|
| Status |
Public on May 16, 2022 |
| Title |
Input_WT1 |
| Sample type |
SRA |
| |
|
| Source name |
Adult heart
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
|
| Treatment protocol |
For the IP experiment, hearts were treated with 100 µg/mL cycloheximide upon excision.
|
| Growth protocol |
For the IP experiment, hearts were homogenized using the homogenization buffer (50 mM Tris-HCl, pH 7.5; 100 mM KCl; 12 mM MgCl2; 1% Nonidet P-40 substitute; 1 mM DTT; 200 U/ml RNasin; 1 mg/ml heparin; 100 μg/ml cycloheximide; 1× protease inhibitor mixture). For the input experiment, total RNA was extracted from heart homogenates using TRIzol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For the IP experiment, translating ribosomes were pulled down using anti-HA antibodies (BioLegend, 901513) and Pierce™ Protein A/G Magnetic Beads. Total RNA was extracted from immunoprecipitates using the Qiagen RNeasy extraction kit supplemented with β-mercaptoethanol. For both the IP and Input experiments, Poly(A) enrichment was done using Dynabeads Oligo(dT)25 beads.
Both the IP and Input libraries were prepared using the ONT's sequncing kit SQK-DCS109, and barcoding expansion kit: EXP-NBD104.
Libraries were multiplexed using the barcoding expansion kit and sequenced in a MinION flowcell (FLO-MIN106).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
MinION |
| |
|
| Data processing |
Library strategy: Nano-TRAP
Basecalling: guppy (v.3.6.1)
Demultiplexing: guppy (v.3.6.1)
Alignment to genome: minimap2 (v.2.14)
Counting at per-gene level: bambu (v.0.3.0) + DESeq2 (v.1.34.0)
Genome_build: GRCm38.primary_assembly.genome.fa
Supplementary_files_format_and_content: Tab delimited file with counts at per-gene level
|
| |
|
| Submission date |
Nov 30, 2021 |
| Last update date |
May 16, 2022 |
| Contact name |
Eva Maria Novoa |
| E-mail(s) |
[email protected]
|
| Phone |
+34933160260
|
| Organization name |
Center for Genomic Regulation
|
| Lab |
Epitranscriptomics and RNA Dynamics
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24973 |
| Series (1) |
| GSE189872 |
Nano-TRAP Input and IP sequencing of WT and Rpl3l-/- mouse hearts |
|
| Relations |
| BioSample |
SAMN23515342 |
| SRA |
SRX13262421 |
