|
| Status |
Public on Jan 31, 2024 |
| Title |
eIF4E-BP1 TMEM119 cKO BL 1 IP |
| Sample type |
SRA |
| |
|
| Source name |
spinal cord
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spinal cord
cell type: microglia
genotype: TMEM119
treatment: Immunoprecipitation (IP) with eGFP antibody
|
| Growth protocol |
Transgenic mice expressing Cre recombinase under the control of the TMEM119 promoter and reporter mouse line eGFPL10a were generated. Mice expressed egfp on l10a location of ribosomes. All experiments were carried out using male mice aged 8 to 12 weeks old.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol RNA kit (Zymo Research)
rRNA-depleted stranded (HMR)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
BP 1 IP
B11
|
| Data processing |
RNA-seq read files (fastq files) were checked for quality by FastQC and read trimming was done based on the Phred score and per-base sequence content
Trimmed Reads were then mapped against the reference genome and transcriptome (Gencode vM16 and GRCm38.p5) using STAR v2.2.1
Relative abundances in Transcripts Per Million (TPM) for every gene of every sample was quantified by stringtie v1.3.5
Assembly: Genome Reference Consortium Mouse Build 38 patch release 5
Supplementary files format and content: gene id (Gencode), gene name, locus, and TPMs for each RNA-seq and trap replicate for all coding genes
|
| |
|
| Submission date |
Jan 29, 2024 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Arkady Khoutorsky |
| E-mail(s) |
arkady.khoutorsky@mail.mcgill.ca
|
| Organization name |
McGill University
|
| Street address |
3655 Promenade Sir-William-Osler
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3G 1Y6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE254472 |
4E-BP1-dependent translation in microglia controls mechanical hypersensitivity |
|
| Relations |
| BioSample |
SAMN39596326 |
| SRA |
SRX23390364 |
