U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX14000018: GSM5851860: Spt5KD_D_3; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 6.5M spots, 2G bases, 619.4Mb downloads

External Id: GSM5851860_r1
Submitted by: Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München
Study: Characterization and function of transcriptional elongation during zygotic genome activation in mouse embryos [RNA-seq]
show Abstracthide Abstract
The work associated to these datasets focuses on the investigation of transcriptional regulation during the earliest stages of mammalian embryogenesis. In particular, ChILseq and RNAseq datasets were generated to study the process of zygotic genome activation in mouse embryos. After fertilisation, the mouse embryo activates its own genome for the first time in a process known as zygotic genome activation, which occurs primarily on two main waves. The first wave occurs in zygotes, and the second one at the late 2-cell stage. To understand how the RNA Polymerase II functions during these waves, we have implemented a ChILseq approach to generate genome-wide maps of Ser5 and Ser2 phosphorylated forms of RNA Polymerase II in zygotes, 2- and 8-cell stage embryos. In addition, we have investigated how elongation factors, such as NELF and DSIF regulate major ZGA by performing single embryo RNAseq using SMART-seq2 in 2-cell stage embryos upon depletion of Spt5, NELFE and upon chemical inhibition of Cdk9. Overall design: RNA-seq experiments upon Cdk9 inhibition, Spt5, NELF-E depletion by Trim-Away as well as IgG Trim-Away and no injection control in single 2-cell stage embryos.
Sample: Spt5KD_D_3
SAMN25524644 • SRS11838397 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM5851860
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction 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.
Runs: 1 run, 6.5M spots, 2G bases, 619.4Mb
Run# of Spots# of BasesSizePublished
SRR178389706,499,6302G619.4Mb2022-10-01

ID:
19637095

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...