|
| Status |
Public on Jan 13, 2020 |
| Title |
Syngeneic1 [S1] |
| Sample type |
SRA |
| |
|
| Source name |
Syngeneic_Microglia
|
| Organism |
Mus musculus |
| Characteristics |
strain background: Balb/c
genotype/variation: WT
treatment: Syngeneic Bone Marrow and T cell Transplantation
tissue: brain
cell type: sorted microglia cells
|
| Treatment protocol |
Post transplantation mouse were regularly checked until day 14 which is the peak stage of GvHD
|
| Growth protocol |
Recipient balb/c mice were lethally irradiated and transplanted with either syngeneic or allogeneic bone marrow (5 million cells) and T cells (300000). The mice were sacrificed by perfusion on day 14 and RNA was isolated from microglia. Four mice were analyzed per group
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Microglia were sorted by FACS and RNA was isolated using the Picopure RNA extraction Kit as per manufacturer's instructions.RNA quality was accessed by bio-analyzer. The samples with an RNA integrity value of 8 and above were considered for sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
paired-end reads were aligned to the mm9 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16 --quantMode GeneCounts
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample
|
| |
|
| Submission date |
Dec 09, 2019 |
| Last update date |
Oct 19, 2023 |
| Contact name |
Geoffroy Andrieux |
| Organization name |
University clinics Freiburg
|
| Street address |
Breisacherstr 153
|
| City |
Freiburg |
| ZIP/Postal code |
79110 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE141663 |
RNA sequencing from the microglia of mice with acute GvHD against syngeneic bone marrow transplanted and untreated controls |
|
| Relations |
| BioSample |
SAMN13512741 |
| SRA |
SRX7290945 |
