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| Status |
Public on Sep 04, 2020 |
| Title |
Treat1 |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Mus musculus |
| Characteristics |
group: follicle after the initiation
tissue: ovary
age: 3d+8d
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| Treatment protocol |
ovarian samples in treatment group were isolated from infant mice (3 days old) followed by in vitro culture for eight days. The follicle initiation of each sample was assessed by HE staining. The mice that were caged together for parturition were purchased from center of animal experiment, Nanchang University.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The ovaries were homogenized and ovarian total RNA was extracted in accordance with manufacturer’s instructions from TRIzol (Invitrogen company, USA). the concentration and purity of the total RNA samples were evaluated using a NanoPhotometer (IMPLEN, Munich, Germany) with optical density measurements at 1.8 < A260/A280 < 2.0. The integrity of RNA was always checked by electrophoresis in 1.5% agarose gels.
Strand-specific LncRNA library was generated with the TruSeq® Stranded kit. The sequencing was conducted using Illumina HiSeqTM 4000 with PE100 according to the manufacturer’s instructions developed by BGI (Wuhan, China). About 10 G clean data were used to bioinformatic analysis.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| 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 mm9 whole genome using HISAT. Ana then the transcripts were assembled using Cufflinks.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Assembly transcripts were compared with annotated lncRNA in NONCODE database (http://www.noncode.org/) using Cuffcompare. The novel transcripts were predicted with CPC, txCdsPredict, CNCI and pfam algorithm.
Genome_build: mm9
NONMMUGnnnn IDs and sequences can be found in http://www.noncode.org/
Supplementary_files_format_and_content: txt files include gene_id, transcript_id(s), length expected_count, FPKM values for each Sample
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| Submission date |
Sep 04, 2017 |
| Last update date |
Sep 04, 2020 |
| Contact name |
su tie |
| E-mail(s) |
1148183596@qq.com
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| Phone |
15797693312
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| Organization name |
Nanchang university
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| Department |
Jiangxi Medical College
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| Street address |
XueFu road 999,HongGuTang newly-developed area,NanChang City,JiangXi province
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| City |
Nanchang |
| ZIP/Postal code |
330031 |
| Country |
China |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE103433 |
The expression profiles of lncRNA before and after the initiation of primordial follicle |
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| Relations |
| BioSample |
SAMN07622356 |
| SRA |
SRX3170799 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2771236_Treat1.gene.FPKM.lncRNA.txt.gz |
553.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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