GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2321997

Query DataSets for GSM2321997

Status

Public on Jul 27, 2017

Title

Drosha-deficient ES cells mRNA

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: mRNA 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_mRNA

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