title: myo5:9Myc IP JCY39-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71267.gif

source_name: aa-amplified reference, whole cell extract

source_name: IP of JCY39 (myo5:9Myc strain), aa-amplified


title: B_Jun_fem_rep2

status: Public on Jan 27 2012

type: RNA

city: Barcelona

first: Anna

last: Navarro Cuenca

state: Barcelona

address: C/Jordi Girona 18-26

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of the fragmentation mixture was added to 25 ul of GEx hybridization buffer. Final volumen of 40ul of each mix was dispensed into a costum array for D. Polymorpha (GPL15152) and placed in a rotating Agilent hybridization oven for 17 hours at 65°C After the hybridization, microarrays slides were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and a last step of 1 minute in acid nitril bath, then dried and placed in a holder.

scan_protocol: The slides were scanned using Agilent G2565CA and signals were extracted using the Agilent Feature Extraction Software v9.5.

data_processing: Normalized signal intensity using Loess normalization protocol by JMP Software v5.

molecule: total RNA

organism: Dreissena polymorpha

label_protocol: The preparations of the samples were performed according the Agilent One-Color Microarray –Based Gene Expression Analysis protocol using Cyanine 3 (Cy3) dye. A total 500ng of total RNA for each sample was used as starter material. After the amplification, labeling and purification procedure, samples were evaluated for yield and effectiveness of Cy3 dye incorporation using the NanoDrop spectrophotometer..

extract_protocol: Total RNA was isolated from the samples using Trizol reagent® protocol (Invitrogene). RNA concentration was measured by spectrophotometric absorption at 260 nm in a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Delaware, DE) and it was treated with DNAseI to remove genomic DNA contamination. RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). The samples that did not show degradation were used in the process of microarray analysis

tag: tissue

value: Half Body

tag: gender

value: female

tag: season


title: B_Jun_male_rep1

value: male


title: B_Feb_male_rep1


title: Myo4:9Myc IP rep #1 w/ 2 ug/ml LatB lysis Bf

city: Stanford

first: Jason

last: Casolari

state: CA

address: 279 Campus Drive

department: Dept. of Biochemistry

country: USA

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74217.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4200A

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)

organism: Saccharomyces cerevisiae

source_name: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: IP 9E11 anti-c-myc, Dynal pan-mouse IgG beads, JCY 19, amino-allyl amplified

extract_protocol: Latrunculin B purification of motors; Immunopurifications of 9Myc- or GFP-tagged motor proteins from cultures treated with latrunculin B were carried out in a manner similar to that described for crosslinking cells with some modifications.  250 ml cultures were grown to mid-log phase, harvested by centrifugation, and washed with 25 mls and then 10 mls of cold Tris-buffered saline.  Pellets were placed on ice and resuspended in 600 ul of lysis buffer with the addition of 2 ug/ml latrunculin B, then mechanically disrupted by a beadbeater.  Lysates were cleared by centrifugation at 4,000g for 1 min at 4 oC, the volume was brought up to 1.4 ml using lysis buffer, and 200 ul was removed for reference RNA isolation.  100 ul of pan-mouse IgG Dynal magnetic beads pre-incubated with antibody (see above) was combined with the remaining lysate and incubated for 4 h at 4 oC with gentle rotation.  Washes were performed as described above.Protein/RNA complexes were eluted with elution buffer (see above), incubation at 70 oC for 10 min, and vigorous vortexing.  Immunopurified and total lysate RNA were extracted with phenol:chloroform:isoamyl alcohol (25:24:1; Invitrogen) twice and chloroform once using 2.0 ml Phase Lock Heavy tubes (Eppendorf) followed by ethanol precipitation in the presence of 7.5 ug Glycoblue (Ambion) as carrier

tag: compound based treatment

value: LatB

tag: tag used for ip


title: Myo4:9Myc IP rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74445.gif

value: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA


title: B_Feb_fem_rep1


title: Myo5:9Myc IP rep #2 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74463.gif

source_name: whole cell extract, decrosslinked, amino-allyl amplified RNA

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 39, amino-allyl amplified

value: formaldehyde


title: Myo1:GFP IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76105.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 49, amino-allyl amplified

value: GFP


title: Gon_male_non treated_rep2

source_name: Gonad_male_non treated

label_protocol: The preparations of the samples were performed according the Agilent One-Color Microarray –Based Gene Expression Analysis protocol using Cyanine 3 (Cy3) dye. A total 500ng of total RNA for each tissue and 200 ng for larvae was used as starter material. After the amplification, labeling and purification procedure, samples were evaluated for yield and effectiveness of Cy3 dye incorporation using the NanoDrop spectrophotometer.

value: Gonad

value: Male

tag: age


title: Gon_female_non treated_rep1

source_name: Gonad_female_non treated

value: Female


title: DG_non treated_rep1

source_name: Digestive gland_female_non treated

value: Digestive gland


title: Gill_non treated_rep2

source_name: Gills_female_non treated

value: Gill


title: Gon_male_non treated_rep1


title: HB_female_non treated_rep1

source_name: Half body_female_non treated


title: HB_male_non treated_rep1

source_name: Half body_male_non treated


title: DG_non treated_rep2


title: myo5:9Myc IP JCY39-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71266.gif

value: aa-amplified reference, whole cell extract


title: myo3-1:9Myc IP JCY38-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71274.gif

source_name: IP of JCY38 (myo3:9Myc strain), aa-amplified


title: Las17:GFP IP rep #2 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74452.gif

value: whole cell extract, decrosslinked, amino-allyl amplified RNA

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 44, amino-allyl amplified


title: mock IP (BY4741) rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76090.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 12, amino-allyl amplified


title: mock 9Myc IP JCY18-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71250.gif

source_name: mock IP of JCY18 (untagged strain)


title: Larv_24h_non_treated_rep2

source_name: Larvae_24h pf non treated

value: Larvae

value: 24h pf


title: Larv_24h_non_treated_rep1


title: Myo4:GFP IP 10' crosslink, Dynal beads

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72449.gif

source_name: whole cell extract, amino-allyl amplified

source_name: Myo4:GFP IP, amino-allyl amplified


title: Myo4:9Myc IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74218.gif

source_name: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA

source_name: IP 9E11 anti-c-myc, Dynal pan-mouse IgG beads, JCY 19, amino-allyl amplified


title: Vrp1:GFP IP rep #3 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74451.gif

source_name: whole cell extract, decrosslinked, amino-allyl amplified RNA

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 43, amino-allyl amplified


title: mock IP #3, 20' crosslink, Dynal beads

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72430.gif

value: whole cell extract, amino-allyl amplified

source_name: mock IP, amino-allyl amplified


title: Myo4:GFP IP 20' crosslink, Dynal beads

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72437.gif


title: Gill_non treated_rep1


title: Myo3:9Myc IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74227.gif

source_name: IP 9E11 anti-c-myc,  Dynal pan-mouse IgG beads, JCY 38, amino-allyl amplified


title: myo5:9Myc IP JCY39-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71268.gif

source_name: aa-amplified reference, whole cell extract

source_name: IP of JCY39 (myo5:9Myc strain), aa-amplified


title: Smy1:GFP, 20' crosslink formaldehyde, BUBBLE

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72348.gif

source_name: IP from JCY34, amino-allyl amplified


title: Smy1:GFP IP rep #3 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74443.gif

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 34, amino-allyl amplified


title: Myo2:GFP IP rep #3 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74449.gif

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 42, amino-allyl amplified


title: Smy1:GFP IP 5' crosslink, Dynal beads

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72439.gif

source_name: Smy1:GFP IP, amino-allyl amplified


title: Myo1:GFP IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76104.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 49, amino-allyl amplified


title: Las17:GFP IP rep #3 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74453.gif

