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Sample GSM7906610 Query DataSets for GSM7906610
Status Public on Nov 18, 2023
Title Smarca4 cKO pooled DN2 and DN3 thymocytes Rep2
Sample type SRA
 
Source name bone marrow
Organism Mus musculus
Characteristics tissue: bone marrow
strain: C57BL/6J
age: 2-4 months
Sex: pooled male and female
cell type: DN2 and DN3 thymocytes
replicate: 2
genotype: Smarca4f/f; Rosa26nTnG/CreERT2
treatment: Tamoxifen
Extracted molecule total RNA
Extraction protocol RNA-seq library preparation was performed by UChicago genomics core facility. Briefly: 50,000-100,000 primary thymocytes or DN cells from OP9-DL4 co-cultures were FACS-sorted directly into RULT lysis buffer from Qiagen RNeasy UCP Micro Kit and total RNA was extracted using manufacturer’s instructions.
mRNA was enriched and RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Kit. Paired-end, dual-index sequencing was performed on the Illumina NovaSeq 6000 platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Adaptor sequences were trimmed using SeqPurge (v2019_11)
Trimmed RNA-seq reads were mapped to the mm10 mouse genome assembly using TopHat (v2.1.1) with settings –microexon-search
Unmapped, unpaired and low quality reads (MAPQ < 5) were removed using samtools (v1.9) view with settings -q 5 -f 2
Paired reads were counted for each gene using featureCounts from Subread (v2.0.1)
‘Transcripts-per-million’ (TPM) values were calculated for each gene to quantify the relative abundance of transcripts for clustering analysis.
‘Trimmed mean of M values’ (TMM) was calculated for each gene for differential comparisons across samples using edgeR (calcNormFactors). Common dispersions were estimated using estimateCommonDisp and Benjamini-Hochberg false discovery rates (FDRs) were calculated for pairwise comparisons using exactTest. Genes exhibiting FDR < 0.05 were regarded as significant.
Assembly: mm10
Supplementary files format and content: RNA_Master_Matrix.txt
 
Submission date Nov 17, 2023
Last update date Nov 18, 2023
Contact name Alexandra Bradu
E-mail(s) abradu@uchicago.edu
Organization name University Of Chicago
Department Pathology
Lab Koh Lab
Street address 924 East 57th Street
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL24247
Series (2)
GSE234331 PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape
GSE248159 PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape [RNA-seq]
Relations
BioSample SAMN38023042
SRA SRX22254858

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

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