|
| Status |
Public on Nov 01, 2021 |
| Title |
Tcf7 knock-out natural killer thymic cells replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Tcf7 knock-out natural killer thymic cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Tcf7 knock-out
gender: male
cell type: thymus
tissue: natural killer thymic cells
|
| Growth protocol |
Thymi were collected and single-cell suspensions were generated by forcing organs through 70 μm sieves. TCRbeta-CD3-CD8-CD1dtetramer-NK1.1+NKp46+ cells were sorted using a FACS Aria III machine from BD Biosciences.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed and RNA purified using a Qiagen Rneasy Micro Plus kit.
Total RNA were prepared and indexed separately for illumina sequencing using the SMART-Seq v4 Ultra Low Input RNA Kit as per manufacturer’s instructions. The indexed libraries were pooled and diluted to 1.5pM for paired end sequencing on a NextSeq instrument using the v2 150 cycle High Output kit (illumina) as per manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
NK_thymic_Tcf7_KO_1
|
| Data processing |
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the human genome by Rsubread version 1.22.2
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene
|
| |
|
| Submission date |
Jan 09, 2017 |
| Last update date |
Nov 01, 2021 |
| Contact name |
Alexandra Garnham |
| E-mail(s) |
garnham.a@wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE93348 |
Role of Tcf-1 (Tcf7) in thymic NK cells |
| GSE93349 |
Gene expression analysis of Tcf7-deficient thymocytes and natural killer cells |
|
| Relations |
| BioSample |
SAMN06214017 |
| SRA |
SRX2480795 |
