|
| Status |
Public on Jan 07, 2020 |
| Title |
Fmr1_KO_CA1_TRAP_3 |
| Sample type |
SRA |
| |
|
| Source name |
TRAP RNA from CA1 pyramidal neurons Fmr1 KO
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Camk2a-Cre +/- RiboTag +/- Fmr1 -/Y
strain: C57BL/6J
tissue: hippocampus
Sex: male
age: postnatal day 28-32
|
| Growth protocol |
Hippocampal tissue from postnatal day 28-32 male littermates or Cerebellar tissue from 6-8 week old male littermates
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For input samples, RNA was extracted directly from tissue lysate with Trizol LS. For TRAP samples, ribosome bound transcripts were immunoprecipitated with anti-HA and eluted from the bead with Trizol. RNA was further purified using the High Pure RNA isolation kit with on-column DNase treatment (Roche)
Illumina Ribo-Zero rRNA removal kit and Illumina TruSeq RNA library prep kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
TRAP RNA from CA1 pyramidal neurons Fmr1 KO
processed data file:
featureCounts_CA1_input_and_trap.txt
|
| Data processing |
Library strategy: TRAP
alignment with STAR to mm10 genome
read counts per gene with featureCounts and GENCODE annotation
Genome_build: mm10
|
| |
|
| Submission date |
Mar 05, 2019 |
| Last update date |
Jan 07, 2020 |
| Contact name |
Kirsty Sawicka |
| E-mail(s) |
Kirsty.sawicka@cruk.cam.ac.uk
|
| Organization name |
CRUK Cambridge Insititute
|
| Department |
University of Cambridge
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE127845 |
TRAP from CA1 pyramidal neurons and cerebellar granule cells in Fmr1 KO and wildtype mice |
| GSE127847 |
The Fragile X protein, FMRP, has a cell-type specific role in CA1 hippocampal neurons to regulate transcripts encoding autism-spectrum proteins and circadian memory |
|
| Relations |
| BioSample |
SAMN11055138 |
| SRA |
SRX5465169 |
