title: 13OctM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14047

value: male


title: L96_647

status: Public on Feb 01 2012

type: RNA

city: Ithaca

first: Jesse

middle: D.

last: Munkvold

state: NY

address: 240 Emerson

department: Plant Breeding and Genetics

country: USA

institute: Cornell University

description: Array Batch: 20050

hyb_protocol: Perhybridization and hybridization was done using the Pronto! Hybridization Kit (Corning) with accompanying protocols. Labeled A555 and A647 samples were combined in balanced dye ratios and hybridization was done in Corning Microarray Hybridization chammber II with Erie Scientific Raised Coverslips (25x60mm). Hybridization was carried out for 18hrs. in a 42C water bath.

scan_protocol: Scanning was done using an Axon 6000B scanner with automatic PMT gain, 100% laser power, and 10um resolution.

data_processing: Array, block, and spot detection was done automatically and inspected by hand. Bad spots were automatically and hand-flagged.Background was calculated by morphological opening followed by closing using the GenePix 6 software.

label: Alexa 555

molecule: total RNA

organism: Triticum aestivum

source_name: Pre-anthesis spike bulk

label_protocol: 10ug of total RNA were reverse transcribed using anchored poly-T primers and a 2:3 amino-allyl dUTP:dTTP ratio. RNA was hydrolyzed with NaOH and the amino-allyl cDNA was cleaned with a Qiagen Qiaquick column and phosphate buffers. Alexa 555 or 647 (Invitrogen #A32755) dyes were coupled according to accompanying protocols. Labeled cDNA  was cleaned using a Qiaquick column and incorporation was measured by spectrophotometry.

growth_protocol: Plants were grown in the  field (Helfer 2004) near Ithaca, NY. Spike samples were harvested at physiological maturity as described in Munkvold et al. 2009. TAG. 119. Samples were stored at -20C for two months while embryo samples were harvested. Primary and secondary position seeds were selected from five spikes and embryos (~100) were isolated by hand, frozen in liquid nitrogen, and stored at -80C.

extract_protocol: Total RNA extraction from isolated embryos was done using the Trizol reagent with only slight modifications to the manufacturer protocol. Total RNA was treated with RQ1 DNAse and cleaned using Qiagen Rneasy columns.

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Helfer, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

label: Alexa 647

source_name: CxC Line 96, embryo at physiological maturity

value: embryo at physiological maturity


title: L95_647

description: Array Batch: 20050

source_name: CxC Line 95, embryo at physiological maturity


title: v2 aCGH GSY2195

type: genomic

city: Stanford

first: Barbara

last: Dunn

state: CA

department: Genetics

institute: Stanford University

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86253.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: G2505C

data_processing: Agilent Feature Extraction

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

label_protocol: not provided

extract_protocol: not provided

tag: test

source_name: 165 ng sonicated genomic DNA from GSY2195

tag: lab database strain name

tag: type

value: Wine - commercially produced strain

tag: strain

value: LVCB


title: 13MafM2

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14042

hyb_protocol: Affymetrix standard protocol The arrays were washed and stained using the Affymetrix Fluidics Station 450.  Fluidics Protocol FS450-0007. Amount labeled  target hybridization to array: Approximately 2.5 µg into the hybridization cocktail, approximately 2.1 µg were hybridized to the array.

scan_protocol: Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and Affymetrix GeneChip Command Console (AGCC) Software version 3.1.1.

data_processing:
Analysis method: Partek
GCOS Tgt value: 500

label: Biotin

organism: Mus musculus

source_name: Gonad, Embryo 13.5 dpc interstitial cell subset and fetal Leydig cells

label_protocol: Nugen Encore Biotin Module (4200)

treatment_protocol:
Pooled sample: Yes
Pool size: one or more litters
Dissection method: Dissected out the gonad, trypsinized and FACS sorted.  Capel protocol: FACS Protocol
Experimental design: Female mice were time-mated and the embryos were collected. The gonads were removed and the males and females were separately pooled. The gonads were incubated in Trypsin EDTA for 5-10 minutes. The trypsin was removed, PBS (often with DNase) was added, and the gonadal cells were dissociated by pipetting and pulling through a syringe. The samples were passed through a strainer and then FACS sorted. Capel protocol: FACS protocol.

tag: gene reported

value: Mafbtm1Jeng / MGI:3663168

value: Progeny of CD-1 crossed to mixed background

tag: sex

tag: developmental stage

tag: theiler stage


title: L91_647

description: Array Batch: 20050

source_name: CxC Line 91, embryo at physiological maturity


title: L86_647

description: Array Batch: 20038

source_name: CxC Line 86, embryo at physiological maturity


title: 14249018 - 6h_2ip_2 vs 1d10h_2ip_2

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

description: Study of the molecular mechanism during transdifferenciation from root apical meristem to shoot apical meristem

hyb_protocol: 1d10h_2ip_2 Cy5 / 6h_2ip_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: roots - germination and growth on MS10+NPA (5 days) transfert on MS10+ANA during 1 day and 18 hours transfert on MSgluc+2iP

extract_protocol: 1d10h_2ip_2:3.5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: Columbia

tag: age

extract_protocol: 6h_2ip_2:6ug. (Qiagen_RNeasy.pdf)


title: 13MafM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14043


title: L89_647

description: Array Batch: 20050

source_name: CxC Line 89, embryo at physiological maturity


title: 14249019 - 1d10h_2ip_2 vs 6h_2ip_2

hyb_protocol: 6h_2ip_2 Cy5 / 1d10h_2ip_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: v2 aCGH GSY2233

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85734.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2233


title: v2 aCGH GSY2219

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85747.gif

value: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2219


title: v2 aCGH GSY2196-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85764.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng in-complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2196


title: 13MafM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14041


title: EP cells, biological replicate 2

city: Philadelphia

first: Paul

last: Gadue

state: PA

address: 3501 Civic center Blvd, CTRB 5012

institute: Children's Hospital of Philadelphia

description: Gene expression data from human endodermal progenitor cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA normalization method through Affymetrix expression console.

label: biotin

organism: Homo sapiens

source_name: human endodermal progenitor cell

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

growth_protocol: ES cells were growing in human ES media containg 20% knockout serum and 10 ng/ml bFGF. DE cells were cultured in high activin media and EP cells were in high BMP media.

extract_protocol: Total RNA was extracted and purified with Qiangen Rneasy Micro Kit  according to the manufacturer's instructions.

