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Sample GSM6692988 Query DataSets for GSM6692988
Status Public on Nov 01, 2022
Title miR-142 KO LSK, from KO females [424]
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: female
genotype: Mir142 KO
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 424
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 Steven T Rosen
Organization name City of Hope
Department Department of Hematology and Hematopoietic Cell Transplantation
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]
BioSample SAMN31508474
SRA SRX18064020

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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