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Sample GSM1634470 Query DataSets for GSM1634470
Status Public on Nov 03, 2015
Title Hira-KO6_RNA-Seq [Gdf9-Cre+]
Sample type SRA
Source name MII oocyte, Hira-KO
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: Hiraf/f, Gdf9-Cre+
cell type: oocyte
developmental stage: MII
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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description KO6
Data processing mRNA-seq reads were aligned to the mouse genome (mm9, NCBI build 37) with Bowtie v0.12.8/Tophat v2.0.2 (, 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
Submission date Mar 16, 2015
Last update date May 15, 2019
Contact name Gopuraja Dharmalingam
Organization name MRC London Institute of Medical Sciences
Department Epigenetics section
Street address Faculty of Medicine, Imperial College, Hammersmith Hospital Campus
City London
ZIP/Postal code W12 0NN
Country United Kingdom
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
BioSample SAMN03418237
SRA SRX957374

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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