|
| Status |
Public on Nov 18, 2021 |
| Title |
IFNgamma_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells polyA RNA
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: treated with IFN gamma for 24h
cell line: HeLa cells (ATCC)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The library preparation followed the protocol of Direct RNA Sequencing Kit (SQK-RNA002) provided by Oxford Nanopore Technology. Briefly, ~500 ng of Poly(A)+ RNA sample was used for each run. Each single run contained one biological replicate of one sample. The RT Adaptor (RTA) was ligated to the 3’ end of Poly(A)+ RNA by T4 DNA ligase (NEB M0202S) and then reverse transcribed by SuperScript III Reverse Transcriptase (ThermoFisher 12574018). The RNA was purified by 1.8x RNAClean XP beads (72 µL) (Beckman Coulter A63987) and then the RNA Adaptor (RMX) was ligated to the 3’ end of Poly(A)+ RNA using T4 DNA ligase (NEB M0202S) and then the RNA was purified with 1x RNAClean XP beads (40 µL). The sample was eluted with 21 µl Elution Buffer. Then the sample was loaded onto a R9.4.1 flow cell (FLO-MIN106D) in a MinION sequencer. Each flow cell was sequenced for 72 hours.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
MinION |
| |
|
| Description |
HeLa cells (ATCC) were cultured in the presence of 500 U/mL human interferon gamma (Peprotech) for 24 hours. RNA were extracted via the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol. PolyA+ RNA from 50 µg total RNA of each sample was extracted by Promega PolyATtract® mRNA Isolation Systems Z5312.
|
| Data processing |
Library strategy: Nanopore direct RNA sequencing
base called by guppy base caller (version 3.2.2+9fe0a78) with min_qscore 7
aligned to by minimap2 (version 2.18-r1015) with parameters -ax splice -uf -k14
reads were piled up by samtools-v1.9
Genome_build: hg38 (Samples 1-6). rfam family RF02541, RF00177, human (NCBI: NR_003286.4, NR_003287.4), yeast (RNACentral: URS00005F2C2D_559292, URS000061F377_4932), C. elegans (RNACentral: URS00005A42AA_6239, URS00008C9AB9_6239), and Drosophila (RNACentral: URS000030AF9A_7227, URS000008C6A9_7227) (Sample 7).
Supplementary_files_format_and_content: csv files containing gene expression levels
Supplementary_files_format_and_content: csv files containing rRNA feature values used for model training
Supplementary_files_format_and_content: csv files containing psU predicted probabilities by model 3.0
|
| |
|
| Submission date |
Jul 22, 2021 |
| Last update date |
Feb 15, 2022 |
| Contact name |
Tao Pan |
| E-mail(s) |
taopan@uchicago.edu
|
| Phone |
(773) 702-4179
|
| Organization name |
University of Chicago
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
929 E. 57th Street
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL24106 |
| Series (2) |
| GSE180654 |
Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Nanopore) |
| GSE180656 |
Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling |
|
| Relations |
| BioSample |
SAMN20350374 |
| SRA |
SRX11523044 |
