|
| Status |
Public on Jan 04, 2023 |
| Title |
KO_rep1_rnaseq |
| Sample type |
SRA |
| |
|
| Source name |
BMDC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: dentritic cells
strain: C57BL/6
genotype: CreER;CTCF fl/fl
treatment: none
|
| Treatment protocol |
Bone marrow-derived dendritic cells were stimulated with LPS at the concentreation of 100ng/ml for 3 hours.
|
| Growth protocol |
Bone marrow cells prepared from CreER or CreER;CTCFfl/fl mice were culutred under the presence of murine GM-CSF for 6 days with chaning medium every 2 days. For the deletion of Ctcf allele, 4-OH tamoxifen is added only on the first day of culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were PBS washed, and RNA was harvested and isolated using Hybrid-R Total RNA kits (Gene All Biotechnology) and rRNAs were depleted by using the NEBNext rRNA Depletion Kit (NEB #E6350).
TruSeq RNA sample prep kit (illumina #FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
sequnced using Illumina Hiseq platform
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using STAR v2.5.1 with parameters --sjdbOverhang 100 --twopassMode Basic --chimSegmentMin 20 --quantMode TranscriptomeSAM
Fragments Per Kilobase Million (FPKM), Transcripts Per Kilobase Million(TPM) and raw counts were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: RSEM output files including raw counts, FPKM, TPM values
|
| |
|
| Submission date |
Oct 13, 2021 |
| Last update date |
Jan 04, 2023 |
| Contact name |
Hyoung-Pyo Kim |
| E-mail(s) |
kimhp@yuhs.ac
|
| Organization name |
Yonsei University College of Medicine
|
| Department |
Department of Tropical Medicine
|
| Street address |
Yonsei-ro 50-1
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE185881 |
Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells (RNA-seq) |
| GSE185884 |
Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells |
|
| Relations |
| BioSample |
SAMN22252106 |
| SRA |
SRX12601733 |
