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| Status |
Public on Jun 12, 2017 |
| Title |
SSCs rep3 |
| Sample type |
SRA |
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| Source name |
SSCs
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: testis
cell type: spermatogonial stem cells
age: 3–5 days
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the SSCs and FGSCs were isolated using TRIzol reagent (Invitrogen, life Technologies, USA) according to the manufacturer's protocol. Total RNA from each sample was quantified using Agilent 2100, and RNA integrity was assessed using Agilent 2100.
After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA from the total RNA with kit. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments (about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 when necessary.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Alignment/mapping reads to reference genome by TopHat2
Transcripts assembling by Cufflinks
Merge assembles by Cuffmege
Coding potential calculation by CNCI and CPC
The genes expression levels were estimated by FPKM (fragments per kilobase of exon per million fragments mapped) and assessed using Cuffdiff v2.1.1
Genome_build: UCSC mm10
Supplementary_files_format_and_content: RPKM values for novel lncRNAs
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| Submission date |
Oct 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ji Wu |
| E-mail(s) |
jiwu@sjtu.edu.cn
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| Organization name |
Shanghai Jiao Tong University
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| Street address |
No.800, Dongchuan Road, Minhang District
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| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE87824 |
Systematic identification and comparison of expressed profiles of lncRNAs and circRNAs in male and female germline stem cells |
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| Relations |
| BioSample |
SAMN05894735 |
| SRA |
SRX2236903 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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