|
| Status |
Public on Aug 01, 2024 |
| Title |
mESC_ZFP524_day0_C2 |
| Sample type |
SRA |
| |
|
| Source name |
H1
|
| Organism |
Mus musculus |
| Characteristics |
cell line: H1
cell type: Mouse embryonic stem cells (mESCs)
genotype: ZFP524 KO
treatment: Differentiation day0
|
| Treatment protocol |
During differentiation, LIF, MEK1/2 inhibitor and GSK3 inhibitor were removed from the medium.
|
| Growth protocol |
H1 mESCs were grown in standard medium (DMEM supplemented with 15% FBS (ES-qualified, ThermoFisher Scientific, 16141-079), 1000 U/mL LIF (Millipore), 1× MEM non-essential amino acids, 1 mM of Sodium Pyruvate, 1× GlutaMAX™ Supplement, 1× Penicillin and streptomycin, and 0.1 mM of 2-mercaptoethanol) supplemented with 1µM MEK1/2 inhibitor (PD0325901, Sigma) and 3 1µM GSK3 inhibitor (CHIR99021, Sigma).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Mini Kit (QIAGEN) following manufacturer’s protocol.
A total of 100ng total RNA was subjected to polyA enrichment and cDNA libraries preparation using NEBNext Ultra II Directional RNA library Preparation Kit for Illumina (NEB, E7760L).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Read quality of RNA-seq data in fastq files was assessed using QoRTs (v1.2.37).
Reads were aligned to mm10 genome using HISAT2 (Version 2.2.1).
Normalized read counts for all genes were obtained using featureCount (v3.18.1).
Differential expression was determined in each of the pair-wise comparisons between experimental and control groups using DESeq (V1.22.1).
Assembly: mm10
Supplementary files format and content: Tabular files include raw counts for each sample.
|
| |
|
| Submission date |
Jun 12, 2023 |
| Last update date |
Aug 01, 2024 |
| Contact name |
Fubo Cheng |
| E-mail(s) |
fubo.cheng@med.uni-tuebingen.de
|
| Organization name |
University of Tuebingen
|
| Department |
Institute of Medical Genetics and Applied Genomics
|
| Street address |
Calwerstrasse 7
|
| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE234677 |
THAP1 is a master regulator of zinc finger transcription factors guiding gastrulation of murine embryos [RNA-seq_mESC] |
| GSE234680 |
THAP1 is a master regulator of zinc finger transcription factors guiding gastrulation of murine embryos |
|
| Relations |
| BioSample |
SAMN35712935 |
| SRA |
SRX20657545 |
