|
| Status |
Public on Mar 27, 2024 |
| Title |
Suv39h1, Suv39h2 double knock-out, RNA-Seq replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
genotype: Suv39h1-/y Suv39h2-/-
gender: Male
cell type: CD4+CD8+ double positive thymocytes
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell suspensions were generated from mouse thymus by mechanical homogenization following by red blood cell lysis (156mM NH4Cl, 11.9mM NaHCO3, 97μM EDTA). DP thymocyte cells were then flow-cytometrically sorted as CD45.2+CD19-CD4+CD8+ cells on a BD FACSAria™ cell sorter.
RNA was extracted using a Qiagen Rneasy Plus Kit.
Illumina TruSeq RNA Library Prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned to the mouse genome by Rsubread version 1.24.0
Read counts were summarized by Ensembl Gene ID using the Rsubread's featureCounts function and Gencode annotation vM22.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files (tsv). Columns represent Ensembl Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene. The supplementary file `Counts_all_samples.txt` provides genewise counts for all samples in one file.
|
| |
|
| Submission date |
Aug 14, 2020 |
| Last update date |
Mar 27, 2024 |
| 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) |
| GSE156296 |
RNA-seq profiles of DP thymocytes from control and Suv39h1/Suv39h2 double knockout mice |
| GSE156297 |
RNA-seq, LaminB1 ChIP-seq and in situ Hi-C of double positive thymocytes from control and Suv39h1/Suv39h2 double knockout mice |
|
| Relations |
| BioSample |
SAMN15824192 |
| SRA |
SRX8949767 |
