ENCORE eCLIP:4047

Experiment Information (Status: Released)

	4047-control	4047
Exp_UID	4047	4047
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR290MTQ	ENCSR224QFQ
ENCODE_alias	gene-yeo:4047-control	gene-yeo:4047
RBP	NSUN4	NSUN4
Cell_Line	K562	K562
Batch	batch11a	batch11a
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB297AWK	ENCAB297AWK
Antibody	720212	720212
Lot_num	SA246721	SA246721
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	8.659184	8.659184
rescue_GRCh38	5.248400	5.248400
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	601	602

Replicate Information


Rep_UID	4047_01	4047_02	4047_INPUT1	4047_INPUT2
Exp UID	4047	4047	4047	4047
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_111915	K562_072016	K562_111915	K562_072016
Biosample_ENCODE_Accession	ENCBS344MAK	ENCBS177POD	ENCBS344MAK	ENCBS177POD
Biosample_ENCODE_Alias	gene-yeo:K562_111915	gene-yeo:K562_072016	gene-yeo:K562_111915	gene-yeo:K562_072016
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-11-19	2016-07-20	2015-11-19	2016-07-20
Culture_End_Date	2015-12-11	2016-08-15	2015-12-11	2016-08-15
Passage	4	5	4	5

QC Stats

Experiment QC

	4047-control	4047
Self_consistency_hg38	8.659184	8.659184
rescue_GRCh38	5.248400	5.248400

Replicate QC


Rep_UID	4047_01	4047_02	4047_INPUT1	4047_INPUT2
eCT	14.80	15.70	6.80	6.60
Usable_reads	2053868	2812450	4508178	4045958
Entropy_hg38	0.785121	3.116889

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4047_01	4047_02	4047_INPUT1	4047_INPUT2
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse	reverse
inline_barcode_1
inline_barcode_2
i5_barcode	GGCTCTGA	GGCTCTGA	CCTATCCT	CCTATCCT
i7_barcode	CGCTCATT	GAGATTCC	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4047_01	4047_02	4047_INPUT1	4047_INPUT2
seq_read_type	single-ended	single-ended	single-ended	single-ended
read_length	75	75	75	75
machine	HiSeq4000	HiSeq4000	HiSeq4000	HiSeq4000
flowcell	flowcell	flowcell	flowcell	flowcell
lane	-	-	-	-

File Information

FASTQ

file_name	Sample ID	file_format	output_type	run_type	read_length	platform	assay_type
4047_CLIP1_S28_L002_R1_001.fastq.gz	4047_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4047_CLIP2_S30_L002_R1_001.fastq.gz	4047_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4047_INPUT1_S27_L002_R1_001.fastq.gz	4047_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4047_INPUT2_S29_L002_R1_001.fastq.gz	4047_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4047_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4047_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4047_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4047_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4047_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4047_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4047_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4047_CLIP1_rep1.vs.4047_CLIP2_rep2.sorted.nh.bb	4047_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4047_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4047_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4047_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4047_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4047_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4047_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4047_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4047_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4047_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4047_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4047_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4047_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4047_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4047_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4047_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4047_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4047_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4047_INPUT2	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29

Data Submission Information

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4047-control	ENCSR290MTQ	experiment	eCLIP	4047-NSUN4-K562-control	Released	ENCODE4
gene-yeo:4047	ENCSR224QFQ	experiment	eCLIP	4047-NSUN4-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_111915-4047_01	ENCLB791ADP	library	eCLIP	4047_01	Released	ENCODE4
gene-yeo:L-K562_072016-4047_02	ENCLB528YLH	library	eCLIP	4047_02	Released	ENCODE4
gene-yeo:L-K562_111915-4047_INPUT1	ENCLB533PAW	library	eCLIP	4047_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4047_INPUT2	ENCLB546CIY	library	eCLIP	4047_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4047_CLIP1_S28_L002_R1_001.fastq.gz	ENCFF197OZT	file_fastq	eCLIP	4047_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF912NYB	file_bam	eCLIP	4047_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF207EDY	file_bam	eCLIP	4047_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF449HBL	file_bw	eCLIP	4047_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF539IFO	file_bw	eCLIP	4047_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF453FNJ	file_quantifications	eCLIP	4047_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF522KVM	file_bed	eCLIP	4047_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF454IDG	file_bb	eCLIP	4047_01	Released	ENCODE4
gene-yeo:4047_CLIP2_S30_L002_R1_001.fastq.gz	ENCFF848WNC	file_fastq	eCLIP	4047_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF541HED	file_bam	eCLIP	4047_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF927RTH	file_bam	eCLIP	4047_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF374TYH	file_bw	eCLIP	4047_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF450ZGX	file_bw	eCLIP	4047_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF280KIG	file_quantifications	eCLIP	4047_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF112LOX	file_bed	eCLIP	4047_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF273FZK	file_bb	eCLIP	4047_02	Released	ENCODE4
gene-yeo:4047_INPUT1_S27_L002_R1_001.fastq.gz	ENCFF005TWX	file_fastq	eCLIP	4047_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF909UNO	file_bam	eCLIP	4047_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF499NFB	file_bam	eCLIP	4047_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF540MYX	file_bw	eCLIP	4047_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF478PGN	file_bw	eCLIP	4047_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF806AZQ	file_quantifications	eCLIP	4047_INPUT1	Released	ENCODE4
gene-yeo:4047_INPUT2_S29_L002_R1_001.fastq.gz	ENCFF765VOG	file_fastq	eCLIP	4047_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF612BLH	file_bam	eCLIP	4047_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF338NHE	file_bam	eCLIP	4047_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF688GAZ	file_bw	eCLIP	4047_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF750LFA	file_bw	eCLIP	4047_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4047_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF533YBU	file_quantifications	eCLIP	4047_INPUT2	Released	ENCODE4