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| Status |
Public on Oct 01, 2018 |
| Title |
ER_WT2 |
| Sample type |
SRA |
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| Source name |
mammary gland
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| Organism |
Mus musculus |
| Characteristics |
genotype/variation: WT.GFP+
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Sep 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
George A Sflomos |
| E-mail(s) |
georgios.sflomos@epfl.ch
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| Phone |
0041(0)216930784
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| Organization name |
EPFL
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| Department |
ISREC
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| Lab |
BRISKEN
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| Street address |
SV 2815, Batiment SV, Station 19
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| City |
Lausanne |
| ZIP/Postal code |
1024 |
| Country |
Switzerland |
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| 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 |
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| Relations |
| BioSample |
SAMN07625925 |
| SRA |
SRX3173685 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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