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Sample GSM2778516 Query DataSets for GSM2778516
Status Public on Oct 01, 2018
Title ER_WT2
Sample type SRA
 
Source name mammary gland
Organism Mus musculus
Characteristics genotype/variation: WT.GFP+
Extracted molecule total RNA
Extraction protocol RNA was extracted from FACS sorted cells derived from intraductally engrafted WT.GFP+ or ERα-/-.GFP+ cells from contralateral glands of the pregnant NSG hosts using miRNeasy Mini Kit (Qiagen, cat.# 217004)
Libraries were prepared in 2 steps. The first step was performed according to Clontech's instructions accompanying the SMART-Seq v4 Ultra Low Input RNA Kit (Part# 634889). Briefly, 10 ng of RNA was reverse transcribed uning a oligo dT primer flanked with a proprietary adapter. Template switching mechanism was then used to append another proprietary adapter on the 3' end of the cDNA (corresponding to the beginning of the mRNA molecule). A PCR specific for the aforementionned adapters was used to create and amplify double-stranded cDNA molecules. The second step was performed according to Illumina's instructions accompanying the Nextera XT kit (Part# FC-131-1096). Briefly, tagmentation of the double-stranded cDNA with hyperactive Tn5 created fragments of a few hundred bp, flanked with Illumina proprietary adapters. DNA was then PCR amplified with Illumina primers for 8 cycles, generating final libraries of ~400 bp (insert plus adaptors). Libraries were sequenced on a NextSeq 500 instrument with single-end reads of 85 nt, following the manufacturer's protocols. Basecalls and Illumina adapters trimming performed using bcl2fastq v2.18. Clontech adapters trimming performed with CLC 9.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing RNA-seq reads were aligned to the mm10 mouse genome using the RNA-Seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTS station http://htsstation.epfl.ch (David, FPA et al. HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis. PLoS ONE 9, e85879 (2014). We applied the ready-to-use pipeline ASAP (the Automated Single-cell Analysis Pipeline) https://asap.epfl.ch/ (https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx337) to the RNA-seq analysis.
Genome_build: mm10
 
Submission date Sep 08, 2017
Last update date May 15, 2019
Contact name George A Sflomos
E-mail(s) georgios.sflomos@epfl.ch
Phone 0041(0)216930784
Organization name EPFL
Department ISREC
Lab BRISKEN
Street address SV 2815, Batiment SV, Station 19
City Lausanne
ZIP/Postal code 1024
Country Switzerland
 
Platform ID GPL19057
Series (1)
GSE103664 The Estrogen Receptor α (ERα) has stage- and cell type-specific roles in the mammary epithelium with distinct requirements for activation function-1 and -2
Relations
BioSample SAMN07625925
SRA SRX3173685

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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