|
| Status |
Public on Nov 23, 2023 |
| Title |
E45_TE_mzKO_RNA_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
E4.5 TE
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Tfap2c mzKO
strain: mix
antibody: none
|
| Growth protocol |
For collection of wildtypes E4.25 blastocyst, 4–6-week-old female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with malemice. E4.25 blastocyst were flushed out from the uterus at E4.25.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells or embyos were lysed in lysis buffer containing RNase inhibitor.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq tracks, gene expression table for RNA-seq data
|
| |
|
| Submission date |
Oct 20, 2022 |
| Last update date |
Nov 23, 2023 |
| Contact name |
Lijia Li |
| E-mail(s) |
lijiali1119@gmail.com
|
| Organization name |
Tsinghua University
|
| Department |
School of Life Science
|
| Lab |
Wei Xie lab
|
| Street address |
Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE216256 |
Lineage regulators TFAP2C and NR5A2 function as bipotency activators in totipotent embryos |
|
| Relations |
| BioSample |
SAMN31394217 |
| SRA |
SRX17979265 |
