|
| Status |
Public on Oct 31, 2021 |
| Title |
S6: NoGC3 |
| Sample type |
SRA |
| |
|
| Source name |
CD8 T cell
|
| Organism |
Mus musculus |
| Characteristics |
strain_recipient: B6D2F1
treatment: vehicle
cell type: CD8 T cell
|
| Treatment protocol |
Recipient mice were injected with water soluble form of dexamethasone (5 mg/kg/day i.p.; Sigma-Aldrich) or vehicle (methyl β-cyclodextrin; Sigma-Aldrich) suspended in PBS solution from days -1 to +5 after BMT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each sorted T cells using a RNeasy micro kit (Qiagen), and each sample was evaluated for the RNA integrity by TapeStation system (Agilent)
cDNA synthesis and enrichment were performed using the SMART v4 protocol (Takara/Clontech), and library preparation was conducted using an Illumina Nextera XT library preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Raw fastq output was generated from Illumina bcl files using bcl2fastq
Fastqs were aligned to the genome (GRCm39; Gencode M26 annotation) using STAR and read counts were calculated using the Bioconductor function SummarizeOverlaps with default parameters
DESeq2 was used to normalize counts using default parameters
Genome_build: GRCm29
Supplementary_files_format_and_content: Normalized counts using DESeq2
|
| |
|
| Submission date |
Sep 28, 2021 |
| Last update date |
Oct 31, 2021 |
| Contact name |
Geoff R Hill |
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
CRD
|
| Lab |
Hill Lab
|
| Street address |
1100 Fairview Ave. N.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE184963 |
Peri-transplant Glucocorticoids Redistribute Donor T-cells to the Bone Marrow and Prevent Relapse after haploidentical SCT |
|
| Relations |
| SRA |
SRX12391835 |
