SRR8950277 Sample ID 2795

Data sources
Paper identifier Zhang2019fundamental
SRP accession SRP193758
GEO accession GSE130266
Samples SRR8950277
Technical details
QC score 1
Replicate 1
Protocol GRO-seq
Library prep ligation
Spike-in None
Single/Paired end paired
Raw strandedness read1 forward
Reverse complemented? True
Mapped strandedness read1 forward
Timecourse False
Control/Experimental experimental
Wildtype & Untreated? False
Outlier No
Unusable No
Downloads
TDF visualization file TDF file 206 Mb
Stranded gene read counts TXT file 921 Kb
Unstranded bidirectional read counts TXT file 17 Mb
Tfit bidirectional regions BED file 4 Mb
dREG bidirectional regions BED file 1 Mb
All data files ZIP archive
Cellular details
Organism M. musculus
Sample type cell line
Cell type CH12F3
Clone/Individual
Strain
Genotype CH +/-; Aid -/-; I-alpha -/-; 3xCTCF-binding element knock-in
Construct
Conditions and treatments
Condition type Treatment Start time End time Duration
treatment TGF-beta (0.5 ng/mL) -24 hr 0 hr 1 day
treatment anti-CD40 (1 microg/mL) -24 hr 0 hr 1 day
treatment interleukin-4 (20 ng/mL) -24 hr 0 hr 1 day
Extended notes
Pipeline info and software versions
Sample notes CH +/-: KO of heavy chain locus non-productive allele; CBE = CTCF binding element
Analysis notes Ran qc redo nextflow
Sample metrics
Sample QC score 1
Sample NRO score 1
Raw read length 76
Read depth after trimming 39,332,218
Duplication proportion 0.28245
Proportion reads mapped 0.8326
Exon/intron ratio 1.72644
Unique read proportion 0.69811
Bidirectionals
Total # Tfit bidirectionals 42460
# Promoter Tfit bidirectionals 8296
# Intronic Tfit bidirectionals 17767
# Intergenic Tfit bidirectionals 11411
Total # dREG bidirectionals 27708
# Promoter dREG bidirectionals 5318
# Intronic dREG bidirectionals 11767
# Intergenic dREG bidirectionals 8290
Part of Tfit master merge? False
Part of dREG master merge? False