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 44, amino-allyl amplified


title: myo2-9Myc IP vs dep supe w EDTA from fresh cells IP rep1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83762.gif

source_name: 8 ug of RNA from dep supe as reference

value: 8 ug of RNA from dep supe as reference

source_name: IP anti-9Myc 9E11, Dynal pan-mouse IgG beads, JCY 304 fresh cells, aa-amplified


title: myo2-9Myc IP vs dep supe w EDTA from fresh cells IP rep2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83766.gif


title: Myo1:GFP IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76103.gif


title: Myo1:GFP IP rep #3 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74459.gif

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 49, amino-allyl amplified


title: Kip3:GFP IP rep #2 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74447.gif

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 41, amino-allyl amplified


title: myo2-GFP IP vs dep supe w EDTA from fixed cells IP rep1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83771.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 42 fixed cells, aa-amplified


title: myo2-9Myc IP vs dep supe w EDTA from fixed cells IP rep1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83773.gif

source_name: IP anti-9Myc 9E11, Dynal pan-mouse IgG beads, JCY 304 fixed cells, aa-amplified


title: mock IP (BY4741) rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76088.gif

source_name: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 12, amino-allyl amplified


title: Myo3:9Myc IP vs dep supe plus EDTA fresh cells high salt washes rep1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87061.gif

source_name: 8 ug IP anti-Myc 9E11, Dynal pan-mouse IgG beads, JCY 38, aa-amplified


title: Smy1:GFP IP rep #2 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74425.gif

source_name: whole cell extract, decrosslinked, amino-allyl amplified RNA


title: Myo2:GFP IP rep #1 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74223.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, decrosslinked, JCY 42, amino-allyl amplified


title: Myo3:9Myc IP vs dep supe plus EDTA fresh cells high salt washes rep2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87062.gif


title: myo2-GFP IP vs dep supe w EDTA from fixed cells IP rep2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83772.gif


title: B_Jun_fem_rep1

value: Half Body

value: female


title: Myo4:9Myc IP #8 20' crosslink, Dynal beads

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72433.gif

source_name: whole cell extract, amino-allyl amplified

source_name: Myo4:9Myc IP, amino-allyl amplified


title: HPV52.1

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v9.5.1 (Agilent Technologies) using the Agilent CGH-v4_95 protocol with default settings

data_processing: Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.

molecule: genomic DNA

organism: Homo sapiens

source_name: Cervical tissue, microdissected

label_protocol: DNA labeling protocol according to Enzo Life Sciences.

extract_protocol: Laser capture microdissection was performed on haematoxylin stained tissue section to obtain the dysplastic cells. Tissues were incubated overnight 37'C in 1M NaSCN. Subsequently, samples were treated with proteinase K for 5 days. DNA was extracted using the DNA Qiagen micro kit (Qiagen).

tag: Stage

value: high-grade cervical intraepithelial neoplasia, HPVtype 52

source_name: Amplified FFPE cervical DNA from 5 individuals

value: normal cervix


title: myo2-9Myc IP vs dep supe w EDTA from fixed cells IP rep2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83774.gif

value: formaldehyde


title: HPV58.2

value: high-grade cervical intraepithelial neoplasia, HPVtype 58


title: HPV58.1


title: Smy1:GFP IP rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76113.gif

value: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 34, amino-allyl amplified

value: LatB

value: GFP


title: HPV52.2


title: HPV45.4

value: high-grade cervical intraepithelial neoplasia, HPVtype 45


title: Myo3:GFP IP vs. WCE, + LatB, rep3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78163.gif

source_name: RNA from WCE (total lysate, pre-IP) as ref

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 50, aa-amplified


title: HPV45.1


title: HPV51.1

value: high-grade cervical intraepithelial neoplasia, HPVtype 51


title: HPV45.2


title: HPV45.3


title: Myo2:GFP IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76096.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 42, amino-allyl amplified


title: HPV33.1

value: high-grade cervical intraepithelial neoplasia, HPVtype 33


title: Dyn1:GFP IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76131.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 59, amino-allyl amplified


title: Smy1:GFP IP, 10' crosslinked formaldehyde, anti-GFP monoclonal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72347.gif

source_name: IP from JCY34, amino-allyl amplified


title: Kar3:GFP IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76120.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 46, amino-allyl amplified


title: Myo5:9Myc IP rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74435.gif

source_name: IP 9E11 anti-c-myc, Dynal pan-mouse IgG beads, JCY 39, amino-allyl amplified


title: HPV31.13

value: high-grade cervical intraepithelial neoplasia, HPVtype 31


title: Myo4:GFP IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76094.gif

source_name: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 33, amino-allyl amplified


title: Myo2:GFP IP rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76099.gif


title: Kar3:GFP IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76119.gif


title: HPV31.14


title: HPV31.9


title: HPV31.6


title: HPV31.8


title: HPV31.10


title: HPV31.5


title: HPV31.12


title: HPV31.11


title: HPV31.7


title: HPV31.3


title: Smy1:GFP IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76111.gif


title: Myo5:GFP IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76100.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 45, amino-allyl amplified


title: Myo2:GFP IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76097.gif


title: Dyn1:GFP IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76132.gif


title: HPV31.4


title: myo2-GFP IP vs dep supe w EDTA from fresh cells IP rep1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83761.gif

source_name: 8 ug of RNA from dep supe as reference

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 42 fresh cells, aa-amplified


title: kip2:9Myc IP JCY36-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71260.gif

source_name: aa-amplified reference, whole cell extract

source_name: IP of JCY36 (kip2:9Myc strain), aa-amplified


title: HPV31.2

description: Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

source_name: Cervical tissue, microdissected


title: Kip1:GFP IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76128.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 57, amino-allyl amplified


title: Myo5:9Myc IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74219.gif


title: Smy1:9Myc IP (#9) with 9E11, crosslinked 20' formaldehyde, Dynal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72345.gif

source_name: whole cell extract, amino-allyl amplified

source_name: IP from JCY31, amino-allyl amplified


title: Myo4:9Myc IP #7 20' crosslink, Dynal beads

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72432.gif

source_name: Myo4:9Myc IP, amino-allyl amplified


title: HPV18.2

value: high-grade cervical intraepithelial neoplasia, HPVtype 18

source_name: Amplified FFPE cervical DNA from 5 individuals


title: HPV31.1


title: Myo5:9Myc IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74220.gif


title: HPV16.16

value: high-grade cervical intraepithelial neoplasia, HPVtype 16


title: HPV18.3


title: Kip2:GFP IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76124.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 51, amino-allyl amplified


title: Kar3:GFP IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76118.gif


title: HPV18.1


title: HPV16.15


title: HPV16.14


title: Kip3:GFP IP rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76117.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 41, amino-allyl amplified


title: HPV16.11


title: Kip1:GFP IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76126.gif


title: HPV16.10


title: HPV16.9


title: Myo4:9Myc IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74431.gif

source_name: IP 9E11 anti-c-myc, Dynal pan-mouse IgG beads, JCY 19, amino-allyl amplified


title: Kip3:GFP IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76115.gif


title: HPV16.12


title: Myo3:9Myc IP with 9E11, crosslinked 20' formaldehyde, Dynal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72341.gif

value: whole cell extract, amino-allyl amplified

source_name: IP from JCY38, amino-allyl amplified


title: Vrp1:GFP IP rep #2 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74450.gif

source_name: whole cell extract, decrosslinked, amino-allyl amplified RNA

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 43, amino-allyl amplified


title: HPV16.8


title: HPV16.7


title: HPV16.6


title: Kip3:GFP IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76116.gif

source_name: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA


title: myo3:9Myc IP JCY38-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71264.gif

