|
| Status |
Public on Apr 11, 2023 |
| Title |
m6A IP sample |
| Sample type |
SRA |
| |
|
| Source name |
protonema 18 d
|
| Organism |
Physcomitrium patens |
| Characteristics |
tissue: protonema 18 d
strain: Grandsen
cell type: Protoplast
genotype: WT
treatment: NAA 1uM, 5 d; kinetin 1 uM, 1d.
antibody: m6A
|
| Treatment protocol |
NAA 1uM, 5 d; kinetin 1 uM, 1d.
|
| Growth protocol |
Protoplasts were grown in PRMB for 4 d, and them moved to PPNH4 medium for 8 d.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For meRIP-seq analysis, polyA+ RNA was extracted with Dynabeads mRNA direct purification kit (Thermo Fisher Scientific).
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) following manufacturer's protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MeRIP_IP
We used the m6A antibody (D9D9W, cat #56593) from Abcam (Cambridge, UK).
|
| Data processing |
Reads were adapter-trimmed with Trim-galore.
Mapping against the P. patens reference genome was done with Bowtie2.
Reads were PCR de-duplicated with PICARD tools.
Peak calling was performed using MACS2.
Assembly: Physcomitrium patens 318 v3
Supplementary files format and content: merip_peaks_narrowPeak.bed includes peaks.
Library strategy: MeRIP-seq
|
| |
|
| Submission date |
Sep 14, 2022 |
| Last update date |
Apr 11, 2023 |
| Contact name |
V Miguel Palomar |
| E-mail(s) |
vpalomar@umich.edu
|
| Phone |
7342195985
|
| Organization name |
University of Michigan
|
| Department |
MCDB
|
| Lab |
Wierzbicki
|
| Street address |
1105 N. University Ave.
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL30955 |
| Series (2) |
| GSE213347 |
N6-Methyladenosine modification of mRNA regulates the transition from 2D to 3D growth in the moss Physcomitrium patens [MeRIP-seq] |
| GSE213348 |
N6-Methyladenosine modification of mRNA regulates the transition from 2D to 3D growth in the moss Physcomitrium patens |
|
| Relations |
| BioSample |
SAMN30853877 |
| SRA |
SRX17571460 |
