ENCORE eCLIP:4083

Experiment Information (Status: Released)

	4083-control	4083
Exp_UID	4083	4083
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR467CNV	ENCSR296TSJ
ENCODE_alias	gene-yeo:4083-control	gene-yeo:4083
RBP	ELAVL1	ELAVL1
Cell_Line	HepG2	HepG2
Batch	batch16	batch16
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB443AAH	ENCAB443AAH
Antibody	MA1-167	MA1-167
Lot_num	SJ260797	SJ260797
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.628823	1.628823
rescue_GRCh38	2.784968	2.784968
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	577	578

Replicate Information


Rep_UID	4083_01	4083_02	4083_INPUT1	4083_INPUT2
Exp UID	4083	4083	4083	4083
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	HepG2_080316	HepG2_062716	HepG2_080316	HepG2_062716
Biosample_ENCODE_Accession	ENCBS133LVQ	ENCBS768GCL	ENCBS133LVQ	ENCBS768GCL
Biosample_ENCODE_Alias	gene-yeo:HepG2_080316	gene-yeo:HepG2_062716	gene-yeo:HepG2_080316	gene-yeo:HepG2_062716
Cell_Line	HepG2	HepG2	HepG2	HepG2
Culture_Start_Date	2016-08-03	2016-06-27	2016-08-03	2016-06-27
Culture_End_Date	2016-08-29	2016-07-25	2016-08-29	2016-07-25
Passage	3	3	3	3

QC Stats

Experiment QC

	4083-control	4083
Self_consistency_hg38	1.628823	1.628823
rescue_GRCh38	2.784968	2.784968

Replicate QC


Rep_UID	4083_01	4083_02	4083_INPUT1	4083_INPUT2
eCT	2.70	2.70	1.00	1.70
Usable_reads	13354846	8438368	4189952	4645650
Entropy_hg38	0.280701	0.351391

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4083_01	4083_02	4083_INPUT1	4083_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	GAATTCGT	ATTCAGAA	ATTCAGAA	GAATTCGT

Sequencing Information


Rep_UID	4083_01	4083_02	4083_INPUT1	4083_INPUT2
seq_read_type	single-ended	single-ended	single-ended	single-ended
read_length	75	75	75	75
machine	NovaSeq6000	NovaSeq6000	NovaSeq6000	NovaSeq6000
flowcell	flowcell	flowcell	flowcell	flowcell
lane	-	-	-	-

File Information

FASTQ

file_name	Sample ID	file_format	output_type	run_type	read_length	platform	assay_type
4083_CLIP1_S44_L002_R1_001.fastq.gz	4083_01	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4083_CLIP2_S46_L002_R1_001.fastq.gz	4083_02	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4083_INPUT1_S43_L002_R1_001.fastq.gz	4083_INPUT1	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4083_INPUT2_S45_L002_R1_001.fastq.gz	4083_INPUT2	fastq	reads	single-ended	101	NovaSeq6000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4083_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4083_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4083_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4083_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4083_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4083_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4083_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4083_CLIP1_rep1.vs.4083_CLIP2_rep2.sorted.nh.bb	4083_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4083_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4083_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4083_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4083_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4083_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4083_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4083_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4083_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4083_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4083_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4083_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4083_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4083_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4083_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4083_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4083_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4083_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4083_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:4083-control	ENCSR467CNV	experiment	eCLIP	4083-ELAVL1-HepG2-control	Released	ENCODE4
gene-yeo:4083	ENCSR296TSJ	experiment	eCLIP	4083-ELAVL1-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4083_01	ENCLB625QZP	library	eCLIP	4083_01	Released	ENCODE4
gene-yeo:L-HepG2_062716-4083_02	ENCLB221VBG	library	eCLIP	4083_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4083_INPUT1	ENCLB167ZBG	library	eCLIP	4083_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_062716-4083_INPUT2	ENCLB688BDV	library	eCLIP	4083_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4083_CLIP1_S44_L002_R1_001.fastq.gz	ENCFF555QVU	file_fastq	eCLIP	4083_01	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF680DLI	file_bam	eCLIP	4083_01	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF299GKP	file_bam	eCLIP	4083_01	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF454LBF	file_bw	eCLIP	4083_01	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF497CRW	file_bw	eCLIP	4083_01	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF617IUR	file_quantifications	eCLIP	4083_01	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF278GLJ	file_bed	eCLIP	4083_01	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF216ZVD	file_bb	eCLIP	4083_01	Released	ENCODE4
gene-yeo:4083_CLIP2_S46_L002_R1_001.fastq.gz	ENCFF144YIL	file_fastq	eCLIP	4083_02	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF250JRA	file_bam	eCLIP	4083_02	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF777LGD	file_bam	eCLIP	4083_02	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF214RKG	file_bw	eCLIP	4083_02	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF247ABJ	file_bw	eCLIP	4083_02	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF404EKR	file_quantifications	eCLIP	4083_02	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF648KMJ	file_bed	eCLIP	4083_02	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF717SVC	file_bb	eCLIP	4083_02	Released	ENCODE4
gene-yeo:4083_INPUT1_S43_L002_R1_001.fastq.gz	ENCFF756IZM	file_fastq	eCLIP	4083_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF566APE	file_bam	eCLIP	4083_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF300IUA	file_bam	eCLIP	4083_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF594COU	file_bw	eCLIP	4083_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF002OFI	file_bw	eCLIP	4083_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF487UVM	file_quantifications	eCLIP	4083_INPUT1	Released	ENCODE4
gene-yeo:4083_INPUT2_S45_L002_R1_001.fastq.gz	ENCFF650SFM	file_fastq	eCLIP	4083_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF835AOE	file_bam	eCLIP	4083_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF762LVB	file_bam	eCLIP	4083_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF743UMT	file_bw	eCLIP	4083_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF891JTX	file_bw	eCLIP	4083_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4083_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF216IAY	file_quantifications	eCLIP	4083_INPUT2	Released	ENCODE4