ENCORE eCLIP:4044

Experiment Information (Status: Released)

	4044-control	4044
Exp_UID	4044	4044
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR327BBW	ENCSR090LNQ
ENCODE_alias	gene-yeo:4044-control	gene-yeo:4044
RBP	ELAVL1	ELAVL1
Cell_Line	K562	K562
Batch	batch11a	batch11a
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB443AAH	ENCAB443AAH
Antibody	MA1-167	MA1-167
Lot_num	SD251451	SD251451
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.646078	1.646078
rescue_GRCh38	2.543148	2.543148
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	597	598

Replicate Information


Rep_UID	4044_01	4044_02	4044_INPUT1	4044_INPUT2
Exp UID	4044	4044	4044	4044
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

	4044-control	4044
Self_consistency_hg38	1.646078	1.646078
rescue_GRCh38	2.543148	2.543148

Replicate QC


Rep_UID	4044_01	4044_02	4044_INPUT1	4044_INPUT2
eCT	9.00	9.10	5.70	5.80
Usable_reads	15310724	10828714	3251271	3554172
Entropy_hg38	0.527471	0.964452

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4044_01	4044_02	4044_INPUT1	4044_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	GGCTCTGA	GGCTCTGA	CCTATCCT	CCTATCCT
i7_barcode	ATTACTCG	TCCGGAGA	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4044_01	4044_02	4044_INPUT1	4044_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
4044_CLIP1_S18_L002_R1_001.fastq.gz	4044_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4044_CLIP2_S20_L002_R1_001.fastq.gz	4044_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4044_INPUT1_S17_L002_R1_001.fastq.gz	4044_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4044_INPUT2_S19_L002_R1_001.fastq.gz	4044_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4044_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4044_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4044_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4044_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4044_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4044_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4044_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4044_CLIP1_rep1.vs.4044_CLIP2_rep2.sorted.nh.bb	4044_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4044_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4044_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4044_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4044_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4044_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4044_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4044_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4044_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4044_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4044_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4044_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4044_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4044_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4044_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4044_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4044_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4044_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4044_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:4044-control	ENCSR327BBW	experiment	eCLIP	4044-ELAVL1-K562-control	Released	ENCODE4
gene-yeo:4044	ENCSR090LNQ	experiment	eCLIP	4044-ELAVL1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_111915-4044_01	ENCLB739TEB	library	eCLIP	4044_01	Released	ENCODE4
gene-yeo:L-K562_072016-4044_02	ENCLB327WKM	library	eCLIP	4044_02	Released	ENCODE4
gene-yeo:L-K562_111915-4044_INPUT1	ENCLB655LUQ	library	eCLIP	4044_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4044_INPUT2	ENCLB159WWB	library	eCLIP	4044_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4044_CLIP1_S18_L002_R1_001.fastq.gz	ENCFF786UGT	file_fastq	eCLIP	4044_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF022MBI	file_bam	eCLIP	4044_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF085ZSE	file_bam	eCLIP	4044_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF631NUT	file_bw	eCLIP	4044_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF642YDN	file_bw	eCLIP	4044_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF948STA	file_quantifications	eCLIP	4044_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF742QQK	file_bed	eCLIP	4044_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF389DKM	file_bb	eCLIP	4044_01	Released	ENCODE4
gene-yeo:4044_CLIP2_S20_L002_R1_001.fastq.gz	ENCFF452ZWM	file_fastq	eCLIP	4044_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF150XON	file_bam	eCLIP	4044_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF245TBA	file_bam	eCLIP	4044_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF985QYQ	file_bw	eCLIP	4044_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF667MNK	file_bw	eCLIP	4044_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF540EUV	file_quantifications	eCLIP	4044_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF856NLY	file_bed	eCLIP	4044_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF797ZAP	file_bb	eCLIP	4044_02	Released	ENCODE4
gene-yeo:4044_INPUT1_S17_L002_R1_001.fastq.gz	ENCFF752UQK	file_fastq	eCLIP	4044_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF393UIG	file_bam	eCLIP	4044_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF162XUI	file_bam	eCLIP	4044_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF125VFV	file_bw	eCLIP	4044_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF058BIF	file_bw	eCLIP	4044_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF014AQG	file_quantifications	eCLIP	4044_INPUT1	Released	ENCODE4
gene-yeo:4044_INPUT2_S19_L002_R1_001.fastq.gz	ENCFF336EAH	file_fastq	eCLIP	4044_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF816NOS	file_bam	eCLIP	4044_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF604KNU	file_bam	eCLIP	4044_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF264AUP	file_bw	eCLIP	4044_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF227BLI	file_bw	eCLIP	4044_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4044_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF932HCK	file_quantifications	eCLIP	4044_INPUT2	Released	ENCODE4