title: Patient#325-IgG


title: Patient#323-IgG

status: Public on Mar 07 2016

type: protein

city: Budapest

first: Krisztian

last: Papp

address: 1/C Pazmany P.

country: Hungary

institute: MTA-ELTE Immunology Research Group

hyb_protocol: Probe: DyLight 649-conjugated F(ab’)2 fragment goat anti-human IgG (gamma chain specific) (Jackson ImmunoResearch)

scan_protocol: Arrays were scanned by FLAIR Fluorescent Array Imaging Reader (Sensovation).

data_processing: Local background of spot ('Bkg.Median') was substracted from the value of signal ('Spot.Median'). Values were multiplied by 65535 and rounded to be integers. Negative signals values were clamped to arbitrary value 1.

label: fluorescent antibodies

molecule: protein

organism: Homo sapiens

source_name: serum

label_protocol: Dried arrays were rinsed in PBS for 15 minutes before use, then incubated with diluted serum at 37°C for 1 hour. Two separated measurements were applied on each sample for detection of bound components. Five-fold serum dilution in 2.5mM Ca2+, 0.7mM Mg2+ and  5% BSA complemented PBS buffer was used for detection of deposited C3 and C4 complement fragments. 125-fold serum dilution in 25mM EDTA, 0.05% Tween 20 and 5% BSA complemented PBS buffer was applied for measurement of bound antigen specific IgG and IgM antibodies. Serum treated slides were washed with PBS containing 0.05% Tween 20, then incubated in the mixture of 1:5,000 diluted FITC-conjugated F(ab’)2 fragment of goat anti-human C3 antibody (Cappel) and 1:1000 diluted Alexa 647 conjugated goat anti-human C4 (Cappel, in-house conjugation) or 1:2500 diluted DyLight 488-conjugated F(ab’)2 fragment goat anti-human IgM (mu chain specific) (Jackson ImmunoResearch) and 1:2,500 diluted DyLight 649-conjugated F(ab’)2 fragment goat anti-human IgG (gamma chain specific) (Jackson ImmunoResearch). Labeling with fluorescent antibodies was carried out at room temperature for 30 minutes in PBS containing 5% BSA and 0.05% Tween 20. After washing in PBS containing 0.05% Tween 20, arrays were dried and scanned

extract_protocol: Serum sample was centrifuged for 6min at 15000g for removing particles

treatment_protocol: Serum samples were stored at -70C

tag: gender

value: Female

tag: disease group (nhs-normal human serum; sle-systemic lupus erythematosus ;uctd-undifferentiated connective tissue disease; sjs-sjörgen's syndrome;ssc-systemic sclerosis; psa-psoriatic arthritis)

value: SSc

tag: age in years

tag: printing batches (1,2)

tag: slide no.


title: Patient#332-IgG

value: Male

value: SLE


title: Patient#314-IgG

value: NHS


title: Patient#324-IgG


title: Patient#328-IgG


title: Patient#313-IgG


title: Patient#319-IgG


title: Patient#318-IgG


title: Patient#310-IgG


title: Patient#322-IgG


title: Patient#304-IgG


title: Patient#342-IgG


title: Patient#303-IgG


title: Patient#308-IgG


title: Patient#302-IgG


title: Patient#309-IgG


title: Patient#316-IgG


title: Patient#317-IgG


title: Patient#335-IgG


title: Patient#301-IgG


title: Patient#333-IgG


title: Patient#326-IgG


title: Patient#312-IgG


title: Patient#311-IgG


title: Patient#306-IgG


title: Patient#307-IgG


title: Patient#305-IgG


title: Patient#300-IgG


title: Patient#288-IgG


title: Patient#291-IgG


title: Patient#289-IgG


title: Patient#283-IgG


title: Patient#286-IgG


title: Patient#285-IgG


title: Patient#321-IgG


title: Patient#315-IgG


title: Patient#299-IgG


title: Patient#298-IgG


title: Patient#297-IgG


title: Patient#280-IgG


title: Patient#296-IgG

value: UCTD


title: Patient#294-IgG


title: Patient#295-IgG


title: Patient#279-IgG


title: Patient#293-IgG


title: Patient#292-IgG


title: Patient#290-IgG


title: Patient#287-IgG


title: Patient#281-IgG


title: Patient#276-IgG


title: Patient#274-IgG


title: Patient#273-IgG


title: Patient#284-IgG


title: Patient#275-IgG


title: Patient#282-IgG


title: Patient#263-IgG


title: Patient#269-IgG


title: Patient#261-IgG


title: Patient#264-IgG


title: Patient#265-IgG


title: Patient#277-IgG


title: Patient#270-IgG


title: Patient#259-IgG


title: Patient#272-IgG


title: Patient#271-IgG


title: Patient#268-IgG


title: Patient#267-IgG


title: Patient#266-IgG


title: Patient#278-IgG


title: Patient#257-IgG


title: Patient#254-IgG


title: Patient#260-IgG


title: Patient#262-IgG


title: Patient#253-IgG


title: Patient#258-IgG


title: Patient#251-IgG


title: Patient#248-IgG


title: Patient#246-IgG


title: Patient#256-IgG


title: Patient#255-IgG


title: Patient#252-IgG


title: Patient#243-IgG


title: Patient#247-IgG


title: Patient#250-IgG


title: Patient#249-IgG


title: Patient#245-IgG


title: Patient#241-IgG


title: Patient#239-IgG


title: Patient#242-IgG


title: Patient#237-IgG


title: Patient#236-IgG


title: Patient#235-IgG


title: Patient#244-IgG


title: Patient#234-IgG


title: Patient#238-IgG


title: Patient#227-IgG


title: Patient#229-IgG


title: Patient#223-IgG


title: Patient#233-IgG


title: Patient#231-IgG


title: Patient#232-IgG


title: Patient#230-IgG


title: Patient#240-IgG


title: Patient#222-IgG


title: Patient#225-IgG


title: Patient#224-IgG


title: Patient#228-IgG


title: Patient#221-IgG


title: Patient#226-IgG


title: Patient#218-IgG


title: Patient#214-IgG


title: Patient#216-IgG


title: Patient#219-IgG


title: Patient#207-IgG


title: Patient#205-IgG


title: Patient#204-IgG


title: Patient#217-IgG


title: Patient#215-IgG


title: Patient#212-IgG


title: Patient#213-IgG


title: Patient#211-IgG


title: Patient#198-IgG


title: Patient#199-IgG


title: Patient#206-IgG

value: SjS


title: Patient#210-IgG


title: Patient#208-IgG


title: Patient#194-IgG


title: Patient#202-IgG


title: Patient#193-IgG


title: Patient#220-IgG


title: Patient#197-IgG


title: Patient#203-IgG


title: Patient#191-IgG


title: Patient#209-IgG


title: Patient#201-IgG


title: Patient#195-IgG


title: Patient#184-IgG


title: Patient#189-IgG


title: Patient#192-IgG


title: Patient#183-IgG


title: Patient#180-IgG


title: Patient#188-IgG


title: Patient#185-IgG


title: Patient#187-IgG


title: Patient#186-IgG


title: Patient#177-IgG


title: Patient#190-IgG


title: Patient#175-IgG


title: Patient#172-IgG


title: Patient#170-IgG


title: Patient#169-IgG


title: Patient#181-IgG


title: Patient#179-IgG


title: Patient#182-IgG


title: Patient#196-IgG


title: Patient#164-IgG


title: Patient#166-IgG


title: Patient#178-IgG


title: Patient#176-IgG


title: Patient#165-IgG


title: Patient#174-IgG


title: Patient#159-IgG


title: Patient#161-IgG


title: Patient#167-IgG


title: Patient#168-IgG


title: Patient#157-IgG


title: Patient#163-IgG


title: Patient#153-IgG


title: Patient#154-IgG


title: Patient#152-IgG

value: PsA


title: Patient#160-IgG


title: Patient#162-IgG


title: Patient#158-IgG


title: Patient#150-IgG


title: Patient#148-IgG


title: Patient#147-IgG


title: Patient#173-IgG


title: Patient#149-IgG


title: Patient#171-IgG


title: Patient#156-IgG


title: Patient#141-IgG


title: Patient#142-IgG


title: Patient#140-IgG


title: Patient#155-IgG


title: Patient#143-IgG


title: Patient#136-IgG


title: Patient#138-IgG


title: Patient#151-IgG


title: Patient#144-IgG


title: Patient#146-IgG


title: Patient#135-IgG


title: Patient#139-IgG


title: Patient#145-IgG


title: Patient#130-IgG


title: Patient#137-IgG


title: Patient#125-IgG


title: Patient#126-IgG


title: Patient#127-IgG


title: Patient#123-IgG


title: Patient#122-IgG


title: Patient#133-IgG


title: Patient#117-IgG


title: Patient#119-IgG


title: Patient#118-IgG


title: Patient#116-IgG


title: Patient#129-IgG


title: Patient#113-IgG


title: Patient#132-IgG


title: Patient#121-IgG


title: Patient#128-IgG


title: Patient#134-IgG


title: Patient#115-IgG


title: Patient#131-IgG


title: Patient#108-IgG


title: Patient#110-IgG


title: Patient#111-IgG


title: Patient#106-IgG


title: Patient#120-IgG


title: Patient#102-IgG


title: Patient#99-IgG


title: Patient#100-IgG


title: Patient#109-IgG


title: Patient#124-IgG


title: Patient#114-IgG


title: Patient#112-IgG


title: Patient#104-IgG


title: Patient#98-IgG


title: Patient#97-IgG


title: Patient#96-IgG


title: Patient#95-IgG


title: Patient#93-IgG


title: Patient#107-IgG


title: Patient#91-IgG


title: Patient#88-IgG


title: Patient#101-IgG


title: Patient#103-IgG


title: Patient#89-IgG


title: Patient#86-IgG


title: Patient#105-IgG


title: Patient#83-IgG


title: Patient#87-IgG


title: Patient#85-IgG


title: Patient#94-IgG


title: Patient#82-IgG


title: Patient#80-IgG


title: Patient#77-IgG


title: Patient#92-IgG


title: Patient#73-IgG


title: Patient#79-IgG


title: Patient#78-IgG


title: Patient#72-IgG


title: Patient#75-IgG


title: Patient#76-IgG


title: Patient#71-IgG


title: Patient#65-IgG


title: Patient#64-IgG


title: Patient#90-IgG


title: Patient#84-IgG


title: Patient#60-IgG


title: Patient#61-IgG


title: Patient#74-IgG


title: Patient#58-IgG


title: Patient#200-IgG


title: Patient#69-IgG


title: Patient#66-IgG


title: Patient#70-IgG


title: Patient#55-IgG


title: Patient#67-IgG


title: Patient#63-IgG


title: Patient#81-IgG


title: Patient#50-IgG


title: Patient#51-IgG


title: Patient#59-IgG


title: Patient#46-IgG


title: Patient#56-IgG


title: Patient#44-IgG


title: Patient#57-IgG


title: Patient#43-IgG


title: Patient#38-IgG


title: Patient#68-IgG


title: Patient#40-IgG


title: Patient#36-IgG


title: Patient#52-IgG


title: Patient#54-IgG


title: Patient#53-IgG


title: Patient#34-IgG


title: Patient#47-IgG


title: Patient#62-IgG


title: Patient#30-IgG


title: Patient#28-IgG


title: Patient#32-IgG


title: Patient#48-IgG


title: Patient#45-IgG


title: Patient#41-IgG


title: Patient#27-IgG


title: Patient#42-IgG


title: Patient#37-IgG


title: Patient#25-IgG


title: Patient#22-IgG


title: Patient#35-IgG


title: Patient#23-IgG


title: Patient#33-IgG


title: Patient#20-IgG


title: Patient#49-IgG


title: Patient#31-IgG


title: Patient#29-IgG


title: Patient#19-IgG


title: Patient#21-IgG


title: Patient#24-IgG


title: Patient#17-IgG


title: Patient#16-IgG


title: Patient#15-IgG


title: Patient#26-IgG


title: Patient#10-IgG


title: Patient#13-IgG


title: Patient#9-IgG


title: Patient#6-IgG


title: Patient#39-IgG


title: Patient#14-IgG


title: Patient#4-IgG


title: Patient#425-C4

hyb_protocol: Probe: Alexa 647 conjugated goat anti-human C4 (Cappel, in-house conjugation)


