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Sample GSM5956410 Query DataSets for GSM5956410
Status Public on Jul 19, 2022
Title RNASeq_Cp190-KO_rep1
Sample type SRA
 
Source name Cultured cells
Organism Drosophila melanogaster
Characteristics cell line: CP-R6
mutation: Cp190[3]
Treatment protocol none
Growth protocol Cells were grown to confluence in Schneider's medium (Lonza) supplemented with 10% FBS, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cultured cells using TRI Reagent according to the manufacturer instructions (Sigma-Aldrich #T9424)
200ng of total RNA were used for indexed library preparation using Ovation RNA-Seq Systems 1–16 for Model Organisms Kit (#0350 DROSOPHILA, Nugen Technology).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Paired-end reads were mapped to the Drosophila melanogaster genome (assembly dm3) using the STAR_v2.6.1a with default parameters. Unmapped or non-unique mapped reads were discarded.
wig file is outputed by options "--outWigType bedGraph --outWigStrand Stranded"
Assembly: dm3
Supplementary files format and content: wig in dm3 outputed from STAR, example variableStep chrom=chr2L 6969 0.01899 6970 0.01899
Supplementary files format and content: bed in dm6 transferred by UCSC liftover from above wig, example chr2L 6969 6970 0.01899 chr2L 6970 6971 0.01899
 
Submission date Mar 16, 2022
Last update date Jul 20, 2022
Contact name Jia-Ming Chang
E-mail(s) chang.jiaming@gmail.com
Organization name National Chengchi University
Department Department of Computer Science
Street address NO.64, Sec. 2, ZhiNan Rd., Wenshan District
City Taipei
ZIP/Postal code 11605
Country Taiwan
 
Platform ID GPL17275
Series (2)
GSE198761 Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [RNA-seq]
GSE198763 Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements
Relations
BioSample SAMN26725121
SRA SRX14474375

Supplementary file Size Download File type/resource
GSM5956410_CPR6_rep1_str1_dm3.wig.gz 112.0 Mb (ftp)(http) WIG
GSM5956410_CPR6_rep1_str1_dm6.bed.gz 239.5 Mb (ftp)(http) BED
GSM5956410_CPR6_rep1_str2_dm3.wig.gz 116.1 Mb (ftp)(http) WIG
GSM5956410_CPR6_rep1_str2_dm6.bed.gz 247.6 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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