value: aa-amplified reference, whole cell extract

source_name: IP of JCY38 (myo3:9Myc strain), aa-amplified


title: mock IP (BY4741) rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76091.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 12, amino-allyl amplified


title: HPV16.5

description: Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: Myo2:GFP IP vs. dep supe, + LatB, rep2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78146.gif

source_name: RNA from depleted supe as ref

value: RNA from depleted supe as ref

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 42, aa-amplified


title: Myo4:9Myc IP (#6) with 9E11, crosslinked 20' formaldehyde, Dynal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72344.gif

source_name: IP from JCY19, amino-allyl amplified


title: Kip3:GFP IP rep #1 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74446.gif

value: whole cell extract, decrosslinked, amino-allyl amplified RNA

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 41, amino-allyl amplified


title: HPV16.13

source_name: Cervical tissue, microdissected


title: HPV16.1


title: Myo2:GFP IP rep #2 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74224.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, decrosslinked, JCY 42, amino-allyl amplified


title: Dyn1:GFP IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76130.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 59, amino-allyl amplified


title: Smy1:9Myc IP (#10) with 9E11, crosslinked 20' formaldehyde, Dynal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72346.gif

source_name: whole cell extract, amino-allyl amplified

source_name: IP from JCY31, amino-allyl amplified


title: 1 KO 500

first: Jose

last: Aramburu

address: Carrer Doctor Aiguader 88

department: Experimental and Health Sciences

institute: Universitat Pompeu Fabra

description: Gene expression data from Mouse Embryonic Fibroblasts

hyb_protocol: Sample was hybridized to Mouse Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed using the RMA algorithm and then SAM was applied to calculate significant differential expression between samples using R 2.11.1 and GEOsubmission 1.0.

label: Biotin

organism: Mus musculus

source_name: Total RNA from Mouse Embryonic Fibroblasts NFAT5 knock-out 5.1

label_protocol: 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

extract_protocol: RNeasy Kit QIAGEN

tag: strain

tag: genotype/variation

value: NFAT5 knock-out 5.1

tag: cell type

value: MEFs

tag: treatment

value: hypertonic


title: Kip1:GFP IP rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76129.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 57, amino-allyl amplified


title: Myo2:GFP IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76098.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 42, amino-allyl amplified


title: 2 KO 500


title: Kar3:GFP IP rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76121.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 46, amino-allyl amplified


title: 4 KO 500


title: 2 KO 300

value: isotonic


title: Dyn1:GFP IP rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76133.gif

value: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA


title: 2 WT 500T

source_name: Total RNA from Mouse Embryonic Fibroblasts NFAT5 wild-type 5.4

value: NFAT5 wild-type 5.4

value: hypertonic with 1 h pretreatment using 100 nM Torin1


title: 4 KO 300


title: HPV16.2

source_name: Amplified FFPE cervical DNA from 5 individuals

value: normal cervix


title: Myo5:GFP IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76101.gif

source_name: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 45, amino-allyl amplified

value: LatB

value: GFP


title: Smy1:GFP IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76110.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 34, amino-allyl amplified


title: 4 WT 500T


title: Kip2:GFP IP rep #4 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76125.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 51, amino-allyl amplified


title: 1 KO 300


title: 1 WT 500T


title: 4 WT 500


title: HPV16.3


title: Myo3:9Myc IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74430.gif

source_name: IP 9E11 anti-c-myc, Dynal pan-mouse IgG beads, JCY 38, amino-allyl amplified


title: dyn1:9Myc IP JCY37-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71262.gif

source_name: aa-amplified reference, whole cell extract

source_name: IP of JCY37 (dyn1:9Myc strain), aa-amplified

value: formaldehyde


title: Myo5:9Myc IP rep #1 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74462.gif

source_name: whole cell extract, decrosslinked, amino-allyl amplified RNA

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 39, amino-allyl amplified


title: 2 WT 500


title: 1 WT 500


title: Kip2:GFP IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76123.gif


title: mock IP #1, Dynal pan-mouse IgG, crosslinked

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72339.gif

source_name: whole cell extract, amino-allyl amplified (not IP'd)

source_name: IP sample (untagged strain), amino-allyl amplified


title: 2 WT 300T

value: isotonic with 1 h pretreatment using 100 nM Torin1


title: 2 WT 300


title: 1 WT 300T


title: Kip1:GFP IP rep #2 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76127.gif


title: 4 WT 300T


title: Myo4:GFP IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76092.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 33, amino-allyl amplified


title: Smy1:GFP IP rep #3 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76112.gif


title: Smy1:9Myc IP #12 20' crosslink, Dynal beads

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72435.gif

source_name: whole cell extract, amino-allyl amplified

source_name: Smy1:9Myc IP, amino-allyl amplified


title: 4 WT 300

description: Gene expression data from Mouse Embryonic Fibroblasts


title: 1 WT 300


title: BrpA mutant, independent set #4

status: Public on Jan 26 2012

city: New Orleans

first: Zezhang

middle: Tom

last: Wen

state: LA

address: 1100 Florida Avenue

department: Oral and Craniofacial Biology

institute: LSU Health Sciences Center

description:
TW4
The BrpA mutant was grown similarly as the wild-type, but it does have defects in biofilm formation and stress tolerance response.

hyb_protocol: Hybridized at 37oC in the MAUI Hybridization System.

scan_protocol: Axon GenePix 4000B scanner.

data_processing: After the slides were scanned, single-channel images were loaded into TIGR Spotfinder software (http://www.tm4.org/spotfinder.html) and overlaid. A spot grid was created according to TIGR specifications and then manually adjusted to fit all spots within the grid. The intensity values of each spot were measured and saved into .mev and .tav files. Data were then normalized using LOWESS and iterative log mean centering with default settings, followed by in-slide replicate analysis using TIGR microarray data analysis software (MIDAS, http://www.tm4.org/midas.html). Spots that were flagged as bad because of either low intensity values or signal saturation were automatically discarded and labeled as null in the matrix. Statistical analysis was carried out using BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) and genes that were differentially transcribed were identified using the Group Comparison program at the statistical significance level of P < 0.001 and 0.01.

organism: Streptococcus mutans

source_name: BrpA mutant TW14D, early phase

label_protocol: 10 µg of total RNA was labeled by following the protocols recommended by the Pathogen Functional Genomics Resource Center (PFGRC).

growth_protocol: Grown to early phase (OD=0.3) in plain BHI broth, 37C, 5% CO2.

extract_protocol: Total RNA was extracted using hot phenol.

tag: genotype

value: BrpA mutant

tag: growth phase

value: early

organism: Streptococcus mutans UA159

source_name: Wild-type UA159, mid-exponential phase

growth_protocol: Grown to mid-log phase in BHI broth.

value: wild-type

value: mid-log

tag: sample type

value: reference


title: BrpA mutant, independent set #3

description:
TW3
The BrpA mutant was grown similarly as the wild-type, but it does have defects in biofilm formation and stress tolerance response.


title: Myo1:GFP IP rep #1 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74221.gif

value: whole cell extract, decrosslinked, amino-allyl amplified RNA

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 49, amino-allyl amplified


title: Myo5:9Myc IP (#30) with 9E11, crosslinked 20' formaldehyde, Dynal, BUBBLE

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72350.gif

value: whole cell extract, amino-allyl amplified

source_name: IP from JCY39, amino-allyl amplified


title: Kip2:GFP IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76122.gif

source_name: whole cell extract, uncrosslinked lysate, amino-allyl amplified RNA


title: Kar3:GFP IP rep #2 crosslinked 10' 1% formaldehyde

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74456.gif

source_name: IP anti-GFP , Dynal pan-mouse IgG beads, decrosslinked, JCY 46, amino-allyl amplified


title: BrpA mutant, independent set #2

description:
TW2
The BrpA mutant was grown similarly as the wild-type, but it does have defects in biofilm formation and stress tolerance response.


