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Sample GSM3878607 Query DataSets for GSM3878607
Status Public on Jun 29, 2020
Title Sample_NB_TET2_KO4
Sample type SRA
 
Source name Naïve B-cells
Organism Mus musculus
Characteristics cell type: naive B-cells
tissue: spleen
genotype: TET2 Knock-Out
strain: C57BL/6
Treatment protocol Not applicable
Growth protocol Cells were isolated from mouse spleens
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol and Qiagen Rneasy kit
Illumina's RNA-seq-TruSeq-stranded-mRNA
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Raw reads were trimmed for truseq R1 adapter sequences using Flexbar.
Trimmed reads were mapped to the GRCm38.p3 reference genome using STAR (version 2.3.0e_r291) with the default parameters.
Read Counts per gene were computed using featureCounts (v1.5.1) tool from Subread package with the following parameters: -t "exon", -g "gene_name". GRCm38 Gencode was used as a reference gene annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: nbgcb.genecounts.txt file contain raw read counts per gene.
 
Submission date Jun 12, 2019
Last update date Jun 30, 2020
Contact name Sheng Li
Organization name The Jackson Laboratory
Lab Li Lab
Street address 10 Discovery Drive
City Farmington
State/province CT
ZIP/Postal code 06032
Country USA
 
Platform ID GPL17021
Series (2)
GSE132596 Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells [RNA-seq]
GSE140086 Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells
Relations
BioSample SAMN12037564
SRA SRX6047961

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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