|
| Status |
Public on Jan 19, 2024 |
| Title |
ZT8, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
L4-6 DRG
|
| Organism |
Mus musculus |
| Characteristics |
tissue: L4-6 DRG
strain: C57bl/6
Sex: Male
age: 6-8 weeks
time: ZT8
|
| Treatment protocol |
L4-6 DRGs were dissected at ZT8 or ZT20.
DRGs were dissociated using 1 mg/ml Dispase II, 2.5 mg/ml Collagenase Type II, and Papain. Released cells were placed into 15% BSA in DMEM gradient to obtain a neuronal enriched cell population
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy micro plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Signle Cell/Low Input RNA Library Prep kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
B_S2
|
| Data processing |
Sequence reads and trimmed reads quality control was carried out using FastQC-v0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore!-v0.6.6 (parameter - Phred33 quality limit: 20)
Trimmed sequence reads were mapped to M27 Gencode reference genome (GrCM39) and read counts per transcript obtained using Salmon-v1.6.0 in mapping-based mode (parameters- gcBias, seqBias)
Salmon output files were imported and converted for DESeq2 using Tximeta-v1.12.4
Differential gene expression analysis was carried out using DESeq2-v1.34.0 in R-v4.1.2
Normalised counts were generated using the median of ratios method in DESeq2.
Assembly: M27
Supplementary files format and content: csv file represents TPM, produced by Salmon, and summarized to gene level via DESeq2
|
| |
|
| Submission date |
Jun 23, 2023 |
| Last update date |
Jan 19, 2024 |
| Contact name |
Franziska Müller |
| E-mail(s) |
f.mueller17@imperial.ac.uk
|
| Organization name |
Imperial College London
|
| Department |
Brain Sciences
|
| Lab |
Simone Di Giovanni
|
| Street address |
Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE235687 |
The circadian clock time tunes axonal regeneration |
|
| Relations |
| BioSample |
SAMN35881929 |
| SRA |
SRX20765735 |
