|
| Status |
Public on May 11, 2021 |
| Title |
SLERT_rep2_invivo_NAI |
| Sample type |
SRA |
| |
|
| Source name |
PA1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PA1
type: cDNA
treatment: SLERT DC samples denatured by formamide at 95degreeC
|
| Treatment protocol |
For SHAPE-MaP, PA1 cells were incubated with 900 uL of fresh cell culture medium and 100 μL of 10x SHAPE Chemical in DMSO with the final concentration of NAI at 200 mM for 10 minutes at 37°C.
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For SHAPE-MaP, isolated RNAs were treated with DNase I (Ambion, DNA-freeTM kit) to remove possible DNA contamination. About 50-100 ng of RNAs were obtained under each treatment, and were then used for SHAPE-MaP reverse transcription by adding 1 μL (200 U/μL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for SLERT(5S rRNA was used as a spike-in control). Mn2+ was removed using G-25 micro-spin columns (GE Healthcare) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase and nested PCR was performed to further improve DNA yield.
SHAPE-MaP libraries were prepared from 1 ng of DNAs for SLERT and 5S rRNA, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina X Ten at CAS Key Laboratory of Computational Biology Omics Core, Shanghai, China.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Library strategy: SHAPE-MaP
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Analyses by Shapemapper V2.1.3
Genome_build: Target RNA sequence
Supplementary_files_format_and_content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.
|
| |
|
| Submission date |
May 10, 2021 |
| Last update date |
May 11, 2021 |
| Contact name |
Li Yang |
| E-mail(s) |
liyang_fudan@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Institutes of Biological Sciences
|
| Street address |
131 Dong-An Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE174140 |
lncRNA SLERT controls phase separation of FC/DFCs to facilitate Pol I transcription |
|
| Relations |
| BioSample |
SAMN19092102 |
| SRA |
SRX10827321 |
