SRR8669170 Sample ID 2548

Data sources
Paper identifier Vihervaara2021stress
SRP accession SRP187541
GEO accession GSE127844
Samples SRR8669170
Technical details
QC score 5
Replicate 2
Protocol PRO-seq
Library prep ligation
Spike-in D. melanogaster
Single/Paired end single
Raw strandedness reverse
Reverse complemented? True
Mapped strandedness forward
Timecourse True
Control/Experimental experimental
Wildtype & Untreated? False
Outlier No
Unusable No
Downloads
TDF visualization file TDF file 30 Mb
Stranded gene read counts TXT file 1 Mb
Unstranded bidirectional read counts TXT file 21 Mb
Tfit bidirectional regions BED file 1 Mb
dREG bidirectional regions BED file 625 Kb
All data files ZIP archive
Cellular details
Organism H. sapiens
Sample type cell line
Cell type K562
Clone/Individual
Strain
Genotype
Construct shRNA control
Conditions and treatments
Condition type Treatment Start time End time Duration
treatment heat shock (42 Celsius) -30 min 0 min 30 min
treatment heat shock (42 Celsius) -2970 min -2910 min 1 hr
treatment heat shock (42 Celsius) -3150 min -3090 min 1 hr
treatment heat shock (42 Celsius) -3330 min -3270 min 1 hr
treatment heat shock (42 Celsius) -4410 min -4350 min 1 hr
treatment heat shock (42 Celsius) -4590 min -4530 min 1 hr
treatment heat shock (42 Celsius) -4770 min -4710 min 1 hr
treatment heat shock (42 Celsius) -5850 min -5790 min 1 hr
treatment heat shock (42 Celsius) -6030 min -5970 min 1 hr
treatment heat shock (42 Celsius) -6210 min -6150 min 1 hr
Extended notes
Pipeline info and software versions
Sample notes Cites Kwak2013 for protocol and library prep and also implies ligation with adapters, but not explicitly stated
Analysis notes Previously in DB until 6/29/2021 as Vihervaara2020unpublished - scripts have been changed, but all previous outerr and log files reflect previous id
Sample metrics
Sample QC score 5
Sample NRO score 3
Raw read length 76
Read depth after trimming 4,966,829
Duplication proportion 0.36594
Proportion reads mapped 0.878
Exon/intron ratio 5.68254
Unique read proportion 0.555
Bidirectionals
Total # Tfit bidirectionals 16870
# Promoter Tfit bidirectionals 8678
# Intronic Tfit bidirectionals 6273
# Intergenic Tfit bidirectionals 2311
Total # dREG bidirectionals 14536
# Promoter dREG bidirectionals 8931
# Intronic dREG bidirectionals 4313
# Intergenic dREG bidirectionals 1876
Part of Tfit master merge? True
Part of dREG master merge? True