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Sample GSM1714232 Query DataSets for GSM1714232
Status Public on Oct 11, 2016
Title KO male 4 cell, repeat 4 [Rlim KO]
Sample type SRA
 
Source name Whole embryo
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: Rlim KO
Stage: 4 cell
gender: male
Extracted molecule total RNA
Extraction protocol Whole embryos were dissected at the indicated timepoints and the correct stage was verified under the binocular. Single embryos/trophoblast cells were placed in 10ul TCL Buffer (Qiagen) supplemented with 1% BME, and snap frozen.
RNA libraries were prepared for sequencing using standard Illumina protocols. A total of 187 samples were distributed on two 96-well plates (plus 5 mock wells) and thawed at RT for 10 minutes prior to RNA purification using Ampure RNA beads (Beckmann-Coulter). RNA samples were re-suspended in solution containing 3’ RT primer and dNTPs. Reverse transcription was performed with SSII (Life Technologies), whose terminal transferase activity allows incorporation of a PCR binding site at the 3’ end of the cDNA using a template-switching oligonucleotide (custom synthesized from Exiqon) as a template. Subsequently, cDNA was amplified using 12 cycles of PCR, followed by tagmentation with Nextera kit (Illumina). Final libraries were amplified by 12 cycles of PCR and sequenced on a NextSeq 500.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing The bcl2fastq 2.16.0.10 software package was used to convert base call (BCL) files generated on the NextSeq system to fastq files
Sequenced reads were aligned to the mouse genome (mm10) using TopHat (version 2.0.12) with default setting except set parameter read-mismatches to 2
HTSeq (version 0.6.1p1) was used to count the features after the alignment
Bioconductor packages edgeR (version 3.10.0 ) and ChIPpeakAnno (version 3.2.0) for transcriptome quantification, differential gene expression analysis and annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the raw count values from HTSeq for each sample
 
Submission date Jun 17, 2015
Last update date May 15, 2019
Contact name Ingolf Bach
E-mail(s) ingolf.bach@umassmed.edu
Organization name University of Massachusetts Medical School
Department Molecular, Cell and Cancer Biology
Street address 364 Plantation St
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
Platform ID GPL19057
Series (2)
GSE69970 Transcriptome of mouse preimplantation development [Rlim KO]
GSE71442 Transcriptome of mouse preimplantation development
Relations
BioSample SAMN03780110
SRA SRX1063763

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

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