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Sample GSM1528085 Query DataSets for GSM1528085
Status Public on Oct 01, 2015
Title WT - 471
Sample type SRA
Source name mESC
Organism Mus musculus
Characteristics strain: C57BL/6
Sex: male
cell type: embryonic stem cells
day: 4
clone: E3
genotype: Trimfl/fl
Treatment protocol Trim71 conditional ("WT") cells were treated with 500 nM 4-OHT for 2 days to induce Trim71 mutation. Cells were further cultivated before cell harvest for at least 7 days.
Growth protocol mES cells were cultivated in complete mES medium (FCS+LIF). Before analysis, harvested cells were subjected to SSEA-1 MACS sorting to correct for spontanious differentiation during culture. Two different mES cell clones were used in this study (with each WT and KO condition)
Extracted molecule total RNA
Extraction protocol Cells lysed in TRIZOL (Invitrogen), and total RNA was extracted according to the manufactures’ protocol
Illumina TruSeq RNA Sample Preparation Kit v2
200 bp paired-end run was performed on a HiSeq1500
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 1500
Data processing base calling and de-multipexing using CASAVA version 1.8
Alignment with Bowtie2 version 2.2.1 using the default parameters against mm10 from mirBase v20
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on April 2014
Normalization using DeSeq2
Genome_build: mm10
Submission date Oct 20, 2014
Last update date May 15, 2019
Contact name Joachim Schultze
Organization name LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
Department Genomics and Immunoregulation
Street address Carl-Troll-Strasse 31
City Bonn
State/province NRW
ZIP/Postal code 53115
Country Germany
Platform ID GPL18480
Series (1)
GSE62509 miRNA sequencing of Trim71 conditional ("WT") and Trim71 KO mES cells
BioSample SAMN03120821
SRA SRX736333

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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