title: Kip3:GFP IP rep #1 w/ 2 ug/ml LatB lysis Bf

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76114.gif

source_name: IP anti-GFP, Dynal pan-mouse IgG beads, JCY 41, amino-allyl amplified


title: BrpA mutant, independent set #1

description:
TW1
The BrpA mutant was grown similarly as the wild-type, but it does have defects in biofilm formation and stress tolerance response.


title: Wildtype, independent set #4

description:
UA4
The BrpA mutant was grown similarly as the wild-type, but it does have defects in biofilm formation and stress tolerance response.

source_name: Wild-type UA159, early phase


title: Wildtype, independent set #3

description:
UA3
The BrpA mutant was grown similarly as the wild-type, but it does have defects in biofilm formation and stress tolerance response.


title: Wildtype, independent set #1

description:
UA1
The BrpA mutant was grown similarly as the wild-type, but it does have defects in biofilm formation and stress tolerance response.


title: Wildtype, independent set #2

description:
UA2
The BrpA mutant was grown similarly as the wild-type, but it does have defects in biofilm formation and stress tolerance response.


title: Exosomes isolated by ultracentrifugation

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

description: miRNA expression after data from the K562 cells’ exosomes isolated by ultracentrifugation

hyb_protocol: labeled RNA was hybridized to Agilent miRNA array at 55°C for 20h in rotisserie in a hybridization oven. Disassembled arrays were washed in GE wash buffer 1&2 for 5 minutes each.

scan_protocol: Images was scanned with Agilent scanner at 5µm resolution

data_processing: The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate Gene view file, providing expression data for each gene probed on the array. Features interogating same miRNA were summarized together based on their weight. No interarray normalization method was employed.

label: Cy3 pCp

source_name: Exosomes derived from K562 cells

label_protocol: 100ng total RNA was dephosphorylated at the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was then ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 1.0

extract_protocol: The exosome pellets were obtained by using Exoquick (System Biosciences) or ultracentrifugation from the culture medium of K562 cells. Total RNA in the exosome was isolated using Isogen (NIPPON GENE) according to the manufacture's instructions. For RNA isolation from exosome, the pellets were homogenized in 750 µl of Isogen. Then 200 µl of chloroform was added to the sample and the mixed solution was centrifugated. After an additional chloroform extraction and precipitation with isopropanol, the RNA sample was suspended in 20 µl of nuclease free water.

treatment_protocol: Treatment protocol: The K562 cells were cultured in RPMI 1640 supplemented with penicillin (Sigma Aldrich, Milan, Italy, 100 U/ml), streptomycin (Sigma Aldrich, 100 mg/ml), and 10% heat-inactivated fetal bovine serum (FBS) at 37°C in a humidified atmosphere of 95% air and 5% CO2. K562 cells were pre-cultured in serum-free AIM V medium (Invitrogen, Carlsbad, CA, USA). The next day, the media was replaced with 20 ml fresh media. After incubation for 24 h, the culture media were collected and centrifuged at 2,000 × g for 10 min at room temperature, and the supernatant was centrifuged again at 12,000 × g for 30 min at room temperature, then the supernatant was ultracentrifuged at 110,000 × g for 70 min at 4 ºC. The pellets were washed with PBS, all supernatant was removed by aspiration.

tag: cell line

value: exosome isolated by ultracentrifugation


title: Exosomes isolated by Exoquick

description: miRNA expression after data from the K562 cells’ exosomes isolated by Exoquick

treatment_protocol: The K562 cells were cultured in RPMI 1640 supplemented with penicillin (Sigma Aldrich, Milan, Italy, 100 U/ml), streptomycin (Sigma Aldrich, 100 mg/ml), and 10% heat-inactivated fetal bovine serum (FBS) at 37°C in a humidified atmosphere of 95% air and 5% CO2. K562 cells were pre-cultured in serum-free AIM V medium (Invitrogen, Carlsbad, CA, USA). The next day, the media was replaced with 20 ml fresh media. After incubation for 24 h, the culture medium was collected and centrifuged at 3000 × g for 15 min. The supernatant was filtered through a 0.22-µm PVDF filter (Millipore). The appropriate volume of Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA) was added to the filtered culture medium and mixed well by inverting. After refrigeration for 12 h, the mixture was centrifuged at 1,500 × g for 30 min and all supernatant was removed by aspiration.

value: exosome isolated by Exoquick


title: P14 - nudelcko/ko 1

city: San Diego

first: Tiziano

last: Pramparo

address: 3611 Valley Centre Drive

department: R&D

institute: Travere

description: embryo at P14, biological rep1

hyb_protocol: Fragmented cRNA was  hybridized in the presence of BSA to an Affymetrix GeneChip™ following manufacture instructions. Volume for fragmented cRNA samples was 40 µl.

scan_protocol: GeneChip® Scanner 3000 with 1 number of scans per array with 2x image, pixel value 3 um and wavelenght 570 nm

data_processing: Microarray data was pre-processed via the Robust Multichip Average (RMA) method, as implemented in the Bioconductor suite of programs (http://www.bioconductor.org/) implemented in the R statistical programming language. Analysis of differential expression was performed using bi-weight analysis.

label: biotin

source_name: mutant Ndel ko/cko

label_protocol: manufacture suggested biotin-labeled IVT reaction. 10 µg of total RNA was used in a maximum volume of 10 µl

extract_protocol: Trizol reagent (Invitrogen)

value: brain

value: mutant Ndel ko/cko


title: P14 - nudelcko/ko 2

description: embryo at P14, biological rep2


title: P14 - nudelcko/ko 3

description: embryo at P14, biological rep3


title: HPV16.4

description: Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

source_name: Cervical tissue, microdissected

value: high-grade cervical intraepithelial neoplasia, HPVtype 16

source_name: Amplified FFPE cervical DNA from 5 individuals


title: P14 - nudelko/+ 3

description: embryo at P14, biological rep3

source_name: mutant Ndel ko/+

value: mutant Ndel ko/+


title: N6 5mC

city: Duarte

first: Marc

last: Jung

address: 1500 East Duarte Street

department: Biology

institute: City Of Hope

description: 5mC profile in N6 sample

hyb_protocol: According to standard NimbleGen Protocol

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: Biological replicates were quantile-normalized and arrays were normalized by Nimblegen's recommended method, tukey-biweight. Probe ratios were smoothed for three neighboring probes prior to peak calling. Instead of estimating a cutoff ratio based on a hypothetical normal distribution for non-bound probes (Ringo), a quantile-based approach was chosen to estimate methylation intensities. For this aim, peaks at different quantiles were called, where four probes were above the quantile-based threshold with a distance cutoff of 300 bp. Normalized data is log2 transformed ratios (MIRA/INPUT) after tukey biweight normalization.

source_name: N6  5mC (MIRA) enriched samples

extract_protocol: DNeasy Blood and Tissue kit (Qiagen; Valencia, CA). Genomic DNA was fragmented by sonication to an average size of ~400 bp using a Sonifier cell disruptor 350 (Branson; Danbury, CT).

