|
Status |
Public on Jul 01, 2018 |
Title |
LMP_Replicate2 |
Sample type |
SRA |
|
|
Source name |
Mouse CMP derived plasmacytoid dendritic cells
|
Organism |
Mus musculus |
Characteristics |
cell type: Myeloid 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 LMP 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 |
SAMN07822805 |
SRA |
SRX3313916 |