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Sample GSM2514237

Query DataSets for GSM2514237

Status

Public on Sep 08, 2017

Title

Naive_RNA_Rep9

Sample type

SRA

Source name

Hippocampus

Organism

Rattus norvegicus

Characteristics

strain: Sprague-Dawley
tissue: CA1 area of the hippocampus
age: 90-120 d

Extracted molecule

polyA RNA

Extraction protocol

RNA was extracted, DNase-treated, and purified (RNeasy, Qiagen).
2 µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 8.0), and was prepared for directional, PolyA+ RNA sequencing at Hudson Alpha using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

RNAseq_FPKM_GRCm38.txt

Data processing

RNA-seq: Raw paired-end sequenced reads were quality controlled, filtered for read quality (FASTX toolkit, Galaxy)
RNA-seq: Aligned to the rat Rn5 genome sequence in Galaxy using Tophat v1.4.0 (with custom settings –p 8 –r 175)
RNA-seq: Gene expression differences between groups were calculated using DESeq2 via R plugin in Seqmonk software release v0.28.0 (Babraham Institute), using Ensembl release v70 gene and feature annotations
RNA-seq: For independent PolyA+ samples, transcript expression levels were determined by computing the fragments per kilobase of exon per million mapped reads (FPKM) and multiple comparisons were corrected using a false-discovery rate of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: a single tab-delimited text file includes FPKM values for each sample; MBD-seq: One tab-delimited text file includes RPKM values for each sample over 500nt windows and another text file includes RPKM values for each gene
MBD-seq: Raw single-end sequenced reads were quality controlled, filtered for read quality (FASTX toolkit, Galaxy)
MBD-seq: Aligned to the rat genome (Rn5 assembly) in Galaxy using Bowtie
MBD-seq: CpG coverage and saturation analyses were performed using the program MEDIPS from the Bioconductor open source software package, and each sample was required to have > 90% signal saturation with a false positive rate of < 20% to pass quality control
MBD-seq: Differentially methylated genes (DMGs) were quantified using the EdgeR algorithm (FDR < 0.1)
MBD-seq: Differentially methylated regions (DMRs) were assessed by dividing the rat genome (rn5) into 500nt windows using the MEDIPS software package, which allows for the identification of DMRs in the context of CpG density, and these 500nt regions were quantified using the EdgeR algorithm (FDR < 0.3)

Submission date

Feb 27, 2017

Last update date

May 15, 2019

Contact name

Andrew John Kennedy

E-mail(s)

akennedy@bates.edu

Organization name

Bates College

Department

Chemistry