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Sample GSM3317307 Query DataSets for GSM3317307
Status Public on Aug 02, 2018
Title Bone marrow sinusoidal endothelial cells, PBS treated, biological rep 1
Sample type SRA
Source name FACS sorted bone marrow SECS from PBS-treated mice
Organism Mus musculus
Characteristics cell type: Sinusoidal endothelial cells
tissue: bone marrow
treatment: PBS
Treatment protocol 200ng Diphtheria toxin (DT) in 100ul PBS or just 100ul PBS was injected into mice intraperitoneally, and the mice were harvested 1 day after treatment.
Growth protocol Mice were maintained under SPF conditions, and all experimental procedures were performed according to methods approved by the Animal Studies Committee at Washington University.
Extracted molecule total RNA
Extraction protocol Sinusoidal endothelial cells were sorted using flow cytometry, gated as Lineage- (CD45, Ter119, Gr1, CD11b) CD31+ Sca1- cells, and the RNA from these cells was extracted using RNeasy micro Kit (74004, Qiagen).
Library preparation was performed with 1ng of total RNA, integrity was determined using an Agilent bioanalyzer. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Clontech) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles/burst 50, time 120 seconds. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 14 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description Normalized_count_data_FPKM.txt
Data processing All data from RNA sequencing were analyzed using Partek® Flow® software, version 7.0 Copyright ©; 2018 (Partek Inc., St. Louis, MO, USA).
Single reads from Illumina sequencing were aligned to the mm10 mouse reference genome by STAR (v. 2.5.3a).
Aligned reads were then quantified to annotation model (Partek E/M, mm10 Ensembl Transcripts release 88).
Gene counts were all added with 0.0001 and were then normalized to total counts.
Partek GSA algorithm was utilized for differential expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all samples
Submission date Aug 01, 2018
Last update date Aug 03, 2018
Contact name Daniel C Link
Phone 314-362-8771
Organization name Washington University in St Louis
Department Internal Medicine
Street address 660 South Euclid Avenue
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
Platform ID GPL21493
Series (1)
GSE118017 Expression data from mouse bone marrow sinusoidal endothelial cells (SECs) before and after the ablation of classical dendrtic cells (cDCs)
BioSample SAMN09755893
SRA SRX4498265

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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