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Sample GSM6591940 Query DataSets for GSM6591940
Status Public on Nov 25, 2022
Title Single 2 cell embryo. Sample 3 ex2 Condition: SR1848
Sample type SRA
 
Source name single embryo
Organism Mus musculus
Characteristics developmental stage: 2 cell
strain: B6129F1
treatment: 10 uM SR 1848
treatment: SR1848
Treatment protocol From 6 hpf, 10 uM SR1848 (Sigma) or 0.1% DMSO was added to the KSOM in which the embryos were cultured.
Growth protocol Mouse zygotes were isolated at 5 hours post fertilization and cultured. Due to the hydrophobic nature of the inhibitor, embryos were cultured in wet chambers without oil.
Extracted molecule polyA RNA
Extraction protocol Single embryo SmartSeq2 protocol with oligo dT priming
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Base calling was performed using bcl2fastq Conversion Software by the Department of Totipotency, MPIB
Low quality reads were trimmed out using TrimGalore (version 0.6.2) using parameters: --nextera --trim-n --paired --quality 20 --nextera
Reads have been checked for contamination with BBMap (version 38.90) using parameters: ref=mm10,hg19 ambig2=all
Read pseudoalignment was done using Kallisto (version 0.46.1) using parameters: -b 100. All reads were aligned to mm10 genome index file.
Count tables have been created in R (version 3.5.1) with tximport (version 1.20.0). Differential expression was assesed with DESeq2 (version 1.32.0).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Sep 19, 2022
Last update date Nov 25, 2022
Contact name Pavel Andreevich Kravchenko
E-mail(s) pkravchenko@biochem.mpg.de
Phone +4915110675513
Organization name Max-Planck-Institute of Biochemistry
Department Totipotency
Lab Tachibana
Street address Am Klopferspitz 18
City Munich
State/province Planegg
ZIP/Postal code 82152
Country Germany
 
Platform ID GPL19057
Series (2)
GSE178661 Zygotic genome activation by the totipotency pioneer factor Nr5a2
GSE213682 Zygotic genome activation by the totipotency pioneer factor Nr5a2 IV
Relations
BioSample SAMN30926338
SRA SRX17628949

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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