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Status |
Public on Jan 10, 2020 |
Title |
CD31p_Ckitm_CD41p_CD45m_Control1 |
Sample type |
SRA |
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|
Source name |
Embryonic
|
Organism |
Mus musculus |
Characteristics |
cell type: Embryonic Hematopoietic cells strain: C57BL/6J antibody: anti-human IgG
|
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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
1_3_21635_GCCAAT
|
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
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|
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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 |
SAMN10719727 |
SRA |
SRX5236124 |