title: AD1_REP3_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58068.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 4/2/2008 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 4/2/2008

label_protocol:
Approx RNA yield = 9 ug; Type of in-vitro transcription = Epicentre; Date performed = 3/30/2008; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD1 salt root; Date performed = 3/31/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 11/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD1 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"

label_protocol:
Approx RNA yield = 21 ug; Date performed = 3/30/2008; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 3/31/2008; Tube label = AD1 no-salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 11/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD1 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD4_REP1_LEAF

status: Public on Jan 21 2010

type: RNA

city: Athens

first: Alan

middle: R

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

country: USA

institute: University of Georgia

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58085.gif

hyb_protocol: not provided

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 6/11/2007 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 6/11/2007

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: total RNA

organism: Gossypium mustelinum

source_name: AD4 no-salt leaf

label_protocol:
Approx RNA yield = 21 ug; Type of in-vitro transcription = Epicentre; Date performed = Jun-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD4 no-salt leaf; Date performed = 6/8/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD4 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

treatment_protocol: BYU growth chamber

tag: treatment

value: no-salt

tag: name

tag: genome

tag: polyploid level

tag: tissue type

value: leaf

source_name: AD4 salt leaf

label_protocol:
Approx RNA yield = 38 ug; Date performed = Jun-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 6/8/2007; Tube label = AD4 salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD4 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA

value: salt


title: AD3_REP4_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58083.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 8/28/2007 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 8/28/2007

organism: Gossypium tomentosum

source_name: AD3 salt leaf

label_protocol:
Approx RNA yield = 15 ug; Type of in-vitro transcription = Epicentre; Date performed = Aug-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD3 salt leaf; Date performed = 8/17/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD3 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"

source_name: AD3 no-salt leaf

label_protocol:
Approx RNA yield = 10 ug; Date performed = Aug-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 8/17/2007; Tube label = AD3 no-salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD3 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD3_REP4_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58084.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 12/4/2007 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 12/4/2007

source_name: AD3 no-salt root

label_protocol:
Approx RNA yield = 9 ug; Type of in-vitro transcription = Epicentre; Date performed = 11/28/2007; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD3 no-salt root; Date performed = 11/29/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/15/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD3 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"

value: root

source_name: AD3 salt root

label_protocol:
Approx RNA yield = 18 ug; Date performed = 11/28/2007; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 11/29/2007; Tube label = AD3 salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/15/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD3 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"; Name = Rozaura; Extracted molecule = RNA


title: BTU 26 Tumor Fibroblasts

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich

description: Cell Type: Human Primary breast Fibroblasts

scan_protocol: GenePix 4100A 01

organism: Homo sapiens

source_name: stratagene human reference plus doping controls.

label_protocol:
MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Michal,,Rajski
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH1; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab ? 04/14/2006 (update 05/25/2006).; Protocol Type = Labeling; Performer: Michal,,Rajski

extract_protocol: StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer: Michal,,Rajski

tag: reference

source_name: BTU 26 Tumor Fibroblasts

label_protocol:
MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Michal,,Rajski
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH2; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab ? 04/14/2006 (update 05/25/2006).; Protocol Type = Labeling; Performer: Michal,,Rajski

extract_protocol: RNeasy; Total RNA was isolated using the RNeasy mini kit (QIAGEN), according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Michal,,Rajski

tag: cell type

value: Human Primary breast Fibroblasts


title: BTU 26 Tumor Fibroblasts with IGF I

value: stratagene human reference plus doping controls.

source_name: BTU 26 Tumor Fibroblasts with IGF I


title: AD3_REP2_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58081.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 9/12/2007 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 9/12/2007

label_protocol:
Approx RNA yield = 50 ug; Type of in-vitro transcription = Epicentre; Date performed = Sep-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD3 no-salt leaf; Date performed = 9/5/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD3 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"

label_protocol:
Approx RNA yield = 42.5 ug; Date performed = Sep-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 9/5/2007; Tube label = AD3 salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD3 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"; Name = Rozaura; Extracted molecule = RNA


title: BTU 26 Normal Fibroblasts

source_name: BTU 26 Normal Fibroblasts


title: AD1_REP3_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58067.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 7/26/2007 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 7/26/2007

organism: Gossypium hirsutum

source_name: AD1 salt leaf

label_protocol:
Approx RNA yield = 16 ug; Type of in-vitro transcription = Epicentre; Date performed = Jul-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD1 salt leaf; Date performed = 7/23/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = Jun-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD1 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"

source_name: AD1 no-salt leaf

label_protocol:
Approx RNA yield = 15.5 ug; Date performed = Jul-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 7/23/2007; Tube label = AD1 no-salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = Jun-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD1 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"; Name = Rozaura; Extracted molecule = RNA


title: BTU 15 Normal Fibroblasts with IGF I

source_name: BTU 15 Normal Fibroblasts with IGF I


title: AD3_REP1_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58080.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 3/20/2008 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 3/20/2008

label_protocol:
Approx RNA yield = 15 ug; Type of in-vitro transcription = Epicentre; Date performed = Mar-08; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD3 salt root; Date performed = 3/15/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD3 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

label_protocol:
Approx RNA yield = 10 ug; Date performed = Mar-08; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 3/15/2008; Tube label = AD3 no-salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD3 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: Detroit 562 P29 rep1

status: Public on Jan 22 2010

city: Woolloongabba

first: Sarina

last: Cameron

state: QLD

address: Level 4, R wing, PA Hospital

country: Australia

institute: Diamantina Institute

description:
Replicate 1
4375521025D

hyb_protocol: Standard illumina hybridization protocol

scan_protocol: Standard illumina scanning protocol

data_processing: Data was normalised using quanatile normalisation with Lumi software.

label: biotin

source_name: Detroit 562 HNSCC Cell line

label_protocol: Biotinylated cRNA was prepared with the ambion amplification kit for illumina arrays.

growth_protocol: Grown as per ATCC recommendations.

extract_protocol: RNA was isolated with Trizol reagent, followed by Clean-up and DNase 1 treatment using the QIAGEN RNA easy mini kit as per the kit protocol. Agilent Bioanalysier was employed for quality control.

tag: sex

value: female

value: Metastatic HNSCC of the Pharynx

tag: cell line

value: Detroit 562

tag: cell culture passage number


title: AD1_REP2_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58066.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 2/22/2007 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 2/22/2007

source_name: AD1 no-salt root

label_protocol:
Approx RNA yield = 7 ug; Type of in-vitro transcription = Epicentre; Date performed = 1/9/2008; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD1 no-salt root; Date performed = 2/18/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/25/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD1 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"

source_name: AD1 salt root

label_protocol:
Approx RNA yield = 9 ug; Date performed = 1/9/2008; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 2/18/2008; Tube label = AD1 salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/25/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD1 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD1_REP1_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58064.gif

label_protocol:
Approx RNA yield = 10 ug; Type of in-vitro transcription = Epicentre; Date performed = Jun-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD1 no-salt leaf; Date performed = 6/8/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD1 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

label_protocol:
Approx RNA yield = 22 ug; Date performed = Jun-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 6/8/2007; Tube label = AD1 salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD1 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD1_REP2_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58065.gif

label_protocol:
Approx RNA yield = 16 ug; Type of in-vitro transcription = Epicentre; Date performed = Sep-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD1 no-salt leaf; Date performed = 9/5/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

