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Sample GSM4030257 Query DataSets for GSM4030257
Status Public on Dec 23, 2019
Title Human-ChIPseq-H3K4me3_ChIP-A17
Sample type SRA
Source name Testis
Organism Homo sapiens
Characteristics tissue: Testis
developmental stage: Adult
chip antibody: anti-H3K4me3
Extracted molecule genomic DNA
Extraction protocol Total DNA was extracted from frozen tissues.
Briefly, frozen tissues were cut into small pieces on dry ice and transferred to 1.7 ml tubes containing cold PBS. Samples were then cross-linked with 2% (w/v) formaldehyde at room temperature for 30 min using end-over-end tumbler. Thereafter, fixed tissues were crushed in the presence of ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) by 40 strokes with a “B” pestle of Dounce homogenizer (Kimble-Chase, Vineland, USA). Furthermore, lysed samples were sonicated using Covaris ultrasonicator (Covaris, E220) to shear the chromatin into 150 to 200 bp. Sonicated lysate was then diluted 1:10 with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-1001.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl) and we performed immunoprecipitation using 5.5 µg of anti-A‑MYB (Sigma, HPA008791) and 4.5 µg of anti-H3K4me3 (Abcam, ab8580). Following the immunoprecipitation of the chromatin with the antibody of interest, we extracted DNA by phenol:chloroform:isoamyl alcohol (25:24:1) (pH 8) and prepared ChIP-seq libraries for anti-AMYB, anti-H3K4me3 and input DNA as previously described.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
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
BioSample SAMN10936583
SRA SRX5376167

Supplementary file Size Download File type/resource 89.2 Mb (ftp)(http) BW
GSM4030257_8246NT-H3K4me3-Id10_S6_peaks.narrowPeak.gz 630.6 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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