treatment_protocol: ES cells were sorted with SSEA3 and SSEA4. DE and EPC cells were sorted with CXCR4 and CD117.

tag: cell type

value: human endodermal progenitor cell


title: ESC, biological replicate 2

description: Gene expression data from human embryonic stem cell

source_name: human embryonic stem cell, undifferentiated


title: EP cells, biological replicate 3


title: ESC, biological replicate 1

value: human embryonic stem cell, undifferentiated


title: v2 aCGH GSY2116

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86572.gif

value: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA of GSY2116

value: "Bread - native or ""wild"" strain"


title: ESC, biological replicate 3


title: v2 aCGH GSY2187-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86346.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2187-2


title: v2 aCGH GSY2173-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86251.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2173


title: 13MafF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14038

source_name: Gonad, Embryo 13.5 dpc female vascular associated mesenchymal stromal cells

value: female


title: L82_647

description: Array Batch: 20050

source_name: Pre-anthesis spike bulk

source_name: CxC Line 82, embryo at physiological maturity


title: 13FlkM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14037

source_name: Gonad, Embryo 13.5 dpc male endothelial cells

tag: Sex


title: 13FlkM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14036


title: L84_647

description: Array Batch: 20050

source_name: CxC Line 84, embryo at physiological maturity


title: 14249010 - 6h_2ip_2 vs 1d18h_ANA_2

hyb_protocol: 1d18h_ANA_2 Cy5 / 6h_2ip_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1d18h_ANA_2:8.5ug. (Qiagen_RNeasy.pdf)


title: L76_647

description: Array Batch: 20050

source_name: CxC Line 76, embryo at physiological maturity


title: 13FlkF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14032

source_name: Gonad, Embryo 13.5 dpc female endothelial cells


title: L81_647

description: Array Batch: 20050

source_name: CxC Line 81, embryo at physiological maturity


title: L70_647

description: Array Batch: 20038

source_name: CxC Line 70, embryo at physiological maturity


title: 13MafF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14040


title: 14249014 - 2d10h_2ip_2 vs 1d10h_2ip_2

hyb_protocol: 1d10h_2ip_2 Cy5 / 2d10h_2ip_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 2d10h_2ip_2:9ug. (Qiagen_RNeasy.pdf)


title: L72_647

description: Array Batch: 20050

source_name: CxC Line 72, embryo at physiological maturity


title: 14249017 - 1d10h_2ip_1 vs 6h_2ip_1

hyb_protocol: 6h_2ip_1 Cy5 / 1d10h_2ip_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 6h_2ip_1:5.7ug. (Qiagen_RNeasy.pdf)

extract_protocol: 1d10h_2ip_1:8ug. (Qiagen_RNeasy.pdf)


title: 12Sox9M3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14031

source_name: Gonad, 12.5 dpc male Sertoli cells

value: Tg(Sox9-ECFP)2Capl / PMID:17940049

value: Progeny of CD-1 crossed to C57BL/6J


title: 14249013 - 1d10h_2ip_2 vs 2d10h_2ip_2

description: Study of the molecular mechanism during transdifferenciation from root apical meristem to shoot apical meristem

hyb_protocol: 2d10h_2ip_2 Cy5 / 1d10h_2ip_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: L69_647

description: Array Batch: 20038

value: Cayuga x Caledonia, DH

source_name: CxC Line 69, embryo at physiological maturity


title: 13FlkF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14033


title: 13FlkF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14034


title: 14249016 - 6h_2ip_1 vs 1d10h_2ip_1

hyb_protocol: 1d10h_2ip_1 Cy5 / 6h_2ip_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14249003 - 1d10h_2ip_1 vs 2d10h_2ip_1

hyb_protocol: 2d10h_2ip_1 Cy5 / 1d10h_2ip_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 2d10h_2ip_1:11ug. (Qiagen_RNeasy.pdf)


title: 14249009 - 1d18h_ANA_2 vs 6h_2ip_2

hyb_protocol: 6h_2ip_2 Cy5 / 1d18h_ANA_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: L73_647

description: Array Batch: 20050

value: Helfer, Cornell University, Ithaca, NY

source_name: CxC Line 73, embryo at physiological maturity


title: 14248988 - 6h_2ip_1 vs 1d18h_ANA_1

hyb_protocol: 1d18h_ANA_1 Cy5 / 6h_2ip_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1d18h_ANA_1:5.4ug. (Qiagen_RNeasy.pdf)


title: 13MafF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14039


title: L71_647

description: Array Batch: 20050

value: Pre-anthesis spike bulk

source_name: CxC Line 71, embryo at physiological maturity


title: 14249004 - 2d10h_2ip_1 vs 1d10h_2ip_1

hyb_protocol: 1d10h_2ip_1 Cy5 / 2d10h_2ip_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13FlkM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14035

value: male


title: v2 aCGH GSY2181-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86340.gif

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY2181-2

value: Wine - commercially produced strain


title: 14248986 - 1d18h_ANA_1 vs 6h_2ip_1

hyb_protocol: 6h_2ip_1 Cy5 / 1d18h_ANA_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 12Sox9M2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14030


title: L62_647

description: Array Batch: 20050

source_name: CxC Line 62, embryo at physiological maturity

value: embryo at physiological maturity


title: L57_647

description: Array Batch: 20050

source_name: CxC Line 57, embryo at physiological maturity


title: L67_647

description: Array Batch: 20050

source_name: Pre-anthesis spike bulk

source_name: CxC Line 67, embryo at physiological maturity


title: L68_647

description: Array Batch: 20050

source_name: CxC Line 68, embryo at physiological maturity


title: 12SryF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14027

source_name: Gonad, 12.5 dpc female supporting cell precursors (follicle cells/pre-Granulosa cells)


title: 12Sox9M1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14029


title: 12SmaaM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14025

source_name: Gonad, 12.5 dpc male interstitial cells

value: Tg(Acta2-EYFP)Jll / PMID:18769072

value: FVB


title: L65_647

description: Array Batch: 20050

source_name: CxC Line 65, embryo at physiological maturity


title: 12SryF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14028


title: L43_647

description: Array Batch: 20050

source_name: CxC Line 43, embryo at physiological maturity


title: L41_647

description: Array Batch: 20050

source_name: CxC Line 41, embryo at physiological maturity


title: L50_647

description: Array Batch: 20050

source_name: CxC Line 50, embryo at physiological maturity


title: 12SryF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14026


title: 12SmaaM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14023


title: 12SmaaF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14022

source_name: Gonad, 12.5 dpc female vascular associated mesenchymal stromal cells


title: L44_647

description: Array Batch: 20050

source_name: CxC Line 44, embryo at physiological maturity


title: 12SmaaM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14024


title: WT-sample6

city: New York

first: Avi

last: Ma'ayan

address: One Gustave L. Levy Place Box 1215

department: Pharmacology and Systems Therapeutics

institute: Mount Sinai School of Medicine

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney coterx from wild type mouse 6

hyb_protocol: Hybridization oven 640, rotate 16-18 hrs.

