|
| Status |
Public on Apr 27, 2022 |
| Title |
AML Gab2 HET mouse 1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole murine bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
tissue: Bone marrow
genotype: Mx1-Cre; Dnmt3a+/-; Flt3ITD/ITD; Gab2+/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified according to manufacturer's protocol (Roboklon, Cat#E3598)
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 2.7.7
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:3 TRAILING:10 MINLEN:25
paired-end reads were aligned to the mm10 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 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16 --quantMode GeneCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample
|
| |
|
| Submission date |
Aug 23, 2021 |
| Last update date |
Apr 27, 2022 |
| 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) |
| GSE182624 |
Transcriptomic differences in murine AML bone marrow samples with different Gab2 genotypes |
|
| Relations |
| BioSample |
SAMN20933965 |
| SRA |
SRX11867574 |