value: Lung

tag: enrichment procedure

value: 5mC (MIRA)

tag: antibodies/kit  information

value: In Lab purified His-MBD3L1 & GST-MBD2b

source_name: N6 input DNA

value: input DNA


title: P14 - nudelko/+ 2

description: embryo at P14, biological rep2

tag: tissue


title: P14 - nudelko/+ 1

description: embryo at P14, biological rep1


title: DMS53 5mC

description: 5mC profile in DMS53 sample

source_name: DMS53  5mC (MIRA) enriched samples

label_protocol: According to standard NimbleGen Protocol

source_name: DMS53 input DNA


title: H1688 5mC

description: 5mC profile in H1688 sample

source_name: H1688  5mC (MIRA) enriched samples

source_name: H1688 input DNA


title: SW1271 5mC

description: 5mC profile in SW1271 sample

source_name: SW1271  5mC (MIRA) enriched samples

source_name: SW1271 input DNA


title: H1836 5mC

description: 5mC profile in H1836 sample

source_name: H1836  5mC (MIRA) enriched samples

source_name: H836 input DNA


title: T18 5mC

description: 5mC profile in T18 sample

source_name: T18  5mC (MIRA) enriched samples

value: SCLC tumor

source_name: T18 input DNA


title: N1 5mC

description: 5mC profile in N1 sample

source_name: N1  5mC (MIRA) enriched samples

source_name: N1 input DNA


title: HBEC 5mC

description: 5mC profile in HBEC sample

source_name: HBEC  5mC (MIRA) enriched samples

value: HBEC

source_name: HBEC input DNA


title: EGS212_MlfabH_rep_5

city: Emeryville

first: Ee-Been

last: Goh

address: 5885 Hollis St, 4th Floor

department: Fuels Synthesis Division

institute: Joint BioEnergy Institute

description: This sample is of Escherichia coli DH1 delta-fadE with pKS1 and pEG205 plasmids. It is the fifth of five biological replicates of the test strain used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed at 42ºC for 20-24 hrs following NimbleGen's standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed on a Axon GenePix 4200A scanner following NimbleGen's standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

label: Alex fluor 555

organism: Escherichia coli K-12

label_protocol: Labeling was carried out by reverse transcription of 10 µg of total RNA primed with 5 µg of random hexamers (Roche, Germany) were reverse transcribed using the SuperScript Indirect cDNA labeling kit (Invitrogen). Alexa Fluor 555 dyes (Invitrogen) were then incorporated into amino-allyl-dUTP-labeled cDNA, the fluorescently labeled cDNA was purified with the QiaQuick PCR purification kit (Qiagen) and dried under vacuum (Vacufuge Speed Vac, Eppendorf).

growth_protocol: Escherichia coli DH1 ∆fadE control and test strains were seeded with OD600nm 0.03 overnight cultures into 15ml tryptic soy broth media and grown at 37°C with 200rpm agitation.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA concentration was determined on a Nanodrop ND-1000 (Thermo Scientific) and RNA quality was determined by analysis with an Agilent 2100 bioanalyzer.

treatment_protocol: After 6 hours of growth both control and test strains were induced with 0.5mM IPTG and harvested 2 hours post-induction.

tag: substrain

value: ∆fadE with overexpression of 'tesA and MlfabH via an IPTG-inudcible promoter

tag: phenotype

value: small improvement in methyl ketone production


title: N3 5mC

description: 5mC profile in N3 sample

source_name: N3  5mC (MIRA) enriched samples

source_name: N3 input DNA


title: T17 5mC

description: 5mC profile in T17 sample

source_name: T17  5mC (MIRA) enriched samples

source_name: T17 input DNA


title: P14 - WTMixB 3

description: embryo at P14, biological rep3

source_name: WT mix background B

value: WT mix background B


title: P14 - WTMixB 2

description: embryo at P14, biological rep2


title: P14 - WTMixB 1

description: embryo at P14, biological rep1


title: P14 - wt129s6 3

description: embryo at P14, biological rep3

source_name: WT inbred background

value: WT inbred background


title: H1417 5mC

description: 5mC profile in H1417 sample

source_name: H1417  5mC (MIRA) enriched samples

source_name: H1417 input DNA


title: T16 5mC

description: 5mC profile in T16 sample

source_name: T16  5mC (MIRA) enriched samples

source_name: T16 input DNA


title: T14 5mC

description: 5mC profile in T14 sample

source_name: T14  5mC (MIRA) enriched samples

source_name: T14 input DNA


title: T15 5mC

description: 5mC profile in T15 sample

source_name: T15  5mC (MIRA) enriched samples

source_name: T15 input DNA


title: EGS212_MlfabH_rep_4

description: This sample is of Escherichia coli DH1 delta-fadE with pKS1 and pEG205 plasmids. It is the fourth of five biological replicates of the test strain used in this experiment, each from separate cultures.


title: EGS212_MlfabH_rep_3

description: This sample is of Escherichia coli DH1 delta-fadE with pKS1 and pEG205 plasmids. It is the third of five biological replicates of the test strain used in this experiment, each from separate cultures.


title: T10 5mC

description: 5mC profile in T10 sample

source_name: T10  5mC (MIRA) enriched samples

source_name: T10 input DNA


title: T13 5mC

description: 5mC profile in T13 sample

source_name: T13  5mC (MIRA) enriched samples

source_name: T13 input DNA


title: N2 5mC

description: 5mC profile in N2 sample

source_name: N2  5mC (MIRA) enriched samples

source_name: N2 input DNA


title: P14 - wt129s6 2

description: embryo at P14, biological rep2


title: T11 5mC

description: 5mC profile in T11 sample

source_name: T11  5mC (MIRA) enriched samples

source_name: T11 input DNA


title: T8 5mC

description: 5mC profile in T8 sample

source_name: T8  5mC (MIRA) enriched samples

source_name: T8 input DNA


title: EGS084_control_rep_6

description: This sample is of Escherichia coli DH1 delta-fadE with pKS1 and pEC-XK99E plasmids. It is the sixth of six biological replicates of the control strain used in this experiment,, each from separate cultures.

value: ∆fadE with overexpression of 'tesA via an IPTG-inudcible promoter

value: normal


title: P14 - wt129s6 1

description: embryo at P14, biological rep1

source_name: WT inbred background


title: P14 - nudelkoMix/+ 3

description: embryo at P14, biological rep3

source_name: mutant Ndel ko/+ mix background

value: mutant Ndel ko/+ mix background


title: T9 5mC

description: 5mC profile in T9 sample

source_name: T9  5mC (MIRA) enriched samples

source_name: T9 input DNA


title: EGS212_MlfabH_rep_2

description: This sample is of Escherichia coli DH1 delta-fadE with pKS1 and pEG205 plasmids. It is the second of five biological replicates of the test strain used in this experiment, each from separate cultures.


title: N5 5mC

description: 5mC profile in N5 sample

source_name: N5  5mC (MIRA) enriched samples

source_name: N5 input DNA


title: EGS084_control_rep_4

description: This sample is of Escherichia coli DH1 delta-fadE with pKS1 and pEC-XK99E plasmids. It is the fourth of six biological replicates of the control strain used in this experiment, each from separate cultures.


title: P14 - nudelkoMix/+ 1

description: embryo at P14, biological rep1

value: brain


title: T6 5mC

description: 5mC profile in T6 sample

source_name: T6  5mC (MIRA) enriched samples

source_name: T6 input DNA


title: EGS084_control_rep_2

description: This sample is of Escherichia coli DH1 delta-fadE with pKS1 and pEC-XK99E plasmids. It is the second of six biological replicates of the control strain used in this experiment, each from separate cultures.


title: P14 - WTMixA 3

description: embryo at P14, biological rep3

source_name: WT mix background A

value: WT mix background A


title: EGS084_control_rep_5

description: This sample is of Escherichia coli DH1 delta-fadE with pKS1 and pEC-XK99E plasmids. It is the fifth of six biological replicates of the control strain used in this experiment,, each from separate cultures.


title: T12 5mC

description: 5mC profile in T12 sample

source_name: T12  5mC (MIRA) enriched samples

source_name: T12 input DNA


title: EGS084_control_rep_1

description: This sample is of Escherichia coli DH1 delta-fadE with pKS1 and pEC-XK99E plasmids. It is the first of six biological replicates of the control strain used in this experiment, each from separate cultures.


title: m50B_negative control IgG

type: protein

first: Chih Long

last: Liu

address: 269 Campus Drive

department: Medicine - Imm. & Rheum

description:
m50B
As a negative control, serum dilutent was applied onto the HEMP V1.0 array, labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.
negative control array, no array features with signal above background (no data obtained)

hyb_protocol: As a negative control, 10% fetal bovine serum with 50 mM Tris pH 7.5, 150 mM sodium chloride and 0.05% NP-40 was incubated overnight at 4 degrees Celsius.

scan_protocol: Fluorescent array images were collected at 635 nm with a GenePix 4000B fluorescent scanner at 10 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 6.1 analysis software.

data_processing: Data were background corrected and flagged values were removed.  The remaining replicate values were averaged.

label: DyLight-649-conjugated goat anti-mouse IgG antibody

molecule: protein

source_name: negative control

label_protocol: Commercially available DyLight 649-conjugated goat anti-mouse or goat anti-human antibody was added to the microarray at 1:500 in 10% fetal bovine serum in phosphate-buffered saline with 0.1% Tween-20.

extract_protocol: Whole antiserum was obtained.

value: negative control


title: P14 - WTMixA 1

description: embryo at P14, biological rep1


title: T3 5mC

description: 5mC profile in T3 sample

source_name: T3  5mC (MIRA) enriched samples

source_name: T3 input DNA


title: EGS084_control_rep_3

description: This sample is of Escherichia coli DH1 delta-fadE with pKS1 and pEC-XK99E plasmids. It is the third of six biological replicates of the control strain used in this experiment, each from separate cultures.


title: P14 - Lis1ko/+ 2

description: embryo at P14, biological rep2

source_name: mutant Lis1 ko/+

value: mutant Lis1 ko/+


title: P14 - nudelkoMix/+ 2

description: embryo at P14, biological rep2


title: P14 - WTMixA 2

description: embryo at P14, biological rep2


title: m25T_NETs + CRAMP 2.0 IgM

description:
m25T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

hyb_protocol: Mouse antiserum was probed on the HEMP array at 1:250 dilution in 10% fetal bovine serum with 50 mM Tris pH 7.5, 150 mM sodium chloride and 0.05% NP-40, and incubated overnight at 4 degrees Celsius.

label: DyLight-649-conjugated goat anti-mouse IgM antibody

source_name: Murine antiserum

value: Balb/c

value: NETs + CRAMP


title: EGS212_MlfabH_rep_1

description: This sample is of Escherichia coli DH1 delta-fadE with pKS1 and pEG205 plasmids. It is the first of five biological replicates of the test strain used in this experiment, each from separate cultures.


title: m23B_NETs + CRAMP 2.3 IgM

description:
m23B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs + 10 ug CRAMP at 3 months. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: m50T_negative control IgM

description:
m50T
As a negative control, serum dilutent was applied onto the HEMP V1.0 array, labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: m25B_NETs + CRAMP 3.0 IgM

description:
m25B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: m24T_NETs + CRAMP 3.3 IgM

description:
m24T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs + 10 ug CRAMP at 3 months. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: P14 - Lis1ko/+ 3

description: embryo at P14, biological rep3


title: m49B_MRL/lpr positive control IgM

description:
m49B
Murine antiserum was obtained from blood collected from an individual MRL/lpr mouse exhibiting lupus-like symptoms. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

source_name: MRL/lpr positive control

value: positive control


title: P14 - Lis1cko/ko 3

description: embryo at P14, biological rep3

source_name: mutant Lis1 ko/cko

value: mutant Lis1 ko/cko


title: P14 - Lis1cko/ko 1

description: embryo at P14, biological rep1


title: P14 - Lis1ko/+ 1

description: embryo at P14, biological rep1


title: P14 - Lis1cko/ko 2

description: embryo at P14, biological rep2


title: m23T_NETs + CRAMP 1.3 IgM

description:
m23T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs + 10 ug CRAMP at 3 months. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: P0 - DCXko/Y 1

description: embryo at P0, biological rep1

source_name: mutant Dcx ko/Y

value: mutant Dcx ko/Y


title: m24B_NETs + CRAMP 1.0 IgM

description:
m24B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: P0 - DCXko/Y 2

description: embryo at P0, biological rep2


title: P0 - DCXko/Y 3

description: embryo at P0, biological rep3


title: T7 5mC

description: 5mC profile in T7 sample

source_name: T7  5mC (MIRA) enriched samples

value: SCLC tumor

value: 5mC (MIRA)

value: In Lab purified His-MBD3L1 & GST-MBD2b

source_name: T7 input DNA

value: input DNA


title: T1 5mC

description: 5mC profile in T1 sample

source_name: T1  5mC (MIRA) enriched samples

source_name: T1 input DNA


title: P0 - nudelcko/ko 3

description: embryo at P0, biological rep3

source_name: mutant Ndel ko/cko

value: mutant Ndel ko/cko


title: T4 5mC

description: 5mC profile in T4 sample

source_name: T4  5mC (MIRA) enriched samples

source_name: T4 input DNA


title: m21T_NETs + CRAMP 3.3 IgG

description:
m21T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs + 10 ug CRAMP at 3 months. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: m22B_MRL/lpr positive control IgG

description:
m22B
Murine antiserum was obtained from blood collected from an individual MRL/lpr mouse exhibiting lupus-like symptoms. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

value: MRL/lpr


title: m49T_NETs + CRAMP 2.0 IgG

description:
m49T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: m20T_NETs + CRAMP 1.3 IgG

description:
m20T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs + 10 ug CRAMP at 3 months. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: m21B_NETs + CRAMP 1.0 IgG

description:
m21B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: P0 - nudelcko/ko 2

description: embryo at P0, biological rep2


title: 36B_negative control IgM

description:
36B
A mixture of human positive control antiserum was obtained from a commercial vendor (Immunovision). A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

hyb_protocol: Human antiserum was probed on the HEMP array at 1:250 dilution in 10% fetal bovine serum with 50 mM Tris pH 7.5, 150 mM sodium chloride and 0.05% NP-40, and incubated overnight at 4 degrees Celsius.

label: DyLight-649-conjugated goat anti-human IgM antibody

source_name: Dilution buffer

tag: sample group


title: 35B_HC003 IgM

description:
35B
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

source_name: Human antiserum

value: healthy control


title: m20B_NETs + CRAMP 2.3 IgG

description:
m20B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs + 10 ug CRAMP at 3 months. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: m22T_NETs + CRAMP 3.0 IgG

description:
m22T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: P0 - nudelcko/ko 1

description: embryo at P0, biological rep1


title: P0 - nudelko/+ 3

description: embryo at P0, biological rep3

source_name: mutant Ndel ko/+

value: mutant Ndel ko/+


title: P0 - WTMixB 3

description: embryo at P0, biological rep3

source_name: WT mix background B

value: brain

value: WT mix background B


title: P0 - nudelko/+ 1

description: embryo at P0, biological rep1


title: 35T_HC002 IgM

description:
35T
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 34B_HC006 IgM

description:
34B
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 3B_HC011 IgM

description:
3B
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 33T_HC010 IgM

description:
33T
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: P0 - epsilon129s6 2

description: embryo at P0, biological rep2

source_name: mutant 14-3-3 ko/ko inbred

value: mutant 14-3-3 ko/ko inbred


title: P0 - epsilon129s6 3

description: embryo at P0, biological rep3


title: P0 - nudel129s6 2

description: embryo at P0, biological rep2

source_name: mutant Ndel ko/+ inbred

value: mutant Ndel ko/+ inbred


title: 37B_HC019 IgM

description:
37B
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: P0 - nudel129s6 1

