ENCORE eCLIP:4050

Experiment Information (Status: Released)

	4050-control	4050
Exp_UID	4050	4050
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR058PIY	ENCSR631HUN
ENCODE_alias	gene-yeo:4050-control	gene-yeo:4050
RBP	DDX47	DDX47
Cell_Line	K562	K562
Batch	batch11b	batch11b
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB088DCV	ENCAB088DCV
Antibody	A302-976A	A302-976A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.204762	1.204762
rescue_GRCh38	2.318352	2.318352
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	587	588

Replicate Information


Rep_UID	4050_01	4050_02	4050_INPUT1	4050_INPUT2
Exp UID	4050	4050	4050	4050
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

	4050-control	4050
Self_consistency_hg38	1.204762	1.204762
rescue_GRCh38	2.318352	2.318352

Replicate QC


Rep_UID	4050_01	4050_02	4050_INPUT1	4050_INPUT2
eCT	12.80	12.60	7.20	5.80
Usable_reads	1309764	1234198	1596708	1837343
Entropy_hg38	0.281511	0.241184

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4050_01	4050_02	4050_INPUT1	4050_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	ATAGAGGC	ATAGAGGC	TATAGCCT	TATAGCCT
i7_barcode	GAGATTCC	CGCTCATT	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4050_01	4050_02	4050_INPUT1	4050_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
4050_CLIP1_S75_L005_R1_001.fastq.gz	4050_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4050_CLIP2_S77_L005_R1_001.fastq.gz	4050_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4050_INPUT1_S74_L005_R1_001.fastq.gz	4050_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4050_INPUT2_S76_L005_R1_001.fastq.gz	4050_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4050_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4050_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4050_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4050_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4050_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4050_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4050_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4050_CLIP1_rep1.vs.4050_CLIP2_rep2.sorted.nh.bb	4050_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4050_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4050_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4050_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4050_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4050_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4050_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4050_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4050_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4050_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4050_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4050_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4050_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4050_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4050_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4050_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4050_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4050_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4050_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:4050-control	ENCSR058PIY	experiment	eCLIP	4050-DDX47-K562-control	Released	ENCODE4
gene-yeo:4050	ENCSR631HUN	experiment	eCLIP	4050-DDX47-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_111915-4050_01	ENCLB204LRA	library	eCLIP	4050_01	Released	ENCODE4
gene-yeo:L-K562_072016-4050_02	ENCLB298ALX	library	eCLIP	4050_02	Released	ENCODE4
gene-yeo:L-K562_111915-4050_INPUT1	ENCLB904DTL	library	eCLIP	4050_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4050_INPUT2	ENCLB044CBL	library	eCLIP	4050_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4050_CLIP1_S75_L005_R1_001.fastq.gz	ENCFF418BKS	file_fastq	eCLIP	4050_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF748LDX	file_bam	eCLIP	4050_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF782BXA	file_bam	eCLIP	4050_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF602MAB	file_bw	eCLIP	4050_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF107VSH	file_bw	eCLIP	4050_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF622JHF	file_quantifications	eCLIP	4050_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF228BKM	file_bed	eCLIP	4050_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF590MBQ	file_bb	eCLIP	4050_01	Released	ENCODE4
gene-yeo:4050_CLIP2_S77_L005_R1_001.fastq.gz	ENCFF375INH	file_fastq	eCLIP	4050_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF832UJF	file_bam	eCLIP	4050_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF433TOE	file_bam	eCLIP	4050_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF278RTY	file_bw	eCLIP	4050_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF270ZTY	file_bw	eCLIP	4050_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF501UKO	file_quantifications	eCLIP	4050_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF766SEA	file_bed	eCLIP	4050_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF470AXV	file_bb	eCLIP	4050_02	Released	ENCODE4
gene-yeo:4050_INPUT1_S74_L005_R1_001.fastq.gz	ENCFF306KCA	file_fastq	eCLIP	4050_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF384XPB	file_bam	eCLIP	4050_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF858EZY	file_bam	eCLIP	4050_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF668TBM	file_bw	eCLIP	4050_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF199WPZ	file_bw	eCLIP	4050_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF172NPI	file_quantifications	eCLIP	4050_INPUT1	Released	ENCODE4
gene-yeo:4050_INPUT2_S76_L005_R1_001.fastq.gz	ENCFF313UGS	file_fastq	eCLIP	4050_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF351MRE	file_bam	eCLIP	4050_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF655QAC	file_bam	eCLIP	4050_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF766QQD	file_bw	eCLIP	4050_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF900NAX	file_bw	eCLIP	4050_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4050_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF935GMC	file_quantifications	eCLIP	4050_INPUT2	Released	ENCODE4