ENCORE eCLIP:4160

Experiment Information (Status: Released)

	4160-control	4160
Exp_UID	4160	4160
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR816TOM	ENCSR008MQM
ENCODE_alias	gene-yeo:4160-control	gene-yeo:4160
RBP	DDX43	DDX43
Cell_Line	K562	K562
Batch	batch21	batch21
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB412ETD	ENCAB412ETD
Antibody	A302-328A	A302-328A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.152023	1.152023
rescue_GRCh38	2.221942	2.221942
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	535	536

Replicate Information


Rep_UID	4160_01	4160_02	4160_INPUT1	4160_INPUT2
Exp UID	4160	4160	4160	4160
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_081815	K562_102015	K562_081815	K562_102015
Biosample_ENCODE_Accession	ENCBS175JIH	ENCBS592SHU	ENCBS175JIH	ENCBS592SHU
Biosample_ENCODE_Alias	gene-yeo:K562_081815	gene-yeo:K562_102015	gene-yeo:K562_081815	gene-yeo:K562_102015
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-08-18	2015-10-20	2015-08-18	2015-10-20
Culture_End_Date	2015-09-08	2015-11-17	2015-09-08	2015-11-17
Passage	5	5	5	5

QC Stats

Experiment QC

	4160-control	4160
Self_consistency_hg38	1.152023	1.152023
rescue_GRCh38	2.221942	2.221942

Replicate QC


Rep_UID	4160_01	4160_02	4160_INPUT1	4160_INPUT2
eCT	9.00	9.70	4.60	6.60
Usable_reads	5597683	5469509	4746075	3682038
Entropy_hg38	0.847912	0.651810

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4160_01	4160_02	4160_INPUT1	4160_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	GGCTCTGA	TATAGCCT	CCTATCCT
i7_barcode	ATTACTCG	ATTACTCG	ATTACTCG	ATTACTCG

Sequencing Information


Rep_UID	4160_01	4160_02	4160_INPUT1	4160_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
4160_CLIP1_S79_L005_R1_001.fastq.gz	4160_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4160_CLIP2_S61_L004_R1_001.fastq.gz	4160_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4160_IN1_S78_L005_R1_001.fastq.gz	4160_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4160_IN2_S60_L004_R1_001.fastq.gz	4160_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4160_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4160_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4160_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4160_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4160_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4160_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4160_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4160_CLIP1_rep1.vs.4160_CLIP2_rep2.sorted.nh.bb	4160_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4160_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4160_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4160_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4160_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4160_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4160_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4160_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4160_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4160_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4160_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4160_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4160_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4160_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4160_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4160_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4160_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4160_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4160_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:4160-control	ENCSR816TOM	experiment	eCLIP	4160-DDX43-K562-control	Released	ENCODE4
gene-yeo:4160	ENCSR008MQM	experiment	eCLIP	4160-DDX43-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4160_01	ENCLB505KRK	library	eCLIP	4160_01	Released	ENCODE4
gene-yeo:L-K562_102015-4160_02	ENCLB705DYM	library	eCLIP	4160_02	Released	ENCODE4
gene-yeo:L-K562_081815-4160_INPUT1	ENCLB247MAV	library	eCLIP	4160_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4160_INPUT2	ENCLB712KAX	library	eCLIP	4160_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4160_CLIP1_S79_L005_R1_001.fastq.gz	ENCFF884KLU	file_fastq	eCLIP	4160_01	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF353FMJ	file_bam	eCLIP	4160_01	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF006VBB	file_bam	eCLIP	4160_01	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF848XEG	file_bw	eCLIP	4160_01	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF251YSP	file_bw	eCLIP	4160_01	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF199MLA	file_quantifications	eCLIP	4160_01	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF456RNY	file_bed	eCLIP	4160_01	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF199AAM	file_bb	eCLIP	4160_01	Released	ENCODE4
gene-yeo:4160_CLIP2_S61_L004_R1_001.fastq.gz	ENCFF338ZLQ	file_fastq	eCLIP	4160_02	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF561HQU	file_bam	eCLIP	4160_02	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF781FNG	file_bam	eCLIP	4160_02	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF768HEE	file_bw	eCLIP	4160_02	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF245LIH	file_bw	eCLIP	4160_02	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF845JPA	file_quantifications	eCLIP	4160_02	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF032BJT	file_bed	eCLIP	4160_02	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF894LGZ	file_bb	eCLIP	4160_02	Released	ENCODE4
gene-yeo:4160_IN1_S78_L005_R1_001.fastq.gz	ENCFF913RUT	file_fastq	eCLIP	4160_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF734XPC	file_bam	eCLIP	4160_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF280KEZ	file_bam	eCLIP	4160_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF759ORV	file_bw	eCLIP	4160_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF391DSJ	file_bw	eCLIP	4160_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF263KKB	file_quantifications	eCLIP	4160_INPUT1	Released	ENCODE4
gene-yeo:4160_IN2_S60_L004_R1_001.fastq.gz	ENCFF146CPZ	file_fastq	eCLIP	4160_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF698EUP	file_bam	eCLIP	4160_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF730DCR	file_bam	eCLIP	4160_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF342XVA	file_bw	eCLIP	4160_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF729RER	file_bw	eCLIP	4160_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4160_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF957KNS	file_quantifications	eCLIP	4160_INPUT2	Released	ENCODE4