|
Status |
Public on Nov 25, 2022 |
Title |
Single 2 cell embryo Exp3 NT 21 |
Sample type |
SRA |
|
|
Source name |
single embryo
|
Organism |
Mus musculus |
Characteristics |
developmental stage: 2 cell strain: B6129F1 treatment: negative control
|
Treatment protocol |
Isolated GV oocytes were microinjected with sets of two siRNAs against targets (20µM each) or control. As a control of successful injection 150 ng/µl H2B-EGFP (for control) or 150 ng/µl H2B-rsEGFP (for target) was co-injected.
|
Growth protocol |
Isolated mouse oocytes were cultured in microdrops under 5% O2, 5% CO2, 90% N2. Oocytes were isolated in M2 medium supplemented with dbcAMP (Sigma, 300 mM) and FBS (20%), microinjected and further cultured for 5 hours in M16 supplemented with dbcAMP. Oocytes were released from dbcAMP and cultured for 12 hours in M16, followed by in vitro fertilization (In Vitro Fert, Cooks; supplemented with GSH (Sigma)). Fertilized embryos were cultured in KSOM
|
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 |
|
|
Description |
txi.kallisto_counts_normalized.csv txi.kallisto_counts_batchcorrected_counts.csv txi.kallisto_counts_raw.csv C88_KD_RNA-Seq_DESeq2_all.csv C88_KD_RNA-Seq_DESeq2_10th_percentile_th.csv
|
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). Batch correction have been done with BatchCorrectedCounts from CountClust (version 1.18.0). Differential expression was assesed with DESeq2 (version 1.32.0). Genome_build: mm10 Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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|
|
Submission date |
Jun 22, 2021 |
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) |
GSE178654 |
Zygotic genome activation by the totipotency pioneer factor Nr5a2 II |
GSE178661 |
Zygotic genome activation by the totipotency pioneer factor Nr5a2 |
|
Relations |
BioSample |
SAMN19812656 |
SRA |
SRX11195944 |