title: Patient#424-C4


title: Patient#423-C4


title: Patient#12-IgG


title: Patient#11-IgG


title: Patient#7-IgG


title: Patient#8-IgG


title: Patient#1-IgG


title: Patient#419-C4


title: Patient#416-C4


title: Patient#3-IgG


title: Patient#422-C4


title: Patient#18-IgG


title: Patient#5-IgG


title: Patient#2-IgG


title: Patient#420-C4


title: Patient#421-C4


title: Patient#409-C4


title: Patient#408-C4


title: Patient#417-C4


title: Patient#407-C4


title: Patient#404-C4


title: Patient#414-C4


title: Patient#400-C4


title: Patient#411-C4


title: Patient#412-C4


title: Patient#415-C4


title: Patient#397-C4


title: Patient#410-C4


title: Patient#413-C4


title: Patient#390-C4


title: Patient#393-C4


title: Patient#418-C4


title: Patient#405-C4


title: Patient#403-C4


title: Patient#402-C4


title: Patient#406-C4


title: Patient#387-C4


title: Patient#395-C4


title: Patient#396-C4


title: Patient#394-C4


title: Patient#389-C4


title: Patient#398-C4


title: Patient#384-C4


title: Patient#381-C4


title: Patient#382-C4


title: Patient#379-C4


title: Patient#391-C4


title: Patient#378-C4


title: Patient#392-C4


title: Patient#376-C4


title: Patient#388-C4


title: Patient#385-C4


title: Patient#386-C4


title: Patient#401-C4


title: Patient#371-C4


title: Patient#373-C4


title: Patient#399-C4


title: Patient#375-C4


title: Patient#368-C4


title: Patient#383-C4


title: Patient#372-C4


title: Patient#377-C4


title: Patient#374-C4


title: Patient#365-C4


title: Patient#380-C4


title: Patient#363-C4


title: Patient#361-C4


title: Patient#360-C4


title: Patient#364-C4


title: Patient#367-C4


title: Patient#369-C4


title: Patient#366-C4


title: Patient#358-C4


title: Patient#357-C4


title: Patient#362-C4


title: Patient#370-C4


title: Patient#359-C4


title: Patient#353-C4


title: Patient#355-C4


title: Patient#349-C4


title: Patient#347-C4


title: Patient#346-C4


title: Patient#356-C4


title: Patient#354-C4


title: Patient#351-C4


title: Patient#343-C4


title: Patient#352-C4


title: Patient#350-C4


title: Patient#348-C4


title: Patient#345-C4


title: Patient#334-C4


title: Patient#342-C4


title: Patient#338-C4


title: Patient#340-C4


title: Patient#333-C4


title: Patient#339-C4


title: Patient#344-C4


title: Patient#330-C4


title: Patient#341-C4


title: Patient#337-C4


title: Patient#335-C4


title: Patient#331-C4


title: Patient#336-C4


title: Patient#328-C4


title: Patient#327-C4


title: Patient#324-C4


title: Patient#326-C4


title: Patient#325-C4


title: Patient#323-C4


title: Patient#329-C4


title: Patient#322-C4


title: Patient#332-C4


title: Patient#317-C4


title: Patient#318-C4


title: Patient#319-C4


title: Patient#316-C4


title: Patient#313-C4


title: Patient#308-C4


title: Patient#315-C4


title: Patient#306-C4


title: Patient#309-C4


title: Patient#314-C4


title: Patient#320-C4


title: Patient#312-C4


title: Patient#303-C4


title: Patient#321-C4


title: Patient#304-C4


title: Patient#311-C4


title: Patient#305-C4


title: Patient#299-C4


title: Patient#300-C4


title: Patient#302-C4


title: Patient#301-C4


title: Patient#297-C4


title: Patient#298-C4


title: Patient#296-C4


title: Patient#294-C4


title: Patient#293-C4


title: Patient#295-C4


title: Patient#307-C4


title: Patient#289-C4


title: Patient#290-C4


title: Patient#310-C4


title: Patient#292-C4


title: Patient#288-C4


title: Patient#283-C4


title: Patient#285-C4


title: Patient#281-C4


title: Patient#284-C4


title: Patient#282-C4


title: Patient#280-C4


title: Patient#278-C4


title: Patient#279-C4


title: Patient#277-C4


title: Patient#271-C4


title: Patient#272-C4


title: Patient#275-C4


title: Patient#286-C4


title: Patient#274-C4


title: Patient#276-C4


title: Patient#269-C4


title: Patient#268-C4


title: Patient#270-C4


title: Patient#291-C4


title: Patient#273-C4


title: Patient#265-C4


title: Patient#267-C4


title: Patient#262-C4


title: Patient#264-C4


title: Patient#287-C4


title: Patient#260-C4


title: Patient#261-C4


title: Patient#263-C4


title: Patient#259-C4


title: Patient#266-C4


title: Patient#258-C4


title: Patient#246-C4


title: Patient#255-C4


title: Patient#257-C4


title: Patient#245-C4


title: Patient#252-C4


title: Patient#248-C4


title: Patient#249-C4


title: Patient#240-C4


title: Patient#256-C4


title: Patient#242-C4


title: Patient#254-C4


title: Patient#241-C4


title: Patient#250-C4


title: Patient#253-C4


title: Patient#243-C4


title: Patient#244-C4


title: Patient#247-C4


title: Patient#239-C4


title: Patient#238-C4


title: Patient#237-C4


title: Patient#235-C4


title: Patient#234-C4


title: Patient#236-C4


title: Patient#233-C4


title: Patient#230-C4


title: Patient#231-C4


title: Patient#232-C4


title: Patient#251-C4


title: Patient#229-C4


title: Patient#225-C4


title: Patient#215-C4


title: Patient#228-C4


title: Patient#213-C4


title: Patient#219-C4


title: Patient#222-C4


title: Patient#210-C4


title: Patient#221-C4


title: Patient#209-C4


title: Patient#220-C4


title: Patient#217-C4


title: Patient#207-C4


title: Patient#227-C4


title: Patient#202-C4


title: Patient#223-C4


title: Patient#218-C4


title: Patient#201-C4


title: Patient#216-C4


title: Patient#206-C4


title: Patient#203-C4


title: Patient#205-C4


title: Patient#214-C4


title: Patient#200-C4


title: Patient#208-C4


title: Patient#204-C4


title: Patient#199-C4


title: Patient#224-C4


title: Patient#226-C4


title: Patient#212-C4


title: Patient#211-C4


title: Patient#196-C4


title: Patient#198-C4


title: Patient#190-C4


title: Patient#192-C4


title: Patient#187-C4


title: Patient#188-C4


title: Patient#185-C4


title: Patient#180-C4


title: Patient#193-C4


title: Patient#197-C4


title: Patient#183-C4


title: Patient#178-C4


title: Patient#182-C4


title: Patient#189-C4


title: Patient#181-C4


title: Patient#176-C4


title: Patient#175-C4


title: Patient#179-C4


title: Patient#184-C4


title: Patient#173-C4


title: Patient#172-C4


title: Patient#186-C4


title: Patient#174-C4


title: Patient#170-C4


title: Patient#171-C4


title: Patient#169-C4


title: Patient#195-C4


title: Patient#191-C4


title: Patient#177-C4


title: Patient#168-C4


title: Patient#166-C4


title: Patient#165-C4


title: Patient#164-C4


title: Patient#156-C4


title: Patient#158-C4


title: Patient#161-C4


title: Patient#157-C4


title: Patient#160-C4


title: Patient#154-C4


title: Patient#153-C4


title: Patient#152-C4


title: Patient#150-C4


title: Patient#149-C4


title: Patient#167-C4


title: Patient#146-C4


title: Patient#148-C4


title: Patient#147-C4


title: Patient#162-C4


title: Patient#151-C4


title: Patient#163-C4


title: Patient#159-C4


title: Patient#140-C4


title: Patient#141-C4


title: Patient#145-C4


title: Patient#144-C4


title: Patient#142-C4


title: Patient#143-C4


title: Patient#194-C4


title: Patient#137-C4


title: Patient#138-C4


title: Patient#135-C4


title: Patient#136-C4


title: Patient#155-C4


title: Patient#133-C4


title: Patient#132-C4


title: Patient#134-C4


title: Patient#129-C4


title: Patient#126-C4


title: Patient#127-C4


title: Patient#123-C4


title: Patient#124-C4


title: Patient#125-C4


title: Patient#122-C4


title: Patient#119-C4


title: Patient#139-C4


title: Patient#121-C4


title: Patient#113-C4


title: Patient#131-C4


title: Patient#120-C4


title: Patient#128-C4


title: Patient#118-C4


title: Patient#117-C4


title: Patient#130-C4


title: Patient#116-C4


title: Patient#114-C4


title: Patient#111-C4


title: Patient#115-C4


title: Patient#108-C4


title: Patient#109-C4


title: Patient#107-C4


title: Patient#106-C4


title: Patient#110-C4


title: Patient#105-C4


title: Patient#102-C4


title: Patient#101-C4


title: Patient#99-C4


title: Patient#97-C4


title: Patient#100-C4


title: Patient#98-C4


title: Patient#96-C4


title: Patient#95-C4


title: Patient#94-C4


title: Patient#93-C4


title: Patient#92-C4


title: Patient#90-C4


title: Patient#88-C4


title: Patient#91-C4


title: Patient#85-C4


title: Patient#89-C4


title: Patient#112-C4


title: Patient#103-C4


title: Patient#84-C4


title: Patient#86-C4


title: Patient#87-C4


title: Patient#104-C4


title: Patient#82-C4


title: Patient#83-C4


title: Patient#81-C4


title: Patient#78-C4


title: Patient#74-C4


title: Patient#79-C4


title: Patient#75-C4


title: Patient#77-C4


title: Patient#76-C4


title: Patient#69-C4


title: Patient#71-C4


title: Patient#73-C4


title: Patient#72-C4


title: Patient#70-C4


title: Patient#68-C4


title: Patient#66-C4


title: Patient#67-C4


title: Patient#80-C4


title: Patient#63-C4


title: Patient#65-C4


title: Patient#60-C4


title: Patient#57-C4


title: Patient#61-C4


title: Patient#59-C4


title: Patient#55-C4


title: Patient#56-C4


title: Patient#62-C4


title: Patient#58-C4


title: Patient#51-C4


title: Patient#52-C4


title: Patient#53-C4


title: Patient#50-C4


title: Patient#49-C4


title: Patient#54-C4


title: Patient#45-C4


title: Patient#48-C4


title: Patient#40-C4


title: Patient#39-C4


title: Patient#47-C4


title: Patient#42-C4


title: Patient#43-C4


title: Patient#41-C4


title: Patient#38-C4


title: Patient#37-C4


title: Patient#64-C4


title: Patient#34-C4


title: Patient#33-C4


title: Patient#35-C4


title: Patient#36-C4


title: Patient#31-C4


title: Patient#30-C4


title: Patient#28-C4


title: Patient#32-C4


title: Patient#46-C4


title: Patient#26-C4


title: Patient#27-C4


title: Patient#29-C4


title: Patient#25-C4


title: Patient#23-C4


title: Patient#44-C4


title: Patient#24-C4


title: Patient#20-C4


title: Patient#18-C4


title: Patient#22-C4


title: Patient#21-C4


title: Patient#19-C4


title: Patient#16-C4


title: Patient#15-C4


title: Patient#9-C4


title: Patient#14-C4


title: Patient#12-C4


title: Patient#13-C4


title: Patient#10-C4


title: Patient#11-C4


title: Patient#7-C4


title: Patient#6-C4


title: Patient#8-C4


title: Patient#17-C4


title: Patient#4-C4


title: Patient#2-C4


title: Patient#5-C4


title: Patient#424-C3

hyb_protocol: Probe: FITC-conjugated F(ab’)2 fragment of goat anti-human C3 antibody (Cappel)


