|
Status |
Public on Sep 09, 2021 |
Title |
BMR2_Liver_S44 |
Sample type |
SRA |
|
|
Source name |
Liver
|
Organism |
Nannospalax ehrenbergi |
Characteristics |
strain: Wild-caught tissue: Liver
|
Treatment protocol |
No treatment
|
Growth protocol |
Fibroblasts were maintained at 37 °C incubator in an atmosphere of 5% CO2 and 3% O2 on treated polystyrene culture dishes (Corning) in EMEM media (ATCC) with 15% (vol/vol) fetal bovine serum (FBS).
|
Extracted molecule |
total RNA |
Extraction protocol |
For RNAseq, was extracted using a Quick-RNA MiniPrep Kit (Zymo), with a DNase I on column digestion to remove genomic DNA contamination; For MeDIP, genomic DNA was extracted using a Zymo Quick-DNA Miniprep Plus Kit. For RNAseq, the RNA samples were processed with the Illumina TruSeq stranded total RNA RiboZero Gold kit and then subjected to Illumina HiSeq 4000 paired-end 150bp sequencing; For MeDIP, genomic DNA samples were processed using the NEBNext UltraII DNA Library Prep kit.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
raw fastq reads files were cleaned by Trimmomatic-0.36 cleaned reads were mapped to the genome by STAR_2.5.2b gene expression (TPM and reads counts) were calculated by salmon 1.4.0 regions of differential methylation were called by edgeR package in 100 window resolution (R version 3.3.2) Genome_build: Mouse (Mus musculus): mm10 Genome_build: Blind mole rat (Spalax ehrenbergi):GCF_000622305.1_S.galili_v1.0
|
|
|
Submission date |
Aug 03, 2021 |
Last update date |
Sep 09, 2021 |
Contact name |
Yang Zhao |
E-mail(s) |
yangzhao926@outlook.com
|
Organization name |
University of Rochester
|
Department |
Biology
|
Street address |
60 Crittenden Blvd, Apt1240
|
City |
Rochester |
State/province |
NY |
ZIP/Postal code |
14620 |
Country |
USA |
|
|
Platform ID |
GPL30472 |
Series (2) |
GSE181413 |
Transposon-triggered innate immune response confers cancer resistance to the blind mole rat [seq] |
GSE181733 |
Transposon-triggered innate immune response confers cancer resistance to the blind mole rat |
|
Relations |
BioSample |
SAMN20558531 |
SRA |
SRX11644658 |