WDR43      eCLIP in HepG2

Experiment Information (Status: Released)
602602-control
Exp_UID602602
RBPARK_Exp_name
ENCODE_ACCESSIONENCSR085JPBENCSR722KGI
ENCODE_aliasgene-yeo:602gene-yeo:602-control
RBPWDR43WDR43
Cell_LineHepG2HepG2
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
ID389444




Replicate Information
Rep_UID602_01602_02602_INPUT
Exp UID602602602
Replicate_typerep1rep2control
ENCODE_ACCESSIONENCLB407VOFENCLB707GOEENCLB441OYG
ENCODE_aliasgene-yeo:602_01gene-yeo:602_02gene-yeo:602_INPUT
Biosample NameHepG2_081815HepG2_111915HepG2_081815
Biosample_ENCODE_AccessionENCBS881CIFENCBS492SDYENCBS881CIF
Biosample_ENCODE_Aliasgene-yeo:HepG2_081815gene-yeo:HepG2_111915gene-yeo:HepG2_081815
Cell_LineHepG2HepG2HepG2
Culture_Start_Date2015-08-182015-11-192015-08-18
Culture_End_Date2015-09-102015-12-102015-09-10
Passage444




QC Stats
Experiment QC
602602-control
Self_consistency_hg38
rescue_GRCh38


Replicate QC
Rep_UID602_01602_02602_INPUT
eCT
Usable_reads
Entropy_hg38




Library-Prep Information
Rep_UID602_01602_02602_INPUT
library_size_selection_methodagarose gel extractionagarose gel extractionagarose gel extraction
strand_specificityreversereversereverse
inline_barcode_1A04A03none
inline_barcode_2F05G07none
i5_barcode501501502
i7_barcode704704703




Sequencing Information
Rep_UID602_01602_02602_INPUT
seq_read_typepaired-endedpaired-endedpaired-ended
read_length505050
machine
flowcell
lane




File Information

FASTQ

file_nameSample IDfile_formatoutput_typerun_typepaired_endread_lengthplatformassay_type
602_01_WDR43.R1.fastq.gz602_01fastqreadspaired-ended150HiSeq4000eCLIP
602_01_WDR43.R2.fastq.gz602_01fastqreadspaired-ended250HiSeq4000eCLIP
602_02_WDR43.R1.fastq.gz602_02fastqreadspaired-ended150HiSeq4000eCLIP
602_02_WDR43.R2.fastq.gz602_02fastqreadspaired-ended250HiSeq4000eCLIP
602_INPUT_WDR43.R1.fastq.gz602_INPUTfastqreadspaired-ended150HiSeq4000eCLIP
602_INPUT_WDR43.R2.fastq.gz602_INPUTfastqreadspaired-ended250HiSeq4000eCLIP


GRCh38

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
GRCh38/602.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz602final_peakspeakseCLIPGRCh38
GRCh38_602_01_WDR43.merged.bam602_01bamalignmentseCLIPGRCh38
GRCh38_602_01_WDR43.merged.r2.norm.neg.bw602_01bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_602_01_WDR43.merged.r2.norm.pos.bw602_01bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/602_01.basedon_602_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz602_01bed_eCLIPpeakseCLIPGRCh38
GRCh38/602_01.basedon_602_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb602_01bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_602_02_WDR43.merged.bam602_02bamalignmentseCLIPGRCh38
GRCh38_602_02_WDR43.merged.r2.norm.neg.bw602_02bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_602_02_WDR43.merged.r2.norm.pos.bw602_02bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/602_02.basedon_602_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz602_02bed_eCLIPpeakseCLIPGRCh38
GRCh38/602_02.basedon_602_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb602_02bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_602_INPUT_S49_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam602_INPUTbamalignmentseCLIPGRCh38
GRCh38_602_INPUT_S49_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw602_INPUTbigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_602_INPUT_S49_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw602_INPUTbigWig+uniqueplus strand signal of unique readseCLIPGRCh38


hg19

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
602.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz602final_peakspeakseCLIPhg19
602_01_WDR43.merged.bam602_01bamalignmentseCLIPhg19
602_01_WDR43.merged.r2.norm.neg.bw602_01bigWig-uniqueminus strand signal of unique readseCLIPhg19
602_01_WDR43.merged.r2.norm.pos.bw602_01bigWig+uniqueplus strand signal of unique readseCLIPhg19
602_01.basedon_602_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz602_01bed_eCLIPpeakseCLIPhg19
602_01.basedon_602_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb602_01bigBed_eCLIPpeakseCLIPhg19
602_02_WDR43.merged.bam602_02bamalignmentseCLIPhg19
602_02_WDR43.merged.r2.norm.neg.bw602_02bigWig-uniqueminus strand signal of unique readseCLIPhg19
602_02_WDR43.merged.r2.norm.pos.bw602_02bigWig+uniqueplus strand signal of unique readseCLIPhg19
602_02.basedon_602_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz602_02bed_eCLIPpeakseCLIPhg19
602_02.basedon_602_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb602_02bigBed_eCLIPpeakseCLIPhg19
602_INPUT_S49_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam602_INPUTbamalignmentseCLIPhg19
602_INPUT_S49_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw602_INPUTbigWig-uniqueminus strand signal of unique readseCLIPhg19
602_INPUT_S49_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw602_INPUTbigWig+uniqueplus strand signal of unique readseCLIPhg19






Data Submission Information

Files

ENCODE_aliasENCODE_accessionobject_typeassay_typeSample_IDStatusProject
gene-yeo:4081_CLIP1_rep1.vs.4081_CLIP2_rep2.sorted.nh.narrowPeak.gzENCFF831PMSfile_finalPeakseCLIP4081ReleasedENCODE4
gene-yeo:4161_CLIP1_rep1.vs.4161_CLIP2_rep2.sorted.nh.bbENCFF311XEJfile_finalPeaks_bbeCLIP4081ReleasedENCODE4
gene-yeo:4082_CLIP1_rep1.vs.4082_CLIP2_rep2.sorted.nh.narrowPeak.gzENCFF704ZXVfile_finalPeakseCLIP4082ReleasedENCODE4
gene-yeo:4164_CLIP1_rep1.vs.4164_CLIP2_rep2.sorted.nh.bbENCFF199SPHfile_finalPeaks_bbeCLIP4082ReleasedENCODE4