|
| Status |
Public on Feb 24, 2021 |
| Title |
cDC1 WT replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Splenic conventional dendritic cells 1
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/BL6
genotype: zfp366+/+
gender: Female
biological replicate (mouse pool): 6
|
| Treatment protocol |
ex-vivo isolated splenic DCs (tissue digested with collagenase and DNAse)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNeasy Plus Mini kit (Qiagen).
TruSeq RNA Sample preparation kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
2789 cDC1
|
| Data processing |
Sequencing was undertaken on an Illumina NextSeq 500 to produce 86bp paired-end reads.
Read-pairs were aligned to the GRCm38/mm10 build of the Mus musculus genome using Rsubread::align.
Genewise counts were obtained using featureCounts with Rsubread's inbuilt mm10 annotation.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text giving Entrez Gene IDs, gene length (number of bases in union of all exons) and the number of read-pairs assigned to that read.
|
| |
|
| Submission date |
Jan 19, 2021 |
| Last update date |
Feb 26, 2021 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| 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) |
| GSE165125 |
RNA-seq analysis of mouse cDC1 and cDC2 populations upon DC-SCRIPT depletion |
| GSE165361 |
RNA-seq and CUT&Tag analysis of mouse cDC1 and cDC2 populations upon DC-SCRIPT depletion |
|
| Relations |
| BioSample |
SAMN17384736 |
| SRA |
SRX9898622 |
