|
| Status |
Public on Apr 08, 2024 |
| Title |
LMH cells_PP1C4 |
| Sample type |
SRA |
| |
|
| Source name |
LMH
|
| Organism |
Gallus gallus |
| Characteristics |
cell line: LMH
cell type: liver cells
treatment: PP1
infection: no infection
|
| Treatment protocol |
LMH cells with or without ILTV infection were treated with PP1 dissolved in DMSO at a final concentration of 2 μM or PP2 dissolved in DMSO at a final concentration of 20 μM.
|
| Growth protocol |
LMH cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine. Cell cultures were incubated at 37°C/5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Seperated cell samples were treated by Smart-Seq2 protocol to get amplified cDNA.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
LMH cells, PP1
|
| Data processing |
Useful Perl script was used to filter the original raw data, to trim Smart-seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases .
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12.
Transcript assemble, difference expression anlysis was finished by Cufflinks 2.2.1.
Assembly: Gallus_gallus-4.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Apr 07, 2022 |
| Last update date |
Apr 08, 2024 |
| Contact name |
Hai Li |
| E-mail(s) |
lihai@xjtu.edu.cn
|
| Organization name |
Xi'an Jiaotong University
|
| Department |
Department of Pathogenic Microbiology and Immunology
|
| Street address |
No.76 Yanta West Road
|
| City |
Xi'an |
| ZIP/Postal code |
710061 |
| Country |
China |
| |
|
| Platform ID |
GPL19005 |
| Series (1) |
| GSE200458 |
Exploration of the transcriptional regulation network of the suppression of ILTV infection by PP1 and PP2 in chickenLMH cells |
|
| Relations |
| BioSample |
SAMN27407796 |
| SRA |
SRX14782199 |
