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Sample GSM8042867 Query DataSets for GSM8042867
Status Public on Jan 31, 2024
Title eIF4E-BP1 TMEM119 cKO BL 1 IN
Sample type SRA
 
Source name spinal cord
Organism Mus musculus
Characteristics tissue: spinal cord
cell type: microglia
genotype: TMEM119
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 IN
C11
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 SAMN39596329
SRA SRX23390369

Supplementary file Size Download File type/resource
GSM8042867_NEBNext_dual_i7_179---NEBNext_dual_i5_179.122.assemb.gtf.gz 15.8 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA

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