title: Patient#3-C4


title: Patient#425-C3


title: Patient#420-C3


title: Patient#1-C4


title: Patient#418-C3


title: Patient#422-C3


title: Patient#423-C3


title: Patient#417-C3


title: Patient#415-C3


title: Patient#419-C3


title: Patient#409-C3


title: Patient#406-C3


title: Patient#408-C3


title: Patient#405-C3


title: Patient#413-C3


title: Patient#414-C3


title: Patient#410-C3


title: Patient#412-C3


title: Patient#402-C3


title: Patient#404-C3


title: Patient#411-C3


title: Patient#421-C3


title: Patient#416-C3


title: Patient#398-C3


title: Patient#401-C3


title: Patient#399-C3


title: Patient#395-C3


title: Patient#400-C3


title: Patient#396-C3


title: Patient#397-C3


title: Patient#389-C3


title: Patient#393-C3


title: Patient#394-C3


title: Patient#392-C3


title: Patient#407-C3


title: Patient#390-C3


title: Patient#388-C3


title: Patient#380-C3


title: Patient#387-C3


title: Patient#384-C3


title: Patient#391-C3


title: Patient#403-C3


title: Patient#383-C3


title: Patient#385-C3


title: Patient#386-C3


title: Patient#375-C3


title: Patient#378-C3


title: Patient#376-C3


title: Patient#379-C3


title: Patient#377-C3


title: Patient#374-C3


title: Patient#372-C3


title: Patient#373-C3


title: Patient#369-C3


title: Patient#371-C3


title: Patient#368-C3


title: Patient#367-C3


title: Patient#370-C3


title: Patient#365-C3


title: Patient#364-C3


title: Patient#366-C3


title: Patient#362-C3


title: Patient#361-C3


title: Patient#382-C3


title: Patient#381-C3


title: Patient#359-C3


title: Patient#352-C3


title: Patient#358-C3


title: Patient#353-C3


title: Patient#355-C3


title: Patient#357-C3


title: Patient#356-C3


title: Patient#348-C3


title: Patient#347-C3


title: Patient#354-C3


title: Patient#344-C3


title: Patient#350-C3


title: Patient#360-C3


title: Patient#363-C3


title: Patient#343-C3


title: Patient#346-C3


title: Patient#345-C3


title: Patient#351-C3


title: Patient#338-C3


title: Patient#341-C3


title: Patient#339-C3


title: Patient#337-C3


title: Patient#336-C3


title: Patient#340-C3


title: Patient#342-C3


title: Patient#333-C3


title: Patient#335-C3


title: Patient#332-C3


title: Patient#334-C3


title: Patient#349-C3


title: Patient#331-C3


title: Patient#327-C3


title: Patient#328-C3


title: Patient#329-C3


title: Patient#325-C3


title: Patient#323-C3


title: Patient#322-C3


title: Patient#324-C3


title: Patient#326-C3


title: Patient#314-C3


title: Patient#317-C3


title: Patient#311-C3


title: Patient#309-C3


title: Patient#316-C3


title: Patient#318-C3


title: Patient#315-C3


title: Patient#307-C3


title: Patient#308-C3


title: Patient#312-C3


title: Patient#319-C3


title: Patient#320-C3


title: Patient#321-C3


title: Patient#304-C3


title: Patient#306-C3


title: Patient#303-C3


title: Patient#305-C3


title: Patient#330-C3


title: Patient#302-C3


title: Patient#301-C3


title: Patient#298-C3


title: Patient#299-C3


title: Patient#313-C3


title: Patient#310-C3


title: Patient#296-C3


title: Patient#295-C3


title: Patient#293-C3


title: Patient#297-C3


title: Patient#292-C3


title: Patient#288-C3


title: Patient#294-C3


title: Patient#286-C3


title: Patient#278-C3


title: Patient#276-C3


title: Patient#287-C3


title: Patient#290-C3


title: Patient#280-C3


title: Patient#289-C3


title: Patient#279-C3


title: Patient#284-C3


title: Patient#300-C3


title: Patient#275-C3


title: Patient#282-C3


title: Patient#274-C3


title: Patient#277-C3


title: Patient#273-C3


title: Patient#285-C3


title: Patient#272-C3


title: Patient#291-C3


title: Patient#271-C3


title: Patient#270-C3


title: Patient#269-C3


title: Patient#281-C3


title: Patient#283-C3


title: Patient#268-C3


title: Patient#263-C3


title: Patient#264-C3


title: Patient#261-C3


title: Patient#260-C3


title: Patient#254-C3


title: Patient#258-C3


title: Patient#259-C3


title: Patient#255-C3


title: Patient#253-C3


title: Patient#249-C3


title: Patient#250-C3


title: Patient#251-C3


title: Patient#248-C3


title: Patient#252-C3


title: Patient#257-C3


title: Patient#256-C3


title: Patient#246-C3


title: Patient#267-C3


title: Patient#247-C3


title: Patient#245-C3


title: Patient#265-C3


title: Patient#266-C3


title: Patient#244-C3


title: Patient#240-C3


title: Patient#239-C3


title: Patient#242-C3


title: Patient#241-C3


title: Patient#262-C3


title: Patient#237-C3


title: Patient#236-C3


title: Patient#243-C3


title: Patient#235-C3


title: Patient#234-C3


title: Patient#238-C3


title: Patient#232-C3


title: Patient#233-C3


title: Patient#231-C3


title: Patient#229-C3


title: Patient#226-C3


title: Patient#228-C3


title: Patient#230-C3


title: Patient#223-C3


title: Patient#227-C3


title: Patient#222-C3


title: Patient#216-C3


title: Patient#218-C3


title: Patient#217-C3


title: Patient#219-C3


title: Patient#215-C3


title: Patient#220-C3


title: Patient#214-C3


title: Patient#212-C3


title: Patient#208-C3


title: Patient#210-C3


title: Patient#213-C3


title: Patient#209-C3


title: Patient#211-C3


title: Patient#207-C3


title: Patient#221-C3


title: Patient#225-C3


title: Patient#224-C3


title: Patient#206-C3


title: Patient#204-C3


title: Patient#205-C3


title: Patient#203-C3


title: Patient#202-C3


title: Patient#201-C3


title: Patient#199-C3


title: Patient#198-C3


title: Patient#195-C3


title: Patient#196-C3


title: Patient#191-C3


title: Patient#194-C3


title: Patient#193-C3


title: Patient#187-C3


title: Patient#192-C3


title: Patient#190-C3


title: Patient#189-C3


title: Patient#188-C3


title: Patient#186-C3


title: Patient#182-C3


title: Patient#185-C3


title: Patient#181-C3


title: Patient#184-C3


title: Patient#183-C3


title: Patient#180-C3


title: Patient#175-C3


title: Patient#177-C3


title: Patient#176-C3


title: Patient#200-C3


title: Patient#179-C3


title: Patient#197-C3


title: Patient#174-C3


title: Patient#173-C3


title: Patient#178-C3


title: Patient#172-C3


title: Patient#171-C3


title: Patient#170-C3


title: Patient#168-C3


title: Patient#167-C3


title: Patient#166-C3


title: Patient#162-C3


title: Patient#163-C3


title: Patient#159-C3


title: Patient#164-C3


title: Patient#158-C3


title: Patient#169-C3


title: Patient#157-C3


title: Patient#160-C3


title: Patient#156-C3


title: Patient#153-C3


title: Patient#152-C3


title: Patient#155-C3


title: Patient#149-C3


title: Patient#154-C3


title: Patient#145-C3


title: Patient#151-C3


title: Patient#144-C3


title: Patient#143-C3


title: Patient#146-C3


title: Patient#148-C3


title: Patient#150-C3


title: Patient#165-C3


title: Patient#161-C3


title: Patient#141-C3


title: Patient#147-C3


title: Patient#142-C3


title: Patient#140-C3


title: Patient#139-C3


title: Patient#137-C3


title: Patient#134-C3


title: Patient#135-C3


title: Patient#133-C3


title: Patient#132-C3


title: Patient#130-C3


title: Patient#131-C3


title: Patient#129-C3


title: Patient#121-C3


title: Patient#125-C3


title: Patient#127-C3


title: Patient#116-C3


title: Patient#123-C3


title: Patient#138-C3


title: Patient#120-C3


title: Patient#136-C3


title: Patient#128-C3


title: Patient#115-C3


title: Patient#122-C3


title: Patient#117-C3


title: Patient#113-C3


title: Patient#112-C3


title: Patient#114-C3


title: Patient#119-C3


title: Patient#111-C3


title: Patient#118-C3


title: Patient#108-C3


title: Patient#110-C3


title: Patient#124-C3


title: Patient#126-C3


title: Patient#107-C3


title: Patient#105-C3


title: Patient#104-C3


title: Patient#106-C3


title: Patient#101-C3


title: Patient#102-C3


title: Patient#99-C3


title: Patient#100-C3


title: Patient#90-C3


title: Patient#89-C3


title: Patient#97-C3


title: Patient#96-C3


title: Patient#91-C3


title: Patient#98-C3


title: Patient#93-C3


title: Patient#83-C3


title: Patient#86-C3


title: Patient#85-C3


title: Patient#82-C3


title: Patient#94-C3


title: Patient#95-C3


title: Patient#87-C3


title: Patient#84-C3


title: Patient#81-C3


title: Patient#103-C3


title: Patient#80-C3


title: Patient#79-C3


title: Patient#78-C3


title: Patient#92-C3


title: Patient#77-C3


title: Patient#76-C3


title: Patient#75-C3


title: Patient#88-C3


title: Patient#74-C3


title: Patient#71-C3


title: Patient#73-C3


title: Patient#72-C3


title: Patient#63-C3


title: Patient#64-C3


title: Patient#68-C3


title: Patient#61-C3


title: Patient#69-C3


title: Patient#60-C3


title: Patient#67-C3


title: Patient#65-C3


title: Patient#66-C3


title: Patient#57-C3


title: Patient#62-C3


title: Patient#55-C3


title: Patient#58-C3


title: Patient#59-C3


title: Patient#54-C3


title: Patient#50-C3


title: Patient#49-C3


title: Patient#51-C3


title: Patient#53-C3


title: Patient#48-C3


title: Patient#52-C3


title: Patient#47-C3


title: Patient#70-C3


title: Patient#46-C3


title: Patient#56-C3


title: Patient#45-C3


title: Patient#44-C3


title: Patient#42-C3


title: Patient#43-C3


title: Patient#41-C3


title: Patient#40-C3


title: Patient#39-C3


title: Patient#38-C3


title: Patient#36-C3


title: Patient#35-C3


title: Patient#37-C3


title: Patient#32-C3


title: Patient#33-C3


title: Patient#29-C3


title: Patient#31-C3


title: Patient#28-C3


title: Patient#30-C3


title: Patient#27-C3


title: Patient#26-C3


title: fS248A-Tg mESC_Rep1

type: RNA

city: San Francisco

first: Barbara

last: Panning

state: CALIFORNIA

address: 600, 16TH STREET, S374 - Genentech Hall,

department: Biochemistry and Molecular biology

country: USA

institute: University of California, San Francisco

description: Sample name: fS248ASOX2-1

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v2.0 (8x60K, Agilent-034068). Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, mRNAs that have flags in Present or Marginal in at least 1 out of 6 samples were chosen for differentially expressed mRNAs screening.

molecule: total RNA

organism: Mus musculus

source_name: fS248A-Tg mESC

label_protocol: Each mRNA sample was amplified and transcribed into Cy3-labelled cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Agilent Quick Amp Labeling Kit).

growth_protocol: fSOX2-Tg and fS248A-Tg are the two mESCs used in this study. We generated mESC lines that express either a FLAG-tagged wild-type SOX2 (fSOX2-Tg) or a S248A (fS248A-Tg) transgene as the sole source of SOX2. SOX2 levels in fSOX2-Tg and fS248A-Tg mESCs are comparable to SOX2 levels in the parental cell line 2TS22C (accession number AES0125, Riken BioResource Center) (Masui et al., 2007). The tagged SOX2 cell lines generated were cultured in standard ESC media (KO-DMEM, 10% FBS, 2 mM glutamine, 1x non-essential amino acids, 1x penicillin/streptomycin, 0.1 mM beta-mercaptoethanol and recombinant leukemia inhibitory factor) supplemented with 1ug/mL doxycycline hyclate (Sigma).

extract_protocol: Total RNA was isolated from three biological triplicates per cell line using TRIzol reagent (Life Technologies) and following the manufacturer's instructions. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the Agilent array standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY Eukaryotic mRNA Isolation Kit, Epicentre).

