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Sample GSM3487957 Query DataSets for GSM3487957
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
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
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
BioSample SAMN10475391
SRA SRX5059831

Supplementary file Size Download File type/resource
GSM3487957_GRA15.txt.gz 80.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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