description: embryo at P0, biological rep1


title: P0 - nudelko/+ 2

description: embryo at P0, biological rep2


title: P0 - WTMixB 2

description: embryo at P0, biological rep2


title: 37T_HC014 IgM

description:
37T
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: P0 - epsilon129s6 1

description: embryo at P0, biological rep1


title: P0 - WTMixB 1

description: embryo at P0, biological rep1


title: P0 - nudel129s6 3

description: embryo at P0, biological rep3


title: P0 - lis1cko/ko Mix 3

description: embryo at P0, biological rep3


title: 39B_040_01 IgM

description:
39B
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

value: SLE Histone negative


title: P0 - lis1cko/ko Mix 2

description: embryo at P0, biological rep2


title: P0 - lis1cko/ko Mix 1

description: embryo at P0, biological rep1


title: 41B_047_09 IgM

description:
41B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

value: SLE Histone positive


title: 40T_030_04 IgM

description:
40T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 40B_041_03 IgM

description:
40B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: T2 5mC

description: 5mC profile in T2 sample

source_name: T2  5mC (MIRA) enriched samples

source_name: T2 input DNA


title: 38T_HC020 IgM

description:
38T
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 42B_147_03 IgM

description:
42B
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 42T_199_01 IgM

description:
42T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 43B_099_05 IgM

description:
43B
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: T5 5mC

description: 5mC profile in T5 sample

source_name: T5  5mC (MIRA) enriched samples

source_name: T5 input DNA


title: 39T_011_01 IgM

description:
39T
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 43T_115_07 IgM

description:
43T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 44B_028_03 IgM

description:
44B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 44T_217_03 IgM

description:
44T
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: P0 - WT129s6 3

description: embryo at P0, biological rep3

source_name: WT inbred background

value: WT inbred background


title: P0 - lis1ko/+ Mix 2

description: embryo at P0, biological rep2

source_name: mutant Lis1 ko/+

value: mutant Lis1 ko/+


title: P0 - WTMixA 2

description: embryo at P0, biological rep2

source_name: WT mix background A

value: WT mix background A


title: E14 - 14-3-3Epsilon 3

description: embryo at E14, biological rep3

source_name: mutant 14-3-3 ko/ko

value: mutant 14-3-3 ko/ko


title: E14 - 14-3-3Epsilon 2

description: embryo at E14, biological rep2


title: P0 - lis1ko/+ Mix 3

description: embryo at P0, biological rep3


title: P0 - WT129s6 2

description: embryo at P0, biological rep2


title: P0 - WT129s6 1

description: embryo at P0, biological rep1


title: P0 - lis1ko/+ Mix 1

description: embryo at P0, biological rep1


title: P0 - WTMixA 3

description: embryo at P0, biological rep3


title: E14 - Lis1cko/ko 3

description: embryo at E14, biological rep3

source_name: mutant Lis1 ko/cko

value: mutant Lis1 ko/cko


title: E14 - Lis1cko/ko 2

description: embryo at E14, biological rep2


title: P0 - WTMixA 1

description: embryo at P0, biological rep1


title: 46B_068_04 IgM

description:
46B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 45T_032_01 IgM

description:
45T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 47T_075_03 IgM

description:
47T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 47B_078_03 IgM

description:
47B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 36T_positive control IgM

description:
36T
As a negative control, serum dilutent was applied onto the HEMP V1.0 array, labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

value: negative control


title: 41T_057_03 IgM

description:
41T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 48B_126_02 IgM

description:
48B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 45B_033_02 IgM

description:
45B
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: E14 - Lis1cko/ko 1

description: embryo at E14, biological rep1


title: E14 - 14-3-3Epsilon 1

description: embryo at E14, biological rep1


title: 46T_059_01 IgM

description:
46T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: E14 - WTMixA 3

description: embryo at E14, biological rep3


title: 48T_109_02 IgM

description:
48T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: E14 - Lis1ko/+ 1

description: embryo at E14, biological rep1


title: E14 - Lis1ko/+ 2

description: embryo at E14, biological rep2


title: E14 - Lis1ko/+ 3

description: embryo at E14, biological rep3


title: E14 - WTMixA 2

description: embryo at E14, biological rep2


title: 32T_positive control IgG

description:
32T
A mixture of human positive control antiserum was obtained from a commercial vendor (Immunovision). A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

label: DyLight-649-conjugated goat anti-human IgG antibody

value: positive control


title: 17B_HC006 IgG

description:
17B
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 18B_HC011 IgG

description:
18B
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 19B_HC019 IgG

description:
19B
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 18T_HC010 IgG

description:
18T
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 19T_HC014 IgG

description:
19T
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 32B_negative control IgG

description:
32B
As a negative control, serum dilutent was applied onto the HEMP V1.0 array, labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 20B_HC024 IgG

description:
20B
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 20T_HC020 IgG

description:
20T
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 21B_040_01 IgG

description:
21B
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 21T_011_01 IgG

description:
21T
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: E14 - DCXko/Y 3

description: embryo at E14, biological rep3

source_name: mutant Dcx ko/Y

value: mutant Dcx ko/Y


title: 22B_041_03 IgG

description:
22B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: E14 - nudelcko/ko 3

description: embryo at E14, biological rep3

source_name: mutant Ndel ko/cko

value: mutant Ndel ko/cko


title: 22T_030_04 IgG

description:
22T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: E14 - WTMixA 1

description: embryo at E14, biological rep1


title: E14 - nudelcko/ko 2

description: embryo at E14, biological rep2


title: 23B_047_09 IgG

description:
23B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: E14 - DCXko/Y 2

description: embryo at E14, biological rep2


title: E14 - WTMixB 2

description: embryo at E14, biological rep2


title: E14 - WTMixB 1

description: embryo at E14, biological rep1


title: E14 - WTMixB 3

description: embryo at E14, biological rep3


title: 23T_057_03 IgG

description:
23T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 24T_199_01 IgG

description:
24T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 24B_147_03 IgG

description:
24B
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: BASC-Myc-depletion-2 [mRNA]

city: Rochester

first: Jie

last: Dong

state: MN

address: 200 1st SW

department: Thoracic Surgery

institute: Mayo Clinic

description:
Gene expression data from mouse bronchoalveolar stem cells
BASC-CMYC-depletion-2

hyb_protocol: The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer’s instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays at 45°C for 16 hr and then washed and stained using the GeneChip Fluidics.

scan_protocol: The arrays were scanned by a GeneArray Scanner and patterns of hybridization detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.

data_processing: The data were analyzed with Partek Genomics Suite 6.4 using Affymetrix default analysis settings and GC-RMA as normalization method

source_name: bronchoalveolar stem cells

label_protocol: Lableing was performed according to Affymetrix Gene Chip technical manual

growth_protocol: BASCs were isolated from the lungs of 4-6 week old ICR mice. In brief, Mice were sacrificed, and their lungs were removed and cut into small pieces. Tissue dissociation was performed, then passing the lungs through a 70 μM filter to obtain a single cell suspension. After washing with PBS. cells were stained with Biotin-conjugated anti-CD31 and anti-CD45, APC-conjugated streptavidin, PE-conjugated anti-Scal, and FITC-conjugated anti-CD34. Cells were washed and sorted for CD31neg, CD45neg, CD34pos and ScaIpos cells on an Aria Flow Cytometry machine. Sorted BASCs were cultured onto irradiated MEF (mouse embryonic fibroblast) cells with BASC media.

