|
Status |
Public on Oct 19, 2022 |
Title |
WT Cortex female mRNA rep9 |
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: N/A plate id: Plate 01 well address: G01
|
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_1 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 |
SAMN15149842 |
SRA |
SRX8483509 |