|
| Status |
Public on Dec 18, 2023 |
| Title |
RNASEH1_shRNA2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
PA1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PA1
shRNA: shRNA2
|
| Treatment protocol |
PA1 cells were cultured using standard protocols from ATCC. PA1 cells were maintained in MEMα supplemented with 10% FBS, 1% Glutamine and 0.1% penicillin/streptomycin. We maintained cell lines at 37 ℃ in a 5% CO2 cell culture incubator and tested all cell lines routinely for Mycoplasma contamination.
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from cultured cells were extracted with Trizol Reagent (Life Technologies) according to the manufacturer’s protocol. RNAs were further treated with DNase I (Ambion, DNA-free kit) and cDNAs were reverse transcribed with PrimeScript II RTase (TAKARA) at 42 ℃ for 2hr, and then applied for qPCR analysis using the SYBR Green Realtime PCR Master Mix (TOYOBO).
For RNA-seq samples from PA1 cells treated with scramble or RNase H1 shRNAs, ribo minus RNA libraries were prepared using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit according to the manufacturer’s protocol with slight modifications in the step for synthesizing first strand cDNA, which used PrimeScript enzyme mix (TAKARA) for reverse transcription at 42 ℃ for 2 hr. All libraries were size-selected with AmpureXP beads (Agencourt) and quantified using Agilent Bio analyzer 2100 and Qubit high-sensitivity dsDNA assay.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ribominus RNA-seq
|
| Data processing |
First filtered by using Trimmomatic v0.38; Next removed rRNA by bowtie v1.1.2.
Analyses by HISAT2, TopHat-Fusion v2.0.12, CLEAR and custom python script.
Genome_build: GRCh38/hg38 human reference genome with the GENCODE gene annotation (v28).
Supplementary_files_format_and_content: bw files include the read depths.
Supplementary_files_format_and_content: bb files include position of ciRNAs.
|
| |
|
| Submission date |
Sep 10, 2021 |
| Last update date |
Dec 18, 2023 |
| 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 |
GPL18573 |
| Series (2) |
| GSE183928 |
RNaseH1KD_RNA-seq |
| GSE183930 |
Linking circular intronic RNA degradation and function in transcription by RNase H1 |
|
| Relations |
| BioSample |
SAMN21387019 |
| SRA |
SRX12136117 |
