ENCORE eCLIP:4140

Experiment Information (Status: Released)

	4140-control	4140
Exp_UID	4140	4140
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR407QDZ	ENCSR179MPN
ENCODE_alias	gene-yeo:4140-control	gene-yeo:4140
RBP	RYBP	RYBP
Cell_Line	K562	K562
Batch	batch21	batch21
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB686SDS	ENCAB686SDS
Antibody	PA5-19943	PA5-19943
Lot_num	UCF2796583	UCF2796583
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	6.958506	6.958506
rescue_GRCh38	3.321004	3.321004
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	539	540

Replicate Information


Rep_UID	4140_01	4140_02	4140_INPUT1	4140_INPUT2
Exp UID	4140	4140	4140	4140
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

	4140-control	4140
Self_consistency_hg38	6.958506	6.958506
rescue_GRCh38	3.321004	3.321004

Replicate QC


Rep_UID	4140_01	4140_02	4140_INPUT1	4140_INPUT2
eCT	10.90	9.60	10.60	5.90
Usable_reads	5541537	2495284	3484208	3005177
Entropy_hg38	0.170845	0.029403

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4140_01	4140_02	4140_INPUT1	4140_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	CCTATCCT	CCTATCCT	ATAGAGGC	ATAGAGGC
i7_barcode	ATTCAGAA	GAGATTCC	ATTCAGAA	GAGATTCC

Sequencing Information


Rep_UID	4140_01	4140_02	4140_INPUT1	4140_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
4140_CLIP1_S67_L004_R1_001.fastq.gz	4140_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4140_CLIP2_S69_L004_R1_001.fastq.gz	4140_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4140_IN1_S66_L004_R1_001.fastq.gz	4140_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4140_IN2_S68_L004_R1_001.fastq.gz	4140_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4140_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4140_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4140_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4140_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4140_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4140_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4140_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4140_CLIP1_rep1.vs.4140_CLIP2_rep2.sorted.nh.bb	4140_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4140_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4140_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4140_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4140_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4140_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4140_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4140_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4140_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4140_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4140_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4140_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4140_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4140_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4140_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4140_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4140_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4140_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4140_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:4140-control	ENCSR407QDZ	experiment	eCLIP	4140-RYBP-K562-control	Released	ENCODE4
gene-yeo:4140	ENCSR179MPN	experiment	eCLIP	4140-RYBP-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4140_01	ENCLB808PTW	library	eCLIP	4140_01	Released	ENCODE4
gene-yeo:L-K562_102015-4140_02	ENCLB477WMP	library	eCLIP	4140_02	Released	ENCODE4
gene-yeo:L-K562_081815-4140_INPUT1	ENCLB107ZXT	library	eCLIP	4140_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4140_INPUT2	ENCLB056WFA	library	eCLIP	4140_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4140_CLIP1_S67_L004_R1_001.fastq.gz	ENCFF604OCB	file_fastq	eCLIP	4140_01	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF422UZN	file_bam	eCLIP	4140_01	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF501SLN	file_bam	eCLIP	4140_01	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF925UUJ	file_bw	eCLIP	4140_01	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF898AFN	file_bw	eCLIP	4140_01	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF835WIF	file_quantifications	eCLIP	4140_01	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF905GCD	file_bed	eCLIP	4140_01	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF907OXS	file_bb	eCLIP	4140_01	Released	ENCODE4
gene-yeo:4140_CLIP2_S69_L004_R1_001.fastq.gz	ENCFF264WXA	file_fastq	eCLIP	4140_02	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF945ORL	file_bam	eCLIP	4140_02	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF824YGM	file_bam	eCLIP	4140_02	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF613ILE	file_bw	eCLIP	4140_02	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF747XIS	file_bw	eCLIP	4140_02	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF515QLS	file_quantifications	eCLIP	4140_02	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF851PEL	file_bed	eCLIP	4140_02	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF184EXI	file_bb	eCLIP	4140_02	Released	ENCODE4
gene-yeo:4140_IN1_S66_L004_R1_001.fastq.gz	ENCFF155CNX	file_fastq	eCLIP	4140_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF098KNI	file_bam	eCLIP	4140_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF774HTQ	file_bam	eCLIP	4140_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF082WKG	file_bw	eCLIP	4140_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF801UVA	file_bw	eCLIP	4140_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF679ZRS	file_quantifications	eCLIP	4140_INPUT1	Released	ENCODE4
gene-yeo:4140_IN2_S68_L004_R1_001.fastq.gz	ENCFF942VJP	file_fastq	eCLIP	4140_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF616WBQ	file_bam	eCLIP	4140_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF220MSI	file_bam	eCLIP	4140_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF252AJB	file_bw	eCLIP	4140_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF262MCE	file_bw	eCLIP	4140_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4140_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF417MUA	file_quantifications	eCLIP	4140_INPUT2	Released	ENCODE4