tag: parental cell line

tag: cell line

tag: cell type

value: mouse embryonic stem cell line


title: fS248A-Tg mESC_Rep2

description: Sample name: fS248ASOX2-2


title: fSOX2-Tg mESC_Rep3

description: Sample name: fSOX2-3

source_name: fSOX2-Tg mESC


title: fS248A-Tg mESC_Rep3

description: Sample name: fS248ASOX2-3


title: Patient#34-C3


title: fSOX2-Tg mESC_Rep2

description: Sample name: fSOX2-2


title: fSOX2-Tg mESC_Rep1

description: Sample name: fSOX2-1


title: WFR, 26°C, biological rep1

city: Albany

first: ByungHoon

middle: Brian

last: Kim

state: GA

address: 504 College Dr.

institute: Albany State University

description: Gene expression data from 10-day old plants

hyb_protocol: The labeled cRNA was fragmented to between 35nt and 200nt segments by metal induced hydrolysis at 94°C for 30 min.  The fragments were hybridized to the arrays in standard hybridization buffer by first heating to 95°C for 5min then placed immediately at 45°C for 5 min prior to loading into the arrays.  Hybridization was done using the Affymetrix rotating Hyb oven 640 at 60rpm for 16 hrs. Following hybridization the arrays were transferred to the Affymetrix Fluidics Station 450 for processing.  The arrays were washed using the EukGE-WS2v4_450 program.  The arrays were stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned using the Affymetrix 3000 7G scanner as described by the manufacturer.

data_processing: The data were RMA normalized with Affy package of Bioconductor. In addition, expression calls were identified by MAS5.

label: biotin

organism: Arabidopsis thaliana

source_name: Treated with supplemental far-red light at 26°C

label_protocol: RNA was converted to cRNA with an intermediate cDNA step as per the manufacturer’s instructions.  Briefly, one microgram of total RNA was reverse transcribed with an oligo-dT-T7 primer by first heating the total RNA and primer mixture to 65°C for 5min followed by incubation at 25°C for 5min.  Following primer annealing reverse transcription buffer, dNTPs, DTT and Reverse Transcriptase (SuperScript III, Invitrogen, Carlsbad CA) were incubated at 48°C for 90 min.  The cDNA second strand was synthesized using second strand reaction buffer, dNTPs, E. coli polymerase, E. coli ligase and RNAse H with incubation at 16°C for 2hrs immediately followed by addition of T4 DNA Polymerase and incubation for an additional 10min at 16°C.  Double stranded cDNA was purified using column purification by standard techniques.  To produce the labeled cRNA required for hybridization the cDNA was incubated with in vitro transcription (IVT) components including the biotin labeled uracil and T7 RNA polymerase for 16hrs at 37°C.  The cRNA was then cleaned using standard column purification as per the manufacturer’s instructions (Qiagen).

growth_protocol: Plants were grown under standard condition for 9 days: 24 hr continuous white light (cool fluorescent light, 80 mmol/m2sec) at 22°C

extract_protocol: Total RNAs were extracted using TRIreagent (SIGMA). Samples were DNase treated and further purified through RNeasy spin column (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Nine-day old plants were treated with one of the four different conditions for 24 hr: combinations of light (white light alone or white light w/ supplemental far-red light, 6 mmol/m2sec) and temperature (22°C or 26°C).

tag: treatment

tag: genotype

value: Wild type, ecotype Columbia

tag: tissue

value: Aerial part

tag: age

value: 10-day old


title: WFR, 26°C, biological rep3

value: Treated with supplemental far-red light at 26°C


title: Patient#25-C3


title: WFR, 26°C, biological rep2


title: Patient#24-C3


title: Patient#23-C3


title: WL, 26°C, biological rep3

source_name: Treated with white light at 26°C

value: Treated with white light at 26°C


title: Patient#21-C3


title: Patient#19-C3


title: Patient#18-C3


title: Patient#20-C3


title: Patient#17-C3


title: Patient#22-C3


title: Patient#15-C3


title: WL, 26°C, biological rep2


title: Patient#16-C3


title: WFR, 22°C, biological rep3

source_name: Treated with supplemental far-red light at 22°C


title: WFR, 22°C, biological rep1

value: Treated with supplemental far-red light at 22°C


title: Patient#14-C3


title: WL, 26°C, biological rep1


title: WFR, 22°C, biological rep2


title: Patient#13-C3


title: WL, 22°C, biological rep3

source_name: Treated with white light at 22°C

value: Treated with white light at 22°C


title: WL, 22°C, biological rep1


title: Control_26

city: Saint John

first: Andrew

middle: M

last: Cowie

state: New Brunswick

address: 100 Tucker Park Rd.

department: Biochemistry and Molecular Biology

country: Canada

institute: Dalhousie University

description: Feed control for 21 days_5

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is LOWESS Normalization.

organism: Danio rerio

source_name: hypothalamus, adult

label_protocol: Agilent one color protocol for Cy3

extract_protocol: Qiagen Miniprep extraction kit

treatment_protocol: Reproductively mature zebrafish were exposed to different concentrations of dieldrin by feeding for 21 days.

tag: Sex

value: female

tag: developmental stage

value: adult

value: hypothalamus


title: Patient#11-C3

value: Female


title: Patient#10-C3

value: Male


title: Control_16

description: Feed control for 21 days_3


title: Medium_33

description: Feed medium for 21 days_5


title: WL, 22°C, biological rep2


title: Control_31

description: Feed control for 21 days_4


title: Patient#9-C3

value: SLE


title: High_18

description: Feed high for 21 days_5


title: Patient#12-C3


title: High_32

description: Feed high for 21 days_6


title: High_24

description: Feed high for 21 days_4


title: Medium_22

description: Feed medium for 21 days_4


title: Patient#109-C3

value: NHS


title: Medium_10

description: Feed medium for 21 days_3


title: Patient#7-C3


title: Patient#8-C3


title: Patient#6-C3


title: Patient#5-C3


title: Patient#4-C3

value: SjS


title: Patient#3-C3


title: PGE_3

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in R

source_name: buffy coats of peripheral blood

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

growth_protocol: freshly isolated CD4+ T cells and CD4+ T cells separated into CD25 negativ and positiv subpopulation activated with variuos conditions

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 NanoDrop ThermoScientific.

treatment_protocol: immediately after isolation, cells were lysed in Trizol reagent or activated with CD3, Cd3CD28, CD3IL2

value: CD4+ T cell

value: activated via CD3CD28 and treated with PGE2


title: Patient#2-C3

value: UCTD


title: High_12

description: Feed high for 21 days_3


title: PGE_1

description: replicate 3


title: High_2

description: Feed high for 21 days_1


title: TGF_1

description: replicate 2

value: activated via CD3CD28 and treated with TGFb1


title: TGF_3

description: replicate 3


title: TGF_2

description: replicate 1


title: Control_11

description: Feed control for 21 days_2


title: IL10_1

description: replicate 3

value: 8 hrs culture with IL10


title: Control_7

description: Feed control for 21 days_1


title: High_13

description: Feed high for 21 days_2


title: IL10_3

description: replicate 2


title: Medium_4

description: Feed medium for 21 days_2


title: D2_CD4

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite 6.6 (v.6.12.1227)

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-g Biotin-aRNA Labeling Kit

growth_protocol: CD4+ T cells were isolated using CD4+ RosetteSep and cultured for 3 days in medium with or without CD3/CD28/MHC-I-coated beads and TNF

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.

treatment_protocol: After extensive washing, cells were lysed in Trizol reagent

tag: donor id

value: Donor 2

value: Peripheral blood

value: CD4+ T cells

tag: stimulation i

tag: stimulation ii


title: PGE_2

description: replicate 1


title: D3_CD4+CD3/CD28+TNF

value: Donor 3

value: CD3/CD28/MHC-I coated beads

value: TNF


title: zf GW rep3

city: Houston

first: Maria

last: Bondesson

state: Texas

address: 3605 Cullen Blvd

department: Biology & Biochemistry

institute: University of Houston

hyb_protocol: The Agilent’s Hybridization Kit was used for the hybridization. After Cy3 labeling, the samples were fragmented and 1.65 µg of sample and hybridization mix was loaded onto each of the 4x44K Expression arrays. The slide was hybridized in Agilent Hybridization Chamber at 65C at a 10rpm rotation for 17 hours. The slide was washed using the Agilent Expression Wash Buffer Set 1 and 2 as per the Agilent protocol. Performed by Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

scan_protocol: The slides were scanned with the Agilent Scanner (G2565BA) using Scanner Version C. Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

data_processing: The Agilent Feature Extraction Software Version 11.0.1.1 was used to analyze the scanned images and processed Signal intensities were obtained after background substraction. Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

source_name: Whole embryo, 6 dpf, 0.1% GW3965 treatment, replicate 3

label_protocol: The Agilent Quick Amp Labeling Kit (for one-color) Protocol Version 6.5 was used. The Labeling Kit (Agilent p/n 5190-0442) was used along with Agilent’s RNA Spike-In Kit and Agilent’s Wash Buffers 1 and 2. The RNA Spike-Ins was added to the sample. The sample was simultaneously amplified and Cy3 dye labeled as cRNA was generated using T7 RNA Polymerase. The cRNA was purified using Qiagen RNeasy mini spin columns. Samples were then measured again on the Nanodrop for yield and dye incorporation. Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

extract_protocol: Total RNA from pooled embryos was extracted using Trizol (Invitrogen Corporation, Carlsbad, CA) and RNeasy spin columns (Qiagen, Chatsworth, CA) according to the manufacturer’s protocols. On-column DNase I (Qiagen, Chatsworth, CA) digestion was performed to remove remaining DNA. RNA concentrations were measured with NanoDrop 1000 spectrophotometer (Agilent Technologies, Palo Alto, CA) and RNA integrity was analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Wild type zebrafish WIK embryos were collected after spawning. At 4 days post fertilization (dpf), zebrafish larvae were transferred to 6-well plates (pools of 30 embryos/well) in 3 mL of embryo media. Larvae at 4 dpf were treated with DMSO as vehicle control, 2 mM T0901317 (T0) or 1 mM GW3965 (GW). Final DMSO concentration in all treatments and control was 0.1%. Treatments were renewed after 24 h and larvae were collected for RNA extraction at 6 dpf.


title: D1_CD4+CD3/CD28

value: Donor 1


title: Patient#1-C3

tag: gender

value: Female


title: Rest_1

description: replicate 3

value: 8 hrs culture


title: D1_CD4+TNF


title: Medium_8

description: Feed medium for 21 days_1

value: female

value: adult

value: hypothalamus


title: Rest_3

description: replicate 2

value: CD4+ T cell


title: zf GW rep4

source_name: Whole embryo, 6 dpf, 0.1% GW3965 treatment, replicate 4


title: zf GW rep2

source_name: Whole embryo, 6 dpf, 0.1% GW3965 treatment, replicate 2


title: Rest_2

description: replicate 1


title: D3_CD4+CD3/CD28


title: D1_CD4+CD3/CD28+TNF


title: IL10_2

description: replicate 1


title: CTLA4_3

description: replicate 3

value: 8 hrs CD3CD28 activation + CTLA4


title: zf T0 rep4

source_name: Whole embryo, 6 dpf, 0.1% T0901317 treatment, replicate 4


title: zf GW rep1

source_name: Whole embryo, 6 dpf, 0.1% GW3965 treatment, replicate 1


title: CTLA4_2

description: replicate 1


title: D3_CD4+TNF


title: D3_CD4


title: zf DMSO rep3

source_name: Whole embryo, 6 dpf, 0.1% DMSO control treatment, replicate 3

tag: treament

value: control (DMSO)


title: D2_CD4+CD3/CD28


title: D1_CD4


title: PD1_2

description: replicate 1

value: 12 hrs culture, then 8 hrs CD3CD28 activation + PD1


title: CTLA4_1

description: replicate 2


title: zf T0 rep3

source_name: Whole embryo, 6 dpf, 0.1% T0901317 treatment, replicate 3


title: zf DMSO rep4

source_name: Whole embryo, 6 dpf, 0.1% DMSO control treatment, replicate 4


title: zf T0 rep1

source_name: Whole embryo, 6 dpf, 0.1% T0901317 treatment, replicate 1


title: zf DMSO rep2

source_name: Whole embryo, 6 dpf, 0.1% DMSO control treatment, replicate 2


title: D2_CD4+CD3/CD28+TNF


title: PD1_3

description: replicate 3


title: zf T0 rep2

description: (removed from microarray data analysis)

source_name: Whole embryo, 6 dpf, 0.1% T0901317 treatment, replicate 2


title: CD28_3

description: replicate 3

value: activated via CD3CD28


title: CD28_2

description: replicate 2


title: PD1_1

description: replicate 2


title: zf DMSO rep1

source_name: Whole embryo, 6 dpf, 0.1% DMSO control treatment, replicate 1


title: CD28_1

description: replicate 1


title: M32_cCD4_PD1-_Control

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite 6.6 (v.6.12.1227) with subsequent batch removal on the array barcode

growth_protocol: CD4+PD-1+ and CD4+PD-1- T cells were isolated using FACS after Infliximab or control-treatment in chronic LCMV infected animals

tag: strain background

tag: mouse id

value: Mouse 32

tag: disease status

value: chronic LCMV infected

value: Control

value: spleen

value: CD4+PD-1- T cells


title: PLACEBO                  [5368138003_K]

