fl/fl mice.

extract_protocol: Whole hearts were dissected and total RNA was extracted using the Qiagen Rneasy Kit, according to manufacturers protocols

value: Whole heart


title: actinomycin D treatment_3h_rep4

description: replicate 4 of 4. actinomycin D treated cells - 3h vs. untreated control cells.

source_name: actinomycin D treated cells - 3h

value: HeLa (ATCC CCL-2)


title: actinomycin D treatment_6h_rep4

description: replicate 4 of 4. actinomycin D treated cells - 6h vs. untreated control cells.

source_name: actinomycin D treated cells - 6h


title: PBS_inj_dc_mouse_1

address: Bâtiment CERVI, 83 bvd de l'Hôpital


title: Heart WT E13.5 4


title: 2013-T32-PAX3-ARHS-Ref-RMS-N

city: Tokyo

first: Masafumi

last: Seki

state: Tokyo

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Pediatrics

institute: The University of Tokyo

description: Hybridized to 250K_Nsp

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:
CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR 3.0
primary_data_description = Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: RMS tumor tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from fresh frozen tumor of rhabdomyosarcoma. DNA quality and quantity was assessed using a Nanodrop Spectrophotometers and agarose gel electrophoresis.

tag: tumor

value: Rhabdomyosarcoma


title: actinomycin D treatment_1h_rep4

description: replicate 4 of 4. actinomycin D treated cells - 1h vs. untreated control cells.

source_name: actinomycin D treated cells - 1h


title: 2013-T31-PAX3-ARHS-DS-RMS-N

description: Hybridized to 250K_Nsp


title: Heart WT E13.5 2


title: LV_1_vac_dc_mouse_1


title: 2013-T25-RMS-N

description: Hybridized to 250K_Nsp


title: Heart WT E13.5 1


title: 2013-T37-RMS-N

description: Hybridized to 250K_Nsp


title: 2013-T23-RMS-N

description: Hybridized to 250K_Nsp


title: actinomycin D treatment_0h_rep4

description: replicate 4 of 4. actinomycin D treated cells - 0h vs. untreated control cells.

source_name: actinomycin D treated cells - 0h


title: Heart Chd7fl/fl;Mesp1Cre E13.5 4

source_name: Heart E13.5 Chd7fl/fl


title: Heart Chd7fl/fl;Mesp1Cre E13.5 2


title: Heart Chd7fl/fl;Mesp1Cre E13.5 3


title: Heart Chd7fl/fl;Mesp1Cre E13.5 1


title: actinomycin D treatment_8h_rep3

description: replicate 3 of 4. actinomycin D treated cells - 8h vs. untreated control cells.


title: actinomycin D treatment_6h_rep3

description: replicate 3 of 4. actinomycin D treated cells - 6h vs. untreated control cells.


title: Heart WT E11.5 3

source_name: Heart E11.5 WT


title: 2013-T22-RMS-N

description: Hybridized to 250K_Nsp


title: 2013-T19-RMS-N

description: Hybridized to 250K_Nsp


title: 2013-T24-RMS-rec-N

description: Hybridized to 250K_Nsp


title: Heart WT E11.5 4


title: 2013-T21-RMS-N

description: Hybridized to 250K_Nsp


title: 2013-T38-RMS-N

description: Hybridized to CytoscanHD_array


title: 2012-T40-RMS-rec_N

description: Hybridized to 250K_Nsp


title: Heart WT E11.5 1


title: Heart WT E11.5 2


title: Heart Chd7fl/fl;Mesp1Cre E11.5 4

source_name: Heart E11.5 Chd7fl/fl


title: actinomycin D treatment_3h_rep3

description: replicate 3 of 4. actinomycin D treated cells - 3h vs. untreated control cells.


title: Heart Chd7fl/fl;Mesp1Cre E11.5 3


title: Heart Chd7fl/fl;Mesp1Cre E11.5 2


title: actinomycin D treatment_1h_rep3

description: replicate 3 of 4. actinomycin D treated cells - 1h vs. untreated control cells.


title: Satellite_cells_Injured_Muscle_CTX3days_biological_replicate_4

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

hyb_protocol: After fragmentation, 600 ng of labeled cDNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).  The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was taken from the Feature Extraction output files and was corrected for background noise using the normexp [Ritchie ME, Silver J, Oshlack A, Silver J, Holmes M, Diyagama D, Holloway A, Smyth GK. (2007). A comparison of background correction methods for two-colour microarrays. Bioinformatics, 23, 2700-2707] method. To assure comparability across samples we used quantile normalization [Bolstad, B. (2001). Probe Level Quantile Normalization of High Density Oligonucleotide Array Data. Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf].  Differential expression analysis was carried out on non control probes with an empirical Bayes approach on linear models (limma) [Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, 3(1):3]. Results were corrected for multiple testing according to the False Discovery Rate (FDR) method [Benjamini Y, Hochberg Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B, 57 (1): 289-300].  All statistical analyses were performed with the Bioconductor project (http://www.bioconductor.org/) in the R statistical environment (http://cran.r‐project.org/) [Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biology, 5: R80].

