PABPC4      eCLIP in K562

Experiment Information (Status: Released)
406406-control
Exp_UID406406
RBPARK_Exp_name
ENCODE_ACCESSIONENCSR958FKZENCSR192TPA
ENCODE_aliasgene-yeo:406gene-yeo:406-control
RBPPABPC4PABPC4
Cell_LineK562K562
Batch
Exp_typeeCLIPcontrol
ENCODE_Antibody_IDENCAB596MHXENCAB596MHX
AntibodyA301-466AA301-466A
Lot_num11
crosslinking_methodultraviolet irradiationultraviolet irradiation
queried_RNP_size_range175-300175-300
Self_consistency_hg38
rescue_GRCh38
StatusReleasedReleased
ProjectENCODE4ENCODE4
ID381436




Replicate Information
Rep_UID406_01406_02406_INPUT
Exp UID406406406
Replicate_typerep1rep2control
ENCODE_ACCESSIONENCLB407STOENCLB599SHTENCLB248UAI
ENCODE_aliasgene-yeo:406_01gene-yeo:406_02gene-yeo:406_INPUT
Biosample NameK562_040915K562_051215K562_040915
Biosample_ENCODE_AccessionENCBS931MQOENCBS489LOCENCBS931MQO
Biosample_ENCODE_Aliasgene-yeo:K562_040915gene-yeo:K562_051215gene-yeo:K562_040915
Cell_LineK562K562K562
Culture_Start_Date2015-04-092015-05-122015-04-09
Culture_End_Date2015-05-082015-06-112015-05-08
Passage545




QC Stats
Experiment QC
406406-control
Self_consistency_hg38
rescue_GRCh38


Replicate QC
Rep_UID406_01406_02406_INPUT
eCT
Usable_reads
Entropy_hg38




Library-Prep Information
Rep_UID406_01406_02406_INPUT
library_size_selection_methodagarose gel extractionagarose gel extractionagarose gel extraction
strand_specificityreversereversereverse
inline_barcode_1A03A04none
inline_barcode_2G07F05none
i5_barcode502502502
i7_barcode704704703




Sequencing Information
Rep_UID406_01406_02406_INPUT
seq_read_typepaired-endedpaired-endedpaired-ended
read_length505050
machine
flowcell
lane




File Information

FASTQ

file_nameSample IDfile_formatoutput_typerun_typepaired_endread_lengthplatformassay_type
406_01_PABPC4.R1.fastq.gz406_01fastqreadspaired-ended150HiSeq4000eCLIP
406_01_PABPC4.R2.fastq.gz406_01fastqreadspaired-ended250HiSeq4000eCLIP
406_02_PABPC4.R1.fastq.gz406_02fastqreadspaired-ended150HiSeq4000eCLIP
406_02_PABPC4.R2.fastq.gz406_02fastqreadspaired-ended250HiSeq4000eCLIP
406_INPUT_PABPC4.R1.fastq.gz406_INPUTfastqreadspaired-ended150HiSeq4000eCLIP
406_INPUT_PABPC4.R2.fastq.gz406_INPUTfastqreadspaired-ended250HiSeq4000eCLIP


GRCh38

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
GRCh38/406.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz406final_peakspeakseCLIPGRCh38
GRCh38_406_01_PABPC4.merged.bam406_01bamalignmentseCLIPGRCh38
GRCh38_406_01_PABPC4.merged.r2.norm.neg.bw406_01bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_406_01_PABPC4.merged.r2.norm.pos.bw406_01bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/406_01.basedon_406_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz406_01bed_eCLIPpeakseCLIPGRCh38
GRCh38/406_01.basedon_406_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb406_01bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_406_02_PABPC4.merged.bam406_02bamalignmentseCLIPGRCh38
GRCh38_406_02_PABPC4.merged.r2.norm.neg.bw406_02bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_406_02_PABPC4.merged.r2.norm.pos.bw406_02bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/406_02.basedon_406_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz406_02bed_eCLIPpeakseCLIPGRCh38
GRCh38/406_02.basedon_406_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb406_02bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_406_INPUT_CGCTCATT-ATAGAGGC_L004_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam406_INPUTbamalignmentseCLIPGRCh38
GRCh38_406_INPUT_CGCTCATT-ATAGAGGC_L004_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw406_INPUTbigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_406_INPUT_CGCTCATT-ATAGAGGC_L004_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw406_INPUTbigWig+uniqueplus strand signal of unique readseCLIPGRCh38


hg19

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
406.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz406final_peakspeakseCLIPhg19
406_01_PABPC4.merged.bam406_01bamalignmentseCLIPhg19
406_01_PABPC4.merged.r2.norm.neg.bw406_01bigWig-uniqueminus strand signal of unique readseCLIPhg19
406_01_PABPC4.merged.r2.norm.pos.bw406_01bigWig+uniqueplus strand signal of unique readseCLIPhg19
406_01.basedon_406_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz406_01bed_eCLIPpeakseCLIPhg19
406_01.basedon_406_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb406_01bigBed_eCLIPpeakseCLIPhg19
406_02_PABPC4.merged.bam406_02bamalignmentseCLIPhg19
406_02_PABPC4.merged.r2.norm.neg.bw406_02bigWig-uniqueminus strand signal of unique readseCLIPhg19
406_02_PABPC4.merged.r2.norm.pos.bw406_02bigWig+uniqueplus strand signal of unique readseCLIPhg19
406_02.basedon_406_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz406_02bed_eCLIPpeakseCLIPhg19
406_02.basedon_406_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb406_02bigBed_eCLIPpeakseCLIPhg19
406_INPUT_CGCTCATT-ATAGAGGC_L004_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam406_INPUTbamalignmentseCLIPhg19
406_INPUT_CGCTCATT-ATAGAGGC_L004_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw406_INPUTbigWig-uniqueminus strand signal of unique readseCLIPhg19
406_INPUT_CGCTCATT-ATAGAGGC_L004_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw406_INPUTbigWig+uniqueplus strand signal of unique readseCLIPhg19






Data Submission Information

Files

ENCODE_aliasENCODE_accessionobject_typeassay_typeSample_IDStatusProject
gene-yeo:4158_CLIP1_rep1.vs.4158_CLIP2_rep2.sorted.nh.narrowPeak.gzENCFF923KPPfile_finalPeakseCLIP4158ReleasedENCODE4
gene-yeo:4132_CLIP1_rep1.vs.4132_CLIP2_rep2.sorted.nh.bbENCFF430AOKfile_finalPeaks_bbeCLIP4158ReleasedENCODE4
gene-yeo:4164_CLIP1_rep1.vs.4164_CLIP2_rep2.sorted.nh.narrowPeak.gzENCFF894YJAfile_finalPeakseCLIP4164ReleasedENCODE4
gene-yeo:4137_CLIP1_rep1.vs.4137_CLIP2_rep2.sorted.nh.bbENCFF029EYGfile_finalPeaks_bbeCLIP4164ReleasedENCODE4