ENCORE eCLIP:4010

Experiment Information (Status: Released)

	4010-control	4010
Exp_UID	4010	4010
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR206NIG	ENCSR448IDP
ENCODE_alias	gene-yeo:4010-control	gene-yeo:4010
RBP	NPM1	NPM1
Cell_Line	K562	K562
Batch	batch7	batch7
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB147WFE	ENCAB147WFE
Antibody	325200	325200
Lot_num	TD268297	TD268297
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.660194	1.660194
rescue_GRCh38	1.157895	1.157895
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	491	492

Replicate Information


Rep_UID	4010_01	4010_02	4010_INPUT1	4010_INPUT2
Exp UID	4010	4010	4010	4010
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_012016	K562_072016	K562_012016	K562_072016
Biosample_ENCODE_Accession	ENCBS039CVO	ENCBS177POD	ENCBS039CVO	ENCBS177POD
Biosample_ENCODE_Alias	gene-yeo:K562_012016	gene-yeo:K562_072016	gene-yeo:K562_012016	gene-yeo:K562_072016
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2016-01-20	2016-07-20	2016-01-20	2016-07-20
Culture_End_Date	2016-02-17	2016-08-15	2016-02-17	2016-08-15
Passage	5	5	5	5

QC Stats

Experiment QC

	4010-control	4010
Self_consistency_hg38	1.660194	1.660194
rescue_GRCh38	1.157895	1.157895

Replicate QC


Rep_UID	4010_01	4010_02	4010_INPUT1	4010_INPUT2
eCT	16.10	12.70	11.90	5.60
Usable_reads	377573	239515	5949586	2780072
Entropy_hg38	12.860967	10.531572

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4010_01	4010_02	4010_INPUT1	4010_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	AGGCGAAG	GGCTCTGA	AGGCGAAG	AGGCGAAG
i7_barcode	TCCGGAGA	CGCTCATT	ATTACTCG	CGCTCATT

Sequencing Information


Rep_UID	4010_01	4010_02	4010_INPUT1	4010_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
4010_CLIP1_S136_L008_R1_001.fastq.gz	4010_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4010_CLIP2_S138_L008_R1_001.fastq.gz	4010_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4010_IN1_S135_L008_R1_001.fastq.gz	4010_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4010_IN2_S137_L008_R1_001.fastq.gz	4010_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4010_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4010_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4010_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4010_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4010_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4010_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4010_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4010_CLIP1_rep1.vs.4010_CLIP2_rep2.sorted.nh.bb	4010_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4010_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4010_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4010_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4010_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4010_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4010_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4010_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4010_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4010_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4010_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4010_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4010_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4010_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4010_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4010_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4010_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4010_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4010_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:4010-control	ENCSR206NIG	experiment	eCLIP	4010-NPM1-K562-control	Released	ENCODE4
gene-yeo:4010	ENCSR448IDP	experiment	eCLIP	4010-NPM1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_012016-4010_01	ENCLB250CSR	library	eCLIP	4010_01	Released	ENCODE4
gene-yeo:L-K562_072016-4010_02	ENCLB968MXJ	library	eCLIP	4010_02	Released	ENCODE4
gene-yeo:L-K562_012016-4010_INPUT1	ENCLB236DXV	library	eCLIP	4010_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4010_INPUT2	ENCLB799XVO	library	eCLIP	4010_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4010_CLIP1_S136_L008_R1_001.fastq.gz	ENCFF583EBH	file_fastq	eCLIP	4010_01	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF697IZA	file_bam	eCLIP	4010_01	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF617WKC	file_bam	eCLIP	4010_01	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF810PZB	file_bw	eCLIP	4010_01	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF022FCJ	file_bw	eCLIP	4010_01	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF707UHR	file_quantifications	eCLIP	4010_01	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF180ZUC	file_bed	eCLIP	4010_01	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF174CTH	file_bb	eCLIP	4010_01	Released	ENCODE4
gene-yeo:4010_CLIP2_S138_L008_R1_001.fastq.gz	ENCFF302QIO	file_fastq	eCLIP	4010_02	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF539FUU	file_bam	eCLIP	4010_02	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF260IBI	file_bam	eCLIP	4010_02	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF160QUT	file_bw	eCLIP	4010_02	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF068YAK	file_bw	eCLIP	4010_02	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF596LUR	file_quantifications	eCLIP	4010_02	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF255YRN	file_bed	eCLIP	4010_02	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF431PVA	file_bb	eCLIP	4010_02	Released	ENCODE4
gene-yeo:4010_IN1_S135_L008_R1_001.fastq.gz	ENCFF577BCD	file_fastq	eCLIP	4010_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF308EFN	file_bam	eCLIP	4010_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF236YLN	file_bam	eCLIP	4010_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF713KHM	file_bw	eCLIP	4010_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF072GNO	file_bw	eCLIP	4010_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF382XJO	file_quantifications	eCLIP	4010_INPUT1	Released	ENCODE4
gene-yeo:4010_IN2_S137_L008_R1_001.fastq.gz	ENCFF929LLC	file_fastq	eCLIP	4010_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF855YNQ	file_bam	eCLIP	4010_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF630FUX	file_bam	eCLIP	4010_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF481KIW	file_bw	eCLIP	4010_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF074TCX	file_bw	eCLIP	4010_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4010_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF725UCT	file_quantifications	eCLIP	4010_INPUT2	Released	ENCODE4