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| Status |
Public on Jan 31, 2024 |
| Title |
2X MS2 and 2X PP7 alternating and 50 bp apart, PP7-TadA-8e_Replicate-2 |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
cell line: HEK293XT
cell type: immortalized cell line
reporter: 2X MS2 and 2X PP7 alternating and 50 bp apart
enzyme fusion/s: PP7-TadA-8e
replicate: 2
treatment: doxycycline-induced expression
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| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol RNA Miniprep Kits, Zymo Research (Cat # R2052)
Nextera XT DNA Library Preparation Kit (Illumina, Cat # FC-131-2002 or Cat # FC-131-1024)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Data processing |
remove adapter with Cutadapt
align to genome using bowtie2 or bwa-mem
generate count tables along reporter sequence using Pysamstats
Assembly: 6X MS2 and 6X PP7 stem-loop-bearing mRNAs (alternating): 6X MS2 and 6X PP7 alternating and 50 bp apart mRNA.fa, 6X MS2 and 6X PP7 alternating and 50 bp apart mRNA features.txt
Assembly: 2X MS2 and 2X PP7 stem-loop-bearing mRNAs (alternating): 2X MS2 and 2X PP7 alternating and 50 bp apart mRNA.fa, 2X MS2 and 2X PP7 alternating and 50 bp apart mRNA features.txt
Assembly: 2X MS2 and 2X PP7 stem-loop-bearing mRNAs (50bp apart): 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart) mRNA.fa, 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart) mRNA features.txt
Supplementary files format and content: count tables with called edits along reporter sequences
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| Submission date |
May 15, 2023 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Brian Yee |
| E-mail(s) |
brian.alan.yee@gmail.com
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| Organization name |
UCSD
|
| Department |
Health
|
| Lab |
Yeo
|
| Street address |
9500 Gilman Dr
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL15520 |
| Series (2) |
| GSE232519 |
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (5) |
| GSE232520 |
Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies |
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| Relations |
| BioSample |
SAMN35085021 |
| SRA |
SRX20341417 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7349721_8_S8_L001_R1_001.sorted.bam.pysam.tsv.gz |
46.9 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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