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Status |
Public on Apr 29, 2024 |
Title |
1 month cortex from WT mouse 1 [S_CX_WT1] |
Sample type |
SRA |
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Source name |
cortex
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Organism |
Mus musculus |
Characteristics |
tissue: cortex cell type: mix genotype: WT
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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).
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Submission date |
Oct 14, 2022 |
Last update date |
Apr 29, 2024 |
Contact name |
Thomas Roule |
E-mail(s) |
roulet@chop.edu
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Organization name |
CHOP
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Lab |
Akizu Lab
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Street address |
3501 Civic Center Boulevard 5th Floor CTRB-5400
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City |
Philadelphia |
State/province |
Pennsylvania |
ZIP/Postal code |
19104 |
Country |
USA |
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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. |
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Relations |
BioSample |
SAMN31289123 |
SRA |
SRX17896894 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6642061_CX_WT1.bw |
36.5 Mb |
(ftp)(http) |
BW |
GSM6642061_CX_WT1.txt.gz |
4.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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