NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6211267 Query DataSets for GSM6211267
Status Public on Jun 30, 2023
Title MEFs, MT194, Cre, RNA-seq, biol rep1
Sample type SRA
 
Source name Embryo
Organism Mus musculus
Characteristics tissue: Embryo
cell type: Mouse Embryonic Fibroblasts (MEFs)
genotype: Nelfb flox/-
treatment: pLenti-MT194; 7 days after Ad-Cre-GFP
Growth protocol 10% FBS in DMEM
Extracted molecule total RNA
Extraction protocol RNA was harvested using RNeasy kit
RNA libraries were prepared following the Illumina TruSeq stranded mRNA-seq sample preparation guide.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Raw RNA-seq data in FASTQ format were aligned to mm10 reference genome using bowtie2. The Sequence Alignment Map (SAM) file was converted to a Binary Alignment Map (BAM) file, and then sorted by Samtools. Alignments with MAPQ score smaller than 30 were skipped.
HTSeq was used to calculate the number of mapped reads to each gene. The count matrix was imported to DESeq2 for normalization, visualization and analysis of differential gene expression. Empirical Bayes shrinkage estimators were applied to shrink the limit fold change (LFC). The shrinkage of effect size (LFC estimates) was then used for visualization and ranking of genes.
The significantly differentially expressed genes (DEGs) were identified by two thresholds: (1) the absolute value of log2 fold change (LFC) greater than 0.5; (2) the adjust p-value (p-adj) less than 0.05.
These DEGs were used for further GO term enrichment analysis by R package clusterProfiler
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each sample
 
Submission date Jun 02, 2022
Last update date Jun 30, 2023
Contact name Haihui Pan
E-mail(s) panh@email.gwu.edu
Organization name George Washington University
Department Biochemistry and Molecular Medicine
Street address 2121 I St NW
City Washington
State/province DC
ZIP/Postal code 20052
Country USA
 
Platform ID GPL21493
Series (1)
GSE205388 Essential Signaling Function of Cytoplasmic NELFB Independent of RNA Polymerase II Pausing
Relations
BioSample SAMN28842323
SRA SRX15576475

Supplementary file Size Download File type/resource
GSM6211267_MTA_GFP_Cre_D1_count.txt.gz 99.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap