|
| Status |
Public on Oct 19, 2022 |
| Title |
WT Cortex female mRNA rep10 |
| Sample type |
SRA |
| |
|
| Source name |
Cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Cerebral Cortex
genotype: Wild type
strain/background: C57BL/6
age: 6 months
Sex: female
batch: Ece2 group
corresponding striatum sample name: WT Striatum female mRNA rep52
plate id: Plate 01
well address: C06
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Brain cortical tissues were dissected from all mice at 6 months of age. RNA was extracted using Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded libraries preparation protocol (Illumina Inc).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Ece2_2_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt
|
| Data processing |
Libraries for RNA-seq were sequenced using an Illumina HiSeq 4000 PE-75.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.3a with default parameter settings.
Raw counts were obtained with HTSeq 0.10.0 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Genome_build: Genome version Mouse GRCm38 (mm10)
Supplementary_files_format_and_content: FPKM_ensembl.txt: Tab-delimited text file includes FPKM values for each Sample (reference: RefSeq).
Supplementary_files_format_and_content: FPKM_ensembl.txt: Tab-delimited text file includes FPKM values for each Sample (reference: Ensembl).
Supplementary_files_format_and_content: metaReadCount_refSeq.txt: Tab-delimited text file includes Count values for each Sample (reference: RefSeq).
Supplementary_files_format_and_content: metaReadCount_ensembl.txt: Tab-delimited text file includes Count values for each Sample (reference: Ensembl).
|
| |
|
| Submission date |
Jun 05, 2020 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Jeff Aaronson |
| E-mail(s) |
jeff.aaronson@chdifoundation.org
|
| Phone |
(609) 945-9616
|
| Organization name |
CHDI
|
| Department |
Discovery & Systems Biology
|
| Street address |
155 Village Boulevard, Suite 200
|
| City |
Princeton |
| State/province |
New Jersey |
| ZIP/Postal code |
08540 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE151923 |
Transcriptional profiling of cortex from 6-month-old wildtype C57BL/6 mice |
|
| Relations |
| BioSample |
SAMN15149841 |
| SRA |
SRX8483510 |