scan_protocol: Genechip Scanner 3000-7G.

data_processing:
Expression Console (1.1.2800.29167), affymetrix-algorithm-name = rma
One-way analysis of variance test (ANOVA) with BH correction at 0.05 FDR was applied to the dataset to identify the genes that were differentially expressed between groups.

source_name: Kidney coterx from wild type mouse 6

label_protocol: Following standard procedures according to the manufacturer's instructions as applied at the MSSM core facility.

growth_protocol: Mice were sacrificed at 8 weeks. Each sample in the Tg and WT mice are from different individual animals. One mice developed significant scarring and since the array results were significantly different this sample was not used for further analysis. HEK 293 and HK2 cells were obtained from ATCC and cultured as described in Rosenstiel, P.E., et al. Kidney Int 74, 1049-1058 (2008).

extract_protocol: Total RNA was extracted from kidney cortices of five Tg26 and five WT for gene expression microarrays. RNA was isolated by using RNAesay kit from Qiagen.

value: Kidney cortex

tag: genotype/variation

value: wild type

tag: gender

value: FVB/N background


title: L55_647

description: Array Batch: 20050

hyb_protocol: Perhybridization and hybridization was done using the Pronto! Hybridization Kit (Corning) with accompanying protocols. Labeled A555 and A647 samples were combined in balanced dye ratios and hybridization was done in Corning Microarray Hybridization chammber II with Erie Scientific Raised Coverslips (25x60mm). Hybridization was carried out for 18hrs. in a 42C water bath.

tag: population

tag: field location

source_name: CxC Line 55, embryo at physiological maturity


title: HSMM-noAb48h-rep1

city: Boston

first: Martha

middle: L

last: Bulyk

state: MA

address: 77 Avenue Louis Pasteur

department: Division of Genetics

institute: Brigham and Women's Hospital

description: mock IP 48 h after serum removal for myoblast differentiation

hyb_protocol: Arrays were hybridized at 65 degrees with rotation for 40 hours and then washed according to the Agilent ChIP-chip protocol.

scan_protocol: Arrays were scanned at 5-micron resolution on an Agilent scanner according to manufacturer recommendations.

data_processing: Agilent Feature Extraction software (version 9.1.3.1; Agilent Technologies Inc., Santa Clara, CA) was used to calculate log10 ratios of IP DNA/Input DNA (Cy5/Cy3) for each microarray spot in each experiment and to remove spots flagged as outliers because of debris on the slide or excessively high background.

source_name: Human skeletal muscle myoblasts mock IP 48 h post-differentiation

label_protocol: The purified DNA from each ChIP was amplified and labeled with Cy5 (IPed DNA) or Cy3 (Input DNA) according to the published ChIP-chip protocol from Agilent.

growth_protocol: Adult male primary human skeletal myoblasts (Lonza) were grown in SkGM-2 medium (Lonza). Myogenic differentiation was stimulated by switching the culture medium to DMEM-F12 with 2% horse serum (Sigma) when the cells reached about 70% confluence. All time points referred are with respect to the time of switching to differentiation medium.

extract_protocol:
Cells were lysed by adding cold cell lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40; PMSF; protease inhibitors) in a ratio of 1 mL/100 million cells, douncing 3 times to aid in nuclei release, and then incubating on ice for 10 minutes.  Nuclei were then pelleted by centrifugation at 2300xg for 5 min at 4 degrees C.  Nuclei were permeabilized by incubation in nuclei lysis buffer (50 mM Tris-Cl pH 8.1, 10 mM EDTA, 1% SDS, protease inhibitors) for 10 min on ice and then were sonicated until the chromatin was an average size of 600 bp.  Sheared chromatin for use in immunoprecipitation was isolated by centrifugation for 10 min at 18,000xg at 4 degrees C.
ChIP experiments were performed using the ChIP protocol published by Farnham and colleagues and modified by Warner and colleagues. After cell lysis, crosslinked chromatin was sheared by sonication to an average length of ~600 bp, and then immunoprecipitated with relevant TF-specific antibodies (MyoD: sc-760 LOT F1610; Myogenin: sc-576 LOT H0603; SRF: sc-335 LOT B272; p300: sc-585 LOT C2009; all from Santa Cruz Biotechnology, Inc.). A separate, mock ‘no antibody’ (i.e., protein A beads without antibody) sample was processed as a negative control. The supernatant from the mock IP was saved as ‘Input’ DNA.

treatment_protocol: At 0 or 48 h post-differentiation, cells were crosslinked with 1% formaldehyde for 20 min and then quenched by glycine addition.  Cells were harvested by scraping.

tag: tissue

value: primary skeletal muscle myoblasts

value: 48 h post-differentiation

source_name: Human skeletal muscle myoblasts Input genomic DNA 48 h post-differentiation


title: HSMM-MyoD48h-rep1a

description: MyoD IP 48 h after serum removal for myoblast differentiation; technical replicate 1/2

source_name: Human skeletal muscle myoblasts MyoD IP 48 h post-differentiation


title: 12SmaaF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14021

hyb_protocol: Affymetrix standard protocol The arrays were washed and stained using the Affymetrix Fluidics Station 450.  Fluidics Protocol FS450-0007. Amount labeled  target hybridization to array: Approximately 2.5 µg into the hybridization cocktail, approximately 2.1 µg were hybridized to the array.


