|
| Status |
Public on Nov 21, 2023 |
| Title |
superior colliculus, left, chow, 1423 |
| Sample type |
SRA |
| |
|
| Source name |
superior colliculus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: superior colliculus
hemisphere: left
diet: chow
diet kcal: 3227
animal id: 1423
rna concentration_qbit: 56.52
"experiment start": 2019-06-24T11:00:00Z
time of_euthanasia: 2019-06-25T11:00:00Z
"experiment duration": 24
box id: 1423
bodyweight start_acclimation: 25.5
bodyweight start_experiment: 25.9
bodyweight before_euthanasia: 25.8
bodyweight change: -0.0999999999999978
bodyweight change_percent: -0.00386100386100377
bodyweight change_percent_per_hour: -1.61E-04
food weight_start_experiment: 593.1
food weight_end_experiment: 589.1
kcal intake: 12908
kcal per_hour: 537.833333333333
notes: Sup. Colliculus for 142.3 is in tube 145.4
qc: ok
flowcell: S2
|
| Treatment protocol |
In the 24 hour study sample processing was randomized in blocks of 24
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the RNeasy Micro Kit
RNA libraries for RNA-seq were prepared using NEBNext Kits with rRNA depletion and Multiplex Oligos for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
S0037_1423_chow_SC
|
| Data processing |
Basecalling was performed using Illumina's bcl2fastq (v2.20.0).
Sequenced reads were then mapped to the GRCm39 build of the Mus musculus genome using STAR (v2.7.3a) with an overhang length of 50.
The files for the reads, specified in the format of fastq, were processed individually.
The read files were provided as input to STAR, using a "zcat" command to read the compressed files.
Quantification mode was set to GeneCounts in the STAR alignment to obtain count data for each gene.
Following the alignment process, raw counts for each sample were combined using R (v4.1.3) and the tidyverse (v2.0.0) package to create a count matrix.
Assembly: The metadata for sample 142.3_SCL_chow and sample 145.4_SCL_fast were corrected to account for the fact that they were erroneously swapped during handling and sequencing.
Supplementary files format and content: GRCm39
Supplementary files format and content: csv file of raw read counts for each sample
|
| |
|
| Submission date |
Jun 28, 2023 |
| Last update date |
Nov 21, 2023 |
| Contact name |
Lars Roed Ingerslev |
| E-mail(s) |
[email protected]
|
| Organization name |
Copenhagen University
|
| Department |
NNF Center for Basic Metabolic Research
|
| Lab |
Integrative Physiology
|
| Street address |
Blegdamsvej 3B
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE236077 |
An RNA-seq atlas of mouse brain areas during fasting and diet-induced obesity |
|
| Relations |
| BioSample |
SAMN36028119 |
| SRA |
SRX20810565 |
