|
| Status |
Public on Feb 13, 2018 |
| Title |
B3_PLX |
| Sample type |
SRA |
| |
|
| Source name |
olfactory bulb
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
tissue: olfactory bulb
diet: PLX5622 diet (inducing a near-complete microglia depletion)
|
| Treatment protocol |
Mice received PLX5622 diet or control diet for 25 days before they were sacrificed and the olfactory bulbs were removed and flash frozen in liquid nitrogen for later processing
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using PerfectPure RNA Tissue Kit, 5 PRIME
Inhouse poly A based RNA seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adapters were trimmed using the cutadapt tool. Following adapter removal, reads that were shorter than 40 nucleotides were discarded (cutadapt option –m 40).
Reads that had either a percentage of Adenine bases above 50% or a percentage of Thymine bases above 50% were discarded using a custom script.
TopHat (v2.0.10) was used to align the reads to the mouse genome (mm10)
Counting reads on mm10 refseq genes was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.6.3)
Supplementary_files_format_and_content: Excel file includes the normalized counts
|
| |
|
| Submission date |
Nov 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Raz Yirmiya |
| Organization name |
Hebrew University of Jerusalem
|
| Street address |
Mount Scopus
|
| City |
Jerusalem |
| ZIP/Postal code |
91905 |
| Country |
Israel |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE106857 |
The role of microglia in maturation of adult-born neurons |
|
| Relations |
| BioSample |
SAMN08023366 |
| SRA |
SRX3389388 |
