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| Status |
Public on Nov 03, 2015 |
| Title |
Hira-WT4_RNA-Seq [Gdf9-Cre+] |
| Sample type |
SRA |
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| Source name |
MII oocyte, Hira-WT
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: Hiraf/f
cell type: oocyte
developmental stage: MII
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| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA synthesis and amplification was performed directly on single Hiraf/f and Hiraf/f Gdf9-Cre+ MII oocytes with the SMARTer Ultra Low Input RNA kit (Clontech). 0.5 uL of ERCC RNA spike-in mix 1 (Life Technologies), diluted 1:105, was added to each reaction prior to cDNA synthesis. The amplified cDNA was fragmented by Covaris S2 sonicator (Covaris) and converted to sequencing libraries following the NEBNext DNA Library Prep (NEB) using the NEBNext Multiplex Oligos for Illumina (NEB). Bar-coded libraries were pooled and sequenced on two lanes of the Illumina HiSeq 2500 instrument.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
WT4
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| Data processing |
mRNA-seq reads were aligned to the mouse genome (mm9, NCBI build 37) with Bowtie v0.12.8/Tophat v2.0.2 (http://tophat.cbcb.umd.edu), which allows mapping across splice sites by reads segmentation. Annotations from Ensembl Gene version 67 were used as gene model with Tophat. Spike-in reads were aligned to ERCC spike-in sequences using bowtie2 with the following settings: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50. For differential expression analysis, read counts per annotated gene were computed using HTSeq and expression level of each gene was quantified with FPKM using R script. Differential expression analysis was performed using edgeR (version 3.1.10)
Genome_build: mm9
Supplementary_files_format_and_content: FPKM
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| Submission date |
Mar 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Gopuraja Dharmalingam |
| Organization name |
MRC London Institute of Medical Sciences
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| Department |
Epigenetics section
|
| Street address |
Faculty of Medicine, Imperial College, Hammersmith Hospital Campus
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| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE66931 |
Single cell RNA-Seq of Hira-KO and control MII oocytes [Gdf9-Cre+] |
| GSE73382 |
Single cell RNA-Seq of Hira-KO and control MII oocytes |
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| Relations |
| BioSample |
SAMN03418230 |
| SRA |
SRX957369 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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