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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 27, 2024 |
| Title |
PRL01_F4 |
| Sample type |
SRA |
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| Source name |
paw
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
Sex: female
treatment: 0.1ug 12d PRL
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| 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)
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| Growth protocol |
None
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| 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
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| Submission date |
Mar 09, 2021 |
| Last update date |
Feb 27, 2024 |
| Contact name |
YI ZOU |
| E-mail(s) |
zou@uthscsa.edu
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| Organization name |
UTHSA-GCCRI
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| Street address |
8403 Floyd Curl Drive
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| City |
SAN ANTONIO |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE168563 |
Prolong elevation of prolactin and sex-depnendt regulation of pain chronicity |
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| Relations |
| BioSample |
SAMN18228542 |
| SRA |
SRX10293138 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5145934_PRL01_F4_Genes_ReadCount.txt.gz |
97.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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