|
| Status |
Public on Sep 26, 2021 |
| Title |
γ-H2AX-IP-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
spermatocytes from testis of 3-week old wildtype mice
|
| Organism |
Mus musculus |
| Characteristics |
tissue: testis
cell type: spermatocytes
age: 3-week old
genotype: wildtype
treatment: RNA-ChIP by γ-H2AX
ip antibody: Rabbit γH2AX antibody, NOVUS BIOLOGICALS, #NB100-384, #G
|
| Treatment protocol |
IgG or γH2AX immunoprecipitated RNA in mouse spermatocytes.
|
| Growth protocol |
Mouse spermatocytes were isolated from testis of 3-week old wildtype mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and RNA-DNA-protein complexes were isolated with antibody. DNA was digested and RNA was extrated.
Library preparation and sequencing were finished by LC-Bio Technology CO., Ltd., Hangzhou, China. The protocol is as follows: 1) RNA fragment and reverse transcription; 2) End repair, add A and adaptor ligation; 3) PCR; 4)Single strand separation and cyclization; 5) DNA nanoball synthesis; 7) Sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
γ-H2AX-IP RNA from spermatocytes
|
| Data processing |
Library strategy: RNA-ChIP
The STAR reference genome of mouse 45S rRNA is built with parameters: STAR --runThreadN 8 --runMode genomeGenerate --genomeDir mmu_45S --genomeFastaFiles mmu_rRNA_45S.fa --sjdbGTFfile mmu_rRNA_45S.gtf --sjdbOverhang 150
RNA-seq reads were aligned to the pre-built mouse 45S ribosomal RNA using STAR version 2.7.6a with the following parameters: STAR --runMode alignReads --genomeLoad NoSharedMemory --runThreadN 8 --readFilesCommand gunzip -c --genomeDir [dir_of_mmu_rRNA_45S] --readFilesIn [read1.fq.gz] [read2.fq.gz] --twopassMode Basic --outFileNamePrefix [outdir_bam] --sjdbOverhang 150 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --outSAMunmapped Within --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 50000000000 --outFilterMultimapNmax 50 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0
The aligned BAM files were processed using featureCounts v2.0.2 with 10nt-binned gtf annotation file to get binned read statistics. The parameter is shown below: featureCounts -T 8 -p -t exon -g gene_id -a [binned_gtf.gtf] -o [featureCounts.binned.txt] [Aligned.sortedByCoord.out.bam]
Genome_build: The mouse 45S rRNA sequence is extracted from NCBI (GenBank:X82564.1), and the GTF annotation is generated from submitted mouse ribosomal RNA sequences (GenBank: M20154.1, AH002077.2 and X00525.1). GTF file is then processed for a 10nt-binned read statistics.
Supplementary_files_format_and_content: TXT, FASTA and GTF
|
| |
|
| Submission date |
Sep 23, 2021 |
| Last update date |
Sep 27, 2021 |
| Contact name |
Xiaochun Yu |
| Organization name |
Westlake University
|
| Street address |
18 Shilongshan Street
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310024 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE184711 |
γH2AX-associated RNA in mouse spermatocytes |
|
| Relations |
| BioSample |
SAMN21583681 |
| SRA |
SRX12323205 |
