|
| Status |
Public on Oct 01, 2022 |
| Title |
Cdk9in_A_4 |
| Sample type |
SRA |
| |
|
| Source name |
2-cell embryo
|
| Organism |
Mus musculus |
| Characteristics |
protocol: RNA-seq
treatment: Cdk9 inhibitor (BAY1251152)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zygotes were collected at 17h post hCG injection and cultured with or without BAY1251152 (Cdk9in or Noinject), or subjected to Trim-Away for SPT5 (Spt5KD), NELF-E (NelfEKD) or IgG. Embryos were cultured until 46h post hCG, washed in PBS and flash-frozen in lysis buffer.
Libraries for single embryo RNA-seq were prepared with Smart-Seq2 protocol (PMID: 24385147). The quality of the libraries was assessed using a 2100 Bioanalyzer (Agilent). Samples were paired-end sequenced at PE150 on an Illumina NovaSeq 6000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The reference genome (GRCm38.dna.primary_assembly.fa) and annotation files (GRCm38.101.gtf) were modified by concatenating the mouse genome with ERCC (source: Thermofisher) and the construct ‘pGEMHE-mCherry-mTrim21’ fasta and gtf files, respectively. The endogenous Trim21 locus was masked using bedtools (version 2.29.0).
The modified reference fasta file was used to prepare STAR index files using rsem-prepare-reference (rsem version 1.3.3). Paired-end reads were aligned using STAR (version 2.7.6a) with parameters --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate.
Downstream analysis was carried out on read counts per gene calculated by STAR.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab files of read counts per gene
|
| |
|
| Submission date |
Jan 31, 2022 |
| Last update date |
Oct 02, 2022 |
| Contact name |
Tamas Schauer |
| E-mail(s) |
tamas.schauer@helmholtz-munich.de
|
| Organization name |
Helmholtz Zentrum München
|
| Department |
Institute of Epigenetics and Stem Cells
|
| Street address |
Feodor-Lynen-Straße 21
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE195839 |
Characterization and function of transcriptional elongation during zygotic genome activation in mouse embryos [RNA-seq] |
| GSE195840 |
Characterization and function of transcriptional elongation during zygotic genome activation in mouse embryos |
|
| Relations |
| BioSample |
SAMN25524698 |
| SRA |
SRX13999964 |
