|
| Status |
Public on May 24, 2023 |
| Title |
CH-4-1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryo stage HH27
|
| Organism |
Gallus gallus |
| Characteristics |
developmental stage: HH27
tissue: embryo
merip antibody: input
|
| Growth protocol |
Fertile chicken eggs (Gallus gallus; Henry Stewart, UK) were incubated and the chicken embryos were collected after 5.5 days at Hamburger and Hamilton stage 27 (HH 27) (44). The samples were snap frozen in liquid nitrogen and stored at –80°C until further use
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was prepared from cells and tissues using Trizol reagent (Invitrogen). The poly(A) RNA was prepared using two rounds of oligo(dT) magnetic beads purification (New England Biolabs).
Libraries were prepared using ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
input, sample3
|
| Data processing |
Library strategy: MeRIPSeq
Basecalls performed using CASAVA version 1.4
Adapter sequences and reads with phred <30 were removed using the TrimGalore wrapper for Cutadapt and FastQC
Reads were aligned to the reference chicken genome (Gallus_gallus, GRCg6a) using STAR (v2.5.3a)
Genome_build: Gallus gallus (GRCg6a)
Supplementary_files_format_and_content: Bedgraph files were generated using Bedtools genomecov
|
| |
|
| Submission date |
Sep 30, 2021 |
| Last update date |
May 24, 2023 |
| Contact name |
Nigel P Mongan |
| Organization name |
University of Nottingham
|
| Department |
Biodiscovery Institute
|
| Street address |
University Park
|
| City |
Nottingham |
| ZIP/Postal code |
NG7 2RD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19787 |
| Series (1) |
| GSE185078 |
An antibody independent verification method quantifies m6A in the chicken β-actin zipcode |
|
| Relations |
| BioSample |
SAMN21917062 |
| SRA |
SRX12413404 |
