|
| Status |
Public on Jun 25, 2020 |
| Title |
JMML rep3 [N393-2M] |
| Sample type |
SRA |
| |
|
| Source name |
JMML
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Juvenile myelomonocytic leukemia (JMML)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq samples were prepared using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, catalog number 20020599) according to manufacturer recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
N393-2M_TSTRLT_a787eb5f_GCL-YL-P0054-SB0110_S3
|
| Data processing |
BCL to FastQ file conversion with bcl2fastq2 v2.18.0.12 (default Illumina adapter trimming performed during conversion).
STAR v2.5.3a was used to align each sample’s paired-end reads to the Ensembl Mus Musculus reference genome build GRCm38 (using STAR’s 2-pass method)
Picard v2.0.1 was used to add read group information. Aligned files were also processed using Sambamba v0.6.5 to mark duplicates and sort reads.
Each sample’s BAM file was initially processed using StringTie v1.3.3b, using Ensembl gene annotations to guide transcriptome (limiting output to only annotated genes). The StringTie option to output “Ballgown-ready” files was enabled.
Using R v3.5.0, Ballgown-ready files were imported into DESeq2 v1.22.2 (using tximport v1.10.1).
Genome_build: Ensembl Mus musculus (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include raw/unnormalized gene count data for each sample.
|
| |
|
| Submission date |
Sep 09, 2019 |
| Last update date |
Jun 25, 2020 |
| Contact name |
Y. Lucy Liu |
| E-mail(s) |
ylliu19@stanford.edu
|
| Organization name |
Stanford Medical School
|
| Department |
Pediatrics
|
| Street address |
240 Pasteur Drive, BMI Suite 2550
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5139 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE137152 |
Sustained fetal hematopoiesis causes juvenile death from leukemia: evidence from a dual-age-specific mouse model |
|
| Relations |
| BioSample |
SAMN12719256 |
| SRA |
SRX6822878 |
