|
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
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Library strategy |
RIP-Seq |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
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|
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).
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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 |