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Sample GSM4486844 Query DataSets for GSM4486844
Status Public on Nov 25, 2020
Title Chopp14: Immature CD4SP thymocytes replicate 1
Sample type SRA
 
Source name Thymus
Organism Mus musculus
Characteristics strain: Chimeric mice:Thpok-GFP Runx3-RFP reporter donor, b2m deficient recipient
surface markers: CD44low MHC-I-low CD8alow CD69+ ThpokGFP+ CD4+
tissue: Thymus
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
SMART-seq Ultra Low Input RNA kit (Takara) and Nextera XT DNA (Illumina), paired-end 2x150
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Basecalls performed with Illumina RTA 1.18.66.3
Demultiplexing with Bcl2fastq 2.17
Filtering with Trimmomatic 0.36
Alignment--STAR aligner 2.4.0 to mm10
Counts per million normalized BigWig files performed with DeepTools
Read counts with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Htseq count table, counts per million normalized bigwig
 
Submission date Apr 20, 2020
Last update date Nov 26, 2020
Contact name Remy Bosselut
E-mail(s) bosselur@helix.nih.gov
Phone 240-760-6866
Organization name National Cancer Institute, National Institute of Health
Department Laboratory of Immune Cell Biology
Lab Bosselut
Street address 9000 Rockville Pike, Building 37
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL21493
Series (2)
GSE148973 An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (RNAseq EXP1)
GSE148981 An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development
Relations
BioSample SAMN14646755
SRA SRX8143972

Supplementary file Size Download File type/resource
GSM4486844_ImmatureCD4SP_rep1.bw 37.1 Mb (ftp)(http) BW
GSM4486844_LC14_htseq.tab.gz 165.0 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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