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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 11, 2014 |
| Title |
Sf1+ mouse adrenocortical cells vs. Wnt-responsive mouse adrenocortical cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
We sought to determine which gene transcripts are enriched in Wnt-responsive adrenocortical mouse cells compared to the entire adrenocortical mouse cell population in vivo. To this end, we employed transgenic reporter mice that label Wnt-responsive cells with GFP expression (TCF/Lef:H2B-GFP mice) or label all adrenocortical cells with GFP expression (Sf1:eGFP mice). GFP-positive adrenocortical cells were obtained from 6-week-old male TCF/Lef:H2B-GFP mice and Sf1:eGFP mice independently. 10 adrenals per genotype per sort were minced and digested by incubation in DMEM:F12 containing 0.1% collagenase/ 0.01% DNaseI solution for 1 h at 37°C. A single cell suspension was obtained following mechanical dispersion, filtration through a 40 micron nylon cell strainer, centrifugation at 1500rpm for 5 min followed by re-suspension in sterile 1X PBS containing 10% cosmic calf serum and 10μg/mL Propidium iodide. 10,000-50,000 viable GFP-positive cells were isolated via FACS using a BD FACSAria III cell sorter. RNA was extracted using an RNeasy Micro Kit (Qiagen) from 4 independent sorts per genotype. cDNA were prepared according to the NuGen WT-Pico V2 kit protocol from 5 ng total RNA (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA were prepared from 3ug of cDNA (Encore Biotin Module P/N 4200-12, 4200-60, 4200-A01). Targets were assayed on the Mouse Gene ST 1.1 strip arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267). One TCF/Lef:H2B-GFP array was deemed low-quality and discarded. Two-sample T-tests were used to compare the two groups of samples. We also supply a supplementary file holding the data and some statistical analysis, as well as probe-set annotation that we used at that time (users may wish to obtain new annotation though). We analyzed only 28944 probe-sets with category "main", "---", and "flmrna->unmapped" according to Affymetrix annotation.
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| Overall design |
GFP-positive adrenocortical cells were obtained from 6-week-old male TCF/Lef:H2B-GFP mice and Sf1:eGFP mice independently. 10 adrenals per genotype per sort were minced and digested by incubation in DMEM:F12 containing 0.1% collagenase/ 0.01% DNaseI solution for 1 h at 37°C. A single cell suspension was obtained following mechanical dispersion, filtration through a 40 micron nylon cell strainer, centrifugation at 1500rpm for 5 min followed by re-suspension in sterile 1X PBS containing 10% cosmic calf serum and 10μg/mL Propidium iodide. 10,000-50,000 viable GFP-positive cells were isolated via FACS using a BD FACSAria III cell sorter. RNA was extracted using an RNeasy Micro Kit (Qiagen) from 4 independent sorts per genoytpe. cDNA were prepared according to the NuGen WT-Pico V2 kit protocol from 5 ng total RNA (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA were prepared from 3ug of cDNA (Encore Biotin Module P/N 4200-12, 4200-60, 4200-A01). Targets were assayed on the Mouse Gene ST 1.1 strip arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).
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| Contributor(s) |
Walczak E, Kuick R, Hammer G |
| Citation(s) |
25029241 |
| Submission date |
Jan 10, 2014 |
| Last update date |
Apr 18, 2017 |
| Contact name |
Rork Kuick |
| E-mail(s) |
rork@umich.edu
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| Phone |
734-936-9241
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| Organization name |
University of Michigan
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| Street address |
University of Michigan, SPH II, 1415 Washington Heights, Room M2533
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109-2029 |
| Country |
USA |
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| Platforms (1) |
| GPL11533 |
[MoGene-1_1-st] Affymetrix Mouse Gene 1.1 ST Array [transcript (gene) version] |
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| Samples (7)
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| GSM1304761 |
SF1+ mouse adrenocortical cells, biological replicate 1 |
| GSM1304762 |
SF1+ mouse adrenocortical cells, biological replicate 2 |
| GSM1304763 |
SF1+ mouse adrenocortical cells, biological replicate 3 |
| GSM1304764 |
SF1+ mouse adrenocortical cells, biological replicate 4 |
| GSM1304765 |
Wnt+ mouse adrenocortical cells, biological replicate 1 |
| GSM1304766 |
Wnt+ mouse adrenocortical cells, biological replicate 2 |
| GSM1304767 |
Wnt+ mouse adrenocortical cells, biological replicate 3 |
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| Relations |
| BioProject |
PRJNA234273 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE53981_RAW.tar |
27.9 Mb |
(http)(custom) |
TAR (of CEL) |
| GSE53981_supplementB1.xlsx.gz |
8.1 Mb |
(ftp)(http) |
XLSX |
| Processed data included within Sample table |
| Processed data are available on Series record |
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