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description:
5368138003_K
Post LPS

hyb_protocol: Illumina standard

scan_protocol: Illumina standard

data_processing: beadarray, neqc normalization

source_name: whole blood

label_protocol: Illumina standard

extract_protocol: Qiacube paxgene mRNA

treatment_protocol: PAXgene blood tubes

value: male

value: whole blood

value: PLACEBO

tag: status

value: Post LPS


title: SRT2104 2.0g/day         [5368138003_J]

description:
5368138003_J
Post LPS


title: PLACEBO + SRT2104 2.0g/d [5368138003_I]

description:
5368138003_I
Post LPS

value: PLACEBO + SRT2104 2.0g/d


title: PLACEBO + SRT2104 2.0g/d [5368138003_L]

description:
5368138003_L
Post LPS


title: M31_cCD4_PD1-_Control

value: Mouse 31


title: D2_CD4+TNF

value: Donor 2

value: Peripheral blood

value: CD4+ T cells

value: TNF


title: PLACEBO                  [5368138003_H]

description:
5368138003_H
Post LPS


title: M43_cCD4_PD1-_Inf

value: Mouse 43

value: Infliximab


title: M13_cCD4_PD1-_Control

value: Mouse 13


title: M14_cCD4_PD1-_Control

value: Mouse 14

value: chronic LCMV infected


title: HIV positive PD-1 positive case 7

description: HIV positive PD-1 positive

source_name: HIV positive PD-1 positive case 7

growth_protocol: CD4+ T cells were isolated from HIV infected individuals

extract_protocol: Cells were lysed in Trizol

treatment_protocol: CD4+ T cells were not further manipulated

value: CD4+ T cell

tag: hiv rna (cop./ml)

tag: cd4+ t cell count

tag: disease state

value: HIV positive

tag: pd-1 status

value: PD-1 positive


title: HIV positive PD-1 positive case 10

description: HIV positive PD-1 positive

source_name: HIV positive PD-1 positive case 10

tag: cell type


title: PLACEBO + SRT2104 2.0g/d [5368138003_D]

description:
5368138003_D
Post LPS

value: male

tag: tissue

value: whole blood

tag: treatment


title: PLACEBO                  [5368138003_F]

description:
5368138003_F
Post LPS

tag: Sex

value: PLACEBO

value: Post LPS


title: M42_cCD4_PD1-_Inf

value: Mouse 42

value: spleen

value: CD4+PD-1- T cells


title: M10_cCD4_PD1-_Control

value: Mouse 10

value: Control


title: HIV positive PD-1 positive case 8

description: HIV positive PD-1 positive

source_name: HIV positive PD-1 positive case 8


title: HIV positive PD-1 positive case 9

description: HIV positive PD-1 positive

source_name: HIV positive PD-1 positive case 9


title: SRT2104 2.0g/day         [5368138003_G]

description:
5368138003_G
Post LPS


title: HIV positive PD-1 positive case 6

description: HIV positive PD-1 positive

source_name: HIV positive PD-1 positive case 6


title: M11_cCD4_PD1-_Inf

value: Mouse 11


title: PLACEBO                  [5368138003_B]

description:
5368138003_B
Post LPS


title: HIV positive PD-1 positive case 5

description: HIV positive PD-1 positive

source_name: HIV positive PD-1 positive case 5


title: SRT2104 2.0g/day         [5368138003_A]

description:
5368138003_A
Post LPS


title: SRT2104 2.0g/day         [5368138003_E]

description:
5368138003_E
Post LPS


title: HIV positive PD-1 positive case 3

description: HIV positive PD-1 positive

source_name: HIV positive PD-1 positive case 3


title: HIV positive PD-1 positive case 4

description: HIV positive PD-1 positive

source_name: HIV positive PD-1 positive case 4


title: M12_cCD4_PD1-_Inf

value: Mouse 12

value: Infliximab


title: PLACEBO + SRT2104 2.0g/d [5368138003_C]

description:
5368138003_C
Post LPS

value: PLACEBO + SRT2104 2.0g/d


title: normal adrenal tissue: ACC77

type: genomic

city: Phoenix

first: Bodour

last: Salhia

state: AZ

address: 445 N Fifth Street

department: Integrated Cancer Genomics Division

institute: Translational Genomics Research Institute

hyb_protocol: Standard Illumina protocol

scan_protocol: Illumina HiScan

data_processing:
GenomeStudio V2011.1
Unmethylated and methylated signal intensities in Series supplementary file

label: Cy5 and Cy3

molecule: genomic DNA

source_name: surgical specimen

label_protocol: Standard Illumina protocol

extract_protocol: All Prep DNA/RNA extraction kit (Qiagen)

value: normal adrenal


title: normal adrenal tissue: ACC79


title: normal adrenal tissue: ACC74


title: normal adrenal tissue: ACC70


title: M19_cCD4_PD1-_Inf

value: Mouse 19

value: chronic LCMV infected


title: PLACEBO                  [5368138011_L]

description:
5368138011_L
Post LPS


title: HIV positive PD-1 positive case 1

description: HIV positive PD-1 positive

source_name: HIV positive PD-1 positive case 1

value: CD4+ T cell

value: HIV positive

value: PD-1 positive


title: SRT2104 2.0g/day         [5368138011_K]

description:
5368138011_K
Post LPS

value: male

value: whole blood


title: HIV positive PD-1 positive case 2

description: HIV positive PD-1 positive

source_name: HIV positive PD-1 positive case 2


title: M32_cCD4_PD1+_Control

value: Mouse 32

value: CD4+PD-1+ T cells


title: HIV positive PD-1 negative case 10

description: HIV positive PD-1 negative

source_name: HIV positive PD-1 negative case 10

value: PD-1 negative


title: M14_cCD4_PD1+_Control

value: Mouse 14

value: spleen


title: M13_cCD4_PD1+_Control

value: Mouse 13

value: Control


title: SRT2104 2.0g/day         [5368138011_I]

description:
5368138011_I
Post LPS

value: Post LPS


title: normal adrenal tissue: ACC54


title: adrenal cortical cancer tissue: ACC125

value: adrenal cortical cancer


title: normal adrenal tissue: ACC80

value: normal adrenal


title: PLACEBO + SRT2104 2.0g/d [5368138011_H]

description:
5368138011_H
Post LPS

value: PLACEBO + SRT2104 2.0g/d


title: M10_cCD4_PD1+_Control

value: Mouse 10

value: chronic LCMV infected


title: M43_cCD4_PD1+_Inf

value: Mouse 43

value: Infliximab


title: adrenal cortical cancer tissue: ACC144


title: adrenal cortical cancer tissue: ACC150


title: HIV positive PD-1 negative case 8

description: HIV positive PD-1 negative

source_name: HIV positive PD-1 negative case 8

value: CD4+ T cell

value: HIV positive


title: HIV positive PD-1 negative case 9

description: HIV positive PD-1 negative

source_name: HIV positive PD-1 negative case 9


title: HIV positive PD-1 negative case 6

description: HIV positive PD-1 negative

source_name: HIV positive PD-1 negative case 6


title: M42_cCD4_PD1+_Inf

value: Mouse 42


title: M6_aCD4_PD1-_Inf

growth_protocol: CD4+PD-1+ and CD4+PD-1- T cells were isolated using FACS after Infliximab or control-treatment in acute LCMV infected animals

tag: mouse id #

value: Mouse 6

value: acute LCMV infected

value: CD4+PD-1- T cells


title: adrenal cortical cancer tissue: ACC132


title: SRT2104 2.0g/day         [5368138011_F]

description:
5368138011_F
Post LPS

value: male

value: whole blood


title: HIV positive PD-1 negative case 7

description: HIV positive PD-1 negative

source_name: HIV positive PD-1 negative case 7

value: PD-1 negative


title: M13_cCD4_PD1+_Inf

value: Mouse 13

value: spleen

value: CD4+PD-1+ T cells


title: PLACEBO                  [5368138011_E]

description:
5368138011_E
Post LPS

source_name: whole blood

value: PLACEBO

value: Post LPS


title: HIV positive PD-1 negative case 5

description: HIV positive PD-1 negative

source_name: HIV positive PD-1 negative case 5


title: PLACEBO                  [5368138011_G]

description:
5368138011_G
Post LPS


title: PLACEBO                  [5368138011_D]

description:
5368138011_D
Post LPS


title: PLACEBO + SRT2104 2.0g/d [5368138011_J]

description:
5368138011_J
Post LPS

value: PLACEBO + SRT2104 2.0g/d


title: PLACEBO + SRT2104 2.0g/d [5368138011_C]

description:
5368138011_C
Post LPS


title: HIV positive PD-1 negative case 4

description: HIV positive PD-1 negative

source_name: HIV positive PD-1 negative case 4


title: adrenal cortical cancer tissue: ACC140

value: adrenal cortical cancer


title: adrenal cortical cancer tissue: ACC134


title: HIV positive PD-1 negative case 3

description: HIV positive PD-1 negative

source_name: HIV positive PD-1 negative case 3


title: M1_aCD4_PD1-_Control

value: Mouse 1

value: Control


title: adrenal cortical cancer tissue: ACC136


title: M5_aCD4_PD1+_Inf

value: Mouse 5

value: Infliximab


title: M4_aCD4_PD1+_Inf

value: Mouse 4


title: M3_aCD4_PD1+_Control

value: Mouse 3

value: acute LCMV infected


title: adrenal cortical cancer tissue: ACC129


title: adrenal cortical cancer tissue: ACC45


title: M4_aCD4_PD1-_Inf

value: CD4+PD-1- T cells


title: SRT2104 2.0g/day         [5368138011_B]

description:
5368138011_B
Post LPS

value: male

value: whole blood


title: HIV positive PD-1 negative case 1

description: HIV positive PD-1 negative

source_name: HIV positive PD-1 negative case 1

value: CD4+ T cell

value: HIV positive

value: PD-1 negative


title: PLACEBO + SRT2104 2.0g/d [5368138011_A]

description:
5368138011_A
Post LPS


title: adrenal cortical cancer tissue: ACC13


title: HIV positive PD-1 negative case 2

description: HIV positive PD-1 negative

source_name: HIV positive PD-1 negative case 2


title: SRT2104 2.0g/day         [5368138005_J]

description:
5368138005_J
Pre SRT

value: Pre SRT


title: PLACEBO + SRT2104 2.0g/d [5368138005_L]

description:
5368138005_L
Pre SRT


title: M3_aCD4_PD1-_Control

value: spleen


title: PLACEBO                  [5368138005_K]

description:
5368138005_K
Pre SRT

value: PLACEBO


title: PLACEBO + SRT2104 2.0g/d [5368138005_I]

description:
5368138005_I
Pre SRT

value: PLACEBO + SRT2104 2.0g/d


title: adrenal cortical cancer tissue: ACC123

value: adrenal cortical cancer


title: M6_aCD4_PD1+_Inf

value: Mouse 6

value: CD4+PD-1+ T cells


title: adrenal cortical cancer tissue: ACC35


title: adrenal cortical cancer tissue: ACC12


title: PLACEBO                  [5368138005_H]

description:
5368138005_H
Pre SRT


title: adrenal cortical cancer tissue: ACC118


title: M5_aCD4_PD1-_Inf

value: Mouse 5

value: Infliximab


title: SRT2104 2.0g/day         [5368138005_G]

description:
5368138005_G
Pre SRT


title: adrenal cortical cancer tissue: ACC117


title: M2_aCD4_PD1-_Control

value: Mouse 2

value: Control


title: SRT2104 2.0g/day         [5368138005_E]

description:
5368138005_E
Pre SRT


title: M1_aCD4_PD1+_Control

value: Mouse 1

value: acute LCMV infected


title: PLACEBO + SRT2104 2.0g/d [5368138005_D]

description:
5368138005_D
Pre SRT

value: male

value: whole blood


title: BMDM t=420 to 450 mins, Ifng, total RNA

city: Edinburgh

first: Peter

last: Ghazal

state: Lothian

address: 49 Little France Crescent

department: Division of Infection and Pathway Medicine

country: United Kingdom

institute: University of Edinburgh

description:
Gene expression data from interferon gamma treated BMDM
420-450_Ifng_totRNA

hyb_protocol: Standard Affymetrix hybridisation and wash procedure Mouse GeneST V1.0

scan_protocol: GeneChips were scanned using the Affymetrx GeneChip Scanner 3000 HR using the GCOS software tool

data_processing: R/Bioconductor using RMA normalisation

source_name: BMDM_Ifng_total RNA

label_protocol: Biotinylated cRNA were prepared with the standard Affymetrix GeneChip IVT labeling kit.

