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Sample GSM3637735

Query DataSets for GSM3637735

Status

Public on Jan 11, 2020

Title

hippocampus_CD_20.1

Sample type

SRA

Source name

hippocampus

Organism

Mus musculus

Characteristics

strain: FVB/ANTJ x C57BL6/J F1 cross
genotype: CD
Sex: male
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