|
| Status |
Public on May 24, 2022 |
| Title |
RNA-seq_Fear_conditioned_Rep3_Scrambled_shRNA |
| Sample type |
SRA |
| |
|
| Source name |
mouse hippocampus area CA1
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
gender: male
mouse id: Mouse 34
condition: 1 hour after fear conditioning
|
| Treatment protocol |
mice were left in their home cage or subjected to Fear conditioning, 3 shocks, 0.5 mA and euthanized 1h or 6 h after
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Brains were flash frozen and dissection of hippocampi was carried out on ice. RNA was extracted using Qiagen Rneasy mini kit
Library prep was conducted by Princess Margaret Genomics Centre using NEBNext Ultra II library prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Scrambled_KD_Control_RNA-seq
SCR23_1h_S5
|
| Data processing |
Brains were collected from home cage controls or from mice who underwent fear conditioning 1 hour and 6 hour before
RNA was extracted using Qiagen Rneasy mini kit
Library prep was conducted by Princess Margaret Genomics Centre using NEBNext Ultra II library prep kit
Adapters: IlluminaTruSeq LT
Reads were aligned using STAR
Reads were count using featureCounts
Differential expression anaslysi was done using DEseq2
Genome_build: UCSC mm10
|
| |
|
| Submission date |
Dec 20, 2021 |
| Last update date |
May 24, 2022 |
| Contact name |
Iva Toronto Zovkic |
| E-mail(s) |
iva.zovkic@utoronto.ca
|
| Phone |
9058283961
|
| Organization name |
University of Toronto Mississauga
|
| Street address |
3359 Mississauga Road North, CCT Building Room 4071
|
| City |
Mississauga |
| State/province |
Ontario |
| ZIP/Postal code |
L5L1C6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE147445 |
Histone variant macroH2A1 is a stronger regulator of hippocampal transcription and memory than macroH2A2 in mice |
|
| Relations |
| BioSample |
SAMN24245251 |
| SRA |
SRX13454094 |
