|
| Status |
Public on Nov 24, 2022 |
| Title |
Single cell RNA-Seq 65736 WT 2cellG2 |
| Sample type |
SRA |
| |
|
| Source name |
small batch of oocytes/embryos
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: G2 2C embryo
strain: B6CASTF1
treatment: untreated
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Isolated mouse oocytes were cultured in microdrops under 5% O2, 5% CO2, 90% N2. s 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 |
Small batch (10-15 oocytes/embryos) 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 NGS core facility of the Vienna BioCenter
Fastq files were pseudo-aligned by Kallisto (kallisto quant --threads=8) to Mus musculus cDNA (mm10)
Kallisto results were imported to R by txiimport on the gene level. Differential expression was analysed by DESeq2 in R and DeSeq2 tables were generated.
To generate bam files, read mapping was done with tophat using the parameters -N 2 --read-gap-length 2 --read-edit-dist 2 -I 500000. All reads were mapped to mm10 genome.
Fastq files can be re-generated from bam files with picard SamToFastq: java -XX:ParallelGCThreads=8 -jar picard.jar SamToFastq.
Genome_build: mm10
|
| |
|
| Submission date |
Jun 21, 2021 |
| Last update date |
Nov 24, 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) |
| GSE178638 |
Zygotic genome activation by the totipotency pioneer factor Nr5a2 I |
| GSE178661 |
Zygotic genome activation by the totipotency pioneer factor Nr5a2 |
|
| Relations |
| BioSample |
SAMN19801999 |
| SRA |
SRX11192651 |
