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| Status |
Public on Jan 08, 2024 |
| Title |
RBM25_rep1 |
| Sample type |
SRA |
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| Source name |
Flp-In T-Rex HEK293
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Flp-In T-Rex HEK293
genotype: RBM25_noFP
molecule subtype: RNAseI digested RNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were crosslnked with 0.199 mj/cm2 UV-C light, lysed with 1xNLB buffer, protein-of-interest purified with streptavidin beads, co-purifying RNA isolated with proteinase K digestion and purified with Oligo clean and concentrator-5 columns (Zymo).
Custom library prep, described in Ilik et al., 2020. Isolated RNA is ligated to s-oligo on beads, reverse-transcribed, RNaseH digested, circularized with CircLigase and PCR amplified.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
library strategy: FLASH-seq (Ilik et al., 2020)
Illumina base calling, demultiplexing and FASTQ conversion
Merging with bbmerge v. 38.72
Demultiplexing with flexbar v. 3.5.0
UMI extraction with umi_tools extract v. 1.0.0
Alignment to human (hg38), mouse (mm10) or Drosophila genomes (dm6) with bowtie2 v. 2.3.5 and bbmap v. 38.72
bigWigs generation using bamCoverage 3.3.1
Assembly: hg38, mm10, dm6
Supplementary files format and content: Raw RNA-seq coverage in bigWig format, separate files for plus and minus strands
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| Submission date |
Jan 19, 2023 |
| Last update date |
Jan 09, 2024 |
| Contact name |
IBRAHIM AVSAR ILIK |
| E-mail(s) |
ilik@molgen.mpg.de
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| Organization name |
Max-Planck-Institut für molekulare Genetik
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| Lab |
OWL Aktas
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| Street address |
Ihnestraße 63-73
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| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE223253 |
Autonomous transposons tune their sequences to ensure somatic suppression [FLASH] |
| GSE223263 |
Autonomous transposons tune their sequences to ensure somatic suppression. |
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| Relations |
| BioSample |
SAMN32798160 |
| SRA |
SRX19076319 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6943955_RBM25_noFP_reps-merged.minus.CPM.bw |
27.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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