|
| Status |
Public on Mar 11, 2020 |
| Title |
F_DC2_CD206_d2 |
| Sample type |
SRA |
| |
|
| Source name |
Cord blood HSPC derived mononuclear phagocytes
|
| Organism |
Homo sapiens |
| Characteristics |
donor status: healthy donor
donor: 2
tissue: In vitro differentiated cells
cell type: CD1c+ CD206+ cells
culture condition: Co-cultured with MS5_FS12
|
| Growth protocol |
CD34+ hematopoietic progenitors isolated from human cord blood were differentiated in vitro by culturing them with engineered mesenchymal stromal cells expressing human transmembrane FLT3L, SCF and soluble CXCL12 (MS5_FS12) for 14 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
in vitro differentiated cells and human PBMCs isolated from healthy donors were FACS sorted in 96-well plates (100 cells/well) containing lysis buffer (RLT).
RNA-seq libraries were prepared using Labcyte Echo 525 contactless liquid handling system (Labcyte Inc). In brief, ERCC mix (Thermo Fisher) was added to each sample and first strand full length cDNA was generated with a modified protocol of the SMARTseq v4 Ultra Low Input RNA Kit (Takara Clontech) using poly dT primers and a template switching oligo. Full length cDNA was amplified using SeqAmp™ DNA Polymerase (Takara Clontech). 12 ng of amplified cDNA from each sample was used to generate non-stranded RNA libraries using a modified protocol of the Ovation Ultralow System V2 1-96 kit (NuGEN). In brief, amplified cDNA was fragmented through sonication on Covaris E220 (Covaris Inc), repaired and polished followed by ligation of indexed adapters. Adapter ligated cDNA were pooled before final amplification to add flow cell primers. Libraries were sequenced on HiSeq2500 (Illumina Cambridge) for 100 cycles PE in Rapid mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
F-moDC-d2_S19_L001
|
| Data processing |
Base-calling was performed on Illumina bcl2fastq v2.19.1.403
The raw sequencing data was initially processed using open source, web-based platform Galaxy (version 18.05.rc1).
Reads were filtered for quality with more than 80% of the sequence having quality score > 33 using FastQC tool.
Mapping against reference genome was performed with Hisat2 v2.1.0 to the hg38 human genome.
Adapter sequences were detected automatically with TrimGalore!. Reads under 20bp were discarded.
All processed sequencing files were imported in Partek® Flow® software (Partek Inc., build 7.0.18.0514) and the gene count data was normalised using FPKM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for each sample
|
| |
|
| Submission date |
Jan 29, 2020 |
| Last update date |
Mar 11, 2020 |
| Contact name |
Kristine Vaivode |
| E-mail(s) |
kristine.vaivode@kcl.ac.uk
|
| Phone |
02078486907
|
| Organization name |
King's College London
|
| Department |
Centre for Inflammation Biology and Cancer Immunology
|
| Lab |
Dr Pierre Guermonprez lab
|
| Street address |
CIBCI, First Floor, New Hunt's House, Great Maze Pond
|
| City |
London |
| ZIP/Postal code |
SE1 1UL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE144435 |
Transcriptional comparison of in vitro generated human dendritic cells and peripheral blood circulating dendritic cells. |
|
| Relations |
| BioSample |
SAMN13939819 |
| SRA |
SRX7645899 |
