|
| Status |
Public on Mar 16, 2023 |
| Title |
M-3294_G34W_10W_crx_RNA |
| Sample type |
SRA |
| |
|
| Source name |
mouse cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Cortex
age: 10 weeks
Sex: Male
gentoype: Hf3fa+/G34W
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from pulverized tissue using the Aurum Total RNA Mini Kit (Bio-Rad) according to manufacturer’s instructions.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were trimmed using Trimmomatic v0.32. First, adaptors and other Illumina-specific sequences from each read were removed using palindrome mode. Then, a four-nucleotide sliding window removes the bases once the average quality within the window falls below 30. Next, the first four bases at the start of each read were removed. Finally, reads shorter than 30 base pairs were dropped.
Cleaned reads were aligned to the mouse reference genome build mm10 using STAR v2.3.0e with default settings. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
Bedgraph files were generated with bedtools 2.27.1 genomeCoverageBed function using a normalization factor of number of mapping read/100,000,000. Then bedGraphtoBigWig was used to convert the bedgraph files to bigwig.
Gene expression levels were estimated by quantifying primary alignments mapping to at most 2 locations (MAPQ >= 3) to exonic regions (the maximal genomic locus of each gene and its known isoforms) using featureCounts v1.4.4 and the mm10 ensGene annotation set from Ensembl.
Assembly: mm10
Supplementary files format and content: bigWig files generated with bedtools 2.27.1, read coverage for each sample over the mouse genome
Supplementary files format and content: mm10.Ensembl.raw_counts.tsv, tab-separated values file, raw counts of all the RNA-seq samples.
|
| |
|
| Submission date |
Mar 31, 2022 |
| Last update date |
Mar 16, 2023 |
| Contact name |
Claudia L Kleinman |
| E-mail(s) |
claudia.kleinman@mcgill.ca
|
| Phone |
514-340-8222 25139
|
| Organization name |
Lady Davis Institute for Medical Research
|
| Department |
Human Genetics
|
| Street address |
3999 Côte Ste-Catherine Road
|
| City |
Montréal |
| State/province |
Québec |
| ZIP/Postal code |
H3T 1E2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE199882 |
Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration [RNA-seq] |
| GSE199885 |
Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration |
|
| Relations |
| BioSample |
SAMN27155548 |
| SRA |
SRX14689813 |