growth_protocol: Bone marrow was flushed from the femurs and tibia of 10 week old C57BL/6J mice. Cells were then cultured for 7 days in DMEM F12-glutamax with 10%FCS, 10%L929 conditioned medium and penicillin/streptomycin. Cells were phenotyped by flow cytometry analysis of surface CD11b and F4/80 expression and were >92% positive for both.

extract_protocol: Total RNA was extracted using and Rneasy Midi kit according to manufacturers protocol. QC was carried out usin an Agilent Bioanalyzer and quantitation was by Nanodrop. Newly transcribed RNA was isolated using a protocol described in Dolken et al. RNA. 2008 Sep;14(9):1959-72

treatment_protocol: On day 7 of culture, cells were treated with 10U/ml Ifng

tag: strain

tag: age

value: 10 week-old

value: femurs and tibia

value: Bone Marrow derived macrophages (BMDM)

tag: cell culture age

value: day 7

tag: treated with

value: 10U/ml interferon gamma

tag: molecule subtype

value: total RNA


title: Summer RAO affected Quarter Horse male (SPA-H4-2 )

city: College Station

first: Sharmila

last: Ghosh

state: TX

address: VMS Building, Rm 107, 4458 TAMUS

department: VIBS

institute: Texas A&M University

hyb_protocol: After probe denaturation and pre-annealing with Cot1-DNA (to mask repetitive sequences), the samples were hybridized at 65°C in hybridization oven with rotation for 40 hours. Array slides were washed according to Agilent’s washing protocol, two time wash with Wash Buffer 1, 2, and acetonitrile. In the experiment slide washing with Wash Buffer 1 was done 10 minutes instead of 5 minutes. The slides were dried with stabilizing and drying solution.

scan_protocol: Scanned with Agilent SureScan DNA Microarray Scanner and Agilent Scanner Control software v8.3 with the following settings: slide id - auto detect; channels - R+G; resolution – 2 µm; tiff – 16bit; R PMT and G PMT are 100%, and XDR set to “0.05”.

data_processing:
Data normalization was done with the Agilent Feature Extraction software (v11.0.1.1).
Data analysis was done using the CGH analytics software (v5.0). The CNVs were represented by gains and losses of normalized fluorescence intensities relative to the reference and identified using the ADM-2 aberration algorithm (Lipson et al. 2006). Parameters used in this analysis were as follows: Threshold of ADM-2: 6.0; Centralization: ON (Threshold: 6.0, Bin Size: 10); Fuzzy Zero: ON; Aberration Filters: ON (minProbes = 5 & minAvgAbsLogRatio = 0.5 & maxAberrations = 10000 AND percentPenetrance = 0); Feature Level Filters: ON, IntraArray: ON).
The CNVs were called with 5 neighboring probes with an average log2 ratio 0.5 aberration filters.

organism: Equus caballus

label_protocol: Samples were labeled with fluorescence dyes Cy3 and Cy5. The control DNA was labeled with Cy3 and cases with Cy5. The labeling reaction was done by random primer, 10XdNTP, 5X reaction buffer, exo-klenow enzyme and Cy3/Cy5-dUTP for 2 hours at 37C, 10 minutes at 65C. The labeled products were purified with Milipore 30k column and diluted with 1X buffer TE according to Agilent protocol.

extract_protocol: Genomic DNA was isolated from peripheral blood or hair follicles using QIAGEN Gentra PureGene Blood kit (Qiagen) according to manufacturer’s protocol.

tag: gender

value: Male

value: Summer RAO affected

tag: breed

value: Quarter Horse

source_name: Thoroughbred1 (reference)


title: PLACEBO                  [5368138005_F]

description:
5368138005_F
Pre SRT

value: PLACEBO

tag: status

value: Pre SRT


title: PLACEBO                  [5368138005_B]

description:
5368138005_B
Pre SRT


title: BMDM t=420 to 450 mins, Mock, total RNA

description:
Gene expression data from Mock treated BMDM
420-450_Mock_totRNA

source_name: BMDM_Mock_total RNA

value: none (mock-treated)


title: adrenal cortical cancer tissue: ACC115

source_name: surgical specimen

value: adrenal cortical cancer


title: adrenal cortical cancer tissue: ACC8


title: PLACEBO + SRT2104 2.0g/d [5368138005_C]

description:
5368138005_C
Pre SRT

value: PLACEBO + SRT2104 2.0g/d


title: Summer RAO affected Tennessee Walking female (SPA-H4-5)

value: Female

value: Tennessee Walking

source_name: Thoroughbred2 (reference)


title: adrenal cortical cancer tissue: ACC10


title: SRT2104 2.0g/day         [5368138005_A]

description:
5368138005_A
Pre SRT

value: male

value: whole blood


title: RAO affected Belgian Draft female (RAO-372)

value: RAO affected

value: Belgian Draft


title: BMDM t=360 to 390 mins, Ifng, total RNA

description:
Gene expression data from interferon gamma treated BMDM
360-390_Ifng_totRNA

value: 10 week-old

value: femurs and tibia

value: Bone Marrow derived macrophages (BMDM)

value: day 7


title: M2_aCD4_PD1+_Control

tag: strain background

value: Mouse 2

tag: disease status

value: acute LCMV infected

value: Control

value: spleen

value: CD4+PD-1+ T cells


title: BMDM t=300 to 330 mins, Ifng, total RNA

description:
Gene expression data from interferon gamma treated BMDM
300-330_Ifng_totRNA

value: 10U/ml interferon gamma

value: total RNA


title: BMDM t=360 to 390 mins, Mock, total RNA

description:
Gene expression data from Mock treated BMDM
360-390_Mock_totRNA

value: none (mock-treated)


title: BMDM t=300 to 330 mins, Mock, total RNA

description:
Gene expression data from Mock treated BMDM
300-330_Mock_totRNA


title: Summer RAO affected Missouri Foxtrotter female (SPA-H4-4)

value: Female

tag: disease state

value: Summer RAO affected

value: Missouri Foxtrotter


title: BMDM t=240 to 270 mins, Ifng, total RNA

description:
Gene expression data from interferon gamma treated BMDM
240-270_Ifng_totRNA


title: Summer RAO control Thoroughbred male (SPA-H1-5)

value: Male

value: Summer RAO control

value: Thoroughbred


title: RAO affected Thoroughbred female (RAO-361)

value: RAO affected


title: PLACEBO + SRT2104 2.0g/d [5368138002_J]

description:
5368138002_J
Pre SRT

value: male

value: whole blood

value: PLACEBO + SRT2104 2.0g/d

value: Pre SRT


title: SRT2104 2.0g/day         [5368138002_I]

description:
5368138002_I
Pre SRT


title: Summer RAO control Quarter Horse female (SPA-H1-3)

value: Quarter Horse


title: RAO affected Appaloosa male (RAO-354 )

value: Appaloosa


title: PLACEBO + SRT2104 2.0g/d [5368138002_H]

description:
5368138002_H
Pre SRT


title: RAO affected Standardbred female (RAO-40 )

value: Standardbred


title: BMDM t=240 to 270 mins, Mock, total RNA

description:
Gene expression data from Mock treated BMDM
240-270_Mock_totRNA

value: 10 week-old

value: femurs and tibia

value: Bone Marrow derived macrophages (BMDM)

value: day 7


title: BMDM t=120 to 150 mins, Mock, total RNA

description:
Gene expression data from Mock treated BMDM
120-150_Mock_totRNA

value: none (mock-treated)

value: total RNA


title: PLACEBO                  [5368138002_L]

description:
5368138002_L
Pre SRT

value: PLACEBO


title: BMDM t=180 to 210 mins, Mock, total RNA

description:
Gene expression data from Mock treated BMDM
180-210_Mock_totRNA


title: PLACEBO                  [5368138002_E]

description:
5368138002_E
Pre SRT


title: SRT2104 2.0g/day         [5368138002_F]

description:
5368138002_F
Pre SRT


title: BMDM t=120 to 150 mins, Ifng, total RNA

description:
Gene expression data from interferon gamma treated BMDM
120-150_Ifng_totRNA

value: 10U/ml interferon gamma


title: Summer RAO affected Tennessee Walking male (SPA-H4-3)

value: Male

value: Summer RAO affected

value: Tennessee Walking


title: BMDM t=60 to 90 mins, Ifng, total RNA

description:
Gene expression data from interferon gamma treated BMDM
60-90_Ifng_totRNA


title: RAO affected Swiss Warmblood male (H4-1999 )

value: RAO affected

value: Swiss Warmblood


title: BMDM t=180 to 210 mins, Ifng, total RNA

description:
Gene expression data from interferon gamma treated BMDM
180-210_Ifng_totRNA


title: PLACEBO                  [5368138002_D]

description:
5368138002_D
Pre SRT

value: male

value: whole blood

value: Pre SRT


title: PLACEBO                  [5368138002_G]

description:
5368138002_G
Pre SRT


title: BMDM t=0 to 30 mins, Ifng, total RNA

description:
Gene expression data from interferon gamma treated BMDM
0-30_Ifng_totRNA


title: RAO affected Swiss Warmblood male (H4-1998 )


title: PLACEBO + SRT2104 2.0g/d [5368138002_C]

description:
5368138002_C
Pre SRT

value: PLACEBO + SRT2104 2.0g/d


title: RAO affected Swiss Warmblood male (H4-2029 )


title: SRT2104 2.0g/day         [5368138002_B]

description:
5368138002_B
Pre SRT


title: PLACEBO + SRT2104 2.0g/d [5368138001_L]

description:
5368138001_L
Pre SRT


title: RAO affected Swiss Warmblood male (H4-1987 )


title: BMDM t=0 to 30 mins, Mock, total RNA

description:
Gene expression data from Mock treated BMDM
0-30_Mock_totRNA

value: 10 week-old


title: BMDM t=450 to 480 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
450-480_Mock_ntRNA

source_name: BMDM_Mock_newly transcribed RNA

value: femurs and tibia

value: newly transcribed RNA


title: PLACEBO                  [5368138001_K]

description:
5368138001_K
Pre SRT


title: BMDM t=450 to 480 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
450-480_Ifng_ntRNA

source_name: BMDM_Ifng_newly transcribed RNA

value: Bone Marrow derived macrophages (BMDM)

value: day 7


title: PLACEBO + SRT2104 2.0g/d [5368138002_A]

description:
5368138002_A
Pre SRT


title: SRT2104 2.0g/day         [5368138001_J]

description:
5368138001_J
Pre SRT


title: BMDM t=420 to 450 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
420-450_Ifng_ntRNA


title: BMDM t=420 to 450 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
420-450_Mock_ntRNA

value: none (mock-treated)


title: BMDM t=390 to 420 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
390-420_Ifng_ntRNA


title: BMDM t=60 to 90 mins, Mock, total RNA

description:
Gene expression data from Mock treated BMDM
60-90_Mock_totRNA

value: total RNA


title: PLACEBO + SRT2104 2.0g/d [5368138001_I]

description:
5368138001_I
Pre SRT


title: SRT2104 2.0g/day         [5368138002_K]

description:
5368138002_K
Pre SRT


title: SRT2104 2.0g/day         [5368138001_G]

description:
5368138001_G
Pre SRT


title: RAO affected Swiss Warmblood male (H4-1943 )


title: RAO affected Swiss Warmblood female (H4-1892)

value: Female


title: BMDM t=390 to 420 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
390-420_Mock_ntRNA


title: PLACEBO                  [5368138001_H]

