|
| Status |
Public on Apr 30, 2024 |
| Title |
GAD2 D4 SNI IP 1 |
| Sample type |
SRA |
| |
|
| Source name |
spinal cord
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spinal cord
cell type: inhibitory neurons
|
| Treatment protocol |
Spared nerver injury or sham surgery was performed on mice and was followed by eithanization and dissection of tissue at day 4 for early time point and at day 60 or day 63 for late time point.
|
| Growth protocol |
Female C57BL/6 mice were purchased from Charles River Laboratories, Inc. (St. Constant, Quebec, Canada) at 6–7 weeks of age. On arrival at the in-house animal facility, the mice were placed in a group of 5 animals per cage with food and water ad libitum under a 12:12 h light/dark cycle (with the light period from 07:00-19:00 h) with ambient temperature (22 °C) and humidity maintained at 40%.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For TRAP immunoprecipitated (IP) samples were prepared by overnight incubation of cell lyate with with protein washed G-coated Dynabeads (Invitrogen) bound to 50 µg of anti-GFP antibodies (HtzGFP-19F7 and HtzGFP-19C8 antibodies). Subsequently, RNA was extracted from the IP and a fraction of the cell lysate (input) samples using Direct-zol RNA kit (Zymo Research). For Ribosome profiling, a fraction of cell clysate was reserved for mRNA-seq while the remaining was used to extract ribosome footprints (rFPs). rFPs were extracted by incubating the cell lysate with 5 µl of RNase I (Ambion, AM2295) per 250 µg of crude total RNA for 45 min at 4 °C and quenched by adding 20 µl of SUPERase-In (Ambion, AM2694) per 5µl of RNase I used followed by ultracentrifugation through a sucrose cushion at 71,000 rpm at 4 °C. Subsequently, RNA was extracted from both the crude cell lysate reserved for mRNA-seq and the resuspended rFP pellet using hot-phenol RNA extraction method with isopropanol based precipitation.
rRNA-depleted stranded (HMR)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GRP4__SC_GAD2_D04_SNI_IP_1_tpm, GRP4__SC_GAD2_D04_SNI_IP_1_tpm_percentile, GRP4__SC_GAD2_D04_SNI_IP_1_tpm_qn
|
| Data processing |
RNA-seq read files (fastq files) were checked for quality by FastQC and read trimming was done based on the Phred score and per-base sequence content
Trimmed Reads were then mapped against the reference genome and transcriptome (Gencode vM16 and GRCm38.p5) using STAR
Relative abundances in Transcripts Per Million (TPM) for every gene of every sample was quantified by stringtie
Assembly: Genome Reference Consortium Mouse Build 38 patch release 5
Supplementary files format and content: TAR packaging followed by a GNU zip (gzip), tab separated text files with columns for gene id (Gencode), gene name, locus, and TPMs for each RNA-seq and trap replicate for all coding genes [processed files tpms and degs SNI TRAP and RF.xlsx]
Library strategy: TRAP-seq
|
| |
|
| Submission date |
Apr 26, 2024 |
| Last update date |
May 02, 2024 |
| Contact name |
Arkady Khoutorsky |
| E-mail(s) |
arkady.khoutorsky@mail.mcgill.ca
|
| Organization name |
McGill University
|
| Street address |
3655 Promenade Sir-William-Osler
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3G 1Y6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE265957 |
Translational control in the spinal cord regulates gene expression and pain hypersensitivity in the chronic phase of neuropathic pain |
|
| Relations |
| BioSample |
SAMN41096324 |
| SRA |
SRX24380166 |
