|
| Status |
Public on Jun 20, 2017 |
| Title |
WT_3 |
| Sample type |
SRA |
| |
|
| Source name |
Freshly isolated brain microglia
|
| Organism |
Mus musculus |
| Characteristics |
strain: Cx3cr1CreER:Dicer+/-
tissue: brain
age (weeks): 10-12 weeks
transfer: CD45intCD11b+F4/80+Ly6C-Ly6G-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
oligo dT dynabeads
http://www.sciencemag.org/content/343/6172/776.abstract?ijkey=6c89f9e625c6efc35902e948462a6d1dad095f64&keytype2=tf_ipsecsha
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Steady state
Figure 3 WT steady state
|
| 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
FastQ files were indexed and mapped for Mm9 genome assembly using HISAT 0.1.5
SAM files were converted to BAM using SAMtools
Gene count and normalization was done using Homer for Fig3 (analyzeRepeats.pl rna mm9 -d <List of tag dir> -count 3utr -condenseGenes -strand + -norm 1e7 ) and DESEQ2 (single factor) for all other tables
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
|
| |
|
| Submission date |
Apr 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Steffen Jung |
| E-mail(s) |
[email protected]
|
| 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 (2) |
| GSE98142 |
Differential impact of Dicer deficiency on microglia of the developing and adult brain (Bulk RNA-Seq) |
| GSE98144 |
Differential impact of Dicer deficiency on microglia of the developing and adult brain |
|
| Relations |
| BioSample |
SAMN06828966 |
| SRA |
SRX2762938 |
