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Sample GSM4109504 Query DataSets for GSM4109504
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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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