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Sample GSM2913368 Query DataSets for GSM2913368
Status Public on Aug 31, 2018
Title No_dox_Chr_2 (6)
Sample type SRA
 
Source name embryonic stem cells
Organism Mus musculus
Characteristics cells: ESC doxycycline-inducible expressing HA-Flag-AGO2
passages: 8-15
fraction: chromatin
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 the cytoplasmic and nucleoplamic fractions disgarded. The purified chromatin fraction was resuspended in TRIzol and the chromatin bound RNA isolated.
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description Chr_dox_noDox_gene_exp.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
Abundance measurements in cuffdiff output
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file reports RPKMs and log2fold change of average RPKM between noDox and Dox
 
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)
GSE108800 Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation [6_chr_seq]
GSE108801 Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation
Relations
BioSample SAMN08296081
SRA SRX3534041

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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