label_protocol:
Approx RNA yield = 15.5 ug; Date performed = Sep-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 9/5/2007; Tube label = AD1 salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura


title: BTU 15 Normal Fibroblasts

source_name: BTU 15 Normal Fibroblasts


title: BTU 31 Normal Fibroblasts

source_name: BTU 31 Normal Fibroblasts


title: BTU 31 Normal Fibroblasts with IGF I

source_name: BTU 31 Normal Fibroblasts with IGF I


title: BTU 31 Tumor Fibroblasts with IGF I

source_name: BTU 31 Tumor Fibroblasts with IGF I


title: BTU 31 Tumor Fibroblasts

source_name: BTU 31 Tumor Fibroblasts


title: BTU 26 Normal Fibroblasts with IGF I

source_name: BTU 26 Normal Fibroblasts with IGF I


title: BTU 15 Tumor Fibroblasts with IGF I

source_name: BTU 15 Tumor Fibroblasts with IGF I


title: AD5_REP3_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58098.gif

organism: Gossypium darwinii

source_name: AD5 salt root

label_protocol:
Approx RNA yield = 11 ug; Type of in-vitro transcription = Epicentre; Date performed = 3/30/2008; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD5 salt root; Date performed = 3/31/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 11/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD5 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = root tissue

source_name: AD5 no-salt root

label_protocol:
Approx RNA yield = 19 ug; Date performed = 3/30/2008; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 3/31/2008; Tube label = AD5 no-salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 11/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD5 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = root tissue; Name = Rozaura; Extracted molecule = RNA


title: AD1_REP1_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58063.gif

label_protocol:
Approx RNA yield = 14 ug; Type of in-vitro transcription = Epicentre; Date performed = Mar-08; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD1 salt root; Date performed = 3/15/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD1 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

label_protocol:
Approx RNA yield = 20ug; Date performed = Mar-08; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 3/15/2008; Tube label = AD1 no-salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD1 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: CCL171 24h culture slide 2

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71307.gif

source_name: stratagene human reference plus doping controls.

label_protocol:
MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Michal,,Rajski
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH1; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab ? 04/14/2006 (update 05/25/2006).; Protocol Type = Labeling; Performer: Michal,,Rajski

extract_protocol: StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer: Michal,,Rajski

source_name: CCL171 plus doping controls.

label_protocol:
MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Michal,,Rajski
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH2; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab ? 04/14/2006 (update 05/25/2006).; Protocol Type = Labeling; Performer: Michal,,Rajski

growth_protocol: Monoculture cell conditions.; MCF - 7 and CCL - 171 cells were expanded and propagated in Dulbeccos Modified Eagles Medium (DMEM) supplemented with:  10% FBS (GIBCO, Grand Island, N.Y.), L - glutamine, 4.5 g/L glucose, 100 U/ml penicillin and 100 ug/ml streptomycin (GIBCO, Grand Island, N.Y.).  For mono-culture experiments the cells were cultivated for 6 hours at 30,000 cells/cm2 in DMEM medium with 5% FBS. After 6 hours medium was changed to DMEM medium with 0.2% FBS and the cells were cultured for 48 hours(starving period). After 48 hours medium was changed to a fresh DMEM medium with 0.2% FBS and the cells were cultured for 24 hours.; Protocol Type = Biological Sample; Performer: Michal,,Rajski

value: CCL 171 fibroblasts


title: BTU 15 Tumor Fibroblasts

source_name: BTU 15 Tumor Fibroblasts

extract_protocol: RNeasy; Total RNA was isolated using the RNeasy mini kit (QIAGEN), according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Michal,,Rajski


title: CCL171 + IGF I 24h culture slide 2

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71309.gif

source_name: CCL171 plus IGF I plus doping controls.


title: AD5_REP3_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58097.gif

source_name: AD5 salt leaf

label_protocol:
Approx RNA yield = 36 ug; Type of in-vitro transcription = Epicentre; Date performed = Jul-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD5 salt leaf; Date performed = 7/23/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = Jun-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD5 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = leaf tissue

source_name: AD5 no-salt leaf

label_protocol:
Approx RNA yield = 31.5 ug; Date performed = Jul-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 7/23/2007; Tube label = AD5 no-salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = Jun-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD5 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = leaf tissue; Name = Rozaura; Extracted molecule = RNA


title: CD25 Hi CD8 T cells, Biological Replicate 4

city: Atlanta

first: Vandana

last: Kalia

address: 1510 Clifton Road

department: Microbiology and Immunology

institute: Emory University

description: Sorted CD25 Hi P14 CD8 T cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430.20 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridized cRNA was detected using streptavidin coupled to phycoerythrin

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples

data_processing: The array used was GeneChip Mouse Genome 430 2.0 Array. There are 3 groups Naïve, CD25 Lo and CD25 Hi . Naïve group has 3 biological replicates. The CD25 Lo and CD25 Hi group both have 4 biological replicates each. The biological replicates are numbered serially.The trimmed target intensities were arbitarilly set at 100. The data was analyzed using Genespring GX 10.0.2 software using RMA normalization.

label: Biotin

organism: Mus musculus

source_name: Splenocytes

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

growth_protocol: CD8 T-cells were FACS sorted and mRNA isolated for microarray analysis.

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

treatment_protocol: RNA was isolated from cells in Trizol (GIBCO/BRL Life Technologies, Rockville, MD) according to manufacture’s protocol. cDNA was synthesized using SuperScript Choice cDNA synthesis kit (GIBCO/BRL) and an oligo (dT) primer containing a T7 promoter. The MEGAscript T7 kit (Ambion, Austin, TX) was used to amplify cRNA from the cDNA. The cRNA was reverse transcribed with biotinylated nucleotides using Enzo BioArray High Yield RNA Transcript Labeling Kit in the second round of cRNAsynthesis, fragmented, and hybridized on mouse 430.2 Affymetrix microarray chips.

tag: tissue

value: splenocytes

value: CD25 Hi CD8 T cells

tag: days after infection with lcmv

value: Day 3.5


title: CCL171 + IGF I 24h culture slide 1

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71308.gif


title: AD5_REP1_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58094.gif

label_protocol:
Approx RNA yield = 9 ug; Type of in-vitro transcription = Epicentre; Date performed = Mar-08; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD5 salt root; Date performed = 3/15/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD5 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = root tissue

label_protocol:
Approx RNA yield = 14 ug; Date performed = Mar-08; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 3/15/2008; Tube label = AD5 no-salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD5 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = root tissue; Name = Rozaura; Extracted molecule = RNA


title: AD3_REP2_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58082.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 2/22/2008 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 2/22/2008

source_name: AD3 no-salt root

label_protocol:
Approx RNA yield = 8 ug; Type of in-vitro transcription = Epicentre; Date performed = 1/9/2008; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD3 no-salt root; Date performed = 2/18/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/29/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD3 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"

source_name: AD3 salt root

label_protocol:
Approx RNA yield = 15 ug; Date performed = 1/9/2008; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 2/18/2008; Tube label = AD3 salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/29/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD3 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD2_REP4_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58078.gif

organism: Gossypium barbadense

source_name: AD2 no-salt root

label_protocol:
Approx RNA yield = 10 ug; Type of in-vitro transcription = Epicentre; Date performed = 11/28/2007; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD2 no-salt root; Date performed = 11/29/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/10/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD2 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

