|
| Status |
Public on Feb 26, 2024 |
| Title |
E14.5 Female PGC RNAseq Tet1-WT2 |
| Sample type |
SRA |
| |
|
| Source name |
Primordial germ cell
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Primordial germ cell
Sex: Female
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extrated using Quick RNA Microprep Kit by Zymo Research from 5000 cells
mRNA library was generated using Oligo d(T)25 RNA Magnetic Isolation Module followed by UltraII RNA Library Prep Kit (NEB) following manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 1000 |
| |
|
| Description |
WT PGC F2
|
| Data processing |
Quality of raw reads were assessed using FastQC
Raw reads were quality-trimmed Using Trim Galore (v0.6.7)
Reads were aligned to GRCm39 (mm10) using STAR (v2.7.10b) with default parameters and a maximum fragment size of 2000bp
Properly paired primary alignments were retained for downstream analysis using Samtools (v1.9)
Count matrices were generated using featureCounts 2.0.3 against RefSeq gene annotation
Assembly: mm10
Supplementary files format and content: Text file of summary count
|
| |
|
| Submission date |
Jan 18, 2024 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Rexxi Diptya Prasasya |
| E-mail(s) |
rexxi.prasasya@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Bartolomei Lab
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL32159 |
| Series (2) |
| GSE224459 |
TET1 catalytic activity is required for reprogrammign of imprinting control regions and the patterning of sperm-specific hypomethylated regions |
| GSE253636 |
TET1 catalytic activity is required for reprogrammign of imprinting control regions and the patterning of sperm-specific hypomethylated regions [RNA-seq: Female PGCs] |
|
| Relations |
| BioSample |
SAMN39487347 |
| SRA |
SRX23304897 |