title: L34_647

description: Array Batch: 20038

tag: year

source_name: CxC Line 34, embryo at physiological maturity


title: HSMM-noAb0h-rep1

description: mock IP 0 h after serum removal for myoblast differentiation

source_name: Human skeletal muscle myoblasts mock IP 0 h post-differentiation

value: 0 h post-differentiation

source_name: Human skeletal muscle myoblasts Input genomic DNA 0 h post-differentiation


title: HSMM-MyoD0h-rep1

description: MyoD IP 0 h after serum removal for myoblast differentiation

source_name: Human skeletal muscle myoblasts MyoD IP 0 h post-differentiation


title: HSMM-MyoD48h-rep1b

description: MyoD IP 48 h after serum removal for myoblast differentiation; technical replicate 2/2


title: HSMM-SRF48h-rep1

description: SRF IP 48 h after serum removal for myoblast differentiation; biological replicate 1/2

source_name: Human skeletal muscle myoblasts SRF IP 48 h post-differentiation


title: HSMM-SRF0h-rep1c

description: SRF IP 0 h after serum removal for myoblast differentiation; technical replicate 3/3 of biological replicate 1/2

source_name: Human skeletal muscle myoblasts SRF IP 0 h post-differentiation


title: L33_647

description: Array Batch: 20038

source_name: Pre-anthesis spike bulk

source_name: CxC Line 33, embryo at physiological maturity


title: WT-sample3

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney coterx from wild type mouse 3

source_name: Kidney coterx from wild type mouse 3

value: female


title: L30_647

description: Array Batch: 20050

source_name: CxC Line 30, embryo at physiological maturity


title: HSMM-SRF0h-rep2

description: SRF IP 0 h after serum removal for myoblast differentiation; biological replicate 2/2


title: 12OctM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14018

source_name: Gonad, 12.5 dpc male germ cells


title: HSMM-p30048h-rep1

description: p300 IP 48 h after serum removal for myoblast differentiation

source_name: Human skeletal muscle myoblasts p300 IP 48 h post-differentiation


title: HSMM-SRF48h-rep2

description: SRF IP 48 h after serum removal for myoblast differentiation; biological replicate 2/2


title: WT-sample4

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney coterx from wild type mouse 4

source_name: Kidney coterx from wild type mouse 4


title: 12OctM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14019


title: 12OctM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14017


title: L29_647

description: Array Batch: 20050

source_name: CxC Line 29, embryo at physiological maturity


title: 12SmaaF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14020

source_name: Gonad, 12.5 dpc female vascular associated mesenchymal stromal cells


title: WT-sample2

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney coterx from wild type mouse 2

source_name: Kidney coterx from wild type mouse 2


title: HSMM-SRF0h-rep1b

description: SRF IP 0 h after serum removal for myoblast differentiation; technical replicate 2/3 of biological replicate 1/2


title: WT-sample1

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney coterx from wild type mouse 1

source_name: Kidney coterx from wild type mouse 1


title: WT-sample5

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney coterx from wild type mouse 5

source_name: Kidney coterx from wild type mouse 5


title: 12OctF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14016

source_name: Gonad, 12.5 dpc female germ cells


title: HSMM-SRF0h-rep1a

description: SRF IP 0 h after serum removal for myoblast differentiation; technical replicate 1/3 of biological replicate 1/2

source_name: Human skeletal muscle myoblasts Input genomic DNA 0 h post-differentiation


title: Tg26-sample6

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney cortex from HIV mouse model 6

source_name: Kidney cortex from HIV mouse model 6

value: Tg26 HIV


title: 12OctF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14014

value: Progeny of CD-1 crossed to C57BL/6J


title: METH EC10-2

city: Antwerpen

first: Nathalie

last: Dom

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

hyb_protocol: Prior to hybridization, arrays were incubated for 30-45 min at 42°C in a prehybridization solution (50% formamide, 5x saline sodium citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 0.1mg/mL BSA). The vacuum dried targets (both reference and treatment target) were resuspended in a hybridization solution (50% formamide, 5x SSC, 0.1% SDS, 0.1mg/mL BSA and 0.1mg/mL sheared salmon sperm) and denaturated at 95°C. The cooled targets were subsequently applied onto the prehybridized slides and incubated overnight at 42°C. After hybridization, arrays were washed in solutions with increasing stringency (decreasing concentrations of SSC and SDS) and dried with N2. The hybridization design was a universal reference design (a mixture of aliquots from control and exposed samples), which is recommended when class discovery is the main purpose of the experiment. One of the three biological replicates of each exposure condition was labeled with one dye, the remaining two samples were labeled with the second dye.

scan_protocol: Scanning and analysing of the slides was performed using the Genepix personal 4100 Scanner and Genepix pro Software (both Axon instruments, USA). Cy3 and Cy5 fluorescent signals were scanned at respectively 532 and 635nm and the PMT (photomultiplier tube) values were adjusted to reach a ratio (Cy5/Cy3) around 1. Spots were identified and ratio’s quantified by means of the Genepix software 5.0 (Axon Instruments).

data_processing: Statistical analyses were performed using the R package limma (linear models for microarray data). Spots for which red and green median foreground intensity < median background intensity + 2SD on all arrays were deleted before analysis. Median intensity data was background corrected using a normal-exponential convolution model. Subsequently, normalization between-arrays was performed using Variance Stabilization Normalization (vsn). For each probe, a linear model was fitted to intensity ratios, after which probes were ranked in order of evidence of differential expression using an empirical Bayes method. Both high and low concentrations of each chemical stressor were contrasted against their respective controls. Genes with p < 0.05 and log2FC < -0.75 or log2FC > 0.75 (log2 fold change) were considered as differentially transcribed gene fragments.

organism: Daphnia magna

label_protocol: The production of cDNA and subsequent amino-allyl labelling were performed according to the protocol described in detail by Vandenbrouck et al. (2009). In brief, 5µg of total RNA was mixed with Lucidea control mRNA spike mix (Amersham, UK) to be reverse-transcribed using the Superscript II, Random hexamer primers (both Invitrogen) in the presence of dNTPs with 2/3 aa-dTTP/dTTP (Sigma-Aldrich, Belgium). After an overnight incubation period (42°C) the amino-allyl-incorporated cDNA was purified using a modified Qiagen PCR spin colomn protocol (Van der Ven et al., 2005). In a next step, Cy5/Cy3 esters (Amersham) were used for covalent coupling to the amino-allyl labelled cDNA. The vacuum dried cDNA samples (dissolved in a 0,1M carbonate buffer (pH 9.0)) were mixed with the Cy3/Cy5 esters (dissolved in 100% DMSO) and incubated for an hour in the dark at room temperature. Hereafter, a second cleanup reaction was performed to establish the removal of the remaining uncoupled dyes (QIAquick PCR purification kit, Qiagen, USA). The quality of eluted and labelled cDNA was analysed using the Nanodrop® spectrophotometer. Samples with an FOI (frequence of incorporated dye) between 20 and 50 were selected for hybridization and an amount of 50 pmol labelled target was vacuum dried.

