|
| Status |
Public on Jul 01, 2018 |
| Title |
LLP_Replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse CLP derived plasmacytoid dendritic cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Lymphoid derived plasmacytoid dendritic cells
|
| Growth protocol |
Cells were freshly isolated and sorted from mouse bone marrow before placed in Trizol for total RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, total RNAs were extracted using Rneasy plus mini kit (Qiagen).
RNA-sequencing libraries were generated using library prep kits (NEB) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Gene expression data in LLP cells
|
| Data processing |
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using tophat.
For RNA-seq, *.fpkm_tracking files from Cufflinks containing FPKM values are provided.
We used three different sample data to normalize to control sample.
For LLP1.fpkm_tracking, LLP1 is normalized to LMP1/2/3:
q1 is from LLP1 normalized to LMP1
q2 is from LLP1 normalized to LMP2
q3 is from LLP1 normalized to LMP3
q4 is from LLP1 normalized internally
For LLP2.fpkm_tracking, LLP2 is normalized to LMP1/2/3.
For LLP3.fpkm_tracking, LLP3 is normalized to LMP1/2/3.
Genome_build: mm9
Supplementary_files_format_and_content: *.fpkm_tracking files from Cufflinks containing FPKM values
|
| |
|
| Submission date |
Oct 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph D Dekker |
| E-mail(s) |
joedekker@gmail.com
|
| Phone |
5054637855
|
| Organization name |
University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Street address |
2506 Speedway Blvd, NMS 1.264
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE105827 |
Common lymphoid progenitor derivation of plasmacytoid dendritic cells is mediated by Bcl11a |
|
| Relations |
| BioSample |
SAMN07822803 |
| SRA |
SRX3313912 |
