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Sample GSM2640301 Query DataSets for GSM2640301
Status Public on Apr 21, 2019
Title Ctrl5_RNAseq
Sample type SRA
 
Source name hypothalamus
Organism Rattus norvegicus
Characteristics tissue: hypothalamus
gender: Male
age: postnatal day 9
treatment: control
Extracted molecule total RNA
Extraction protocol Extracted and purified using the Qiagen RNeasy kit
Total RNA was isolated from AMC and control hypothalamus using the RNeasy Kit (Qiagen, Valencia, CA). Total RNA samples were then processed with a Gene Read ribosomal RNA depletion kit (Qiagen, Germantown PA) prior to Illumina Hi-Seq library preparation using a directional RNA-seq library kit (NEB, Ipswich, MA). Libraries were checked by Bioanalyzer analysis (Agilent, Santa Clara, CA) for quality, then 50 base pair, single end reads were acquired on a Hi-Seq 2500 (Illumina, San Diego, CA) at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkley.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Post-mortem brain
Data processing The Hi-Seq 2500 reads were trimmed using Trimmomatic and Illuminaclip single end adapter trimming
final quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-seq reads were aligned to the current UCSC rat genome rn6 using the splicing-aware aligner Tophat2 (v2.0.14, stranded, Single End).
Differential expression was analyzed using cufflinks (v2.2.1) with bias, multi-read, and length corrections.
Cuffdiff was performed using a Cuffmerge generated gtf from all assembled transcripts and RefSeq UCSC genes using a genometric pooled dispersion model and minimum alignment of 10 fragments.
Genome_build: rn6
Supplementary_files_format_and_content: Strand specific RNAseq bigwig showing read coverage over the genome
 
Submission date May 24, 2017
Last update date May 15, 2019
Contact name Keith Dunaway
E-mail(s) kwdunaway@ucdavis.edu
Organization name UC Davis
Department MMI
Lab LaSalle Lab
Street address 3318 Tupper Hall
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL18694
Series (2)
GSE99278 Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care [RNA-seq]
GSE99282 Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care
Relations
BioSample SAMN07163656
SRA SRX2851956

Supplementary file Size Download File type/resource
GSM2640301_JLDY109E_neg_strand.bigwig 38.5 Mb (ftp)(http) BIGWIG
GSM2640301_JLDY109E_pos_strand.bigwig 39.0 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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