NIPBL      eCLIP in K562

Experiment Information (Status: Released)
565565-control
Exp_UID565565
RBPARK_Exp_name
ENCODE_ACCESSIONENCSR891RICENCSR816NVJ
ENCODE_aliasgene-yeo:565gene-yeo:565-control
RBPNIPBLNIPBL
Cell_LineK562K562
Batch
Exp_typeeCLIPcontrol
ENCODE_Antibody_IDENCAB695MXGENCAB695MXG
Antibodycustom (Yokomori lab)custom (Yokomori lab)
Lot_num----
crosslinking_methodultraviolet irradiationultraviolet irradiation
queried_RNP_size_range175-300175-300
Self_consistency_hg38
rescue_GRCh38
StatusReleasedReleased
ProjectENCODE4ENCODE4
ID386441




Replicate Information
Rep_UID565_01565_02565_INPUT
Exp UID565565565
Replicate_typerep1rep2control
ENCODE_ACCESSIONENCLB303DXOENCLB434SDQENCLB112XSX
ENCODE_aliasgene-yeo:565_01gene-yeo:565_02gene-yeo:565_INPUT
Biosample NameK562_111915K562_080316K562_111915
Biosample_ENCODE_AccessionENCBS344MAKENCBS839QBDENCBS344MAK
Biosample_ENCODE_Aliasgene-yeo:K562_111915gene-yeo:K562_080316gene-yeo:K562_111915
Cell_LineK562K562K562
Culture_Start_Date2015-11-192016-08-032015-11-19
Culture_End_Date2015-12-112016-08-292015-12-11
Passage434




QC Stats
Experiment QC
565565-control
Self_consistency_hg38
rescue_GRCh38


Replicate QC
Rep_UID565_01565_02565_INPUT
eCT
Usable_reads
Entropy_hg38




Library-Prep Information
Rep_UID565_01565_02565_INPUT
library_size_selection_methodagarose gel extractionagarose gel extractionagarose gel extraction
strand_specificityreversereversereverse
inline_barcode_1A03A04none
inline_barcode_2G07F05none
i5_barcode502502501
i7_barcode704704703




Sequencing Information
Rep_UID565_01565_02565_INPUT
seq_read_typepaired-endedpaired-endedpaired-ended
read_length505050
machine
flowcell
lane




File Information

FASTQ

file_nameSample IDfile_formatoutput_typerun_typepaired_endread_lengthplatformassay_type
565_01_NIPBL.R1.fastq.gz565_01fastqreadspaired-ended150HiSeq4000eCLIP
565_01_NIPBL.R2.fastq.gz565_01fastqreadspaired-ended250HiSeq4000eCLIP
565_02_NIPBL.R1.fastq.gz565_02fastqreadspaired-ended150HiSeq4000eCLIP
565_02_NIPBL.R2.fastq.gz565_02fastqreadspaired-ended250HiSeq4000eCLIP
565_INPUT_NIPBL.R1.fastq.gz565_INPUTfastqreadspaired-ended150HiSeq4000eCLIP
565_INPUT_NIPBL.R2.fastq.gz565_INPUTfastqreadspaired-ended250HiSeq4000eCLIP


GRCh38

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
GRCh38/565.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz565final_peakspeakseCLIPGRCh38
GRCh38_565_01_NIPBL.merged.bam565_01bamalignmentseCLIPGRCh38
GRCh38_565_01_NIPBL.merged.r2.norm.neg.bw565_01bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_565_01_NIPBL.merged.r2.norm.pos.bw565_01bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/565_01.basedon_565_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz565_01bed_eCLIPpeakseCLIPGRCh38
GRCh38/565_01.basedon_565_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb565_01bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_565_02_NIPBL.merged.bam565_02bamalignmentseCLIPGRCh38
GRCh38_565_02_NIPBL.merged.r2.norm.neg.bw565_02bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_565_02_NIPBL.merged.r2.norm.pos.bw565_02bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/565_02.basedon_565_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz565_02bed_eCLIPpeakseCLIPGRCh38
GRCh38/565_02.basedon_565_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb565_02bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_565_INPUT_S28_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam565_INPUTbamalignmentseCLIPGRCh38
GRCh38_565_INPUT_S28_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw565_INPUTbigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_565_INPUT_S28_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw565_INPUTbigWig+uniqueplus strand signal of unique readseCLIPGRCh38


hg19

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
565.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz565final_peakspeakseCLIPhg19
565_01_NIPBL.merged.bam565_01bamalignmentseCLIPhg19
565_01_NIPBL.merged.r2.norm.neg.bw565_01bigWig-uniqueminus strand signal of unique readseCLIPhg19
565_01_NIPBL.merged.r2.norm.pos.bw565_01bigWig+uniqueplus strand signal of unique readseCLIPhg19
565_01.basedon_565_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz565_01bed_eCLIPpeakseCLIPhg19
565_01.basedon_565_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb565_01bigBed_eCLIPpeakseCLIPhg19
565_02_NIPBL.merged.bam565_02bamalignmentseCLIPhg19
565_02_NIPBL.merged.r2.norm.neg.bw565_02bigWig-uniqueminus strand signal of unique readseCLIPhg19
565_02_NIPBL.merged.r2.norm.pos.bw565_02bigWig+uniqueplus strand signal of unique readseCLIPhg19
565_02.basedon_565_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz565_02bed_eCLIPpeakseCLIPhg19
565_02.basedon_565_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb565_02bigBed_eCLIPpeakseCLIPhg19
565_INPUT_S28_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam565_INPUTbamalignmentseCLIPhg19
565_INPUT_S28_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw565_INPUTbigWig-uniqueminus strand signal of unique readseCLIPhg19
565_INPUT_S28_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw565_INPUTbigWig+uniqueplus strand signal of unique readseCLIPhg19






Data Submission Information

Files

ENCODE_aliasENCODE_accessionobject_typeassay_typeSample_IDStatusProject
gene-yeo:4108_CLIP1_rep1.vs.4108_CLIP2_rep2.sorted.nh.narrowPeak.gzENCFF723BSOfile_finalPeakseCLIP4108ReleasedENCODE4
gene-yeo:4152_CLIP1_rep1.vs.4152_CLIP2_rep2.sorted.nh.bbENCFF436WIXfile_finalPeaks_bbeCLIP4108ReleasedENCODE4