|
Status |
Public on Nov 25, 2020 |
Title |
Chopp15: Immature CD4SP thymocytes replicate 2 |
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 |
SAMN14646754 |
SRA |
SRX8143973 |