|
| Status |
Public on Nov 27, 2018 |
| Title |
GRA15 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
transfection: GRA15
cell type: Immortalized bone marrow derived macrophages
genotype: wild type
|
| Treatment protocol |
Cells were infected by lenti-virus containing GRA15II gene and selected by applying puromycin in culture medium
|
| Growth protocol |
Immortalized bone marrow derived macrophages were cultured in DMEM containing 10% FBS, 1% glutamine, 1% streptomycin-penicillin on 10 cm dish for further experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Supernatant was removed and cells were covered with 350ul Buffer RLT at the end of treatment. Total RNA was extracted following the strandard protocol of RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), and sequenced on an Illumina Novaseq platform.
Illumina Casava 1.8 software used for basecalling and raw reads were gained.
After eliminating low-quality reads and reads with adaptors, clean reads were mapped to mouse genome reference sequence (GRCm38/mm10 Ensembl release 81) using HISAT2.
Gene expression was quantified as reads per kilobase of coding sequence per million reads (RPKM) algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ensemble gene ID and RPKM values for each Sample
|
| |
|
| Submission date |
Nov 26, 2018 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Peiyan Wang |
| E-mail(s) |
peiyanwang@hsc.pku.edu.cn
|
| Organization name |
Peking University
|
| Street address |
NO.38 ROAD XUEYUAN, DISTRICT HAIDIAN, BEIJING, CHINA, 北京市海淀区学院路38号北京大学医学部
|
| City |
BEIJING |
| State/province |
北京 |
| ZIP/Postal code |
100191 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE122906 |
mRNA-seq of immortailized bone marrow derived macrophages (iBMDM) overexpressing GRA15II |
|
| Relations |
| BioSample |
SAMN10475391 |
| SRA |
SRX5059831 |