description:
5368138001_H
Pre SRT

value: PLACEBO


title: PLACEBO                  [5368138001_F]

description:
5368138001_F
Pre SRT


title: RAO affected Swiss Warmblood male (H4-2109 )

value: Male


title: RAO affected Swiss Warmblood female (H4-1912)


title: BMDM t=360 to 390 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
360-390_Ifng_ntRNA

value: 10U/ml interferon gamma


title: SRT2104 2.0g/day         [5368138001_E]

description:
5368138001_E
Pre SRT


title: BMDM t=300 to 330 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
300-330_Mock_ntRNA


title: BMDM t=360 to 390 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
360-390_Mock_ntRNA


title: BMDM t=270 to 300 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
270-300_Ifng_ntRNA


title: BMDM t=330 to 360 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
330-360_Mock_ntRNA


title: PLACEBO                  [5368138001_B]

description:
5368138001_B
Pre SRT


title: BMDM t=300 to 330 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
300-330_Ifng_ntRNA


title: PLACEBO + SRT2104 2.0g/d [5368138001_C]

description:
5368138001_C
Pre SRT


title: PLACEBO + SRT2104 2.0g/d [5368138001_D]

description:
5368138001_D
Pre SRT


title: SRT2104 2.0g/day         [5368138010_K]

description:
5368138010_K
Pre SRT


title: PLACEBO                  [5368138010_G]

description:
5368138010_G
Pre SRT


title: SRT2104 2.0g/day         [5368138010_I]

description:
5368138010_I
Pre SRT


title: BMDM t=270 to 300 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
270-300_Mock_ntRNA


title: BMDM t=210 to 240 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
210-240_Mock_ntRNA


title: BMDM t=120 to 150 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
120-150_Ifng_ntRNA


title: BMDM t=180 to 210 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
180-210_Mock_ntRNA


title: SRT2104 2.0g/day         [5368138010_F]

description:
5368138010_F
Pre SRT


title: PLACEBO                  [5368138010_E]

description:
5368138010_E
Pre SRT


title: BMDM t=330 to 360 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
330-360_Ifng_ntRNA


title: BMDM t=180 to 210 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
180-210_Ifng_ntRNA


title: PLACEBO + SRT2104 2.0g/d [5368138010_H]

description:
5368138010_H
Pre SRT


title: SRT2104 2.0g/day         [5368138001_A]

description:
5368138001_A
Pre SRT


title: BMDM t=240 to 270 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
240-270_Mock_ntRNA


title: BMDM t=120 to 150 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
120-150_Mock_ntRNA


title: BMDM t=150 to 180 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
150-180_Mock_ntRNA


title: BMDM t=150 to 180 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
150-180_Ifng_ntRNA


title: BMDM t=210 to 240 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
210-240_Ifng_ntRNA


title: BMDM t=60 to 90 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
60-90_Ifng_ntRNA


title: PLACEBO + SRT2104 2.0g/d [5368138010_A]

description:
5368138010_A
Pre SRT


title: PLACEBO + SRT2104 2.0g/d [5368138010_J]

description:
5368138010_J
Pre SRT


title: PLACEBO + SRT2104 2.0g/d [5368138010_C]

description:
5368138010_C
Pre SRT


title: Kasumi1_NR4A1_WT_replicate2

first: Orla

last: Conneely

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Gene expression data from Kasumi-1 cells electroporated with NR4A1 WT for 6hr
NR4A1 WT 2

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Human Genome hg U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
RMA signal estimates from RMA Express
RMA data were analyzed in TM4 MeV (4_4_0) using Rank Product analysis.

source_name: acute myeloid leukemia

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

growth_protocol: RPMI1640 supplemented with 20%FBS

extract_protocol: Qiagen RNeasy extraction kit according to manfacturer's instructions

tag: cell line

value: acute myeloid leukemia cell line Kasumi-1

value: NR4A1 WT mRNA electroporation

tag: genotype/variation

value: NR4A1 WT


title: BMDM t=60 to 90 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
60-90_Mock_ntRNA

tag: tissue

tag: cell type


title: SRT2104 2.0g/day         [5368138010_B]

description:
5368138010_B
Pre SRT

tag: Sex

value: male

value: whole blood

tag: treatment


title: Kasumi1_NR4A1_CEAA_replicate2

description:
Gene expression data from Kasumi-1 cells electroporated with NR4A1 CEAA for 6hr
NR4A1 CEAA 2

value: NR4A1 CEAA mRNA electroporation

value: NR4A1 CEAA (DBD-mutated)


title: Kasumi1_NR4A1_WT_replicate3

description:
Gene expression data from Kasumi-1 cells electroporated with NR4A1 WT for 6hr
NR4A1 WT 3


title: Kasumi1_NR4A1_CEAA_replicate1

description:
Gene expression data from Kasumi-1 cells electroporated with NR4A1 CEAA for 6hr
NR4A1 CEAA 1


title: Kasumi1_NR4A1_WT_replicate1

description:
Gene expression data from Kasumi-1 cells electroporated with NR4A1 WT for 6hr
NR4A1 WT 1


title: Mγ-Mφs _w2DG

city: Kawasaki-shi

first: Hiroaki

last: Suzuki

state: Kanagawa

address: 1-1, Suzuki-cho, Kawasaki-ku

country: Japan

institute: Ajinomoto Pharmaceuticals Co., LTD.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 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 SurePrint G3 Human GE v2 8x60K Microarray (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k v2 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 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: monocytes derived from peripheral blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Peripheral blood samples were collected from healthy donors, all of whom provided written informed consent. All experiments were approved by the ethics committees of Keio University School of Medicine. Peripheral blood mononuclear cells were isolated from heparinized peripheral blood samples by density gradient centrifugation using LymphoPrep (Nycomed Pharma, Oslo, Norway). Cells were aspirated from the gradient interface, washed with PBS, and resuspended in RPMI-1640 medium (Sigma-Aldrich, St Louis, MO) containing 10% heat-inactivated fetal bovine serum (Life Technologies, Carlsbad, CA), 100 U/ml penicillin and 100 mg/ml streptomycin (Life Technologies). Monocytes were purified using a magnetic cell separation system (MACS; Miltenyi Biotec, Auburn, AL) with anti-human CD14 microbeads (Miltenyi Biotec), and were seeded in 6-well plates at 1 x 10^6 cells/well. The culture medium contained 50 ng/ml macrophage colony-stimulating factor (M-CSF; R&D Systems, Minneapolis, MN) to induce the production of M-CSF differentiated macrophages (M-Mφs), or 50 ng/ml M-CSF and 100 ng/ml interferon-gamma (IFN-γ; R&D) to induce the production of M-CSF and IFN-γ differentiated macrophages (Mγ-Mφs).  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2. After 6 days, the cells were trypsinized and harvested with a cell scraper.

extract_protocol: RNA was prepared using an RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations.

treatment_protocol: Cells were incubated with 3 mM 2-deoxy-D-glucose during differentiation from monocytes to macrophages

value: inflammatory macrophages (Mγ-Mφs)

value: 3 mM 2-DG for 6-days


title: M-Mφs_wo2DG

value: regulatory macrophages (M-Mφs)


title: BMDM t=0 to 30 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
0-30_Mock_ntRNA

tag: strain

value: 10 week-old

value: femurs and tibia

value: Bone Marrow derived macrophages (BMDM)

value: day 7

value: newly transcribed RNA


title: BMDM t=90 to 120 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
90-120_Mock_ntRNA

tag: age

value: none (mock-treated)


title: PLACEBO                  [5368138010_D]

description:
5368138010_D
Pre SRT

value: PLACEBO

value: Pre SRT


title: Mγ-Mφs _wo2DG


title: BMDM t=90 to 120 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
90-120_Ifng_ntRNA

tag: cell culture age

value: 10U/ml interferon gamma


title: M-Mφs_w2DG


title: MOU870_WT4

status: Public on Mar 06 2016

first: Daniel

middle: A

last: Lim

state: CA

address: 35 Medical Center Way RMB 933B

department: Neurological Surgery

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_870_WT_4d

hyb_protocol: Hybridization was performed in the UCSF Genomics Core Facility according to standard Affymetrix protocols.

scan_protocol: Microarray chip scanning was performed in the UCSF Genomics Core Facility according to standard Affymetrix protocols.

data_processing: The raw data (.CEL files) were processed using Affymetrix Power Tools to implement RMA algorithms. Prior to gene coexpression analysis, gene expression data were reverse log-transformed and restricted to probes annotated as category = main (n = 28,350) by Affymetrix (annotation file: MoGene-1_0-st-v1.na32.mm9.transcript.csv). Sample quality control was performed with the SampleNetwork R function (Oldham et al. Network methods for describing sample relationships in genomic datasets: application to Huntington's disease. BMC systems biology (2012) vol. 6 (1) pp. 63). No sample outliers (Z.K < -3) were present, and there was no significant batch effect associated with microarray hybridization date. Gene coexpression module detection was restricted to probes annotated as crosshyb type = 1 (n = 25,232; i.e. probes that uniquely and perfectly match only one target sequence). Gene coexpression module detection was performed as described (Ramos et al. 2013). To identify differentially expressed (DE) genes, data were log-transformed and a Bayesian t-test was applied using the R package bayesreg (Baldi and Long. A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics (2001) vol. 17 (6) pp. 509-19) with the following parameters: betaFit = 1, bayes = TRUE, winSize = 101, conf = 10. Correction for multiple comparisons was performed by controlling the false-discovery rate (FDR) (Benjamini, Y. and Hochberg, Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser B 57 (1), 289 (1995)) using the R package qvalue (Storey, J. D. and Tibshirani, R., Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100 (16), 9440 (2003)). Genes with FDR < .05 were considered to be differentially expressed.

source_name: SVZ NSCs, wild-type, 4d

label_protocol: Standard protocol.

growth_protocol: SVZ single cell suspensions were plated in N5 medium17 containing DMEM/F12 with Glutamax (Gibco, Cat. No. 10565-018), 5% fetal bovine serum (FBS; Hyclone, Cat. No. SH30070.03), N2 supplement (Gibco, Cat. No. 17502-048), 35µg/ml bovine pituitary extract (BPE; Gibco, Cat. No. 13028.014), 20ng/ml recombinant human epidermal growth factor (EGF; Peprotech, Cat. No. AF-100-15), 20ng/ml recombinant human fibroblast growth factor (FGF; Peprotech, Cat. No. 100-18B-1mg), and antibiotic-antimycotic (Gibco, Cat. No. 15240-062). SVZ cultures were maintained with serial passages as previously described. SVZ cultures were differentiated after 5-7 passages. For differentiation, the medium was changed to a serum-free differentiation medium consisting of DMEM/F12 with Glutamax, N2 supplement, BPE, and antibiotic-antimycotic.

extract_protocol: SVZ cultures were homogenized using QIAshredder columns (QIAgen, Cat. No. 79654), and RNA was extracted using QIAgen RNeasy Plus Mini Kit (Cat. No. 74134). RNA quality and integrity were assessed with the Agilent BioAnalyzer 2100 before samples were converted to cDNA.

value: wild-type

value: subventricular zone neural tem cells

tag: condition

value: differentiation

tag: time point


title: MOU870_WT1

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_870_WT_1d

source_name: SVZ NSCs, wild-type, 1d


title: MOU862_WT2

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_862_WT_2d

source_name: SVZ NSCs, wild-type, 2d


title: MOU870_WT0

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_870_WT_0d

source_name: SVZ NSCs, wild-type, 0d


title: BMDM t=30 to 60 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
30-60_Ifng_ntRNA

tag: treated with

tag: molecule subtype


title: Kasumi1_GFP_replicate1

description:
Gene expression data from Kasumi-1 cells electroporated with GFP for 6hr
GFP 1

value: acute myeloid leukemia cell line Kasumi-1

value: GFP mRNA electroporation

value: control


title: MOU862_WT1

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_862_WT_1d


title: MOU862_WT4

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_862_WT_4d


title: MOU858_KO1

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_858_KO_1d

source_name: SVZ NSCs, Mll1-deleted, 1d


title: BMDM t=30 to 60 mins, Mock, newly transcribed RNA

description:
Gene expression data from Mock treated BMDM
30-60_Mock_ntRNA


title: MOU818_WT2

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_818_WT_2d


title: BMDM t=0 to 30 mins, Ifng, newly transcribed RNA

description:
Gene expression data from interferon gamma treated BMDM
0-30_Ifng_ntRNA


title: MOU862_WT0

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_862_WT_0d


title: Kasumi1_GFP_replicate3

description:
Gene expression data from Kasumi-1 cells electroporated with GFP for 6hr
GFP 3


title: MOU818_WT0

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_818_WT_0d


title: Kasumi1_GFP_replicate2

description:
Gene expression data from Kasumi-1 cells electroporated with GFP for 6hr
GFP 2


title: MOU870_WT2

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_870_WT_2d


title: MOU814_KO1

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_814_KO_1d


title: MOU858_KO4

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_858_KO_4d

source_name: SVZ NSCs, Mll1-deleted, 4d


title: MOU489_KO2

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_489_KO_2d

source_name: SVZ NSCs, Mll1-deleted, 2d


title: monocytes

value: monocytes


title: MOU489_KO1

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_489_KO_1d


title: MOU489_KO4

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_489_KO_4d


title: MOU814_KO0

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_814_KO_0d

source_name: SVZ NSCs, Mll1-deleted, 0d


title: MOU858_KO2

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_858_KO_2d


title: MOU858_KO0

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_858_KO_0d


title: PLACEBO                  [5368138010_L]

description:
5368138010_L
Pre SRT

source_name: whole blood

value: male

value: whole blood

tag: status


title: T29H repeat 2

city: wenzhou

first: jianmin

last: wu

state: zhejiang

address: 268 xueyuan Road

country: China

institute: wenzhou medical university

description: low-molecular-weight RNA derived from total RNA

hyb_protocol: The labled RNA were hybridized for 16 hr at 48°C on Affymetrix miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with miRNA QCTool using Affymetrix default analysis settings and quantile as normalization method.