value: pima s7

source_name: AD2 salt root

label_protocol:
Approx RNA yield = 10 ug; Date performed = 11/28/2007; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 11/29/2007; Tube label = AD2 salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/10/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD2 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: CD25 Hi CD8 T cells, Biological Replicate 1

description: Sorted CD25 Hi P14 CD8 T cells


title: CD25 Hi CD8 T cells, Biological Replicate 2

description: Sorted CD25 Hi P14 CD8 T cells


title: CCL171 24h culture slide 1

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71306.gif


title: AD5_REP2_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58096.gif

label_protocol:
Approx RNA yield = 12 ug; Type of in-vitro transcription = Epicentre; Date performed = 1/9/2008; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD5 no-salt root; Date performed = 2/18/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/31/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD5 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = root tissue

label_protocol:
Approx RNA yield = 2 ug; Date performed = 1/9/2008; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 2/18/2008; Tube label = AD5 salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/31/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD5 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = root tissue; Name = Rozaura; Extracted molecule = RNA


title: AD2_REP3_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58076.gif

label_protocol:
Approx RNA yield = 36 ug; Type of in-vitro transcription = Epicentre; Date performed = 3/30/2008; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD2 salt root; Date performed = 3/31/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 11/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD2 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

label_protocol:
Approx RNA yield = 34 ug; Date performed = 3/30/2008; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 3/31/2008; Tube label = AD2 no-salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 11/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD2 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD1_REP4_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58069.gif

source_name: AD1 salt leaf

label_protocol:
Approx RNA yield = 15 ug; Type of in-vitro transcription = Epicentre; Date performed = Aug-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD1 salt leaf; Date performed = 8/17/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD1 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"

source_name: AD1 no-salt leaf

label_protocol:
Approx RNA yield = 12 ug; Date performed = Aug-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 8/17/2007; Tube label = AD1 no-salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD1 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD5_REP1_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58093.gif

label_protocol:
Approx RNA yield = 13 ug; Type of in-vitro transcription = Epicentre; Date performed = Jun-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD5 no-salt leaf; Date performed = 6/8/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD5 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = leaf tissue

label_protocol:
Approx RNA yield = 34 ug; Date performed = Jun-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 6/8/2007; Tube label = AD5 salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD5 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = leaf tissue; Name = Rozaura; Extracted molecule = RNA


title: AD2_REP4_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58077.gif

source_name: AD2 salt leaf

label_protocol:
Approx RNA yield = 11 ug; Type of in-vitro transcription = Epicentre; Date performed = Aug-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD2 salt leaf; Date performed = 8/17/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD2 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

source_name: AD2 no-salt leaf

label_protocol:
Approx RNA yield = 16 ug; Date performed = Aug-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 8/17/2007; Tube label = AD2 no-salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD2 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: MCF7 24h culture slide 1

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71294.gif

label_protocol:
MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Michal,,Rajski
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH1; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab ? 04/14/2006 (update 05/25/2006).; Protocol Type = Labeling; Performer: Michal,,Rajski

extract_protocol: StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer: Michal,,Rajski

source_name: mcf7 plus doping controls.

label_protocol:
MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Michal,,Rajski
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH2; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab ? 04/14/2006 (update 05/25/2006).; Protocol Type = Labeling; Performer: Michal,,Rajski

extract_protocol: RNeasy; Total RNA was isolated using the RNeasy mini kit (QIAGEN), according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Michal,,Rajski

value: MCF-7 breast cancer cells


title: AD4_REP4_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58092.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 12/18/2007 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 12/18/2007

source_name: AD4 no-salt root

label_protocol:
Approx RNA yield = 13 ug; Type of in-vitro transcription = Epicentre; Date performed = 11/28/2007; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD4 no-salt root; Date performed = 11/29/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/15/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD4 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

source_name: AD4 salt root

label_protocol:
Approx RNA yield = 4 ug; Date performed = 12/13/2007; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 12/14/2007; Tube label = AD4 salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/15/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD4 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: MCF7 24h culture slide 2

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71295.gif

source_name: stratagene human reference plus doping controls.


title: MCF7 + IGF I 24h culture slide 1

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71296.gif

source_name: mcf7 plus IGF I plus doping controls.


title: CD25 Lo CD8 T cells, Biological Replicate 4

description: Sorted CD25 Lo P14 CD8 T cells

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

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

value: CD25 Lo CD8 T cells


title: AD3_REP1_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58079.gif

source_name: AD3 no-salt leaf

label_protocol:
Approx RNA yield = 15 ug; Type of in-vitro transcription = Epicentre; Date performed = Jun-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD3 no-salt leaf; Date performed = 6/8/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD3 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

source_name: AD3 salt leaf

label_protocol:
Approx RNA yield = 21 ug; Date performed = Jun-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 6/8/2007; Tube label = AD3 salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD3 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD2_REP3_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58075.gif

label_protocol:
Approx RNA yield = 22.5 ug; Type of in-vitro transcription = Epicentre; Date performed = Jul-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD2 salt leaf; Date performed = 7/23/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = Jun-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD2 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

label_protocol:
Approx RNA yield = 22 ug; Date performed = Jul-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 7/23/2007; Tube label = AD2 no-salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = Jun-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD2 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: CD25 Lo CD8 T cells, Biological Replicate 2

description: Sorted CD25 Lo P14 CD8 T cells


title: AD5_REP2_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58095.gif

source_name: AD5 no-salt leaf

label_protocol:
Approx RNA yield = 17 ug; Type of in-vitro transcription = Epicentre; Date performed = Sep-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD5 no-salt leaf; Date performed = 9/5/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

source_name: AD5 salt leaf

label_protocol:
Approx RNA yield = 41 ug; Date performed = Sep-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 9/5/2007; Tube label = AD5 salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura


title: CD25 Lo CD8 T cells, Biological Replicate 3

description: Sorted CD25 Lo P14 CD8 T cells

source_name: Splenocytes


title: Salt stress condition replicate 3

city: Tsukuba

first: Tomomi

last: Mito

state: Ibaraki

address: Central 4 Higashi 1-1-1

country: Japan

institute: Greensogna,Inc.

description: Biological replicate 3 of 3. Salt stress condition of 35S:AtMYB102-SRDX plant

hyb_protocol: Hybridization was performed with Agilent Gene Expression Hybridization Kit (Agilent, product #5188-5242） according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner according to Agilent manual.

