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Sample GSM5851856 Query DataSets for GSM5851856
Status Public on Oct 01, 2022
Title Spt5KD_C_2
Sample type SRA
 
Source name 2-cell embryo
Organism Mus musculus
Characteristics protocol: RNA-seq
treatment: Spt5 Trim-Away
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 SAMN25524648
SRA SRX14000014

Supplementary file Size Download File type/resource
GSM5851856_MUC26829.ReadsPerGene.out.tab.gz 258.3 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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