|
| Status |
Public on Apr 29, 2024 |
| Title |
1 month cortex from KO mouse 3 [S_CX_KO3] |
| Sample type |
SRA |
| |
|
| Source name |
cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cortex
cell type: mix
genotype: Snx14 KO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse brain tissue were dissected on ice, fast froze in liquid nitrogen, and stored in -80˚C until use. On the day of RNA extraction, 50mg to 100mg tissue from each sample was lysed in 1ml TRIzol (15596026, Invitrogen). Addition of 0.2ml chloroform (288306, Sigma-Aldreich) followed by centrifugation was performed to separate the solution into an aqueous phase and an organic phase. Isopropyl alcohol and 75% ethanol (111000200CSPP, Pharmco) was added in sequence to precipitate and wash the RNA pellets.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were counted using FeatureCounts from the subread package (v2.0.1) with parameters: -p -C -O.
Differential gene expression analysis was performed with DEseq2 (V1.38.3) excluding genes with less than five reads, and all genes from chromosome X and Y. Differential expression was performed using a linear model and as factor the genotypes.
BigWig files were generated using bamCoverage from the deepTools suite with parameters: --normalizeUsing BPM --binSize 10.
Assembly: mm10/GRCm38
Supplementary files format and content: Tab-delimited text file including read count values for each gene (.txt).
Supplementary files format and content: Coverage files in bigWig format (.bw).
|
| |
|
| Submission date |
Oct 14, 2022 |
| Last update date |
Apr 29, 2024 |
| Contact name |
Thomas Roule |
| E-mail(s) |
roulet@chop.edu
|
| Organization name |
CHOP
|
| Lab |
Akizu Lab
|
| Street address |
3501 Civic Center Boulevard 5th Floor CTRB-5400
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE215831 |
Altered lipid homeostasis underlies selective neurodegeneration in SNX14 deficiency [1 month] |
| GSE215834 |
Altered lipid homeostasis underlies selective neurodegeneration in SNX14 deficiency. |
|
| Relations |
| BioSample |
SAMN31289118 |
| SRA |
SRX17896899 |
