|
| 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 |
