|
Status |
Public on Feb 26, 2024 |
Title |
E14.5 Male PGC RNAseq Tet1-WT4 |
Sample type |
SRA |
|
|
Source name |
WT PGC4
|
Organism |
Mus musculus |
Characteristics |
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 |
|
|
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
|
|
|
Submission date |
Dec 08, 2023 |
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 |
GSE249772 |
TET1 catalytic activity is required for reprogrammign of imprinting control regions and the patterning of sperm-specific hypomethylated regions [RNA-Seq] |
|
Relations |
BioSample |
SAMN38732737 |
SRA |
SRX22834973 |