ENCORE eCLIP:4142

Experiment Information (Status: Released)

	4142-control	4142
Exp_UID	4142	4142
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR254NWE	ENCSR153STI
ENCODE_alias	gene-yeo:4142-control	gene-yeo:4142
RBP	RNF187	RNF187
Cell_Line	K562	K562
Batch	batch22	batch22
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB212BNU	ENCAB212BNU
Antibody	PA5-56340	PA5-56340
Lot_num	UF2796809A	UF2796809A
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.737249	1.737249
rescue_GRCh38	3.416069	3.416069
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	531	532

Replicate Information


Rep_UID	4142_01	4142_02	4142_INPUT1	4142_INPUT2
Exp UID	4142	4142	4142	4142
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

	4142-control	4142
Self_consistency_hg38	1.737249	1.737249
rescue_GRCh38	3.416069	3.416069

Replicate QC


Rep_UID	4142_01	4142_02	4142_INPUT1	4142_INPUT2
eCT	10.70	11.60	7.20	8.30
Usable_reads	4387250	6159097	2059689	3632973
Entropy_hg38	0.062553	0.074342

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4142_01	4142_02	4142_INPUT1	4142_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	ATTACTCG	TCCGGAGA	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4142_01	4142_02	4142_INPUT1	4142_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
4142_CLIP1_S117_L007_R1_001.fastq.gz	4142_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4142_CLIP2_S119_L007_R1_001.fastq.gz	4142_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4142_IN1_S116_L007_R1_001.fastq.gz	4142_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4142_IN2_S118_L007_R1_001.fastq.gz	4142_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4142_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4142_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4142_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4142_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4142_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4142_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4142_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4142_CLIP1_rep1.vs.4142_CLIP2_rep2.sorted.nh.bb	4142_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4142_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4142_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4142_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4142_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4142_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4142_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4142_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4142_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4142_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4142_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4142_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4142_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4142_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4142_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4142_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4142_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4142_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4142_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:4142-control	ENCSR254NWE	experiment	eCLIP	4142-RYBP-K562-control	Released	ENCODE4
gene-yeo:4142	ENCSR153STI	experiment	eCLIP	4142-RYBP-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4142_01	ENCLB097RVP	library	eCLIP	4142_01	Released	ENCODE4
gene-yeo:L-K562_102015-4142_02	ENCLB845KZM	library	eCLIP	4142_02	Released	ENCODE4
gene-yeo:L-K562_081815-4142_INPUT1	ENCLB449LJX	library	eCLIP	4142_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4142_INPUT2	ENCLB819ZZT	library	eCLIP	4142_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4142_CLIP1_S117_L007_R1_001.fastq.gz	ENCFF690HVR	file_fastq	eCLIP	4142_01	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF996PJP	file_bam	eCLIP	4142_01	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF417CSC	file_bam	eCLIP	4142_01	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF663VSZ	file_bw	eCLIP	4142_01	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF118LDB	file_bw	eCLIP	4142_01	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF786YMP	file_quantifications	eCLIP	4142_01	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF834BUB	file_bed	eCLIP	4142_01	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF393WEC	file_bb	eCLIP	4142_01	Released	ENCODE4
gene-yeo:4142_CLIP2_S119_L007_R1_001.fastq.gz	ENCFF468HAG	file_fastq	eCLIP	4142_02	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF601TLX	file_bam	eCLIP	4142_02	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF450QWZ	file_bam	eCLIP	4142_02	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF575PGQ	file_bw	eCLIP	4142_02	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF232YAI	file_bw	eCLIP	4142_02	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF656QLZ	file_quantifications	eCLIP	4142_02	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF269GWR	file_bed	eCLIP	4142_02	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF314MKS	file_bb	eCLIP	4142_02	Released	ENCODE4
gene-yeo:4142_IN1_S116_L007_R1_001.fastq.gz	ENCFF726EOS	file_fastq	eCLIP	4142_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF775VAD	file_bam	eCLIP	4142_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF160JIV	file_bam	eCLIP	4142_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF894DIZ	file_bw	eCLIP	4142_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF423KIL	file_bw	eCLIP	4142_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF710SRP	file_quantifications	eCLIP	4142_INPUT1	Released	ENCODE4
gene-yeo:4142_IN2_S118_L007_R1_001.fastq.gz	ENCFF019PZK	file_fastq	eCLIP	4142_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF014NMX	file_bam	eCLIP	4142_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF725VFW	file_bam	eCLIP	4142_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF721KDQ	file_bw	eCLIP	4142_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF657STC	file_bw	eCLIP	4142_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4142_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF065PCT	file_quantifications	eCLIP	4142_INPUT2	Released	ENCODE4