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Sample GSM3637727 Query DataSets for GSM3637727
Status Public on Jan 11, 2020
Title hippocampus_Gtf2i*_13.2
Sample type SRA
 
Source name hippocampus
Organism Mus musculus
Characteristics strain: FVB/ANTJ x C57BL6/J F1 cross
genotype: Gtf2i*
Sex: female
tissue: hippocampus
Extracted molecule total RNA
Extraction protocol hippocampi were dissected and homogenized in 500ul of RIPA buffer with RNAse inhibitors. 250ul of homogenate was added to 750ul of Trizol LS and stored at -80C until RNA extraction. RNA was extracted using the Zymo clean and concentrator-5 kit with on column DNAse digestion and eluted in 30ul of RNAse free water.
1ug of RNA was used as input for the rRNA depletion kit (human/mouse/rat) (NEB#E6310) and then libraries were prepped using the NEBNext Ultra II RNA Library prep kit for Illumina (E7770L)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing raw fastq files were trimmed of adapaters and low quatlity bases using Trimmomatic, then aligned to the mm10 mouse genome using STARv2.6.1b default parameters
Htseq-count v0.9.1 was used to count the number of reads that aligned to features in the Ensembl GRCm38 version 93 gtf file.
Lowly expressed genes were defined as genes that had a cpm less than 2 across all samples. Lowly expressed genes were then filtered out of the dataset.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated file. Each sample is a column and each row is a gene. The entries are read counts that mapped to that gene.
 
Submission date Mar 01, 2019
Last update date Jan 11, 2020
Contact name Joseph D Dougherty
Organization name Washington University
Department Genetics and Psychiatry
Street address 4566 Scott Ave, box 8232
City St Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
 
Platform ID GPL21493
Series (1)
GSE127723 Hippocampus RNA-seq in CD x Gtf2i*
Relations
BioSample SAMN11041893
SRA SRX5447907

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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