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: Wild type Col-0 leaves

label_protocol: Labeling was performed with Low RNA Input Linear Amplification Kit (Agilent, product # 5188-5340) and fragmented according to Agilent protocol.

growth_protocol: Sterilized Arabidopsis seeds were plated on MS medium and grown at 22 ˚C with 16h-light/8h-dark cycle.

extract_protocol: total RNA was extracted from 3 young rosette leaves using Qiagen Rneasy Plant Mini kit (Qiagen,Valencia,CA)

treatment_protocol: 3-week old plant was transferred to MS medium (Control condition) or MS containing 200mM NaCl (Salt stress condition) for 24h.

tag: genotype/variation

value: wild type

tag: ecotype

value: rosette leaves

tag: age

value: 3-weeks old

tag: stress

source_name: 35S:AtMYB102-SRDX leaves


title: Salt stress condition replicate 2

description: Biological replicate 2 of 3. Salt stress condition of 35S:AtMYB102-SRDX plant

value: salt


title: Salt stress condition replicate 1

description: Biological replicate 1 of 3. Salt stress condition of 35S:AtMYB102-SRDX plant


title: KATO-III_DAC

status: Public on Jan 20 2010

type: other

city: Yushima, Bunkyo-ku

first: Yutaka

last: Hashimoto

state: Tokyo

department: Molecular Oncology

institute: Tokyo Medical and Dental University Graduate School

hyb_protocol: A 3x miRNA Hybridization Buffer (Ambion) was added to the fluorescently labeled miRNAs and the solution was heated at 95ºC for 3 min. Slides were hybridized form 12 to 16 h at 42 ºC in sealed cassettes using a water bath.

scan_protocol: The Cy3 fluorescence on the arrays was scanned at an excitation wavelength of 532nm using a GenePix　4000B scanner (Axon Instruments, CA, USA). Raw data were normalized and analyzed using Array-Pro Analyzer Version 4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA).

data_processing: We used Array-Pro Analyzer Ver4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA) to determine the signal intensity of each spot and its local background on microarrays. We calculated net intensity by subtracting the mean intensity of all pixels within the local background area from the mean intensity of all pixels within the spot areas. We normalized biases in net intensity between the one fluorescent dye channel in a microarray by grobal normalization using its software. Analyzed data were selected by using MicroArray Data Analysis Tool (Filgen, Inc.)

label: Cy3 succinimide esters

molecule: other

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

source_name: gastric carcinoma, treated with DAC

label_protocol: mirVana™ miRNA Labeling Kit

growth_protocol: Cells were cultured in RPMI1640 supplemented with 10% Fetal Bovine Serum (FBS) for 3 days at 37°C (5% CO2 - 95% air gas mixture).

extract_protocol: microRNA enriched fraction obtained by passing total RNA through a flashPAGE™ Fractionator apparatus (Ambion, Inc., Austin, TX) and cleaned.

treatment_protocol: Cells were daily treated with 5 micro-mol/L 5'-Aza-2'-deoxycitydine (Sigma-Aldrich, St. Louis, MO) for 72 h.

tag: disease state

value: gastric carcinoma

value: stomach

value: KATO-III

tag: agent

value: 5-aza-2'-deoxycytidine (DAC)

tag: time

value: 72 hours

tag: growth properties

value: mixed, adherent and suspension.

tag: morphology

value: spherical


title: CD25 Lo CD8 T cells, Biological Replicate 1

description: Sorted CD25 Lo P14 CD8 T cells

value: splenocytes


title: Naïve P14 CD8 T cells, Biological Replicate 1

description: Sorted Naïve P14 CD8 T cells

value: Naïve P14 CD8 T cells

value: Day 0


title: Control condition replicate 1

description: Biological replicate 1 of 3. Control condition of 35S:AtMYB102-SRDX plant

value: control


title: Naïve P14 CD8 T cells, Biological Replicate 3

description: Sorted Naïve P14 CD8 T cells


title: AD2_REP2_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58074.gif

source_name: AD2 no-salt root

label_protocol:
Approx RNA yield = 6 ug; Type of in-vitro transcription = Epicentre; Date performed = 1/9/2008; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD2 no-salt root; Date performed = 2/18/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/25/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD2 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"

tag: treatment

value: no-salt

tag: name

value: pima s7

tag: genome

tag: polyploid level

tag: tissue type

value: root

source_name: AD2 salt root

label_protocol:
Approx RNA yield = 3.5 ug; Date performed = 1/9/2008; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 2/18/2008; Tube label = AD2 salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/25/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD2 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD4_REP4_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58091.gif

source_name: AD4 salt leaf

label_protocol:
Approx RNA yield = 16 ug; Type of in-vitro transcription = Epicentre; Date performed = Aug-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD4 salt leaf; Date performed = 8/17/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD4 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

value: leaf

source_name: AD4 no-salt leaf

label_protocol:
Approx RNA yield = 12 ug; Date performed = Aug-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 8/17/2007; Tube label = AD4 no-salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD4 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: Control condition replicate 3

description: Biological replicate 3 of 3. Control condition of 35S:AtMYB102-SRDX plant

value: wild type

value: rosette leaves

value: 3-weeks old


title: MCF7 + IGF I 24h culture slide 2

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71297.gif

label_protocol:
MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Michal,,Rajski
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH1; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab ? 04/14/2006 (update 05/25/2006).; Protocol Type = Labeling; Performer: Michal,,Rajski

tag: reference

value: stratagene human reference plus doping controls.

tag: cell line

value: MCF-7 breast cancer cells


title: AD4_REP3_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58090.gif

label_protocol:
Approx RNA yield = 32 ug; Type of in-vitro transcription = Epicentre; Date performed = 3/30/2008; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD4 salt root; Date performed = 3/31/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 11/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD4 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

value: salt

label_protocol:
Approx RNA yield = 35 ug; Date performed = 3/30/2008; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 3/31/2008; Tube label = AD4 no-salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 11/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD4 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD2_REP2_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58073.gif

source_name: AD2 no-salt leaf

label_protocol:
Approx RNA yield = 16 ug; Type of in-vitro transcription = Epicentre; Date performed = Sep-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 9/5/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD2 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

source_name: AD2 salt leaf

label_protocol:
Approx RNA yield = 30 ug; Date performed = Sep-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 9/5/2007; Tube label = AD2 salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD2 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA


title: Naïve P14 CD8 T cells, Biological Replicate 2

description: Sorted Naïve P14 CD8 T cells

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

tag: tissue

tag: cell type

tag: days after infection with lcmv


title: KATO-III control

data_processing: We used Array-Pro Analyzer Ver4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA) to determine the signal intensity of each spot and its local background on microarrays.  We calculated net intensity by subtracting the mean intensity of all pixels within the local background area from the mean intensity of all pixels within the spot areas. We normalized biases in net intensity between the one fluorescent dye channel in a microarray by grobal normalization using its software. Analyzed data were selected by using MicroArray Data Analysis Tool (Filgen, Inc.)

source_name: gastric carcinoma, untreated

treatment_protocol: Cells were untreated for 72 h.

value: gastric carcinoma

value: stomach

value: KATO-III

value: 72 hours


title: Control condition replicate 2

description: Biological replicate 2 of 3. Control condition of 35S:AtMYB102-SRDX plant

tag: genotype/variation

tag: ecotype

tag: age


title: 1B6 EBV-positive Akata BL clone, 4hr starve, biological rep 3

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

institute: Louisiana State University Health Sciences Center-Shreveport

description: no additional information

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U95Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 3.0 using Affymetrix default analysis settings and global scaling with a target intensity value of 2500 as normalization method.

source_name: EBV-positive Akata  BL clone (1B6)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were seeded at a density fo 1x10^5 cells/ml in RPMI media containing 10% fetal bovine serum, 2 mM L-glutamine, 100 IU/ml penicillin and 100 μg/ml streptomycin and allowed to grow for 3 days.

extract_protocol: STAT60 extration of RNA was performed according to manufacturer's protocol (Tel-test).

treatment_protocol: The cells were transferred to media containing low serum (1% serum) for 4 hours prior to RNA harvest.

