|
| Status |
Public on Jun 13, 2024 |
| Title |
PFA_HEK293T_Buffer_Only_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
cell line: HEK293XT
cell type: immortalized cell line
replicate: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol RNA Miniprep Kits, Zymo Research (Cat # R2052)
Ilumina TruSeq Stranded mRNA Library Prep (Cat # 20020594)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
isSTAMP10_16
|
| Data processing |
remove adapter with Cutadapt
align to hg38 using STAR 2.4.0 (Homo sapiens) or mm10 using STAR 2.5.2 (Mus musculus)
SAILOR analysis to call C-to-U edits and keep only sites with score >0.5 and edit fraction <80%
FLARE analysis to call C-to-U edit clusters
Intersect the edit clusters from 3 replicates, which yields "*confident_peaks.bed"
Subtract STAMP confident clusters to Buffer only control, which yields "*cleaned_confident_peaks.bed"
Assembly: hg38
Assembly: mm10
Supplementary files format and content: SAILOR step yields bed file: *0.5Score0.8Fraction.fastqTr.sorted.STARUnmapped.out.sorted.STARAligned.out.sorted.bam.combined.readfiltered.formatted.varfiltered.snpfiltered.ranked.bed
Supplementary files format and content: FLARE step yields .tsv file: "*merged_sorted_peaks.fdr_0.1.d_15.scored.tsv"
Supplementary files format and content: Intersection step yields .bed file: "*confident_peaks.bed"
Supplementary files format and content: Subtraction step yields .bed file: "*cleaned_confident_peaks.bed"
|
| |
|
| Submission date |
Aug 03, 2023 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Brian Yee |
| E-mail(s) |
brian.alan.yee@gmail.com
|
| Organization name |
UCSD
|
| Department |
Health
|
| Lab |
Yeo
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE240014 |
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP] |
| GSE240326 |
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells |
|
| Relations |
| BioSample |
SAMN36828493 |
| SRA |
SRX21239495 |