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

treatment_protocol: We depleted c-Myc endogenous expression by transfecting lentivirus-delivered c-Myc shRNA into BASCs, After several generations of puromycin selection, stable c-Myc knock down cell lines were established and the degree of c-Myc reduction in both mRNA and protein level was confirmed

value: ICR

value: bronchoalveolar stem cells (BASC)

value: Myc-depleted


title: 25B_099_05 IgG

description:
25B
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

source_name: Human antiserum


title: 28B_068_04 IgG

description:
28B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: BASC-Control-2 [mRNA]

description:
Gene expression data from mouse bronchoalveolar stem cells
BASC-CMYC-C-2

value: control


title: 38B_HC024 IgM

description:
38B
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

value: healthy control


title: 26B_028_03 IgG

description:
26B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 29B_078_03 IgG

description:
29B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: BASC-Myc-depletion-1 [mRNA]

description:
Gene expression data from mouse bronchoalveolar stem cells
BASC-CMYC-depletion-1


title: 28T_059_01 IgG

description:
28T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 25T_115_07 IgG

description:
25T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 27T_032_01 IgG

description:
27T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 26T_217_03 IgG

description:
26T
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 27B_033_02 IgG

description:
27B
Human antiserum was obtained from blood collected from a SLE Histone negative patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 31B_HC003 IgG

description:
31B
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 30T_109_02 IgG

description:
30T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: E14 - DCXko/Y 1

description: embryo at E14, biological rep1

value: brain


title: 30B_126_02 IgG

description:
30B
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 31T_HC002 IgG

description:
31T
Human antiserum was obtained from blood collected from a healthy control subject. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: BASC-Control-1 [mRNA]

description:
Gene expression data from mouse bronchoalveolar stem cells
BASC-CMYC-C-1


title: 29T_075_03 IgG

description:
29T
Human antiserum was obtained from blood collected from a SLE Histone positive patient. A 1:250 dilution of this antiserum was then applied onto the HEMP array V1.0, labeled with a goat anti-human IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 313B_negative control

description:
313B
As a negative control, serum dilutent was applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

hyb_protocol: As a negative control, 5% fetal bovine serum in phosphate-buffered saline with 0.1% Tween-20 was incubated for 1.25 hours at 4 degrees Celsius.

source_name: Dilution buffer

label_protocol: Commercially available DyLight 649-conjugated goat anti-mouse antibody was added to the microarray at 1:2000 in 5% fetal bovine serum in phosphate-buffered saline with 0.1% Tween-20.


title: 313T_MRL/lpr positive control

description:
313T
Murine antiserum was obtained from blood collected from an individual MLR/lpr mouse exhibiting lupus-like symptoms.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

hyb_protocol: Murine antiserum was probed on the antigen microarray at 1:250 dilution in 5% fetal bovine serum in phosphate-buffered saline with 0.1% Tween-20, and incubated for 1.25 hours at 4 degrees Celsius.

source_name: murine antiserum

value: MRL/lpr


title: 306T_NETs alone 3.2

description:
306T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

value: Balb/c

value: NETs


title: MSC from healthy donor 5 +TNF/LT set 2

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

description: Gene expression from Healthy Donnor derived BM-MSC stimulated by TNFalpha and Lymphotoxin alpha1beta6

hyb_protocol: Following fragmentation, 12 µg of cARN were hybridized for 16h at 45°C and 60rpm on GeneChip Human U133Plus2 arrays

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

data_processing:
The data were normalized by the RMA algorithm using GC content from the Partek Genomics Suite software (Partek, St Louis, MO).
set 1: FL-MSC signaturethat includes the genes differentially expressed in FL-MSC compared with HD-MSC (GUILLOTON F et al., Blood, 2012, figure 1 and tableS3)
set 2: TNF/LT signature that includes the genes differentially expressed in HD-MSC+TNF/LT compared with HD-MSC (GUILLOTON F et al., Blood, 2012, figure 2 and tableS4).

source_name: In vitro expanded BM-MSC

label_protocol: Biotinylated cRNA were amplified according to the small sample labelling protocol (TwoCycle amplification kit, Affymetrix, Santa Clara, CA)

growth_protocol: MSC were expanded from bone marrow mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)

extract_protocol: RNA was extracted using AllPrep ARN/ADN/protein kit (Qiagen, Valencia, CA)

tag: pathology

value: Healthy donor

tag: age (y)

tag: gender

value: Male

tag: growth protocol

value: Stimulated by TNF+LT for 3 days

value: Bone-Marrow Mesenchymal Stromal Cells


title: Subject AKA EDTA, biological rep1

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

department: Medicine

country: Canada

institute: University of British Columbia

hyb_protocol: Affymetrix Human Gene 1.0 ST array (Affymetrix, Santa Clara, CA)

scan_protocol: standand Affymetrix protocol

data_processing:
Raw data normalization using the 'farms' package consisted of quantile normalization and  summarization of probe-level data.
Data filtering was also performed using the Informative vs. Non-Informative Calls function in the 'farms' package. Differential gene expression was determined using moderated t-tests in limma using an FDR cut-off of 5%.
All statistical analyses were performed in the statistical computing program R.

source_name: whole blood Pre-challenged

label_protocol: standand Affymetrix protocol

extract_protocol:
Samples were stored at -80⁰C until RNA extraction
From PAXgene tube samples, total RNA was purified from 2.5 mL of whole blood using Rneasy mini kit (Qiagen, Chatsworth, CA, USA)
From EDTA tube samples, total RNA was purified from 3.0 mL of whole blood following modified TRIzol-based extraction method.
The yield and quality of RNA was assessed by NanoDrop 8000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)

value: F

tag: age

tag: site

value: McM

tag: allergen

value: HDMDP

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: % fall in fev1 (late)

tag: rna integrity number

value: whole blood


title: Subject 102 EDTA,  biological rep2

source_name: Post

value: Cat


title: NFs_rep_1

city: Hefei

first: Wei

last: Lan

state: Anhui

address: 96#, Jinzhai Road

department: School of Life Science

country: China

institute: University of Science and Technology of China

description: Gene expression of oral NFs

hyb_protocol: Hybridized to the chip at 65°C for 17 h according to Agilent protocol.

scan_protocol: After wash, the chip was scanned and visualized using the Agilent DNA microarray scanner. Probe set intensities were measured using Agilent Feature Extraction software.

data_processing: Raw data were normalized in the Agilent GeneSpring GX software using the Agilent FE one-color scenario (median normalization).

source_name: NFs replicate 1

label_protocol: 1 μg total RNA pooled respectively from the CAFs and the NFs were reversed transcripted, labeled, and hybridized to the chip at 65°C for 17 h.

extract_protocol: TRIzol reagent (Invitrogen, USA) was used to extract total RNA and ultraviolet spectrophotometry was used to examine the quality of RNA samples.

treatment_protocol: The tissues were isolated, cultured, purified and identified using standard methods. The protocol was reviewed by the Institutional Ethics Committee of West China Hospital of Stomatology and informed consent was obtained from each subject. Briefly, tissues were washed thrice with phosphate-buffered saline (PBS) and antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin). Then epithelial and adipose tissues were separated from surrounding stromal cells. The residual connective tissue was cut into small pieces (1 × 1 × 1 mm) that were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, pH 7.2) containing 20% fetal calf serum at 37°C in an atmosphere containing 5% CO2. To purify the cells, we opted for a method of curettage combined with trypsinization, which was performed when cells fully covered the bottom of the culture bottle. Cultures at passage number three were used for the cellular identification of oral CAFs and NFs. A wide-spectrum a-cytokeratin antibody was used to confirm the absence of contaminating epithelial cells. Finally, antibodies against vimentin and smooth muscle actin (SMA) were used to confirm the myofibroblastic nature of these cells.

tag: cell type

value: oral normal fibroblasts (NFs)