|
| Status |
Public on May 01, 2017 |
| Title |
CX3CR1_3 |
| Sample type |
SRA |
| |
|
| Source name |
CX3CR1_3
|
| Organism |
Mus musculus |
| Characteristics |
cell type: FACS sorted cells
tissue: Brown adipose tissue
selection marker: CD11b+ Ly6C- f4/80+ cd64+ CD14+MerTK+MHCII+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Enzymatic digestion and gradient seperation. Antibodies used throughout the research are: CD11b (clone M1/70), Ly6C (clone AL21), Ly6G (clone H129.19), f4/80 (clone BM8), CD64 (clone 90322), CD14 (clone Sa2-8), MerTK (polyclonal), MHCII (clone M5/114.15.2)
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 NextSeq 500 |
| |
|
| Description |
Steady state untreated cells
RNAseq_pos_neg_all.xlsx
|
| Data processing |
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7
alignment: hisat 0.1.5 with deafult parameters
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count exons -condenseGenes -strand + -norm 1e7
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
|
| |
|
| Submission date |
Mar 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Steffen Jung |
| E-mail(s) |
s.jung@weizmann.ac.il
|
| Phone |
0097289342787
|
| Organization name |
The Weizmann Institute of Science
|
| Department |
Immunology and Regenerative Biology
|
| Lab |
Steffen Jung
|
| Street address |
Herzl
|
| City |
REHOVOT |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE95859 |
Brown adipose tissue macrophages control tissue innervation and homeostatic energy expenditure |
|
| Relations |
| BioSample |
SAMN06554768 |
| SRA |
SRX2628095 |
