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Sample GSM1079799 Query DataSets for GSM1079799
Status Public on Apr 10, 2013
Title Flag-HA-NR6A1_Clone6
Sample type SRA
Source name Dicer f/f murine MSC cell line
Organism Mus musculus
Characteristics cell type: murine MSC cell line
genotype: Dicer f/f
strain: C57BL/6
Treatment protocol Two independent clones of immortalized Dicer WT MSCs (Clone 6 and Clone 12) were infected with puromycin-resistant pMMP-puro retrovirus encoding vector control or Flag-HA-NR6A1.
Growth protocol Monoclonal immortalized Dicer WT MSCs were cultured in Alpha-MEM supplemented with pen/strep and 10% fetal bovine serum.
Extracted molecule polyA RNA
Extraction protocol mRNA-sequencing was carried out with total RNA purified with the RNeasy reagent (Qiagen) and DNase-treated with TURBO Dnase. (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description mRNAs isolated from immortalized clonal lines of Dicerf/f (Dicer WT) mesenchymal stem cells (MSCs), a fibroblast cell type present in adult bone marrow, were infected with puromycin-resistant pMMP-puro retrovirus encoding Flag-HA-NR6A1.
Data processing Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Sequence reads were trimmed to remove traces of adapter sequence (AGATCGGAAGAGCGGTTCAGCAGGAATG). Reads were first mapped to the mouse transcriptome (UCSC annotation, genome build mm9) and un-aligned reads were then mapped to the mouse genome where possible. Read mapping was performed with TopHat version 1.2.0 using default options. Abundance estimation and differential analysis were performed using Cufflinks version 1.0.3 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) value per gene for each sample
Submission date Feb 07, 2013
Last update date May 15, 2019
Contact name A Bhutkar
Organization name MIT
Street address 77 Massachusetts Avenue
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platform ID GPL13112
Series (2)
GSE44158 Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [mRNA-seq_Flag-HA-NR6A1_overexpr]
GSE44163 Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts
Reanalyzed by GSE80797
SRA SRX228561
BioSample SAMN01915291

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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