|
| Status |
Public on Jun 30, 2023 |
| Title |
MEFs, Δ-C60-Cre, RNA-seq, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Embryo
cell type: Mouse Embryonic Fibroblasts (MEFs)
genotype: Nelfb flox/-
treatment: pBabe-delta-C60; Ad-Cre; single clone isolation
|
| 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 |
SAMN28842330 |
| SRA |
SRX15576468 |