extract_protocol: Approximately 30 Daphnia/replicate were collected. Samples were shock-frozen in liquid nitrogen and stored in RNAlater (Ambion, USA) at -80°C. All RNA extractions were performed using the TRIzol® method (Invitrogen, Belgium) followed by a DNAse treatment using 1U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 30µl sample and subsequent phenol/chloroform extractions. The purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were respectively above 1.90 and 2.10. To verify the intactness of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed to visualize the 18S and 28S ribosomal bands.

treatment_protocol: Two sets of structural analogues, defined as narcotics (alcohols: ethanol, methanol and isopropanol) and as polar narcotics (chlorinated anilines: aniline, 4-chloroaniline, 3,5-dichloroaniline and 2,3,4-trichloroaniline) were selected for short-term toxicity experiments. Daphnia magna neonates (between 0 and 24h old) were exposed for 96h in glass recipients to each chemicals’ respective EC1-96h and EC10-96h (determined based on 96h immobilization experiments) to allow multi-level effect assessment (growth, energy reserves and gene transcription was assessed) of different chemicals at the same level of acute toxicity (exposure at equitoxic acute concentration). The experiments were performed in triplicate at a density of 1daphnid/5ml of reconstituted fresh water CaCl2.2H2O, 2mM; MgSO4.7H2O, 500μM; NaHCO3, 771μM; KCl, 77.1μM; water hardness, 250 mg CaCO3; pH 7.8; OECD guideline 203, annex 2). Test media were renewed every 24h for the alcohols (to account for their high(er) volatility) and every 48h for the anilines. Organisms were fed every other day with a mixture of P. subcapitata and C. reinhardtii in a 3:1 ratio. The necessary amounts of organisms for the respective endpoints (growth and energy use) were collected after 48h and 96h of exposure and for gene transcription analyses after 96h of exposures. 30 pooled daphnids per replica were used for gene transcription analyses.

value: whole body extracts (30 organisms)

value: 96h old

tag: effect concentration

tag: agent

value: methanol

source_name: whole body extracts from reference sample

tag: sample type

value: reference


title: 12OctF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14015

tag: gene reported

tag: strain


title: L23_647

description: Array Batch: 20038

value: Cayuga x Caledonia, DH

value: Helfer, Cornell University, Ithaca, NY

value: Pre-anthesis spike bulk

source_name: CxC Line 23, embryo at physiological maturity


title: L26_647

description: Array Batch: 20050

source_name: Pre-anthesis spike bulk

source_name: CxC Line 26, embryo at physiological maturity

value: embryo at physiological maturity


title: L22_647

description: Array Batch: 20038

source_name: CxC Line 22, embryo at physiological maturity


title: Tg26-sample4

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney cortex from HIV mouse model 4

source_name: Kidney cortex from HIV mouse model 4

value: Kidney cortex


title: L21_647

description: Array Batch: 20050

source_name: CxC Line 21, embryo at physiological maturity


title: Tg26-sample3

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney cortex from HIV mouse model 3

source_name: Kidney cortex from HIV mouse model 3

value: male


title: L20_647

description: Array Batch: 20050

source_name: CxC Line20, embryo at physiological maturity


title: Tg26-sample5

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney cortex from HIV mouse model 5

source_name: Kidney cortex from HIV mouse model 5

value: FVB/N background


title: L28_647

description: Array Batch: 20038

source_name: CxC Line 28, embryo at physiological maturity


title: METH EC1-3


title: HSMM-MyoG48h-rep2

description: MyoG IP 48 h after serum removal for myoblast differentiation; biological replicate 2/2

source_name: Human skeletal muscle myoblasts MyoG IP 48 h post-differentiation

value: primary skeletal muscle myoblasts

tag: developmental stage

source_name: Human skeletal muscle myoblasts Input genomic DNA 48 h post-differentiation


title: 12MafM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14012

source_name: Gonad, 12.5 dpc interstitial cell subset and fetal Leydig cells

value: Mafbtm1Jeng / MGI:3663168

value: Progeny of CD-1 crossed to mixed background

tag: sex

tag: theiler stage


title: HSMM-MyoG0h-rep2

description: MyoG IP 0 h after serum removal for myoblast differentiation; biological replicate 2/2

source_name: Human skeletal muscle myoblasts MyoG IP 0 h post-differentiation

value: 0 h post-differentiation


title: 12MafM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14013


title: METH EC10-3

tag: age


title: METH EC1-2


title: METH EC10-1


title: Tg26-sample2

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney cortex from HIV mouse model 2

scan_protocol: Genechip Scanner 3000-7G

source_name: Kidney cortex from HIV mouse model 2

value: Tg26 HIV


title: L18_647

description: Array Batch: 20050

source_name: CxC Line 18, embryo at physiological maturity


title: 12MafF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14010

source_name: Gonad, 12.5 dpc female vascular associated mesenchymal stromal cells

value: female


title: 12MafF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14009


title: L11_647

description: Array Batch: 20038

source_name: CxC Line 11, embryo at physiological maturity


title: wildtype strong 2

city: Zürich

first: Matthias

last: Schäfer

state: ZH

address: Schafmattstrasse 18

department: Department of Cell Biology

country: Switzerland

institute: ETH Zürich

hyb_protocol: 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).

scan_protocol: Standard Affymetrix procedures using a Hewlett-Packard scanner

data_processing: Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the Robust Multichip Average (RMA) method.

source_name: whole skin

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.

growth_protocol: 3 female K5cre-caNrf2 (tg/tg) and 3 female K5cre-wt (tg/wt) mice of one litter were sacrificed at P2.5

extract_protocol: back skin was cut out and snap frozen in N2, RNA was extracted using GSCN and phenol/chloroform

tag: genotype

value: tg/wt

tag: treatment

tag: background strain

value: FVB/N/C57BL/6 mixed


title: Tg26-sample1

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from kidney cortex from HIV mouse model 1

hyb_protocol: Hybridization oven 640, rotate 16-18hrs.

scan_protocol: GeneChip Scanner 3000-7G

source_name: Kidney cortex from HIV mouse model 1

tag: genotype/variation

tag: gender


title: METH Co3

value: whole body extracts (30 organisms)

value: 96h old

value: unexposed control

source_name: whole body extracts from reference sample


title: wildtype strong 1


title: 12MafM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14011


title: METH EC1-1

value: reference

value: methanol


title: 12FlkM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14006

source_name: Gonad, 12.5 dpc male endothelial cells

tag: Sex


title: HSMM-MyoG0h-rep1a

description: MyoG IP 0 h after serum removal for myoblast differentiation; technical replicate 1/2 of biological replicate 1/2

tag: tissue

source_name: Human skeletal muscle myoblasts Input genomic DNA 0 h post-differentiation


title: METH Co1


title: wildtype strong 3


title: L14_647

description: Array Batch: 20050

source_name: Pre-anthesis spike bulk

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Helfer, Cornell University, Ithaca, NY

tag: year

value: Pre-anthesis spike bulk

source_name: CxC Line 14, embryo at physiological maturity

value: embryo at physiological maturity


title: METH Co2

tag: sample type


title: HSMM-MyoG0h-rep1b

description: MyoG IP 0 h after serum removal for myoblast differentiation; technical replicate 2/2 of biological replicate 1/2

value: primary skeletal muscle myoblasts

value: male


title: 12FlkM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14007

tag: gene reported


title: HSMM-MyoG48h-rep1

description: MyoG IP 48 h after serum removal for myoblast differentiation; biological replicate 1/2

value: 48 h post-differentiation


title: ISO EC10

tag: effect concentration

tag: agent

value: isopropanol


title: L8_647

description: Array Batch: 20050

source_name: CxC Line 8, embryo at physiological maturity


title: L7_647

description: Array Batch: 20050

source_name: CxC Line 7, embryo at physiological maturity


title: 12MafF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14008

value: Mafbtm1Jeng / MGI:3663168

tag: strain

value: Progeny of CD-1 crossed to mixed background

tag: sex

tag: developmental stage


title: ISO EC10-2

tag: age


title: transgene strong 1

tag: genotype

value: tg/g

tag: treatment

value: female


title: L5_647

description: Array Batch: 20050

source_name: CxC Line 5, embryo at physiological maturity


title: 12FlkM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14005

tag: theiler stage


title: transgene strong 3

tag: gender

tag: background strain

value: FVB/N/C57BL/6 mixed


title: L1_647

description: Array Batch: 20050

tag: tissue

source_name: CxC Line 1, embryo at physiological maturity


title: 11SryM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14001

source_name: Gonad, 11.5 dpc male supporting cell precursors (pre-Sertoli)

value: Progeny of CD-1 crossed to C57BL/6J

tag: Sex


title: ISO EC10-3

value: whole body extracts (30 organisms)

value: 96h old


title: ISO EC1-3

value: reference


title: 12FlkF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14003

source_name: Gonad, 12.5 dpc female endothelial cells


title: transgene strong 2


title: iPS clone 4 derivated in the absence of ascorbic acid

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description:
MS16
Biological rep 4 of 4.

hyb_protocol: Microarray chip type= Affymetrix GeneChip mouse genome 430 2.0. Affymetrix hybridization oven model 645 and fluidic station model 450. Fluidic protocol was EukGE-WS2v5_450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G controlled by GCOS.

data_processing: The data were analyzed with Affymetrix GCOS (Library file = mouse genome 430 2.0) using the statistic algorithm (alpha1=0.05, alpha2=0.065, tau=0.015). Scaling target value=150.

source_name: iPS cells, without ascorbic acid

label_protocol: Biotinylated cRNA probes were synthesized using Affymetrix one-cycle target labeling and control reagents and the ENZO bioarray high-yield RNA transcript labeling kit following the manufacturer's instructions.

growth_protocol: iPS cells were derivated in ES cell medium (DMEM with FBS, L-Glutamin, penicillin-streptomycin, non-essential amino acids, beta-mercaptoethanol, LIF, doxycycline, in the presence or absence of ascorbic acid) on irradiated MEF feeder cells.

extract_protocol: iPS cells grown on 35mm dishes were harvested when they reached about 50% confluency and preplated on non-gelatinized T25 flasks for 45 minutes to remove feeder cells. Cells were spun down and the pellet used for isolation of total RNA using the miRNeasy Mini Kit (QIAGEN) without DNase digestion. RNA was eluted from the columns using 50 ml RNase-free water or TE buffer, pH7.5 (10 mM Tris-HCl and 0.1 mM EDTA) and quantified using Nanodrop (Nanodrop Technologies).

treatment_protocol: iPS cells were derivated from the reprogrammable mouse MEFs in the presence or absence of ascorbic acid.

tag: cell type

value: induced pluripotent stem cells (iPSCs)


title: L169_555

description: Array Batch: 20050

source_name: CxC Line 169, embryo at physiological maturity

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Helfer, Cornell University, Ithaca, NY

tag: year


title: 11SryM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14000

tag: gene reported


title: L167_555

description: Array Batch: 20038

source_name: CxC Line 167, embryo at physiological maturity

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: 12FlkF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14002


title: L9_647

description: Array Batch: 20038

source_name: CxC Line 9, embryo at physiological maturity


title: iPS clone 2 derivated in the absence of ascorbic acid

description:
MS14
Biological rep 2 of 4.


title: iPS clone 1 derivated in the absence of ascorbic acid

description:
MS13
Biological rep 1 of 4.


title: L174_555

description: Array Batch: 20050

source_name: CxC Line 174, embryo at physiological maturity


title: ISO Co2

tag: sample type

value: unexposed control


title: ISO EC1-1

tag: effect concentration

tag: agent


title: ISO EC1-2


title: ISO Co1


title: ISO Co3


title: iPS clone 3 derivated in the absence of ascorbic acid

description:
MS15
Biological rep 3 of 4.


title: 11SryM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13999

tag: strain

value: male

tag: developmental stage


title: 12FlkF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14004


title: iPS clone 4 derivated in the presence of ascorbic acid

description:
MS12
Biological rep 4 of 4.

source_name: iPS cells, with ascorbic acid

value: ascorbic acid


title: iPS clone 2 derivated in the presence of ascorbic acid

description:
MS10
Biological rep 2 of 4.


title: Eth EC10-3

tag: age

value: ethanol

source_name: whole body extracts from reference sample


title: 11SryF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13998

source_name: Gonad, 11.5 dpc female supporting cell precursors (follicle cells/pre-Granulosa cells)


title: L162_555

description: Array Batch: 20038

source_name: CxC Line 162, embryo at physiological maturity


title: L173_555

description: Array Batch: 20050

source_name: CxC Line 173, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: 11SryF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13996


title: iPS clone 3 derivated in the presence of ascorbic acid

description:
MS11
Biological rep 3 of 4.

