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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 04, 2017 |
| Title |
Sperm-1 |
| Sample type |
SRA |
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| Source name |
Sperm
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Sperm
age: 3-5 months
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from the purified sperm and testes samples using RNeasy® Plus Micro (Qiagen, Duesseldorf, Germany) according to the manufacturer’s instructions with some modifications. We added 1 ml of buffer RLT (a guanidine-thiocyanate lysis buffer supplemented with 10 mM DL-Dithiothreitol) to the sperm pellet and 10 mg testes tissues, and then homogenized the sample by passing the samples through a 20-G needle attached to a 1-ml syringe 10 to 15 times. After total RNA was bound to the membrane and other contaminants were efficiently washed away, on-column DNase digestion was performed to eliminate trace amounts DNA contamination. The concentration and integrity of the total RNA samples were evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and a 2100-Bioanalyzer with the RNA 6000 Nano Chip (Applied Biosystems, Carlsbad, CA, USA), respectively.
RNase H protocol was performed to removal rRNA as previously described (Adiconis et al. 2013). The DNase digested RNA was purified with AMPure Beads and then fragmented to about 140–160 nt. The RNA fragments were further converted into a DNA library through end repair, adaptor ligation, reverse transcription circularization, and PCR amplification. The library was further purified with AMPure Beads and validated using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., CA, USA) and ABI StepOnePlus Real-Time PCR System (Applied Biosystems, CA, USA). The qualified library was sequenced by Illumina Illumina HiSeqTM 4000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: .txt files include RPKM values for each Sample
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| Submission date |
Oct 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaoning Zhang |
| E-mail(s) |
[email protected]
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| Organization name |
Nanchang University
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| Street address |
999 Xuefu R.D., Nanchang
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| City |
Nanchang |
| ZIP/Postal code |
330031 |
| Country |
China |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE88732 |
Systematic Identification and Characterization of Long Non-coding RNAs in Mouse Mature Sperm |
| GSE88739 |
Dysregulation of long non-coding RNAs in mouse testis and sperm after exposure to cadmium |
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| Relations |
| Reanalyzed by |
GSM2344953 |
| BioSample |
SAMN05908351 |
| SRA |
SRX2245385 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2344899_M-sper-con-1.txt.gz |
138.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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