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Sample GSM4728487 Query DataSets for GSM4728487
Status Public on Mar 27, 2024
Title Control, RNA-Seq replicate 2
Sample type SRA
Source name Thymus
Organism Mus musculus
Characteristics background strain: C57BL/6
genotype: Suv39h1+/y Suv39h2+/-
gender: Male
cell type: CD4+CD8+ double positive thymocytes
Extracted molecule polyA RNA
Extraction protocol Single cell suspensions were generated from mouse thymus by mechanical homogenization following by red blood cell lysis (156mM NH4Cl, 11.9mM NaHCO3, 97μM EDTA). DP thymocyte cells were then flow-cytometrically sorted as CD45.2+CD19-CD4+CD8+ cells on a BD FACSAria™ cell sorter.
RNA was extracted using a Qiagen Rneasy Plus Kit.
Illumina TruSeq RNA Library Prep
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned to the mouse genome by Rsubread version 1.24.0
Read counts were summarized by Ensembl Gene ID using the Rsubread's featureCounts function and Gencode annotation vM22.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files (tsv). Columns represent Ensembl Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene. The supplementary file `Counts_all_samples.txt` provides genewise counts for all samples in one file.
Submission date Aug 14, 2020
Last update date Mar 27, 2024
Contact name Gordon K Smyth
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
Platform ID GPL19057
Series (2)
GSE156296 RNA-seq profiles of DP thymocytes from control and Suv39h1/Suv39h2 double knockout mice
GSE156297 RNA-seq, LaminB1 ChIP-seq and in situ Hi-C of double positive thymocytes from control and Suv39h1/Suv39h2 double knockout mice
BioSample SAMN15824195
SRA SRX8949764

Supplementary file Size Download File type/resource
GSM4728487_Counts_Control_2.txt.gz 401.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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