ENCORE eCLIP:4004

Experiment Information (Status: Released)

	4004-control	4004
Exp_UID	4004	4004
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR624YWO	ENCSR691HQP
ENCODE_alias	gene-yeo:4004-control	gene-yeo:4004
RBP	DEK	DEK
Cell_Line	K562	K562
Batch	batch2	batch2
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB872AQT	ENCAB872AQT
Antibody	720215	720215
Lot_num	SD249202	SD249202
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.450000	1.450000
rescue_GRCh38	3.577465	3.577465
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	553	554

Replicate Information


Rep_UID	4004_01	4004_02	4004_INPUT1	4004_INPUT2
Exp UID	4004	4004	4004	4004
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_072016	K562_012016	K562_072016	K562_012016
Biosample_ENCODE_Accession	ENCBS177POD	ENCBS039CVO	ENCBS177POD	ENCBS039CVO
Biosample_ENCODE_Alias	gene-yeo:K562_072016	gene-yeo:K562_012016	gene-yeo:K562_072016	gene-yeo:K562_012016
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2016-07-20	2016-01-20	2016-07-20	2016-01-20
Culture_End_Date	2016-08-15	2016-02-17	2016-08-15	2016-02-17
Passage	5	5	5	5

QC Stats

Experiment QC

	4004-control	4004
Self_consistency_hg38	1.450000	1.450000
rescue_GRCh38	3.577465	3.577465

Replicate QC


Rep_UID	4004_01	4004_02	4004_INPUT1	4004_INPUT2
eCT	12.90	14.20	5.10	4.60
Usable_reads	620390	500690	517990	701007
Entropy_hg38	1.212902	0.606520

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4004_01	4004_02	4004_INPUT1	4004_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	AGGCGAAG	GGCTCTGA	AGGCGAAG
i7_barcode	ATTCAGAA	ATTCAGAA	GAGATTCC	GAGATTCC

Sequencing Information


Rep_UID	4004_01	4004_02	4004_INPUT1	4004_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
4004_CLIP1_S21_L004_R1_001.fastq.gz	4004_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4004_CLIP2_S23_L004_R1_001.fastq.gz	4004_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4004_INPUT1_S20_L004_R1_001.fastq.gz	4004_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4004_INPUT2_S22_L004_R1_001.fastq.gz	4004_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4004_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4004_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4004_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4004_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4004_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4004_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4004_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4004_CLIP1_rep1.vs.4004_CLIP2_rep2.sorted.nh.bb	4004_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4004_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4004_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4004_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4004_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4004_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4004_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4004_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4004_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4004_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4004_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4004_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4004_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4004_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4004_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4004_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4004_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4004_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4004_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:4004-control	ENCSR624YWO	experiment	eCLIP	4004-DEK-K562-control	Released	ENCODE4
gene-yeo:4004	ENCSR691HQP	experiment	eCLIP	4004-DEK-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_072016-4004_01	ENCLB721CQU	library	eCLIP	4004_01	Released	ENCODE4
gene-yeo:L-K562_012016-4004_02	ENCLB957VUU	library	eCLIP	4004_02	Released	ENCODE4
gene-yeo:L-K562_072016-4004_INPUT1	ENCLB654XPT	library	eCLIP	4004_INPUT1	Released	ENCODE4
gene-yeo:L-K562_012016-4004_INPUT2	ENCLB840PWB	library	eCLIP	4004_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4004_CLIP1_S21_L004_R1_001.fastq.gz	ENCFF685AEC	file_fastq	eCLIP	4004_01	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF415SOY	file_bam	eCLIP	4004_01	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF290HNR	file_bam	eCLIP	4004_01	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF626FMV	file_bw	eCLIP	4004_01	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF828VZU	file_bw	eCLIP	4004_01	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF703ZLL	file_quantifications	eCLIP	4004_01	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF687FST	file_bed	eCLIP	4004_01	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF820OHH	file_bb	eCLIP	4004_01	Released	ENCODE4
gene-yeo:4004_CLIP2_S23_L004_R1_001.fastq.gz	ENCFF527VKC	file_fastq	eCLIP	4004_02	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF645JPQ	file_bam	eCLIP	4004_02	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF569WIZ	file_bam	eCLIP	4004_02	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF052ZFL	file_bw	eCLIP	4004_02	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF709RPW	file_bw	eCLIP	4004_02	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF078RGN	file_quantifications	eCLIP	4004_02	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF203FVI	file_bed	eCLIP	4004_02	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF804RCC	file_bb	eCLIP	4004_02	Released	ENCODE4
gene-yeo:4004_INPUT1_S20_L004_R1_001.fastq.gz	ENCFF600WXN	file_fastq	eCLIP	4004_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF817SWP	file_bam	eCLIP	4004_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF896DIF	file_bam	eCLIP	4004_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF742XQC	file_bw	eCLIP	4004_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF498SKZ	file_bw	eCLIP	4004_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF300YKD	file_quantifications	eCLIP	4004_INPUT1	Released	ENCODE4
gene-yeo:4004_INPUT2_S22_L004_R1_001.fastq.gz	ENCFF136VLR	file_fastq	eCLIP	4004_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF171MHY	file_bam	eCLIP	4004_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF847DNS	file_bam	eCLIP	4004_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF137ATW	file_bw	eCLIP	4004_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF122ILM	file_bw	eCLIP	4004_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4004_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF494RAA	file_quantifications	eCLIP	4004_INPUT2	Released	ENCODE4