UTP3      eCLIP in K562

Experiment Information (Status: Released)
475475-control
Exp_UID475475
RBPARK_Exp_name
ENCODE_ACCESSIONENCSR734ZHLENCSR241ALC
ENCODE_aliasgene-yeo:475gene-yeo:475-control
RBPUTP3UTP3
Cell_LineK562K562
Batch
Exp_typeeCLIPcontrol
ENCODE_Antibody_IDENCAB872CCUENCAB872CCU
AntibodyA302-067AA302-067A
Lot_num11
crosslinking_methodultraviolet irradiationultraviolet irradiation
queried_RNP_size_range175-300175-300
Self_consistency_hg38
rescue_GRCh38
StatusReleasedReleased
ProjectENCODE4ENCODE4
ID383438




Replicate Information
Rep_UID475_01475_02475_INPUT
Exp UID475475475
Replicate_typerep1rep2control
ENCODE_ACCESSIONENCLB038BHOENCLB279NAAENCLB278BFU
ENCODE_aliasgene-yeo:475_01gene-yeo:475_02gene-yeo:475_INPUT
Biosample NameK562_061215K562_070715K562_061215
Biosample_ENCODE_AccessionENCBS318IMKENCBS517UIRENCBS318IMK
Biosample_ENCODE_Aliasgene-yeo:K562_061215gene-yeo:K562_070715gene-yeo:K562_061215
Cell_LineK562K562K562
Culture_Start_Date2015-06-122015-07-072015-06-12
Culture_End_Date2015-06-302015-08-042015-06-30
Passage454




QC Stats
Experiment QC
475475-control
Self_consistency_hg38
rescue_GRCh38


Replicate QC
Rep_UID475_01475_02475_INPUT
eCT
Usable_reads
Entropy_hg38




Library-Prep Information
Rep_UID475_01475_02475_INPUT
library_size_selection_methodagarose gel extractionagarose gel extractionagarose gel extraction
strand_specificityreversereversereverse
inline_barcode_1A03A04none
inline_barcode_2G07F05none
i5_barcode506506505
i7_barcode705705706




Sequencing Information
Rep_UID475_01475_02475_INPUT
seq_read_typepaired-endedpaired-endedpaired-ended
read_length505050
machine
flowcell
lane




File Information

FASTQ

file_nameSample IDfile_formatoutput_typerun_typepaired_endread_lengthplatformassay_type
475_01_UTP3.R1.fastq.gz475_01fastqreadspaired-ended150HiSeq4000eCLIP
475_01_UTP3.R2.fastq.gz475_01fastqreadspaired-ended250HiSeq4000eCLIP
475_02_UTP3.R1.fastq.gz475_02fastqreadspaired-ended150HiSeq4000eCLIP
475_02_UTP3.R2.fastq.gz475_02fastqreadspaired-ended250HiSeq4000eCLIP
475_INPUT_UTP3.R1.fastq.gz475_INPUTfastqreadspaired-ended150HiSeq4000eCLIP
475_INPUT_UTP3.R2.fastq.gz475_INPUTfastqreadspaired-ended250HiSeq4000eCLIP


GRCh38

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
GRCh38/475.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz475final_peakspeakseCLIPGRCh38
GRCh38_475_01_UTP3.merged.bam475_01bamalignmentseCLIPGRCh38
GRCh38_475_01_UTP3.merged.r2.norm.neg.bw475_01bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_475_01_UTP3.merged.r2.norm.pos.bw475_01bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/475_01.basedon_475_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz475_01bed_eCLIPpeakseCLIPGRCh38
GRCh38/475_01.basedon_475_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb475_01bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_475_02_UTP3.merged.bam475_02bamalignmentseCLIPGRCh38
GRCh38_475_02_UTP3.merged.r2.norm.neg.bw475_02bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_475_02_UTP3.merged.r2.norm.pos.bw475_02bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/475_02.basedon_475_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz475_02bed_eCLIPpeakseCLIPGRCh38
GRCh38/475_02.basedon_475_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb475_02bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_475_INPUT_S25_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam475_INPUTbamalignmentseCLIPGRCh38
GRCh38_475_INPUT_S25_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw475_INPUTbigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_475_INPUT_S25_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw475_INPUTbigWig+uniqueplus strand signal of unique readseCLIPGRCh38


hg19

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
475.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz475final_peakspeakseCLIPhg19
475_01_UTP3.merged.bam475_01bamalignmentseCLIPhg19
475_01_UTP3.merged.r2.norm.neg.bw475_01bigWig-uniqueminus strand signal of unique readseCLIPhg19
475_01_UTP3.merged.r2.norm.pos.bw475_01bigWig+uniqueplus strand signal of unique readseCLIPhg19
475_01.basedon_475_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz475_01bed_eCLIPpeakseCLIPhg19
475_01.basedon_475_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb475_01bigBed_eCLIPpeakseCLIPhg19
475_02_UTP3.merged.bam475_02bamalignmentseCLIPhg19
475_02_UTP3.merged.r2.norm.neg.bw475_02bigWig-uniqueminus strand signal of unique readseCLIPhg19
475_02_UTP3.merged.r2.norm.pos.bw475_02bigWig+uniqueplus strand signal of unique readseCLIPhg19
475_02.basedon_475_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz475_02bed_eCLIPpeakseCLIPhg19
475_02.basedon_475_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb475_02bigBed_eCLIPpeakseCLIPhg19
475_INPUT_S25_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam475_INPUTbamalignmentseCLIPhg19
475_INPUT_S25_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw475_INPUTbigWig-uniqueminus strand signal of unique readseCLIPhg19
475_INPUT_S25_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw475_INPUTbigWig+uniqueplus strand signal of unique readseCLIPhg19






Data Submission Information

Files

ENCODE_aliasENCODE_accessionobject_typeassay_typeSample_IDStatusProject
gene-yeo:4002_CLIP1_rep1.vs.4002_CLIP2_rep2.sorted.nh.narrowPeak.gzENCFF111LMZfile_finalPeakseCLIP4002ReleasedENCODE4
gene-yeo:4139_CLIP1_rep1.vs.4139_CLIP2_rep2.sorted.nh.bbENCFF694JTMfile_finalPeaks_bbeCLIP4002ReleasedENCODE4
gene-yeo:4001_CLIP1_rep1.vs.4001_CLIP2_rep2.sorted.nh.narrowPeak.gzENCFF089QYNfile_finalPeakseCLIP4001ReleasedENCODE4
gene-yeo:4140_CLIP1_rep1.vs.4140_CLIP2_rep2.sorted.nh.bbENCFF607DJSfile_finalPeaks_bbeCLIP4001ReleasedENCODE4