ENCORE eCLIP:4223

Experiment Information (Status: Released)

	4223-control	4223
Exp_UID	4223	4223
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR818IOS	ENCSR171XCR
ENCODE_alias	gene-yeo:4223-control	gene-yeo:4223
RBP	EED	EED
Cell_Line	K562	K562
Batch	batch25	batch25
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB164MTM	ENCAB164MTM
Antibody	PA5-34430	PA5-34430
Lot_num	UK2881462A	UK2881462A
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.850875	1.850875
rescue_GRCh38	1.666149	1.666149
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	503	504

Replicate Information


Rep_UID	4223_01	4223_02	4223_INPUT1	4223_INPUT2
Exp UID	4223	4223	4223	4223
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

	4223-control	4223
Self_consistency_hg38	1.850875	1.850875
rescue_GRCh38	1.666149	1.666149

Replicate QC


Rep_UID	4223_01	4223_02	4223_INPUT1	4223_INPUT2
eCT	15.60	15.30	6.10	7.90
Usable_reads	5810369	5394687	5848229	6116082
Entropy_hg38	3.112752	1.432126

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4223_01	4223_02	4223_INPUT1	4223_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	ATTACTCG	TCCGGAGA	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4223_01	4223_02	4223_INPUT1	4223_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
4223_CLIP1_S115_L008_R1_001.fastq.gz	4223_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4223_CLIP2_S117_L008_R1_001.fastq.gz	4223_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4223_INPUT1_S114_L008_R1_001.fastq.gz	4223_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4223_INPUT2_S116_L008_R1_001.fastq.gz	4223_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4223_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4223_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4223_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4223_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4223_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4223_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4223_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4223_CLIP1_rep1.vs.4223_CLIP2_rep2.sorted.nh.bb	4223_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4223_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4223_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4223_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4223_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4223_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4223_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4223_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4223_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4223_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4223_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4223_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4223_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4223_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4223_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4223_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4223_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4223_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4223_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:4223-control	ENCSR818IOS	experiment	eCLIP	4223-EED-K562-control	Released	ENCODE4
gene-yeo:4223	ENCSR171XCR	experiment	eCLIP	4223-EED-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4223_01	ENCLB932KTB	library	eCLIP	4223_01	Released	ENCODE4
gene-yeo:L-K562_102015-4223_02	ENCLB771VWY	library	eCLIP	4223_02	Released	ENCODE4
gene-yeo:L-K562_081815-4223_INPUT1	ENCLB460MNA	library	eCLIP	4223_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4223_INPUT2	ENCLB393ORW	library	eCLIP	4223_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4223_CLIP1_S115_L008_R1_001.fastq.gz	ENCFF711WKM	file_fastq	eCLIP	4223_01	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF038HGR	file_bam	eCLIP	4223_01	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF369DFE	file_bam	eCLIP	4223_01	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF523VSN	file_bw	eCLIP	4223_01	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF950ECS	file_bw	eCLIP	4223_01	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF762FXM	file_quantifications	eCLIP	4223_01	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF561ZDH	file_bed	eCLIP	4223_01	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF407TYS	file_bb	eCLIP	4223_01	Released	ENCODE4
gene-yeo:4223_CLIP2_S117_L008_R1_001.fastq.gz	ENCFF288VIR	file_fastq	eCLIP	4223_02	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF067FDO	file_bam	eCLIP	4223_02	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF201GCL	file_bam	eCLIP	4223_02	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF130SHU	file_bw	eCLIP	4223_02	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF488LBE	file_bw	eCLIP	4223_02	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF719TFU	file_quantifications	eCLIP	4223_02	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF005INK	file_bed	eCLIP	4223_02	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF984GXB	file_bb	eCLIP	4223_02	Released	ENCODE4
gene-yeo:4223_INPUT1_S114_L008_R1_001.fastq.gz	ENCFF949FIS	file_fastq	eCLIP	4223_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF548SAV	file_bam	eCLIP	4223_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF199DUX	file_bam	eCLIP	4223_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF732OGF	file_bw	eCLIP	4223_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF944MXJ	file_bw	eCLIP	4223_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF310ZSK	file_quantifications	eCLIP	4223_INPUT1	Released	ENCODE4
gene-yeo:4223_INPUT2_S116_L008_R1_001.fastq.gz	ENCFF694AJG	file_fastq	eCLIP	4223_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF828IYO	file_bam	eCLIP	4223_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF599PJB	file_bam	eCLIP	4223_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF715CVV	file_bw	eCLIP	4223_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF458PTW	file_bw	eCLIP	4223_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4223_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF649CQN	file_quantifications	eCLIP	4223_INPUT2	Released	ENCODE4