NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4030207 Query DataSets for GSM4030207
Status Public on Dec 23, 2019
Title Human-RNAseq-A12
Sample type SRA
 
Source name Testis
Organism Homo sapiens
Characteristics tissue: Testis
developmental stage: Adult
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the human frozen testis tissues using mirVana miRNA isolation kit (Thermo Fisher, AM1560).
Briefly, 186 short antisense (AS) DNA oligos (50–80 nt) that are complementary to rRNAs were designed and pooled (0.05µM/each). 1 µl of pooled rRNA AS oligos were added to 1 µg of total RNA and hybridized to rRNAs in the presence of 100 mM Tris-HCl (pH 7.4) and 200 mM NaCl at 95°C and cooled to 22°C (−0.1°C/sec). Additional incubation at 22°C was performed for 5 min. Thereafter, the DNA:RNA hybrids were digested with ten units of Thermostable RNase h (Epicentre, H39500) in the presence of 50 mM Tris-HCl (pH 7.4), 0.1M NaCl, and 20 mM MgCl2 at 45°C for 30 min. After RNase h digestion, samples were treated with DNase using four units of Turbo DNase (Thermo Fisher, AM2238) at 37°C for 20 min and purified with RNA Clean & Concentrator-5 (Zymo Research, R1015) to enrich RNA >200 nt and remove tRNAs.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing The 3′ adaptor sequence from the reads were removed and those reads whose PHRED score <5 was further filtered. The reads passed the quality check were mapped to human genome (hg19) and or mouse genome (mm10) using piPipes allowing 1 mismatch.
For RNA-seq, CAGE and PAS-seq, we first removed rRNA reads using bowtie 2.2.5 with default parameters48 and then the unaligned reads were further mapped to human genome (hg19) using STAR 2.3 (Ref. 52). Mapped results were generated as SAM format that was further transformed into duplication removed sorted BAM format using SAMtools 1.8 and normalized bigWig files are generated by custom scripts.
Raw reads were mapped to genome using Bowtie 2.2.5 with parameter —very-sensitive. Mapped results were generated as SAM format that was further transformed into duplication removed sorted BAM format using SAMtools 1.8. We, then, normalized genome coverage files in bigWig format that were calculated using homemade script. Data are presented in bigWig file of unique mapping reads as read depth per million reads (rpm). We used Model-based analysis of ChIP-seq (MACS 1.1.2; Ref. 58) with parameter -q 0.01 to detect A-MYB peaks that were significantly enriched over input (1,296 genomic regions; false discovery rate [FDR] < 0.05).
Genome_build: hg19; mm10
Supplementary_files_format_and_content: bigWig; narrowPeak; rpm.txt (text)
 
Submission date Aug 13, 2019
Last update date Dec 23, 2019
Contact name Tianxiong Yu
Organization name Umass Med
Street address 364 Plantation St
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
Platform ID GPL18573
Series (1)
GSE135791 Pachytene piRNA Genes Are Rapidly Diverging Among Modern Humans
Relations
BioSample SAMN10936578
SRA SRX5376208

Supplementary file Size Download File type/resource
GSM4030207_AmbionNT.uniq.crick.bw 162.9 Mb (ftp)(http) BW
GSM4030207_AmbionNT.uniq.watson.bw 168.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap