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Sample GSM3557782 Query DataSets for GSM3557782
Status Public on Jan 10, 2020
Title CD31p_ckitp_CD45m_DIl4_4
Sample type SRA
 
Source name Embryonic
Organism Mus musculus
Characteristics cell type: Embryonic Hematopoietic cells
strain: C57BL/6J
antibody: anti-Dll4
Treatment protocol E10.5 embryos were intracardiacally injected with anti-human IgG and anti-Dll4 and incubated for 5 hours at 37 °C in a humidified atmosphere with 5% CO2 in complete myeloid long-term medium (STEMCELL Technologies - supplemented with 10 ng ml−1 interleukin (IL)-3 and 10 µM hydrocortisone (Sigma-Aldrich) containing 5 μg ml−1 of the relevant antibody.
Extracted molecule polyA RNA
Extraction protocol CD31 B51 were sorted in a FACS ARIA in QIAGEN RLT medium
Samples were digested with 0.1% collagenase and single-cell suspension was stained as described. Different subpopulations were directly sorted in a total volume of 10  ml of reaction buffer and processed for obtaining cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description 8_1_21655_GTGGCC
Data processing Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads
Reads were aligned to the mm10 genome assembly using STAR RNA-seq aligner
QualiMap was run for the quality control of alignment sequencing data
htseq software was used to estimate the raw gene counts
DESeq2 R package was run to infer differentially expressed genes accross samples
Genome_build: mm10
Supplementary_files_format_and_content: txt files are generated from htseq and DESeq2 results using R
 
Submission date Jan 09, 2019
Last update date Jan 10, 2020
Contact name Anna Bigas
E-mail(s) abigas@imim.es
Phone +34933160440
Organization name Institut Hospital del Mar d'Investigacions Mèdiques
Department Cancer Research
Lab Stem Cells and Cancer
Street address Dr. Aiguader 88
City Barcelona
State/province Barcelona
ZIP/Postal code 08003
Country Spain
 
Platform ID GPL13112
Series (1)
GSE124875 Notch ligand Dll4 impairs the recruitment of hemogenic cells into intra-aortic clusters and limits hematopoietic stem cell production.
Relations
BioSample SAMN10719707
SRA SRX5236144

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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