tag: disease state

value: Burkitt's lymphoma

tag: ebv status

value: EBV-positive

tag: treatment protocol

value: 4 hour serum starvation


title: 1B6 EBV-positive Akata BL clone, 4hr starve, biological rep 2

description: no additional information


title: 2A8 EBV-negative Akata BL clone,4hr starve, biological rep 1

description: no additional information

source_name: EBV-negative Akata BL clone (2A8)

value: EBV-negative


title: 2A8 EBV-negative Akata BL clone, 4hr starve, biological rep 3

description: no additional information


title: 2A8 EBV-negative Akata BL clone, 4hr starve, biological rep 2

description: no additional information


title: bb0647 mutant vs. wild-type (s7 B31-Cy3-H3-Cy5)

city: Dallas

first: zhiming

last: ouyang

state: TX

address: 6000 Harry Hines Blvd

department: Department of Microbiology

institute: UT Southwestern Medical Center

hyb_protocol: Cy3- and Cy5-labeled cDNA were mixed and further purified using the Qiaquick PCR purification kit (Qiagen, Valencia, CA). Formamide (Acros Organics, Belgium) and 4×RNA hybridization buffer (Amersham Biosciences, Piscataway, NJ) were added to the labeled probes, and the mixture was denatured by heating at 95°C for 5 minutes, cooled on ice for 1 minute and then applied to slides. Prior to hybridization, slides were pre-hybridized in a solution of 5xSSC (1×SSC = 0.15M sodium chloride/0.015M sodium citrate, pH 7), 0.1% SDS, and 0.1% bovine serum albumin (BSA) for 30 min at 55 oC.  Following pre-hybridization, slides were washed 5 times in distilled water, dipped in isopropanol, dried by centrifugation, and immediately used in the hybridization. After loading probes, slides were covered with lifter coverslips (Erie Scientific Company, Portsmouth, NH), placed into a humidified hybridization chamber (Ambion, Austin, TX), and the chamber was placed into a hybridization oven set at 50oC.  After hybridization overnight, slides were washed twice with 2×SSC/0.1% SDS for 15 min at 42oC, twice with 0.1×SSC/0.1% SDS for 15 min at room temperature, and twice with 0.1×SSC for 1 min at room temperature. Washed slides were then dried by centrifugation and scanned immediately.

scan_protocol: Hybridized slides were scanned on an Axon 4000B microarray scanner using GenePix Pro 6.1 (Molecular Devices, Sunnyvale, CA). Data then were analyzed with Acuity 4.0 (Molecular Devices), using ratio-based normalization method and a cutoff value of a 2-fold change.  Statistical analyses were performed using the one and two-sample significance test (p<0.05) in the Acuity program.

data_processing: Ratio based normalization, which is based on the premise hat most genes on the array will not be differentially expressed, and therefore the arithmetic mean of the ratios from every feature on a given array should be equal to 1. If the mean is not 1, a value is computed which represents the amount by which the ratio data should be scaled such that the mean returns to 1.

organism: Borreliella burgdorferi

source_name: B31 cDNA

label_protocol: cDNA was synthesized from 10 μg total RNA using Amino Allyl cDNA Labeling Kit (Ambion)

growth_protocol: three biological replicates of wild-type parental strain B. burgdorferi B317 and the mutant bb0647 were grown in BSK-H medium at 37 degree with 5% CO2.

extract_protocol: RNA was extracted  using the Trizol reagent (Invitrogen) according to the manufacturer’s protocol, folloed by genomic DNA digestion using Dnase I, and purified again using Rneasy Mini kit (Qiagen).

tag: genotype

source_name: bb0647 OY10/H3 cDNA

value: bb0647 mutant


title: bb0647 mutant vs. wild-type (s6 B31-cy5-H3-cy3)


title: 1B6 EBV-positive Akata BL clone, 4hr starve, biological rep 1

description: no additional information


title: bb0647 mutant vs. wild-type (S3 B31-Cy3-H3-Cy5)


title: bb0647 mutant vs. wild-type (s5 B31-Cy3-H3-Cy5)


title: bb0647 mutant vs. wild-type (s4 B31-cy5-H3-cy3)


title: KATO-III_181c_VS_CONT.txt

description: Human gastric cancer cell line with mock and pre-miR-181c

hyb_protocol: Standard Agilent protocol

scan_protocol: Agilent DNA Microarray scanner and Agilent scan control software

data_processing: Agilent Feature Extraction Software version 9.5.3

source_name: gastric carcinoma cell line, transfected with mock

label_protocol: Standard Agilent protocol

extract_protocol: Trizol and RNeasy Mini Elute Cleanup kit

treatment_protocol: KATO-III cells were transfected with mock using a Solution kit (Digital Bio) with a MicroPorator electroporation device (Digital Bio) according to the manufacturer’s instructions. Total RNA was extracted 24 h after transfection.

tag: properties

value: mixed, adherent and suspension.

tag: morphology

value: spherical

tag: protocol

value: mock transfection

source_name: gastric carcinoma cell line, transfected with miR-181c

treatment_protocol: KATO-III cells were transfected with 100 pmol of Pre-miR miRNA Molecules hsa-miR-181c (Ambion) using a Solution kit (Digital Bio) with a MicroPorator electroporation device (Digital Bio) according to the manufacturer’s instructions. Total RNA was extracted 24 h after transfection.

value: momiR-181c transfection


title: CD25 Hi CD8 T cells, Biological Replicate 3

description: Sorted CD25 Hi P14 CD8 T cells

source_name: Splenocytes

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

value: splenocytes

value: CD25 Hi CD8 T cells

value: Day 3.5


title: AD2_REP1_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58072.gif

label_protocol:
Approx RNA yield = 17 ug; Type of in-vitro transcription = Epicentre; Date performed = Mar-08; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD2 salt root; Date performed = 3/15/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD2 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"

tag: treatment

value: salt

tag: name

value: pima s7

tag: genome

tag: polyploid level

value: root

label_protocol:
Approx RNA yield = 10 ug; Date performed = Mar-08; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 3/15/2008; Tube label = AD2 no-salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD2 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"; Name = Rozaura; Extracted molecule = RNA

value: no-salt


title: AD2_REP1_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58071.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 6/11/2007 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 6/11/2007

source_name: AD1 no-salt leaf

label_protocol:
Approx RNA yield = 33 ug; Type of in-vitro transcription = Epicentre; Date performed = Jun-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 6/8/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 5/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD2 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"

tag: tissue type

value: leaf

source_name: AD1 salt leaf

label_protocol:
Approx RNA yield = 23 ug; Date performed = Jun-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 6/8/2007; Tube label = AD2 salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 5/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD2 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"; Name = Rozaura; Extracted molecule = RNA


title: intestine, ACD-infected, biol rep2

city: Boston

first: Amy

last: Ma

state: MA

address: 200 Longwood Ave D1-411

department: Microbiology

institute: Harvard Medical School

description:
ACD-2
V. cholerae strain also referred to as ATM-6, lacks background toxins rtxA hlyA hapA and the actin cross-linking domain (ACD) of vgrG-1.

hyb_protocol: Affymetrix Hybridization, Wash, Stain Kit.

scan_protocol: Gene Array Scanner 7000, Affymetrix Microarray Suite Software.

