|
| Status |
Public on Dec 14, 2014 |
| Title |
moDC_6 hours PAM |
| Sample type |
SRA |
| |
|
| Source name |
GM-CSF derived cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone Marrow
treatment: 6 hour 100ng/ml PAM3CSK (PAM)
|
| Treatment protocol |
(mentioned in the relevant samples)
|
| Growth protocol |
Samples 1-40:Bone marrows were extracted from femora and tibiae of C57BL/6J female mice (6 to 10 weeks old), growth in presence of GM-CSF (for moDC) or Flt3L (for pDC). Samples 41-50: cells were isolated from the indicated organ, filtered and stained with the indicated antibodies for FACS sorting
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction, cells were harvested in Qiazol lysis solution (Qiagen), and total RNA was extracted using miRNeasy Mini Kit (Qiagen).
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
polyA+ RNA
TLRs_stimulated_moDC_and_pDC.xlsx
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
alignment: TopHat aligner with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
|
| |
|
| Submission date |
Oct 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ido Amit |
| E-mail(s) |
ido.amit@weizmann.ac.il
|
| Phone |
972-8-9343338
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Immunology
|
| Street address |
234 Herzl st.
|
| City |
Rehovot |
| ZIP/Postal code |
760001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE62704 |
A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN03142961 |
| SRA |
SRX742914 |
