|
| Status |
Public on Oct 07, 2020 |
| Title |
32D clone 3_pEGFP-N1_CXCL1/2 treated [C3] |
| Sample type |
SRA |
| |
|
| Source name |
32D clone 3_pEGFP-N1_CXCL1/2 treated
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: bone marrow
cell line: 32D clone 3 cells
genotype/variation: transfected with an empty vector
treatment: CXCL1 (50 ng/mL) and CXCL2 (50 ng/mL) for 4 h
|
| Treatment protocol |
32D clone 3 cells transfected with PEGP-N1(an empty vector) or CXCR2 were cultured in complete medium supplemented with CXCL1 (50 ng/mL) and CXCL2 (50 ng/mL) for 4 h
|
| Growth protocol |
32D clone 3 cells were maintained in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 10% mouse interleukin(IL)-3 culture supplement.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cellular RNA was extracted using Trizol reagent followed by a genomic DNA elimination step. RNA purity was checked using the kaiaoK5500® Spectrophotometer. RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
32D clone 3 cells transfected with an empty vector
|
| Data processing |
Library construction and sequencing on an Illumina HiSeq 2500 instrument
Bowtie2 v2.2.3 was used for building the genome index
Clean data was then aligned to the reference genome using HISAT2 v2.1.0
Gene expression levels were quantified using a software package called FPKM
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates
Genome_build: Mus musculus. GRCm38. 89
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample
|
| |
|
| Submission date |
Nov 20, 2019 |
| Last update date |
Oct 07, 2020 |
| Contact name |
Xianlu Zeng |
| E-mail(s) |
[email protected]
|
| Phone |
8613943182276
|
| Organization name |
Northeast Normal University
|
| Street address |
No. 5268, Renmin Avenue
|
| City |
Changchun |
| ZIP/Postal code |
130024 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE140723 |
RNA-seq of 32D clone 3 cells transfected with CXCR2 (pEGFP-N1-CXCR2) or an empty vector (pEGFP-N1) with CXCL1/2 treatment |
|
| Relations |
| BioSample |
SAMN13336633 |
| SRA |
SRX7191486 |