data_processing: Affymetrix Expression Console, RMA.

source_name: infected intestine, ACD, 4 hours

label_protocol: Affymetrix WT Terminal Labeling Kit.

extract_protocol: TriReagent (Invitrogen), per manufacturer's instructions.

treatment_protocol: 5-day-old infant CD1 mice were infected with 5 x 10^9 V. cholerae for 4 hours. Intestines were harvested and homogenized in TriReagent.

tag: strain

value: 5 days

tag: tissue

value: intestine

tag: v. cholerae infection

value: ACD

tag: infection time

value: 4 hours


title: panicle 3, Zhenshan 97, biological rep1, technical rep2

city: Wuhan

first: Weibo

last: Xie

state: Hubei

address: Luoshi Road

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

hyb_protocol: Microarray hybridization were conducted by the CapitalBio Corporation (Beijing, China) according to the Affymetrix standard protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The probe intensity files (.cel files) for expression profiles were read into R. Background correction, quantile normalization and summarization were performed using the RMA method in Bioconductor affy package.

organism: Oryza sativa Indica Group

source_name: developing panicle with length between 10 and 15 mm, Zhenshan 97

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

growth_protocol: Rice seeds were soaked in fresh water until germination. Then the germinated rice seeds were planted in a seed bed in mid-May, and seedling of 20 days old were transplanted to the field and managed according to normal agricultural conditions in the experimental farm of Huazhong Agricultural University, Wuhan, China.

extract_protocol: Total RNA extraction was performed using Trizol, according to the manufacturer's instructions.

treatment_protocol: Untreated.

tag: subspecies

value: indica

tag: variety

value: Zhenshan 97


title: panicle 2, Zhenshan 97, biological rep2, technical rep1

source_name: developing panicle with length between 3 and 5 mm, Zhenshan 97


title: panicle 2, Zhenshan 97, biological rep3, technical rep2


title: intestine, V52-infected, biol rep1

description:
V52-1
V. cholerae strain also referred to as ATM-1, lacks background toxins rtxA hlyA hapA.

source_name: infected intestine, V52, 4 hours

tag: age


title: intestine, mock-infected, biol rep1

description:
mock-1
Mock group infected with LB.

source_name: infected intestine, mock, 4 hours

value: mock


title: panicle 2, Zhenshan 97, biological rep2, technical rep2


title: intestine, ACD-infected, biol rep3

description:
ACD-3
V. cholerae strain also referred to as ATM-6, lacks background toxins rtxA hlyA hapA and the actin cross-linking domain (ACD) of vgrG-1.


title: intestine, mock-infected, biol rep2

description:
mock-2
Mock group infected with LB.


title: intestine, mock-infected, biol rep3

description:
Mock group infected with LB.
mock-3


title: intestine, V52-infected, biol rep2

description:
V52-2
V. cholerae strain also referred to as ATM-1, lacks background toxins rtxA hlyA hapA.


title: panicle 3, Zhenshan 97, biological rep2, technical rep2


title: panicle 3, Zhenshan 97, biological rep3, technical rep1


title: intestine, V52-infected, biol rep3

description:
V52-3
V. cholerae strain also referred to as ATM-1, lacks background toxins rtxA hlyA hapA.


title: panicle 1, Zhenshan 97, biological rep3, technical rep2

source_name: developing panicle with length less than 1mm, Zhenshan 97


title: panicle 3, Zhenshan 97, biological rep3, technical rep2


title: panicle 2, Zhenshan 97, biological rep1, technical rep2


title: panicle 3, Zhenshan 97, biological rep1, technical rep1


title: panicle 2, Zhenshan 97, biological rep3, technical rep1


title: panicle 1, Zhenshan 97, biological rep1, technical rep2


title: panicle 1, Zhenshan 97, biological rep2, technical rep1


title: panicle 3, Zhenshan 97, biological rep2, technical rep1


title: intestine, ACD-infected, biol rep1

description:
ACD-1
V. cholerae strain also referred to as ATM-6, lacks background toxins rtxA hlyA hapA and the actin cross-linking domain (ACD) of vgrG-1.


title: panicle 2, Zhenshan 97, biological rep1, technical rep1


title: panicle 1, Zhenshan 97, biological rep3, technical rep1


title: Biological replicate 3 - epi vs mes (before vs after EMT)

city: Cambridge

first: Cristian

last: Brocchieri

address: Hills Road

country: United Kingdom

institute: University of Cambridge

description: Analysis used epithelial OSE amplified RNA (control) for comparison to the mesenchymal (experimental) taken after EMT induced by changing the culture conditions from 2.5% FBS to 15% FBS for one week.

hyb_protocol: The Hybridisation kit (Agilent, 5184-3468) was used, following the manufacturer's instructions. The hybridisation was conducted with the dye-swap technique, and for each slide were used 0.5mg of Cy3- or Cy5-labelled cRNA from each of the two samples.

scan_protocol: The Agilent G2565A Microarray Scanner with the Agilent G2567AA Feature Extraction Software  were used.

data_processing: The data were background corrected using the method called minimum in the Limma R library for microarray data analysis within R. In order to normalise all arrays in the same manner, we used a global LOWESS fit to normalise each array. The linear model functionality in Limma was used to combine the replicate array data for the comparison (epithelial versus mesenchymal): the linear model output gives an overall estimate for the differential expression between the two samples for each gene.

source_name: epithelial OSE in 2.5% FBS, before EMT

label_protocol: The amplification of the extracted RNA was made using the Amino Allyl MessageAmp aRNA kit (Ambion, 1752), following the manufactirer's instructions, starting from 4ug of total RNA per sample. The labelling was made using Cy3 Mono-Reactive Dye (Amersham, PA23001) and Cy5 Mono-Reactive Dye (Amersham, PA25001). RNA and Dye concentrations for each sample were determined using the Vysis Nanodrop.

growth_protocol: Superovulation was induced in virgin female C57/Bl6 mice with the following scheme: day 0: administration of Pregnant mare's serum gonadotropin (PMSG); day 1: administration of hCG and mating with stud male; day 3: female culled 12 hours post-coitum and ovaries collected.  The external capsula was removed, the ovaries were dissected and the cells were dissociated by treating them for 10 minutes in collagenase + dispase, then 2 X 10 minutes in trypsin. The OSE cells were then cultured in 25% DMEM, 25% F12, 25% MCDB-105, 25% 199 medium in the absence of antibiotics.

extract_protocol: The cells at 80% confluence were collected by cell scraping in ice cold PBS, spun down for 5 minutes at 1000 rpm at 4deg, snap frozen and stored at -80deg. Total RNA was extracted using the Macherey-Nagel RNA L Kit, following the manufacturer's recommendations, which includes a DNAseI treatment step. Elution was made in RNAse-free wtaer. The RNA quality was checked using the Agilent 2100 bioanalyzer. The RNA concentration was measured using the Vysis Nanodrop.

treatment_protocol: To maintain the epithelial phenotype, the cells were cultured in 2.5% FBS. To induce the mesenchymal phenotype, they were cultured in 15% FBS for one week.

