|
| Status |
Public on Jul 05, 2022 |
| Title |
Zygote.IgG.Input.RNAseq.rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Zygotes
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Zygotes collected after Lsm1 mRNA injection
strain: B6D2F1
rip antibody: none
|
| Treatment protocol |
Lsm1KD group were injected with Lsm1 siRNA; WT group were injected with Lsm1 scramble siRNA; LLsm1FLAGRIP group were injected with Lsm1_3XFlag mRNA; CtrlRIP group were injected with Lsm1 mRNA
|
| Growth protocol |
B6D2F1 female mice (8–10 weeks old) were super-ovulated by injection with 7 IU each of pregnant mare serum gonadotropin (PMSG), followed by injection of 5 IU of human chorionic gonadotropin (hCG) 48 hr later. The super-ovulated female mice were mated with male mice. The zygote were collected at 18-20 hr post-hCG injection, and micro-injected with different RNAs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For Lsm1 knockdown zyogtes, RNA was harvested using Trizol reagent. For RIP-seq zygotes, Protein-RNA complex were isolated by ANTI-FLAG® M2 Affinity Gel, then RNA was harvested using Trizol reagent.
For Lsm1 knockdown zyogtes, RNA libraries were prepared for sequencing using KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (KapaBiosystems, Cat. Nos.KK8483); For RIP-seq zygotes, RNA libraries were prepared for sequencing using SMARTer Stranded Total RNA-Seq Kit v2 (Takara, Cat. Nos. 635005)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
total RNA
|
| Data processing |
Adapter trimming using Trimmomatic with default parameters, followed by a quality control step using FastQC.
FASTQ reads were aligned to the transcriptome (RefSeq transcriptome assembly, and Repbase transposon sequences) using salmon.
TPM values from the salmon results were used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: salmon output .sf file per sample
|
| |
|
| Submission date |
Jul 06, 2021 |
| Last update date |
Jul 05, 2022 |
| Contact name |
Jiang Zhu |
| E-mail(s) |
zhujiang860918@yahoo.com
|
| Organization name |
Tongji University
|
| Street address |
1239 Siping Road
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE179556 |
Non-equilibrium pronucleus histones require gametal factor Lsm1 induced major satellite RNA decay |
|
| Relations |
| BioSample |
SAMN20081367 |
| SRA |
SRX11361543 |
