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Sample GSM6693014 Query DataSets for GSM6693014
Status Public on Nov 01, 2022
Title miR-142 KO CML LSK, from KO CML males [851]
Sample type SRA
 
Source name BM Lin-Sca-1+c-Kit+ (LSK)
Organism Mus musculus
Characteristics cell type: BM Lin-Sca-1+c-Kit+ (LSK)
Sex: male
genotype: Mir142 KO BCR-ABL+
Extracted molecule total RNA
Extraction protocol RNA was extracted using the miRNeasy Micro Kit (Qiagen, Valencia, CA).
RNA sequencing libraries were prepared with Kapa mRNA HyperPrep kit (Kapa Biosystems, Cat KR1352) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit.
RNA-seq was performed on Illumina NovaSeq6000 with S4 Reagent kit v1.5 (Illumina, Cat 20028313) at Tgen with the sequencing length of 2x101. Real-time analysis (RTA) 3.4.4 software was used to process the image analysis.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 851
Data processing Illumina NovaSeq6000
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the mouse genome mm10 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Oct 28, 2022
Last update date Nov 01, 2022
Contact name Li Du
Organization name City of Hope
Department Toni Stephenson Lymphoma Center
Lab KCRB 1028
Street address 1500 E. Duarte Road
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
 
Platform ID GPL24247
Series (1)
GSE216794 Gene profiling changes in BM Lin-Sca-1+c-Kit+ cells (LSKs) from miR-142-/- (KO), miR-142+/+ (WT), miR-142-/- BCR-ABL (BC CML) and miR-142+/+ BCR-ABL (CP CML) mice. [bulk RNA-Seq]
Relations
BioSample SAMN31508460
SRA SRX18064034

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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