|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Nov 18, 2019 |
Title |
LC, cKO rep1 |
Sample type |
SRA |
|
|
Source name |
Locus coeruleus
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: Brain age: post natal day 35 genotype: ASL-LC cKO
|
Extracted molecule |
total RNA |
Extraction protocol |
Brains were removed rapidly, embedded and frozen in OCT on dry ice without fixation. 8μm thick sections were cut from the frozen block, mounted on polyethylene membrane-coated glass slides and kept in -80°C. At the day of the experiment, slides were thawed for 5 minutes in room temperature followed by fixation in 70% ethanol (30s), incubation in DEPC water, stained with 150µl 1% crystal violet acetate, and washed vigorously in 100% ethanol for a total of 30s and air dried for 3m before microdissection. Tissue sections were microdissected using a UV laser-based PALM Microbeam. SMARTer Ultra Low Input RNA followed by in-house DNA Seq protocol
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
455_ko
|
Data processing |
Fastq files for each sample were generated by the usage of bcl2fastq-v2.17.1.14 software (basecalling) Reads were trimmed using cutadapt Reads were aligned to the mouse genome mm10 using, TopHat (v2.0.10). Counting reads on reference genome, RefSeq release mm10, was done with HTSeq-count (version 0.6.1p1) Differential analysis was carried out using DESeq2 (1.6.3) Genome_build: mm10 Supplementary_files_format_and_content: processed1_raw_counts.xlsx Supplementary_files_format_and_content: processed2_normalized_counts.xlsx
|
|
|
Submission date |
Oct 06, 2019 |
Last update date |
Nov 18, 2019 |
Contact name |
Ayelet Erez |
E-mail(s) |
ayelet.erez@weizmann.ac.il
|
Phone |
972-8-934-3714
|
Organization name |
Weizmann Institute of Science
|
Department |
Biological Regulation
|
Street address |
234 Herzl Street
|
City |
Rehovot |
ZIP/Postal code |
76100 |
Country |
Israel |
|
|
Platform ID |
GPL17021 |
Series (1) |
GSE138471 |
Detection of differences in gene expression in the noradrenergic nuclei in the brain |
|
Relations |
BioSample |
SAMN12924301 |
SRA |
SRX6955962 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|