tag: cell type

value: OSE cells

source_name: mesenchymal OSEcultured  in 15% FBS for one week (I.e. after EMT)


title: Biological replicate 2 - epi vs mes (before vs after EMT)


title: Biological replicate 1 - epi vs mes (before vs after EMT)


title: seedling 2, Zhenshan 97, biological rep2, technical rep2

source_name: seedling at trefoil stage, Zhenshan 97


title: seedling 2, Zhenshan 97, biological rep2, technical rep1


title: seedling 2, Zhenshan 97, biological rep3, technical rep1


title: 60 min post-1.2uM Mitomycin C 4098316059_D_MMC2_healthy control_Pool 3

city: Brisbane

first: Logan

last: Walker

address: PO RBH

institute: Queensland Institute of Medical Research

description: Equal quantities of RNA pooled from 3 samples

hyb_protocol: Standard Illumina protocols were followed for hybridisation, washing and staining of Human-Ref8 V2 Beadchips.

scan_protocol: Slides were scanned with an Illumina Beadarray reader at a factor of 2

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

source_name: Lymphoblastoid cell line, 60 min post-1.2uM Mitomycin C

label_protocol: 450 ng of RNA was amplified with the Illumina Totalprep RNA amplification kit (Applied Biosystems)

growth_protocol: lymphoblastoid cell lines were removed from liquid nitrogen and grown for a minimum of 1 week prior to treatment. LCLs were cultered in RPMI 1640 media with 10% serum supreme, and 1% penicillin-streptomycin

extract_protocol: RNA was extracted immediately after the post-treatement culture period using an RNeasy mini kit (Qiagen)

treatment_protocol: 5 hrs prior to treatment, cells were normalised to 500,000 cells/ml. 5 ml cells were untreated, irradiated, or treated with mitomycin C.

tag: gender

value: Female

tag: cell line

value: EBV-transformed lymphoblastoid cell line

tag: patient group

value: Healthy control

tag: pool number

value: Pool 3

tag: pooled sample #1 mutation

value: Healthy Control#34

tag: pooled sample #2 mutation

value: Healthy Control#35

tag: pooled sample #3 mutation

value: Healthy Control#36

value: 1.2 uM Mitomycin C

tag: post-treatment culture period

value: 60 min


title: 120 min post-1.2uM Mitomycin C 4098316059_F_MMC4_healthy control_Pool 3

source_name: Lymphoblastoid cell line, 120 min post-1.2uM Mitomycin C

tag: treatment

value: 120 min


title: seedling 1, Zhenshan 97, biological rep2, technical rep1

source_name: seedling, 3 days after sowing, Zhenshan 97


title: panicle 1, Zhenshan 97, biological rep1, technical rep1


title: seedling 2, Zhenshan 97, biological rep3, technical rep2


title: seedling 2, Zhenshan 97, biological rep1, technical rep2


title: untreated 4098316059_A_untreated_healthy control_Pool 3

source_name: Lymphoblastoid cell line, untreated

value: no treatment


title: seedling 1, Zhenshan 97, biological rep3, technical rep2


title: seedling 1, Zhenshan 97, biological rep2, technical rep2


title: seedling 1, Zhenshan 97, biological rep3, technical rep1


title: endosperm 3, Zhenshan 97, biological rep2

source_name: endosperm, 21 days after pollination, Zhenshan 97


title: seedling 1, Zhenshan 97, biological rep1, technical rep2


title: endosperm 2, Zhenshan 97, biological rep2

source_name: endosperm, 14 days after pollination, Zhenshan 97


title: 120 min post-0.4uM Mitomycin C 4098316059_E_MMC3_healthy control_Pool 3

source_name: Lymphoblastoid cell line, 120 min post-0.4uM Mitomycin C

value: 0.4 uM Mitomycin C


title: endosperm 3, Zhenshan 97, biological rep1


title: seedling 1, Zhenshan 97, biological rep1, technical rep1


title: leaf 4, Zhenshan 97, biological rep1

source_name: flag leaf, 14 days after pollination, Zhenshan 97


title: endosperm 2, Zhenshan 97, biological rep1


title: endosperm 1, Zhenshan 97, biological rep2

source_name: endosperm, 7 days after pollination, Zhenshan 97


title: spikelet, Zhenshan 97, biological rep2

source_name: spikelet, 3 days after flowering, Zhenshan 97


title: 120 min post-0.4uM Mitomycin C 4098316057_E_MMC3_healthy control_Pool 2

value: Pool 2

value: Healthy Control#31

value: Healthy Control#32

value: Healthy Control#33


title: palea/lemma, Zhenshan 97, biological rep1

source_name: palea/lemma, just before heading date, Zhenshan 97

value: indica

value: Zhenshan 97


title: untreated 4098316057_A_untreated_healthy control_Pool 2

value: Female

value: EBV-transformed lymphoblastoid cell line


title: 60 min post-1.2uM Mitomycin C 4098316057_D_MMC2_healthy control_Pool 2

value: Healthy control


title: 60 min post-0.4uM Mitomycin C 4098316059_C_MMC1_healthy control_Pool 3

source_name: Lymphoblastoid cell line, 60 min post-0.4uM Mitomycin C

value: Pool 3

value: Healthy Control#34

value: 0.4uM Mitomycin C


title: palea/lemma, Zhenshan 97, biological rep2


title: panicle 5, Zhenshan 97, biological rep2

source_name: mature panicle, heading stage, Zhenshan 97


title: stamen, Zhenshan 97, biological rep2

source_name: stamen, just before heading date, Zhenshan 97


title: leaf 4, Zhenshan 97, biological rep2


title: 60 min post-10 Gy IR 4098316059_B_IR_healthy control_Pool 3

source_name: Lymphoblastoid cell line, 60 min post-10 Gy IR

value: Healthy Control#35

value: Healthy Control#36

value: 10 Gy gamma radiation


title: 120 min post-1.2uM Mitomycin C 4098316057_F_MMC4_healthy control_Pool 2

value: 1.2 uM Mitomycin C

value: 120 min


title: endosperm 1, Zhenshan 97, biological rep1


title: seedling 2, Zhenshan 97, biological rep1, technical rep1


title: spikelet, Zhenshan 97, biological rep1


title: 60 min post-0.4uM Mitomycin C 4098316057_C_MMC1_healthy control_Pool 2

value: Pool 2

value: 60 min


title: stamen, Zhenshan 97, biological rep1


title: stem 2, Zhenshan 97, biological rep1

source_name: stem, heading stage, Zhenshan 97


title: 60 min post-10 Gy IR 4098316057_B_IR_healthy control_Pool 2

value: Healthy Control#31

value: Healthy Control#32


title: stem 2, Zhenshan 97, biological rep2

value: indica


title: panicle 5, Zhenshan 97, biological rep1

value: Zhenshan 97


title: leaf 3, Zhenshan 97, biological rep1

source_name: flag leaf, just before heading date, Zhenshan 97


title: stem 1, Zhenshan 97, biological rep1

source_name: stem, just before heading date, Zhenshan 97


title: leaf 3, Zhenshan 97, biological rep2


title: stem 1, Zhenshan 97, biological rep2


title: leaf 2, Zhenshan 97, biological rep2

source_name: mature leaf blade of the rice plants with developing panicle whose length is between 40 and 50 mm, Zhenshan 97


title: sheath 2, Zhenshan 97, biological rep1

source_name: mature leaf sheath of the rice plants with developing panicle whose length is between 40 and 50 mm, Zhenshan 97


