 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 03, 2023 |
| Title |
biol WT2 |
| Sample type |
SRA |
| |
|
| Source name |
Cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Cortex
genotype: WT
Sex: male
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
To isolate RNA, mouse cortex was homogenized in 1mL of TRIzol and RNA was purified using chloroform and Isopropyl alcohol
Poly(A)+ transcripts were isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module kit according to the manufacturer’s protocol (New England BioLabs Inc., Massachusetts, USA). RNA samples were randomly primed (5’ d(N6) 3’ [N=A,C,G,T]) and fragmented. The first strand was synthesized with Protoscript II Reverse Transcription with a modified extension period as to what is stated in the manufacturer’s protocol (30 minutes at 42⁰C). The remaining steps of library generation were carried out according to the manufacturer’s protocol NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
s283
|
| Data processing |
RNA sequencing reads were trimmed using Trimmomatic/0.36. Illumina adapters were removed from the reads. The leading and trailing ends of reads were trimmed if the base quality dropped below a Phred score of 20, and a sliding window 4:15
Sequenced reads were aligned to the mouse genome mm10 using STAR/2.7.0f with the default parameters.
Genes with less than 20 reads were dropped and differential gene expression analysis was performed with DESeq2.
DESeq2 was also used to generate VST normalized read counts for each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Feb 24, 2023 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Matthew J Armstrong |
| E-mail(s) |
matthew.armstrong@emory.edu
|
| Organization name |
Emory University
|
| Street address |
615 Michael St
|
| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE226053 |
Role of TET1-mediated epigenetic modulation in Alzheimer’s disease [RNA-Seq] |
| GSE226056 |
Role of TET1-mediated epigenetic modulation in Alzheimer's disease |
|
| Relations |
| BioSample |
SAMN33436010 |
| SRA |
SRX19496132 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7062065_raw_counts_anno_s283_matrix.txt.gz |
190.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