source_name: Satellite cells, Injured muscle CTX 3days, Biological replicate 4

label_protocol: Total cDNA from each sample was labeled with Cy3-UTP and purified using the SureTag Complete DNA Labeling Kit (Agilent).

extract_protocol: FACS sorted satellite cells were collected in lysis buffer. RNA isolation was performed with the RNeasy Micro kit following manufacterurer instructions.

tag: gender

value: Male

value: Skeletal muscle

value: satellite cells

tag: age


title: 2013-T16-RMS-N

description: Hybridized to 250K_Nsp


title: actinomycin D treatment_0h_rep3

description: replicate 3 of 4. actinomycin D treated cells - 0h vs. untreated control cells.

tag: cell line


title: Satellite_cells_Injured_Muscle_CTX3days_biological_replicate_3

source_name: Satellite cells, Injured muscle CTX 3days, Biological replicate 3


title: 2013-T20-RMS-N

description: Hybridized to 250K_Nsp


title: actinomycin D treatment_3h_rep2

description: replicate 2 of 4. actinomycin D treated cells - 3h vs. untreated control cells.


title: mouse spleen at 10 dpi, biological rep1

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

description: Gene expression data from mouse spleen 10 days post-infection with A/HK-x31 influenza virus.

hyb_protocol: cDNA was hybridized with Affymetrix Mouse Gene ST 1.0 arrays overnight using conditions specified in the NuGEN kit. Arrays were washed and stained with phycoerythrin-streptavidin in an Affymetrix hybridization station as recommended by Affyemtrix.

scan_protocol: Stained arrays were scanned with an Affymetrix scanner controlled by Expression Console software, which converted the raw data files to cel files.

data_processing: Cel file data were normalized with the Affymetrix PLIER algorithm using Affymetrix Expresiion Console software. Transcript-level PLIER signals were then quantile-normalized.

source_name: mouse spleen 10 days post-infection with influenza A

label_protocol: Biotinylated cDNA was prepared from RNA using Ovation kits purchased from NuGEN according to instructions provided by NuGEN.

growth_protocol: Mice were housed in microisolator cages with same-sex siblings. They were allowed free access to water and rodent chow.

extract_protocol: Spleens were disrupted by pressing through a strainer with a syringe piston. Cells were were filtered through Nitex mesh (Thermo-Fisher, Waltham, MA) and layered on Lympholyte (Cedarlane, Burlington, NC). TER-119 immunomagnetic beads (BD Bioscience, San Diego, CA) were used to remove red blood cells. RNA was extracted with Qiagen Rneasy kits. RNA integrity was confirmed with an Agilent Bioanalyzer.

treatment_protocol: Mice were anesthetized with Avertin, then inoculated intranasally with 0.03 ml H3N2/Hong Kong/X31 influenza A virus ( 10^5 EID50).

value: spleen

tag: subject

tag: timepoint

tag: Sex

value: Female

tag: mousestrain

tag: weightbaseline

tag: weightunits

value: g

tag: ageatinfection

tag: ageunits

value: weeks

value: infected

tag: virussubtype

tag: virusstrain

tag: infectionroute

tag: infectionvolume

tag: infectionvolumeunits

value: ug

tag: infectiondose

tag: weightatsacrifice


title: actinomycin D treatment_6h_rep2

description: replicate 2 of 4. actinomycin D treated cells - 6h vs. untreated control cells.

tag: agent

tag: time

tag: control composition


title: mouse spleen at 9 dpi, biological rep2

description: Gene expression data from mouse spleen 9 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 9 days post-infection with influenza A

tag: tissue

tag: subject

tag: timepoint

tag: treatment


title: mouse spleen at 9 dpi, biological rep1

tag: Sex

tag: mousestrain

tag: weightbaseline

tag: weightunits


title: mouse spleen at 10 dpi, biological rep2

tag: ageatinfection

tag: ageunits

tag: virussubtype

tag: virusstrain


title: mouse spleen at 9 dpi, biological rep3

tag: infectionroute

tag: infectionvolume

tag: infectionvolumeunits

tag: infectiondose


title: 1995-T22-RMS_N

description: Hybridized to 250K_Nsp

tag: tumor


title: mouse spleen at 10 dpi, biological rep3

tag: tissue

tag: weightatsacrifice


title: mouse spleen at 8 dpi, biological rep3

description: Gene expression data from mouse spleen 8 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 8 days post-infection with influenza A

tag: subject

tag: timepoint


title: 93-69-T-meta-RMS_N

description: Hybridized to 250K_Nsp


title: 2012-T49-RMS-N

description: Hybridized to 250K_Nsp


title: actinomycin D treatment_8h_rep2

description: replicate 2 of 4. actinomycin D treated cells - 8h vs. untreated control cells.

tag: cell line

tag: agent

tag: time

tag: control composition


title: Satellite_cells_Injured_Muscle_CTX3days_biological_replicate_1

source_name: Satellite cells, Injured muscle CTX 3days, Biological replicate 1

tag: gender

tag: strain

tag: cell type

tag: age


title: Satellite_cells_Basal_Muscle_biological_replicate_3

source_name: Satellite cells, Basal muscle, Biological replicate 3


title: mouse spleen at 8 dpi, biological rep2

tag: Sex

tag: mousestrain

tag: weightbaseline

tag: weightunits

tag: ageatinfection

tag: ageunits

tag: treatment

tag: virussubtype

tag: virusstrain

tag: infectionroute


title: Satellite_cells_Basal_Muscle_biological_replicate_4

source_name: Satellite cells, Basal muscle, Biological replicate 4

tag: tissue


title: 1997-T13-RMS-rec_N

description: Hybridized to 250K_Nsp

tag: tumor


title: actinomycin D treatment_1h_rep2

description: replicate 2 of 4. actinomycin D treated cells - 1h vs. untreated control cells.

tag: cell line

tag: agent

tag: time

source_name: pooled samples treated with DMSO vehicle (control)

tag: control composition


title: Satellite_cells_Injured_Muscle_CTX3days_biological_replicate_2

source_name: Satellite cells, Injured muscle CTX 3days, Biological replicate 2

tag: gender

tag: strain

tag: cell type

tag: age


title: Heart Chd7fl/fl;Mesp1Cre E11.5 1


title: Satellite_cells_Basal_Muscle_biological_replicate_1

source_name: Satellite cells, Basal muscle, Biological replicate 1


title: mouse spleen at 7 dpi, biological rep3

description: Gene expression data from mouse spleen 7 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 7 days post-infection with influenza A

tag: subject

tag: timepoint

tag: Sex

tag: mousestrain

tag: weightbaseline

tag: weightunits

tag: infectionvolume

tag: infectionvolumeunits

tag: infectiondose

tag: weightatsacrifice


title: actinomycin D treatment_0h_rep2

description: replicate 2 of 4. actinomycin D treated cells - 0h vs. untreated control cells.

tag: cell line

tag: agent


title: mouse spleen at 8 dpi, biological rep1

tag: tissue

tag: ageatinfection

tag: ageunits

tag: treatment

tag: virussubtype

tag: virusstrain

tag: infectionroute


title: actinomycin D treatment_8h_rep1

description: replicate 1 of 4. actinomycin D treated cells - 8h vs. untreated control cells.

source_name: actinomycin D treated cells - 8h

tag: time

tag: control composition


title: mouse spleen at 6 dpi, biological rep3

description: Gene expression data from mouse spleen 6 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 6 days post-infection with influenza A

tag: subject

tag: timepoint

tag: Sex

tag: mousestrain

tag: weightbaseline


title: Satellite_cells_Basal_Muscle_biological_replicate_2

source_name: Satellite cells, Basal muscle, Biological replicate 2

tag: gender

tag: strain

tag: cell type

tag: age


title: mouse spleen at 7 dpi, biological rep2

tag: tissue

tag: weightunits

tag: ageatinfection

tag: infectionvolume

tag: infectionvolumeunits

tag: infectiondose

tag: weightatsacrifice


title: mouse spleen at 6 dpi, biological rep2

tag: ageunits

tag: treatment

tag: virussubtype

tag: virusstrain

tag: infectionroute


title: actinomycin D treatment_6h_rep1

description: replicate 1 of 4. actinomycin D treated cells - 6h vs. untreated control cells.

source_name: actinomycin D treated cells - 6h

tag: cell line

tag: agent

tag: time

tag: control composition


title: actinomycin D treatment_1h_rep1

description: replicate 1 of 4. actinomycin D treated cells - 1h vs. untreated control cells.

source_name: actinomycin D treated cells - 1h


title: actinomycin D treatment_3h_rep1

description: replicate 1 of 4. actinomycin D treated cells - 3h vs. untreated control cells.

source_name: actinomycin D treated cells - 3h


title: mouse spleen at 5 dpi, biological rep2

description: Gene expression data from mouse spleen 5 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 5 days post-infection with influenza A

tag: subject

tag: timepoint

tag: Sex

tag: mousestrain

tag: weightbaseline


title: 98-T69-3-S96-529_N

description: Hybridized to 250K_Nsp

source_name: RMS tumor tissue

tag: tumor