WDR43      eCLIP in K562

Experiment Information (Status: Released)
517517-control
Exp_UID517517
RBPARK_Exp_name
ENCODE_ACCESSIONENCSR349CMIENCSR404ABA
ENCODE_aliasgene-yeo:517gene-yeo:517-control
RBPWDR43WDR43
Cell_LineK562K562
Batch
Exp_typeeCLIPcontrol
ENCODE_Antibody_IDENCAB350LKSENCAB350LKS
AntibodyA302-478AA302-478A
Lot_num11
crosslinking_methodultraviolet irradiationultraviolet irradiation
queried_RNP_size_range175-300175-300
Self_consistency_hg38
rescue_GRCh38
StatusReleasedReleased
ProjectENCODE4ENCODE4
ID385440




Replicate Information
Rep_UID517_01517_02517_INPUT
Exp UID517517517
Replicate_typerep1rep2control
ENCODE_ACCESSIONENCLB216OEVENCLB619RUWENCLB272OWM
ENCODE_aliasgene-yeo:517_01gene-yeo:517_02gene-yeo:517_INPUT
Biosample NameK562_070715K562_061215K562_070715
Biosample_ENCODE_AccessionENCBS517UIRENCBS318IMKENCBS517UIR
Biosample_ENCODE_Aliasgene-yeo:K562_070715gene-yeo:K562_061215gene-yeo:K562_070715
Cell_LineK562K562K562
Culture_Start_Date2015-07-072015-06-122015-07-07
Culture_End_Date2015-08-042015-06-302015-08-04
Passage545




QC Stats
Experiment QC
517517-control
Self_consistency_hg38
rescue_GRCh38


Replicate QC
Rep_UID517_01517_02517_INPUT
eCT
Usable_reads
Entropy_hg38




Library-Prep Information
Rep_UID517_01517_02517_INPUT
library_size_selection_methodagarose gel extractionagarose gel extractionagarose gel extraction
strand_specificityreversereversereverse
inline_barcode_1A01C01none
inline_barcode_2B06D08fixednone
i5_barcode501501502
i7_barcode704704703




Sequencing Information
Rep_UID517_01517_02517_INPUT
seq_read_typepaired-endedpaired-endedpaired-ended
read_length505050
machine
flowcell
lane




File Information

FASTQ

file_nameSample IDfile_formatoutput_typerun_typepaired_endread_lengthplatformassay_type
517_01_WDR43.R1.fastq.gz517_01fastqreadspaired-ended150HiSeq4000eCLIP
517_01_WDR43.R2.fastq.gz517_01fastqreadspaired-ended250HiSeq4000eCLIP
517_02_WDR43.R1.fastq.gz517_02fastqreadspaired-ended150HiSeq4000eCLIP
517_02_WDR43.R2.fastq.gz517_02fastqreadspaired-ended250HiSeq4000eCLIP
517_INPUT_WDR43.R1.fastq.gz517_INPUTfastqreadspaired-ended150HiSeq4000eCLIP
517_INPUT_WDR43.R2.fastq.gz517_INPUTfastqreadspaired-ended250HiSeq4000eCLIP


GRCh38

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
GRCh38/517.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz517final_peakspeakseCLIPGRCh38
GRCh38_517_01_WDR43.merged.bam517_01bamalignmentseCLIPGRCh38
GRCh38_517_01_WDR43.merged.r2.norm.neg.bw517_01bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_517_01_WDR43.merged.r2.norm.pos.bw517_01bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/517_01.basedon_517_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz517_01bed_eCLIPpeakseCLIPGRCh38
GRCh38/517_01.basedon_517_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb517_01bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_517_02_WDR43.merged.bam517_02bamalignmentseCLIPGRCh38
GRCh38_517_02_WDR43.merged.r2.norm.neg.bw517_02bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_517_02_WDR43.merged.r2.norm.pos.bw517_02bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/517_02.basedon_517_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz517_02bed_eCLIPpeakseCLIPGRCh38
GRCh38/517_02.basedon_517_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb517_02bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_517_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam517_INPUTbamalignmentseCLIPGRCh38
GRCh38_517_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw517_INPUTbigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_517_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw517_INPUTbigWig+uniqueplus strand signal of unique readseCLIPGRCh38


hg19

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
517.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz517final_peakspeakseCLIPhg19
517_01_WDR43.merged.bam517_01bamalignmentseCLIPhg19
517_01_WDR43.merged.r2.norm.neg.bw517_01bigWig-uniqueminus strand signal of unique readseCLIPhg19
517_01_WDR43.merged.r2.norm.pos.bw517_01bigWig+uniqueplus strand signal of unique readseCLIPhg19
517_01.basedon_517_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz517_01bed_eCLIPpeakseCLIPhg19
517_01.basedon_517_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb517_01bigBed_eCLIPpeakseCLIPhg19
517_02_WDR43.merged.bam517_02bamalignmentseCLIPhg19
517_02_WDR43.merged.r2.norm.neg.bw517_02bigWig-uniqueminus strand signal of unique readseCLIPhg19
517_02_WDR43.merged.r2.norm.pos.bw517_02bigWig+uniqueplus strand signal of unique readseCLIPhg19
517_02.basedon_517_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz517_02bed_eCLIPpeakseCLIPhg19
517_02.basedon_517_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb517_02bigBed_eCLIPpeakseCLIPhg19
517_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam517_INPUTbamalignmentseCLIPhg19
517_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw517_INPUTbigWig-uniqueminus strand signal of unique readseCLIPhg19
517_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw517_INPUTbigWig+uniqueplus strand signal of unique readseCLIPhg19






Data Submission Information

Files

ENCODE_aliasENCODE_accessionobject_typeassay_typeSample_IDStatusProject
gene-yeo:4104_CLIP1_rep1.vs.4104_CLIP2_rep2.sorted.nh.narrowPeak.gzENCFF723JLSfile_finalPeakseCLIP4104ReleasedENCODE4
gene-yeo:4146_CLIP1_rep1.vs.4146_CLIP2_rep2.sorted.nh.bbENCFF722RGGfile_finalPeaks_bbeCLIP4104ReleasedENCODE4
gene-yeo:4116_CLIP1_rep1.vs.4116_CLIP2_rep2.sorted.nh.narrowPeak.gzENCFF111TWFfile_finalPeakseCLIP4116ReleasedENCODE4
gene-yeo:4149_CLIP1_rep1.vs.4149_CLIP2_rep2.sorted.nh.bbENCFF203CWYfile_finalPeaks_bbeCLIP4116ReleasedENCODE4