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Sample GSM4072079 Query DataSets for GSM4072079
Status Public on Jun 25, 2020
Title WT rep1 [N411-4M]
Sample type SRA
Source name WT
Organism Mus musculus
Characteristics genotype/variation: wild type
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 N411-4M_TSTRLT_3bbc53ab_GCL-YL-P0054-SB0110_S5
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
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
BioSample SAMN12719255
SRA SRX6822879

Supplementary file Size Download File type/resource
GSM4072079_raw_counts_N411-4M.tsv.gz 175.2 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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