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Sample GSM5284579 Query DataSets for GSM5284579
Status Public on Jun 06, 2023
Title D20-156041
Sample type SRA
 
Source name Tumor
Organism Mus musculus
Characteristics tissue: Thymic Lymphoma
genotype: LCK-Cdc20(+/D); MYCChr6
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from primary cells or tumors, using the RNeasy Plus Mini Kit (Qiagen) and sequenced on an Illumina HiSeq2000. At least 5000 cells were sorted directly in lysis buffer for specifc T cell progenitor populations in the thymus while at least 5 million cells have used for RNA isolation form thymic lymphomas. Unless otherwise indicated samples from tumors were isolated without sorting specific polulations.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description RNASeq200227_gene_counts.txt
Data processing Quality control:QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, sample contamination estimation, intergenic reads percentile calculation, intronic reads percentile calculation, UTR reads percentile calculation, gene coding reads percentile calculation, and rRNA contamination estimation. Besides, sense to antisense reads ratio was calculated to indicate strand specificity. Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.11.1.0.12 basing on log2(fpkm+1) values of the expressed coding genes to observe sample relationship and to detect outliers.
RNA-Seq mapping: against GRCm38/mm10 reference for mouse sequences using STAR/2.5.3a
Gene expression was quantitated using RSEM v. 1.3.0
Gene set enrichment analyses was performed by GSEA 2-2.0.13 basing on normalized expression values
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt file. Each gene per row and each sample per column(raw counts from RSEM)
 
Submission date May 06, 2021
Last update date Jun 06, 2023
Contact name Dunaduan Ma
E-mail(s) maduanduan8@gmail.com
Organization name MIT
Department Koch Institute
Lab Bioinformatics Core
Street address 77 Massachusetts Ave
City Cambridge
State/province Ma
ZIP/Postal code 02139
Country USA
 
Platform ID GPL13112
Series (1)
GSE174012 Bulk RNA sequencing from sorted thymic populations and tumors from control Cdc20(+/D) and aneuploid Cdc20(D/AAA)mice
Relations
BioSample SAMN19057413
SRA SRX10809989

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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