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Sample GSM4030217 Query DataSets for GSM4030217
Status Public on Dec 23, 2019
Title Human-smallRNAseq-A4
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).
In brief, total RNA was run on 15% urea polyacrylamide gel electrophoresis (PAGE) to select small RNAs ranging from 18–34 nt. To prevent microRNAs and siRNAs entering to the library, sRNAs were oxidized with sodium periodate (NaIO4) prior to 3′ adaptor ligation. We then ligated the 3′ adaptor (5′-rApp NNN TGG AAT TCT CGG GTG CCA AGG /ddC/-3′ or 5′-rApp TGG AAT TCT CGG GTG CCA AGG /ddC/-3′; Supplementary file 1) in the presence of 50% (w/v) PEG8000 (Rigaku, 1008063). After 3′ ligation, ligated sRNAs were run on 15% PAGE to eliminate the non-ligated 3′ adaptor; ligated sRNAs that were 42 to 60 nt with 3′ adaptor were purified. Thereafter, 5′ adaptor was ligated.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Description 9268NT_Ox
processed data file: merged.rpm
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 SAMN10936570
SRA SRX5376177

Supplementary file Size Download File type/resource
GSM4030217_9268NT_Ox.rpm.txt.gz 282.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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