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Sample GSM5145928 Query DataSets for GSM5145928
Status Public on Feb 27, 2024
Title PRL01_M2
Sample type SRA
 
Source name paw
Organism Mus musculus
Characteristics strain: C57BL/6J
Sex: male
treatment: 0.1ug 12d PRL
Treatment protocol PBS single i.pl. injection; PBS 12d i.pl. injection (one per day); PRL (0.1ug) i.pl. injection; PRL (0.1ug) 12d i.pl. injection (one per day)
Growth protocol None
Extracted molecule total RNA
Extraction protocol Fresh tissues were homogenized in Rn-easy solution using Bead Mill Homogenizer (Omni International, Kennesaw, GA).
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads, the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp singlle-end protocol with Illumina HiSeq 3000 platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using HTSeq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Genome_build: UCSC mouse genome build mm9
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
 
Submission date Mar 09, 2021
Last update date Feb 27, 2024
Contact name YI ZOU
E-mail(s) zou@uthscsa.edu
Organization name UTHSA-GCCRI
Street address 8403 Floyd Curl Drive
City SAN ANTONIO
State/province TX
ZIP/Postal code 78229
Country USA
 
Platform ID GPL21493
Series (1)
GSE168563 Prolong elevation of prolactin and sex-depnendt regulation of pain chronicity
Relations
BioSample SAMN18228548
SRA SRX10293132

Supplementary file Size Download File type/resource
GSM5145928_PRL01_M2_Genes_ReadCount.txt.gz 95.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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