tag: treatment


title: 11SryF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13997

tag: theiler stage


title: Renal pelvis cell line UO_31-250K_Nsp

city: Rochester

first: xiaoyang

last: ruan

state: MN

address: 200 1st Street

department: Health Science Research

institute: Mayo Clinic

description:
Hybridized to 250K_Nsp
UO_31-250knsp

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G with AutoLoader.

data_processing: Genotype call was made by Affymetrix Power Tool (Linux, version 1.12.0) BRLMM algorithm. ROH was inferred by dChip (Version 2010/01) basic-HMM module, and PLINK (Version 1.07) ROH module. dChip ROH Call: L, R, and N; PLINK ROH Call: 0, 1 [dChip.txt, PLINK_coverted.txt, and PLINK_rawData.txt are provided as Series supplementary files.]

source_name: Renal pelvis cell line

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0.5 x 10^6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 37C. Spin down suspended cells, and resuspend in ~3ml growth media. Count cells. Pass 1x10^6 cells into new T162's w 30 ml media.  Repeat growth cycle until desired amount of cells are available. Cells are not grown past passage 20.

extract_protocol: Genomic DNA was purified from cells using either the QIAamp DNA Blood Maxi Kit, or the Blood & Cell Culture DNA Maxi Kit (Qiagen Inc., Valencia, CA) according to manufacturer's instructions.  Quality was assessed by optical density 260/280 ratio using a spectrophotometer (Beckman-Coulter, Fullerton, CA) and by 0.8% agarose (SeaKem GTG, FMC BioProducts, Rockland, ME) gel electrophoresis in 1x TAE (Roche, Indianapolis, IN).

tag: tissue type

value: Renal pelvis

tag: cell line


title: L166_555

description: Array Batch: 20050

source_name: CxC Line 166, embryo at physiological maturity

extract_protocol: Total RNA extraction from isolated embryos was done using the Trizol reagent with only slight modifications to the manufacturer protocol. Total RNA was treated with RQ1 DNAse and cleaned using Qiagen Rneasy columns.

tag: tissue


title: Eth  EC10-2


title: Prostate cell line DU_145 ATCC-250K_Nsp

description:
Hybridized to 250K_Nsp
DU_145 ATCC-250knsp

source_name: Prostate cell line

value: Prostate

value: DU145 ATCC


title: L153_555

description: Array Batch: 20038

source_name: CxC Line 153, embryo at physiological maturity


title: L151_555

description: Array Batch: 20050

source_name: CxC Line 151, embryo at physiological maturity


title: L158_555

description: Array Batch: 20050

source_name: CxC Line 158, embryo at physiological maturity


title: 11SmaaM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13994

source_name: Gonad, 11.5 dpc male mesenchymal cells

value: Tg(Acta2-EYFP)Jll / PMID:18769072

value: FVB

tag: sex


title: L145_555

description: Array Batch: 20050

source_name: CxC Line 145, embryo at physiological maturity


title: L157_555

description: Array Batch: 20038

source_name: CxC Line 157, embryo at physiological maturity


title: Eth Co3

value: whole body extracts (30 organisms)


title: 11SmaaM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13993


title: 11SmaaM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13995


title: Eth EC1-2

value: 96h old


title: 11SmaaF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13992

source_name: Gonad, 11.5 dpc female mesenchymal cells

value: female


title: L147_555

description: Array Batch: 20038

source_name: CxC Line 147, embryo at physiological maturity


title: Prostate cell line RCO.1-250K_Nsp

description:
Hybridized to 250K_Nsp
RCO.1-250knsp


title: iPS clone 1 derivated in the presence of ascorbic acid

description:
MS9
Biological rep 1 of 4.

source_name: iPS cells, with ascorbic acid

tag: cell type

value: induced pluripotent stem cells (iPSCs)


title: Renal pelvis cell line 786_0-10-250K_Nsp

description:
Hybridized to 250K_Nsp
TK_10-250knsp


title: Renal pelvis cell line SN12C-250K_Nsp

description:
Hybridized to 250K_Nsp
SN12C-250knsp


title: Eth EC10-1

source_name: whole body extracts from reference sample

value: reference


title: Eth EC1-1


title: Eth EC1-3


title: Renal pelvis cell line RXF-393-250K_Nsp

description:
Hybridized to 250K_Nsp
RXF_393-250knsp


title: 11SmaaF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13991


title: L149_555

description: Array Batch: 20050

source_name: CxC Line 149, embryo at physiological maturity

tag: population

value: Cayuga x Caledonia, DH

value: Helfer, Cornell University, Ithaca, NY


title: L138_555

description: Array Batch: 20050

source_name: CxC Line 138, embryo at physiological maturity

tag: field location

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: TCA EC10-3


title: ETH Co1

value: unexposed control


title: 11SmaaF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13990


title: 11OctM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13988

source_name: Gonad, 11.5 dpc male primordial germ cell

treatment_protocol:
Pooled sample: Yes
Pool size: one or more litters
Dissection method: Dissected out the gonad and mesonephros, trypsinized and FACS sorted.  Capel protocol: FACS Protocol
Experimental design: Female mice were time-mated and the embryos were collected. The gonads were removed and the males and females were separately pooled. The gonads were incubated in Trypsin EDTA for 5-10 minutes. The trypsin was removed, PBS (often with DNase) was added, and the gonadal cells were dissociated by pipetting and pulling through a syringe. The samples were passed through a strainer and then FACS sorted. Capel protocol: FACS protocol.

