|
| Status |
Public on Nov 25, 2022 |
| Title |
Single 2 cell embryo Exp3 C88 15 |
| Sample type |
SRA |
| |
|
| Source name |
single embryo
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: 2 cell
strain: B6129F1
treatment: knockdown
|
| 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
|
| |
|
| 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 |
SAMN19812721 |
| SRA |
SRX11195914 |
