|
| Status |
Public on Sep 09, 2021 |
| Title |
O-3_S12_L002 |
| Sample type |
SRA |
| |
|
| Source name |
Fibroblasts
|
| Organism |
Nannospalax ehrenbergi |
| Characteristics |
strain: Wild-caught
tissue: Fibroblasts
|
| 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 HiSeq 4000 |
| |
|
| 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) |
[email protected]
|
| 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 |
GPL30473 |
| 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 |
SAMN20558574 |
| SRA |
SRX11644731 |
