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Sample GSM6944016 Query DataSets for GSM6944016
Status Public on Jan 08, 2024
Title Dmel_control_rep2
Sample type SRA
 
Source name S2R+-MT::Cas9
Organism Drosophila melanogaster
Characteristics cell line: S2R+-MT::Cas9
genotype: Dmel_control
molecule subtype: RNAseI digested RNA
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.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
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
 
Submission date Jan 19, 2023
Last update date Jan 09, 2024
Contact name IBRAHIM AVSAR ILIK
E-mail(s) ilik@molgen.mpg.de
Organization name Max-Planck-Institut für molekulare Genetik
Lab OWL Aktas
Street address Ihnestraße 63-73
City Berlin
State/province Berlin
ZIP/Postal code 14195
Country Germany
 
Platform ID GPL25244
Series (2)
GSE223253 Autonomous transposons tune their sequences to ensure somatic suppression [FLASH]
GSE223263 Autonomous transposons tune their sequences to ensure somatic suppression.
Relations
BioSample SAMN32798099
SRA SRX19076332

Supplementary file Size Download File type/resource
GSM6944016_Dmel_SafB_reps-merged.plus.CPM.bw 4.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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