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Sample GSM8212382 Query DataSets for GSM8212382
Status Public on Apr 16, 2024
Title IRAK4-KD-3
Sample type SRA
 
Source name Hippocampus
Organism Mus musculus
Characteristics tissue: Hippocampus
age: 10 months
genotype: IRAK4-KD
Extracted molecule total RNA
Extraction protocol QIAGEN miRNEasy Micro Kit
KAPA HyperPrep mRNA
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description poly(A) RNA from hippocampus
D3
Data processing 2x150bp reads, Base-calling was done using Offline Base Caller (Illumina) v. 1.9.4
alignment was done using HISAT2 v 2.1.0 under default specfications
BAM files were generated and indexed using Samtools v 1.9 under default specifications
Peak-calling was done using Stringtie v 2.1.0 under parameter -B to first generate a usable list of ballgown files to prep for DESeq2 analysis. A separate python script (prepDE.py) was then used to convert the ballgown list (sample_list.txt) to gene and transcript counts as well as FPKM values for each sample as a list of gtf files (using python2.7 - python 3.7.4 does not work).
Analysis of counts was performed using R v 4.0.5, Rstudio v 1.2.1, DESeq2 v 1.30.1 using the filtering parameters of FDR<.05
Assembly: mm10
Supplementary files format and content: tab delimited file of counts on a per gene basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of counts on a transcript basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of FPKM values on a transcript basis (generated from Stringtie)
 
Submission date Apr 16, 2024
Last update date Apr 16, 2024
Contact name Anthony Vella
E-mail(s) vella@uchc.edu
Organization name UConn Health
Department Immunology
Lab Vella
Street address 263 Farmington Ave
City Farmington
State/province Connecticut
ZIP/Postal code 06030
Country USA
 
Platform ID GPL24247
Series (1)
GSE264121 IRAK4 is an immunological checkpoint in neuropsychiatric systemic lupus erythematosus
Relations
BioSample SAMN40986069
SRA SRX24277045

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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