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag Biotin HSR Labeling Kit. This kit can be used to label any RNA sample, including total RNA, severely degraded RNA, plant RNA, and low molecular weight RNA.

growth_protocol: T29H and T29 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100U/ml penicillin, and 100U/ml streptomycin at 37°C with 5% CO2.

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

value: ovarian epithelial cell


title: MOU818_WT4

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_818_WT_4d


title: MOU814_KO2

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_814_KO_2d


title: MOU814_KO4

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_814_KO_4d


title: MOU818_WT1

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_818_WT_1d


title: IRS2_C6_24_IGF_A

status: Public on Mar 05 2016

city: Rochester

first: Marc

last: Becker

state: MN

address: 200 First St SW

department: Medical Oncology

institute: Mayo Clinic

description: total RNA

hyb_protocol: Following fragmentation, hybridization, washing and staining was performed using Affymetrix GeneTitan® Multi-Channel (MC) Instrument per the manufacturer instructions.

scan_protocol: GeneChips were scanned the Affymetrix GeneTitan® Multi-Channel (MC) Instrument per the manufacturer instructions.

data_processing: Base-2 logarithm transformed intensity data were normalized within each batch using GC-RMA.

source_name: T47D-YA-IRS-2 #6 24h IGF

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

growth_protocol: Cells were plated at a density of 3x10^6 in 150 mm dishes, allowed to equilibrate overnight, and the media replaced by SFM alone for 24 h prior to stimulation.

extract_protocol: Total RNA was collected using RNeasy mini kit (Qiagen) or PerfectPure RNA tissue kit (5Prime). RNA quantity was determined by 260:280 assay and quality using the Agilent Bioanalyzer 2100 (1.8-2.0; Agilent Technologies, Palo Alto, CA) to ensure banding conservation.

treatment_protocol: At time = 0 cells were treated with SFM+FN alone or with IGF-I for 4 h or 24 h.


title: IRS2_C6_4_IGF_C

description: total RNA

source_name: T47D-YA-IRS-2 #6 4h IGF


title: IRS2_C6_24_B

description: total RNA

source_name: T47D-YA-IRS-2 #6 24h SFM


title: IRS2_C6_4_IGF_B

description: total RNA


title: IRS2_C6_4_C

description: total RNA

source_name: T47D-YA-IRS-2 #6 4h SFM


title: Riparia.Glorie_24hr_Stress

city: Reno

first: Grant

last: Cramer

state: Nevada

address: 1664 N. Virginia St

department: Biochemistry & Molecular Biology

institute: University of Nevada, Reno

description: Three grapevine genotypes (Vitis vinifera cv. Cabernet Sauvignon clone 8, Vitis riparia cv. Riparia Gloire, and Vitis champinii cv. Ramsey (a naturally occurring hybrid between Vitis candicans and Vitis rupestris)) were pruned to two shoots and grown in 13.3 liter pots containing 10 L SuperSoil® potting mix supplemented with slow release fertilizer (5-10-10). Vines were grown in a greenhouse with supplemental sodium vapor lamp lighting (day/night cycles of 16 h/8h light (minimum 400 E m-2 s-1) and 28°C/18°C). Fully-developed leaves were subjected to dehydration as previously described (Hopper et al., 2014). Leaves were removed from dehydration boxes at 1, 2, 4, 8, and 24 h and frozen immediately in liquid nitrogen. Control leaves were taken from the second shoot of the intact plant at the corresponding daytime of the dehydration assay to account for circadian effects on transcript abundance.

hyb_protocol: Labeled cDNA was hybridized to a NimbleGen microarray 090818 Vitis exp HX12 (Roche, NimbleGen Inc., Madison, WI, USA), which contains probes targeted to 29,549 grapevine genes predicted from the V1 annotation of the 12x grapevine genome (http://srs.ebi.ac.uk/), and 19,091 random probes as negative controls.

scan_protocol: Each microarray was scanned using an Axon GenePix 4400A (Molecular Devices, Sunnyvale, CA, USA) at 532 nm (Cy3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), which produces pair files containing the raw signal intensity data for each probe and calls files with normalized expression data derived from the average of the intensities of the four probes for each gene.

organism: Vitis riparia

source_name: Vitis riparia cv. Riparia Gloire, own-rooted vines, harvested from fully-developed leaves during a 24-hour dehydration time course

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User's Guide (V 3.2).

extract_protocol: Samples were rapidly frozen in liquid nitrogen before storage at -80°C. Frozen leaves were ground using a Retsch MM 301 ball mill (www.restsch.com) for 1 min at 30 revolutions s-1. Total RNA was extracted from ~100 mg of tissue using a CTAB-based method (Gambino et al., 2008; Tattersall et al., 2005). Three independent experimental (and biological) replicates were harvested to compare between the dehydration-treated and untreated samples at each time point. Each biological replicate was ground in a frozen mortar and pestle. Total RNA was isolated using a cetyltrimethylammonium bromide (CTAB) based method and RNeasy plant mini kit (Quiagen) following the manufacture’s protocol. The total RNA was treated with RNAse-free DNAse I (Qiagen) to eliminate any genomic DNA contamination and then quantified by using a Nanodrop spectrophotometer (Thermo Scientific NanoDrop 2000c). An aliquot of each RNA sample was also analyzed using an Agilent 2100 Bioanalyzer using RNA LabChip® assays according to the manufacturer's instructions.

tag: cultivar

value: Riparia Gloire

value: Stress leaves placed in dehydration box containing 50 mL 333 mM NaCL, harvested at 24 hour

tag: year

tag: location

value: University of Nevada, Reno, USA

value: leaves


title: Riparia.Glorie_4hr_Stress

growth_protocol: Three grapevine genotypes (Vitis vinifera cv. Cabernet Sauvignon clone 8, Vitis riparia cv. Riparia Gloire, and Vitis champinii cv. Ramsey (a naturally occurring hybrid between Vitis candicans and Vitis rupestris)) were pruned to two shoots and grown in 13.3 liter pots containing 10 L SuperSoil® potting mix supplemented with slow release fertilizer (5-10-10). Vines were grown in a greenhouse with supplemental sodium vapor lamp lighting (day/night cycles of 16 h/8h light (minimum 400 E m-2 s-1) and 28°C/18°C).

treatment_protocol: Fully-developed leaves were subjected to dehydration as previously described (Hopper et al., 2014). Leaves were removed from dehydration boxes at 1, 2, 4, 8, and 24 h and frozen immediately in liquid nitrogen. Control leaves were taken from the second shoot of the intact plant at the corresponding daytime of the dehydration assay to account for circadian effects on transcript abundance.

value: Stress leaves placed in dehydration box containing 50 mL 333 mM NaCL, harvested at 4 hour


title: Riparia.Glorie_24hr_Control

value: Control leaves excised with corresponding Stress leaves, harvested at 24 hour


title: IRS2_C6_4_A

description: total RNA

tag: cell line


title: Riparia.Glorie_1hr_Stress

value: Stress leaves placed in dehydration box containing 50 mL 333 mM NaCL, harvested at 1 hour


title: T29 repeat 2

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


title: T29 repeat 1


title: T29H repeat 1

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. The low-molecular-weight (LMW) RNA was isolated from 35μg of total RNA using a PEG6000 solution precipitation method


title: MOU489_KO0

description:
RNA expression of SVZ neural stem cells.
PolyA RNA
Mm_489_KO_0d

tag: genotype/variation


title: Riparia.Glorie_8hr_Control

value: Control leaves excised with corresponding Stress leaves, harvested at 8 hour

tag: tissue


title: Riparia.Glorie_2hr_Stress

value: Stress leaves placed in dehydration box containing 50 mL 333 mM NaCL, harvested at 2 hour


title: Riparia.Glorie_4hr_Control

value: Control leaves excised with corresponding Stress leaves, harvested at 4 hour


title: IRS2_C6_24_IGF_B

description: total RNA


title: Cabernet.Sauvignon_24hr_Stress

organism: Vitis vinifera

source_name: Vitis vinifera L. cv. Cabernet Sauvignon clone 8, own-rooted vines, harvested from fully-developed leaves during a 24-hour dehydration time course

value: Cabernet Sauvignon, Clone 8


title: Cabernet.Sauvignon_8hr_Stress

value: Stress leaves placed in dehydration box containing 50 mL 333 mM NaCL, harvested at 8 hour


title: IRS2_C6_24_IGF_C

description: total RNA


title: IRS2_C6_4_IGF_A

description: total RNA


title: IRS2_C6_24_A

description: total RNA


title: Ramsey_1hr_Control

organism: Vitis x champinii

source_name: Vitis champinii cv. Ramsey, own-rooted vines, harvested from fully-developed leaves during a 24-hour dehydration time course

value: Ramsey

value: Control leaves excised with corresponding Stress leaves, harvested at 1 hour


title: IRS2_C1_4_IGF_C

description: total RNA

source_name: T47D-YA-IRS-2 #1 4h IGF


title: IRS2_C1_24_B

description: total RNA

source_name: T47D-YA-IRS-2 #1 24h SFM


title: IRS2_C6_24_C

description: total RNA


title: IRS2_C1_24_IGF_A

description: total RNA

source_name: T47D-YA-IRS-2 #1 24h IGF


title: Riparia.Glorie_8hr_Stress


title: IRS2_C1_24_IGF_C

description: total RNA


title: Cabernet.Sauvignon_4hr_Control


title: IRS2_C6_4_B

description: total RNA


title: Cabernet.Sauvignon_8hr_Control


title: Cabernet.Sauvignon_1hr_Control


title: Riparia.Glorie_2hr_Control

value: Control leaves excised with corresponding Stress leaves, harvested at 2 hour


title: Riparia.Glorie_1hr_Control


title: Cabernet.Sauvignon_4hr_Stress


title: Ramsey_8hr_Stress


title: IRS2_C1_24_C

description: total RNA


title: Cabernet.Sauvignon_1hr_Stress


title: IRS2_C1_24_A

description: total RNA


title: Cabernet.Sauvignon_24hr_Control


title: Cabernet.Sauvignon_2hr_Stress


title: Ramsey_4hr_Stress


title: Ramsey_24hr_Control


title: Ramsey_24hr_Stress


title: Ramsey_2hr_Stress


title: Ramsey_1hr_Stress


title: Cabernet.Sauvignon_2hr_Control


title: Ramsey_4hr_Control


title: IRS2_C1_4_IGF_B

description: total RNA


title: IRS1_C20_24_IGF_C

description: total RNA

source_name: T47D-YA-IRS-1 #20 24h IGF


title: IRS2_C1_4_IGF_A

description: total RNA


title: IRS2_C1_4_B

description: total RNA

source_name: T47D-YA-IRS-2 #1 4h SFM


title: Ramsey_2hr_Control