value: Progeny of CD-1 crossed to C57BL/6J

tag: Sex

value: male


title: 11OctF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13986

source_name: Gonad, 11.5 dpc female primordial germ cell

tag: gene reported


title: Renal pelvis cell line CAKI-1-250K_Nsp

description:
Hybridized to 250K_Nsp
CAKI_1-250knsp

source_name: Metastasis_Renal pelvis cell line

value: Renal pelvis


title: 11OctM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13989


title: TCA EC10-2

tag: sample type


title: L142_555

description: Array Batch: 20038

source_name: CxC Line 142, embryo at physiological maturity

tag: year

source_name: Pre-anthesis spike bulk


title: ETH Co2


title: L135_555

description: Array Batch: 20038

source_name: CxC Line 135, embryo at physiological maturity


title: L137_555

description: Array Batch: 20050

source_name: CxC Line 137, embryo at physiological maturity


title: 11OctM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13987


title: 11OctF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13985


title: L131_555

description: Array Batch: 20050

source_name: CxC Line 131, embryo at physiological maturity


title: Renal pelvis cell line ACHN-250K_Nsp

description:
Hybridized to 250K_Nsp
ACHN-250knsp

source_name: Renal pelvis cell line

value: ACHN


title: L130_555

description: Array Batch: 20038

source_name: CxC Line 130, embryo at physiological maturity


title: L129_555

description: Array Batch: 20050

source_name: CxC Line 129, embryo at physiological maturity


title: TCA EC10-1

tag: effect concentration

tag: agent


title: 11OctF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13984

tag: strain

tag: developmental stage


title: TCA EC1-2

tag: age


title: Prostate cell line PC_3-250K_Nsp

description:
Hybridized to 250K_Nsp
PC_3-250knsp

source_name: Prostate cell line

value: Prostate


title: TCA EC1-3


title: Ovary cell line SK_OV_3-250K_Nsp

description:
Hybridized to 250K_Nsp
SK_OV_3-250knsp

source_name: Ascites_Ovary cell line

value: Ovary


title: TCA Co3


title: Renal pelvis cell line A498-250K_Nsp

description:
Hybridized to 250K_Nsp
A498-250knsp


title: Renal pelvis cell line 786_0-250K_Nsp

description:
Hybridized to 250K_Nsp
786_0-250knsp


title: TCA EC1-1


title: 11MafM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13983

source_name: Gonad, 11.5 dpc male vascular associated mesenchymal cells

value: Mafbtm1Jeng / MGI:3663168

value: Progeny of CD-1 crossed to mixed background

tag: theiler stage


title: L126_555

description: Array Batch: 20050

source_name: CxC Line 126, embryo at physiological maturity


title: TCA Co1

source_name: whole body extracts from reference sample

value: whole body extracts (30 organisms)

value: 96h old


title: DCA EC10-3


title: TCA Co2


title: Prostate cell line DU_145 DTP-250K_Nsp

description:
Hybridized to 250K_Nsp
DU_145 DTP-250knsp

tag: tissue type

value: DU145 DTP


title: L123_555

description: Array Batch: 20038

source_name: CxC Line 123, embryo at physiological maturity


title: 11MafM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13981


title: L120_555

description: Array Batch: 20050

source_name: CxC Line 120, embryo at physiological maturity


title: L119_555

description: Array Batch: 20050

source_name: CxC Line 119, embryo at physiological maturity


title: 11MafF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13980

source_name: Gonad, 11.5 dpc female vascular associated mesenchymal cells

value: female


title: 11MafM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13982


title: L125_555

description: Array Batch: 20050

source_name: CxC Line 125, embryo at physiological maturity

value: Cayuga x Caledonia, DH


title: Ovary cell line NCI_ADR_RES-250K_Nsp

description:
Hybridized to 250K_Nsp
NCI_ADR_RES-250knsp

source_name: Ovary cell line

tag: cell line

value: NCI/ADR-RES


title: 11MafF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13978


title: L124_555

description: Array Batch: 20050

source_name: CxC Line 124, embryo at physiological maturity

value: Helfer, Cornell University, Ithaca, NY

tag: tissue

value: embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: DCA EC10-1

value: reference


title: 11MafF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13979

tag: sex


title: Ovary cell line OVCAR_8-250K_Nsp

description:
Hybridized to 250K_Nsp
OVCAR_8-250knsp


title: 11FlkM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13976

source_name: Gonad and mesonephros, 11.5 dpc male endothelial cells

treatment_protocol:
Pooled sample: Yes
Pool size: one or more litters
Dissection method: Dissected out the gonad and a portion of the mesonephros, trypsinized and FACS sorted.  Capel protocol: FACS Protocol
Experimental design: Female mice were time-mated and the embryos were collected. The gonads were removed and the males and females were separately pooled. The gonads were incubated in Trypsin EDTA for 5-10 minutes. The trypsin was removed, PBS (often with DNase) was added, and the gonadal cells were dissociated by pipetting and pulling through a syringe. The samples were passed through a strainer and then FACS sorted. Capel protocol: FACS protocol.


title: 11FlkM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13977


title: DCA EC1-3


title: DCA EC1-1


title: L116_555

description: Array Batch: 20038

source_name: CxC Line 116, embryo at physiological maturity

value: Pre-anthesis spike bulk


title: L115_555

description: Array Batch: 20050

source_name: CxC Line 115, embryo at physiological maturity


title: Ovary cell line IGROV1-250K_Nsp

description:
Hybridized to 250K_Nsp
IGROV1-250knsp


title: DCA EC1-2


title: Ovary cell line OVCAR_3-250K_Nsp

description:
Hybridized to 250K_Nsp
OVCAR_3-250knsp


title: DCA Co3

value: unexposed control


title: Ovary cell line OVCAR_5-250K_Nsp

description:
Hybridized to 250K_Nsp
OVCAR_5-250knsp


title: DCA Co2


title: L110_555

description: Array Batch: 20050

source_name: CxC Line 110, embryo at physiological maturity


title: 11FlkF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13974

source_name: Gonad and mesonephros, 11.5 dpc female endothelial cells


title: Ovary cell line OVCAR_4-250K_Nsp

description:
Hybridized to 250K_Nsp
OVCAR_4-250knsp


title: Ovary cell line OVCAR_3-250K.1_Nsp

description:
Hybridized to 250K_Nsp
OVCAR_3-250knsp

source_name: Ascites_Ovary cell line


title: Melanocyte cell line UACC-257-250K_Nsp

description:
Hybridized to 250K_Nsp
UACC_257-250knsp

source_name: Melanocyte cell line

value: Melanocyte


title: L107_555

description: Array Batch: 20038

source_name: CxC Line 107, embryo at physiological maturity


title: 11FlkF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13972


title: L111_555

description: Array Batch: 20050

source_name: CxC Line 111, embryo at physiological maturity


title: DCA Co1

source_name: whole body extracts from reference sample


title: Melanocyte cell line SK_MEL-2-250K_Nsp

description:
Hybridized to 250K_Nsp
SK_MEL_2-250knsp

source_name: Metastasis_Melanocyte cell line


title: 11FlkM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13975

value: male


title: DCA EC10-2