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Sample GSM2913359 Query DataSets for GSM2913359
Status Public on Aug 31, 2018
Title ESC_Total_dox_2 (5)
Sample type SRA
 
Source name embryonic stem cells
Organism Mus musculus
Characteristics cells: ESC doxycycline-inducible expressing HA-Flag-AGO2
passages: 8-15
fraction: Total
rip antibody: Monoclonal ANTI-FLAG® M2 antibody produced in mouse (Sigma-Aldrich, catalog# M8823)
Treatment protocol 15 h before cell harvesting, transgene expression was induced with 2.5 ug/ml doxycycline in ESC.
Growth protocol ESC were grown on 0.1% gelatin in DMEM supplemented with 15% heat-inactivated FBS, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1mM Sodium Pyruvate and 1000 U/ml recombinant leukemia inhibitory factor.
Extracted molecule total RNA
Extraction protocol Cells were fractionated and AGO2 was immunoprecipitated from cytoplasmic and nuclear fraction. The RNA was isolated using Trizol.
Preadenylated, barcoded 3´adapter oligonucleotide was ligated followed by ligation of a 5´adapter. Ligation products were reverse transcribed and amplified by PCR.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 3000
 
Description miRNA_ESC_MT.xlsx
Data processing Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the mm10 genome using TopHat
The miRNA normalized counts was generated as in Farazi et al., Cancer research 2011 (GEO accession number GSE28884)
Genome_build: mm10
Supplementary_files_format_and_content: xlsx reports Normalized counts
 
Submission date Jan 05, 2018
Last update date Aug 31, 2018
Contact name Markus Hafner
E-mail(s) Markus.hafner@nih.gov
Phone 3014026956
Organization name NIH
Department NIAMS
Lab Markus Hafner
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL21493
Series (2)
GSE108799 Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation [5_miRNA-seq]
GSE108801 Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation
Relations
BioSample SAMN08296076
SRA SRX3534032

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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