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| Status |
Public on Oct 10, 2022 |
| Title |
WT-6W-1 |
| Sample type |
SRA |
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| Source name |
Fully-grown GV oocyte
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: oocyte
developmental stage: Fully-grown GV
genotype/variation: WT
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Oocytes were collected from indicated genotypes (10 oocytes per sample) after PMSG treatment for 44-48h. Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
RTCB.FPKM.normbyERCC.txt
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| Data processing |
RNA-Seq was performed with biological replicates for all samples.
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1.
Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Expression level was further normalized with the ERCC spike-in.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples
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| Submission date |
Dec 10, 2021 |
| Last update date |
Oct 10, 2022 |
| Contact name |
Heng-yu Fan |
| E-mail(s) |
Fanhengyu_lab@163.com, 21907079@zju.edu.cn
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| Organization name |
Life Sciences Institute
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| Lab |
Fan heng-yu
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| Street address |
Yuhangtang Road
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE190681 |
RNA Ligase RTCB-mediated mRNA Alternative Splicing is Required for Mouse Oocyte Development and Maintenance |
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| Relations |
| BioSample |
SAMN23893677 |
| SRA |
SRX13379871 |
| 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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