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Sample GSM2321998 Query DataSets for GSM2321998
Status Public on Jul 27, 2017
Title Drosha-deficient ES cells short RNA
Sample type SRA
 
Source name Drosha-deficient ES cells
Organism Mus musculus
Characteristics genotype/variation: Drosha-deficient
cell type: embryonic stem cells (ES cells)
molecule subtype: Short RNA
Growth protocol MethylC-Seq: ES cells were cultured in ES cell media which consists of Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum, 100 IU/mL penicillin, 100mg/mL streptomycin, 2 mmol/L L-glutamine, MEM non-essential amino acids, 0.12 mmol/L β-mercaptoethanol, and leukemia inhibitory factor (LIF); RNA-seq: ES cells were cultured in ES cell media which consists of Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum, 100 IU/mL penicillin, 100mg/mL streptomycin, 2 mmol/L L-glutamine, MEM non-essential amino acids, 0.12 mmol/L β-mercaptoethanol, and leukemia inhibitory factor (LIF)
Extracted molecule total RNA
Extraction protocol RNA-seq: Trizol Extracted total RNA was subsequently fractionated into long and short (using miRVana miRNA Isolation Kit) and mRNA (using Oligotext mRNA Mini Kit)
MethylC-Seq: Genomic DNA was prepared from fresh cell pellets using GeneJET Genomic DNA Purification Kit (ThermoScientific) according to the manufacturer’s protocol; RNA-seq: Libraries were constructed according to NEBNext Multiple Small RNA Library Prep Protocol (NEB)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Ooi_lab_M_musculus_drosha_shortRNA
Data processing RNA-seq: Basecalls performed using bcl2fastq v1.8.4
RNA-seq: Adapter sequence removed using fastq-mcf
RNA-seq: Reads trimmed according to quality score using seqtk trimfq (-q 0.01)
RNA-seq: Reads mapped to mouse genome (mm10) with TopHat2 v2.0.10
RNA-seq: Transcripts assembled for wildtype, Drosha-/- and Dnmt1c/c datasets for each of the RNA types (short, long and mRNA) using Cufflinks v2.1.1 (default settings, -g gencode.vM3.annotation.gtf)
RNA-seq: Wildtype and Drosha-/- transcripts merged using Cuffmerge to obtain master transcriptomes for each pairwise comparison of gene expression, in each RNA type
RNA-seq: Differential gene expression analysis carried out using Cuffdiff (gencode.vM3.annotation.gtf, short RNA was masked using a gtf file containing gencode rRNAs, Mt_tRNAs, snRNAs, Mt_rRNAs and snoRNAs)
Genome_build: Mus musculus GRCm38 reference genome
Supplementary_files_format_and_content: tab delimited text file
 
Submission date Sep 19, 2016
Last update date May 15, 2019
Contact name Robert J Schmitz
E-mail(s) schmitz@uga.edu
Organization name University of Georgia
Department Genetics
Street address B416 Davison Life Sciences
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platform ID GPL17021
Series (1)
GSE86907 A novel requirement for Drosha in maintenance of mammalian CG methylation
Relations
BioSample SAMN05788762
SRA SRX2175618

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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