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Sample GSM3403553 Query DataSets for GSM3403553
Status Public on Mar 06, 2019
Title HEK293T EXOSC10WT rep 2 (iCLip-seq)
Sample type SRA
 
Source name HEK293T EXOSC10WT
Organism Homo sapiens
Characteristics cell line: HEK293T
antibody: anti-FLAG M2 magnetic beads) (Sigma Aldrich)
adapter: AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG
barcode: NNNCCGGNN
treatment: transiently transfected with FLAG-hRRP6 (wild type)
molecule subtype: EXOSC10WT bound RNA
Growth protocol HEK293T transiently transfected with FLAG-hRRP6 (wild type) were expanded in 15 cm plates to 95% confluency
Extracted molecule total RNA
Extraction protocol HEK293T were irradiated, lysed and epitope-tagged proteins were purified following protocol from Konig et al. 2011
iCLIP libraries were constructed FLAG-hRRP6 immunoprecipitates following the protocol from Konig et al. 2011
iCLIP library strategy can be found in Konig et al. 2011
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description 45srDNA.fa
45srDNA.annotation.bed
EXOSC10-WT.45srDNA.bw
EXOSC10-WT.hg38.antisense.bw
EXOSC10-WT.hg38.sense.bw
Data processing [Preprocessing - Demultiplex] flexbar --format i1.5 --barcode-trim-end LEFT_TAIL --barcode-keep --pre-trim-phred 30 --min-read-length 28 --adapter-min-overlap 4
[Preprocessing - Collapsing Redundant Reads] nonRedundant reads were collapsed using custom perl scripts
[Preprocessing - Barcode Removal] fastx_trimmer -f 10 -m 20 -z
[Preprocessing - Merge] biological replicate samples were combined to increase coverage
[Alignment] Tophat VN:2.0.14 --max-multihits 1 --library-type fr-firststrand --num-threads 8 --no-novel-juncs --no-coverage-search --no-novel-indels
[Normalization] bigwig files scaled to reads mapped per million
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files are coverage tracks that have been scaled based on reads mapped per million (RPM).
 
Submission date Sep 27, 2018
Last update date Mar 06, 2019
Contact name Steven West
E-mail(s) [email protected]
Phone 0044(0)1392727458
Organization name University of Exeter
Department Living Systems Institute
Street address Stocker Rd
City Exeter
State/province Devon
ZIP/Postal code EX4 4QD
Country United Kingdom
 
Platform ID GPL11154
Series (1)
GSE120574 The immediate impact of exoribonucleolysis on nuclear RNA processing, turnover and transcriptional control revealed by rapid depletion of DIS3, EXOSC10 or XRN2 from human cells
Relations
Reanalysis of GSM1892062
BioSample SAMN10138453
SRA SRX4745221

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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