title: 60 min post-0.4uM Mitomycin C 4098316006_C_MMC1_healthy control_Pool 1

value: Female

value: Pool 1

value: Healthy Control#28

value: Healthy Control#29

value: Healthy Control#30


title: 120 min post-1.2uM Mitomycin C 4098316006_F_MMC4_healthy control_Pool 1

source_name: Lymphoblastoid cell line, 120 min post-1.2uM Mitomycin C

value: EBV-transformed lymphoblastoid cell line

value: Healthy control


title: 120 min post-0.4uM Mitomycin C 4098316006_E_MMC3_healthy control_Pool 1

value: 0.4 uM Mitomycin C


title: leaf 2, Zhenshan 97, biological rep1


title: sheath 1, Zhenshan 97, biological rep1

source_name: mature leaf sheath of the rice plants with developing panicle whose length is less than 1mm, Zhenshan 97


title: panicle 4, Zhenshan 97, biological rep1

source_name: developing panicle with length between 40 and 50mm, Zhenshan 97


title: 60 min post-1.2uM Mitomycin C 4098316006_D_MMC2_healthy control_Pool 1

source_name: Lymphoblastoid cell line, 60 min post-1.2uM Mitomycin C


title: leaf 1, Zhenshan 97, biological rep2

source_name: mature leaf blade of the rice plants with developing panicle whose length is less than 1mm, Zhenshan 97


title: leaf 1, Zhenshan 97, biological rep1


title: sheath 2, Zhenshan 97, biological rep2


title: untreated 4098316006_A_untreated_healthy control_Pool 1

source_name: Lymphoblastoid cell line, untreated

value: no treatment


title: root, Zhenshan 97, biological rep2

source_name: root of the seedling with 2 tillers, Zhenshan 97


title: 60 min post-10 Gy IR 4098316006_B_IR_healthy control_Pool 1

value: 10 Gy gamma radiation


title: root, Zhenshan 97, biological rep1


title: shoot, Zhenshan 97, biological rep1

source_name: shoot of the seedling with 2 tillers, Zhenshan 97


title: untreated 4098316060_C_untreated_non-BRCA1/2_Pool 3

value: non-BRCA1/2 mutation

value: Pool 3


title: shoot, Zhenshan 97, biological rep2


title: E_1, exon-level analysis

first: Jianlong

last: Sun

address: 1 Blackfan Street

department: Hematology/Oncology

institute: Boston Children's Hospital

description: Exon RMA expression value derived from Arrayassist software (Stratagene); core-exon analysis; genome build hg18.

hyb_protocol: Hybridization service was provided by Expression Analysis Inc. (Durham, NC).  Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) according to manufacturer's instructions.

scan_protocol: Scan service was provided by Expression Analysis Inc. (Durham, NC) and was performed according to manufacturer's instructions (Affymetrix).

data_processing: The exon array data were analyzed using ArrayAssist (Stratagene) and GeneSpring GX 10 (Agilent) with default settings.  The CEL files were imported and the triplicates from the same siRNA treatment were assigned into the same group.  Probe sets at the Core level were summarized by using the ExonPLIER algorithm.  Quantile normalization was performed and antigenomic probes were used as background probes.  For variance stabilization, the number of 16 was added to probe set intensity values before transformation to a log2 scale.  Once the summarized dataset was obtained, a series of analysis were applied to assess the quality of the samples, hybridization procedures, and actual data. Through these analyses, one of the siNELF-B samples was found to be an outlier, and data from the three arrays of the siNELF-B group were therefore excluded from subsequent analysis.  Probe sets below the noise level was filtered out by the Detection Above Background (DABG) analysis.  A transcript was retained if one of its probe sets had p-value < 0.05 in at least 6 of the remaining 12 arrays.  Gene level expression was estimated with the same algorithm from all probe sets in each transcript.  A splicing index was then calculated for all probe sets using siControl samples as the reference group.  Pairwise analysis was conducted to compare all groups with the siControl reference group using unpaired T test.  Transcripts that were commonly changed in siNELF-A, -C, and –E groups with fold change > 1.5 and p-value < 0.05 were selected as the differentially expressed genes.  And probe sets with absolute value of differential splicing index > 1 and p-value < 0.05 were selected as the alternatively spliced probe sets.  The list of probe sets with significant splicing index was further filtered to retain those with at least two non-overlapping probes and unique hybridization pattern.

source_name: breast cancer cell line, siNELF-E

label_protocol: Sample label service was provided by Expression Analysis Inc. (Durham, NC).  1 ug of total RNA from each sample was used to generate labeled probes for array hybridization.  Quality of isolated RNA was first measured by Bioanalyzer QC Assay (Agilent).  Ribosomal RNA was then removed with the RiboMinus Kit (Invitrogen) and the reduction efficiency was verified by capillary electrophoresis.  Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: siRNA transfected T47D cells are grown in DMEM with 10% FBS.

extract_protocol: Total RNA is extracted with Trizol reagent (Invitrogen) following manufacturer's protocol.

treatment_protocol: Transfection of the siRNA duplex into T47D cells was carried out by using RNAiMAX reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions.  Briefly, 1.5 x 10^6 cells in a 10 cm culture dish were transfected with 10 nM of siRNA duplex with 15 ul of RNAiMAX reagent.  Growth medium was replenished 48 hours after transfection, and cells were allowed to grow for additional 48 hours before harvest.

value: breast cancer

tag: sirna

value: siNELF-E


title: E_3, exon-level analysis


title: 60 min post-0.4uM Mitomycin C 4098316060_E_MMC1_non-BRCA1/2_Pool 3

source_name: Lymphoblastoid cell line, 60 min post-0.4uM Mitomycin C

value: 0.4uM Mitomycin C

value: 60 min


title: C_3, exon-level analysis

source_name: breast cancer cell line, siNELF-C

value: siNELF-C


title: radicle 2, Zhenshan 97, biological rep2

source_name: radicle, dark, Zhenshan 97

value: indica

value: Zhenshan 97


title: seedling 3, Zhenshan 97, biological rep1

description:
Z14A
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone NAA treatment

source_name: seedling at trefoil stage, treated by NAA, Zhenshan 97


title: 120 min post-0.4uM Mitomycin C 4098316060_G_MMC3_non-BRCA1/2_Pool 3

source_name: Lymphoblastoid cell line, 120 min post-0.4uM Mitomycin C

value: Female

value: 120 min


title: 60 min post-10 Gy IR 4098316060_D_IR_non-BRCA1/2_Pool 3

source_name: Lymphoblastoid cell line, 60 min post-10 Gy IR


title: 120 min post-1.2uM Mitomycin C 4098316060_H_MMC4_non-BRCA1/2_Pool 3

value: 1.2 uM Mitomycin C


title: 60 min post-1.2uM Mitomycin C 4098316060_F_MMC2_non-BRCA1/2_Pool 3

value: EBV-transformed lymphoblastoid cell line


title: seedling 3, Zhenshan 97, biological rep2

description:
Z14B
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone NAA treatment


title: radicle 2, Zhenshan 97, biological rep1


title: seedling 5, Zhenshan 97, biological rep1

description:
Z16A
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone KT treatment

source_name: seedling at trefoil stage, treated by KT, Zhenshan 97


title: seedling 4, Zhenshan 97, biological rep1

description:
Z15A
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone GA3 treatment

source_name: seedling at trefoil stage, treated by GA3, Zhenshan 97