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Sample GSM2936896 Query DataSets for GSM2936896
Status Public on Jun 04, 2018
Title CD49fHi Lgr5Hi biological replicate 1
Sample type RNA
 
Source name CD49fHi Lgr5Hi mammary cells from Lgr5-IRES-GFP female embryos isolated at E14
Organism Mus musculus
Characteristics tissue: Embryonic mouse mammary gland FACS purified cells
Treatment protocol Pregnant females bearing Lgr5-IRES-GFP embryos were sacrificed at 14 days of gestation and E14 embryos were collected and epidermis + mammary gland were digested in Collagenase+hyaluronidase. Single cells were stained with the appropriate antibodies and FACS sorted.
Growth protocol Mice were maintained in a certified animal house according to European guidelines
Extracted molecule total RNA
Extraction protocol RNA isolation and cDNA amplification was performed as described by Gonzalez-Roca et al. (2010).In brief, 813 or 2000 cells were sorted into lysis buffer and RNA was purified using magnetic beads (RNAClean XP beads, Agencourt).RNA was reverse transcribed and cDNA was amplified using Whole Transcriptome Amplification chemistry (WTA2, Sigma Aldrich). For monitoring amplification, SYBR Green was added to the reaction; it was stopped after 25 cycles when SYBR Green signal reached a plateau. cDNA was purified using Genelute PCR Clean-Up kit (Sigma Aldrich).
Label Biotin
Label protocol cDNA was labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.
 
Hybridization protocol Affymetrix MG-430 PM array strips were hybridized with 8 mg of labeled cDNA, washed, stained and scanned according to the protocol described in GeneAtlas 3’IVT express kit User Manual.
Scan protocol Arrays were scanned with GeneAtlasImaging station scanner (Affymetrix, Santa Clara, CA)
Description Gene expression of 2000 CD49fHi Lgr5Hi mammary cells from Lgr5-IRES-GFP female embryos isolated at E14, biological replicate 1
Data processing All the results were normalized using the RMA normalization algorithm using R-bioconductor affy package with standard parameters. Cross experiment normalization was further performed to eliminate the batch effect using non-parametric empirical Bayes frameworks for adjusting data implemented in ComBat function of the Surrogate Variable Analysis package (SVA) in R-bioconductor for the two different microarrays used here and then between this experiment and the previously published data under the accession number GSE69290.
 
Submission date Jan 17, 2018
Last update date Jun 04, 2018
Contact name Alexandra Van Keymeulen
Organization name Université Libre de Bruxelles
Department IRIBHM
Lab Blanpain
Street address 808, route de Lennik CP602
City Bruxelles
ZIP/Postal code 1070
Country Belgium
 
Platform ID GPL11180
Series (2)
GSE109306 Early lineage segregation of multipotent embryonic mammary gland progenitors [expression]
GSE109711 Early lineage segregation of multipotent embryonic mammary gland progenitors

Data table header descriptions
ID_REF
VALUE RMA expression estimate

Data table
ID_REF VALUE
1428118_PM_at
1436602_PM_x_at
1436741_PM_at
1459030_PM_at
1425425_PM_a_at 98.94796847
1428455_PM_at 169.3296083
1460049_PM_s_at 26.39235584
1457273_PM_at 102.0540007
1434458_PM_at 32.10822742
1450988_PM_at 145.1372742
1418457_PM_at 370.4326735
1450440_PM_at 109.2023279
1423261_PM_at 69.59611417
1436044_PM_at 60.06321019
1450928_PM_at 51.22360589
1458268_PM_s_at 200.2175514
1423259_PM_at 38.14111927
1418456_PM_a_at 854.3832763
1418666_PM_at 63.78101716
1423062_PM_at 175.6344407

Total number of rows: 45141

Table truncated, full table size 1159 Kbytes.




Supplementary file Size Download File type/resource
GSM2936896_1476_2016.ga.cel.gz 2.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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