|
| Status |
Public on Nov 05, 2020 |
| Title |
Control(h0) rep1 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Raw264.7
cell type: Monocyte-derived cell line
treatment: Control
time point: hour 0
|
| Treatment protocol |
Total RNA was isolated from RAW264.7 cells at 0, 4, 14 and 24h after RANKL, RANKL/I-BET, or I-BET treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction: Nucleospin RNA kit (Macherey-Nagel).
Libraries preparation: NEBNext poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra RNA Library Prep kit; Sequenced: Illumina HiSeq 2500 paired-end 100bp reads. Two replicates per time point and treatment were made.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_4-neg1
|
| Data processing |
Quality Check (FastQC).
Sequence reads aligned to the GRCm38 by STAR (version 2.5.3a) --alignTranscriptsPerReadNmax 100000 --limitGenomeGenerateRAM 20000000000, and chimeric outputs were allowed.
Raw counts of each library were obtained using the Rsubread (version 1.24.2) R/Bioconductor package.
The DESeq2 (version 1.16.1) R/Bioconductor package was used for normalizing the counts and implementing the DE analysis.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: allsamples_RPKM_withmm10.csv: Normalized counts (RPKM) file for all samples; comma-separated text file.
Supplementary_files_format_and_content: brd_allrawcounts.csv: Raw counts for all samples; comma-separated text file.
|
| |
|
| Submission date |
Nov 04, 2020 |
| Last update date |
Nov 05, 2020 |
| Contact name |
Anastasios Karadimitris |
| E-mail(s) |
a.karadimitris@imperial.ac.uk
|
| Phone |
+44 20 3313 8438
|
| Organization name |
Imperial College London
|
| Department |
Department of Immunology and Inflammation
|
| Lab |
Karadimitris' Lab
|
| Street address |
Hammersmith Campus, Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE160834 |
Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development [RNA-seq] |
| GSE160840 |
Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development |
|
| Relations |
| BioSample |
SAMN16663131 |
| SRA |
SRX9431939 |
