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Sample GSM4411290 Query DataSets for GSM4411290
Status Public on Nov 22, 2021
Title W1homing
Sample type SRA
 
Source name CD45.2+Lin-Sca-1+ cells from recipients that received BM cells from WT mice
Organism Mus musculus
Characteristics cell type: CD45.2+Lin-Sca-1+ cells isolated from primary recipients 6h after transplantation
donor cell source: From bone marrow (BM) of WT mice
genotype: WT
Treatment protocol For BMT, 2×10^7 donor cells from bone marrow (BM) of HEMGN-/- (CD45.2+) and WT were injected intravenously via the retro-orbital route into recipients mice(CD45.1+) previously irradiated with a split dose of 9Gy. Each group contains three replicates.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the QIAshredder and RNeasy Mini Kit (QIAGEN).
RNA libraries were constructed using TruSeq kits (Illumina). The RNA libraries were sequenced on an Illumina Hiseq 2000/2500 at the ANNOROAD GENOME Co., Ltd. (Beijing, CN) following the vendor's recommended protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data). The steps are: 1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads);
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2 , which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates. Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate
Genome_build: Mus_musculus.GRCm38.90.chr
Supplementary_files_format_and_content: Processed values are FPKM
 
Submission date Mar 13, 2020
Last update date Nov 22, 2021
Contact name Xian Liu
E-mail(s) Liux.bio@gmail.com
Phone 010-80728330
Organization name Beijing Institute of Life Omics
Street address 38 Life Science Park Street
City Beijing
ZIP/Postal code 102206
Country China
 
Platform ID GPL21273
Series (1)
GSE146949 Gene Expression Profiling of HEMGN-/- and WT HSPCs sorted from primary recipients 6h after transplantation (early homing cells)
Relations
BioSample SAMN14374621
SRA SRX7909615

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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