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| Status |
Public on Nov 18, 2019 |
| Title |
LC, cKO rep2 |
| Sample type |
SRA |
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| Source name |
Locus coeruleus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Brain
age: post natal day 35
genotype: ASL-LC cKO
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
459_ko
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| 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
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| Submission date |
Oct 06, 2019 |
| Last update date |
Nov 18, 2019 |
| Contact name |
Ayelet Erez |
| E-mail(s) |
ayelet.erez@weizmann.ac.il
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| Phone |
972-8-934-3714
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| Organization name |
Weizmann Institute of Science
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| Department |
Biological Regulation
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| Street address |
234 Herzl Street
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| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE138471 |
Detection of differences in gene expression in the noradrenergic nuclei in the brain |
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| Relations |
| BioSample |
SAMN12924300 |
| SRA |
SRX6955963 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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