ENCORE eCLIP:4082

Experiment Information (Status: Released)

	4082-control	4082
Exp_UID	4082	4082
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR729XJN	ENCSR383BCQ
ENCODE_alias	gene-yeo:4082-control	gene-yeo:4082
RBP	EIF4E	EIF4E
Cell_Line	HepG2	HepG2
Batch	batch16	batch16
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB864VOP	ENCAB864VOP
Antibody	MA1-089	MA1-089
Lot_num	TD257774	TD257774
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.008389	1.008389
rescue_GRCh38	1.432700	1.432700
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	575	576

Replicate Information


Rep_UID	4082_01	4082_02	4082_INPUT1	4082_INPUT2
Exp UID	4082	4082	4082	4082
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

	4082-control	4082
Self_consistency_hg38	1.008389	1.008389
rescue_GRCh38	1.432700	1.432700

Replicate QC


Rep_UID	4082_01	4082_02	4082_INPUT1	4082_INPUT2
eCT	7.60	7.60	1.60	1.50
Usable_reads	2561172	3006605	4124768	4184342
Entropy_hg38	0.531752	0.472848

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4082_01	4082_02	4082_INPUT1	4082_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	GAGATTCC	CGCTCATT	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4082_01	4082_02	4082_INPUT1	4082_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
4082_CLIP1_S10_L001_R1_001.fastq.gz	4082_01	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4082_CLIP2_S12_L001_R1_001.fastq.gz	4082_02	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4082_INPUT1_S9_L001_R1_001.fastq.gz	4082_INPUT1	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4082_INPUT2_S11_L001_R1_001.fastq.gz	4082_INPUT2	fastq	reads	single-ended	101	NovaSeq6000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4082_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4082_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4082_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4082_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4082_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4082_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4082_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4082_CLIP1_rep1.vs.4082_CLIP2_rep2.sorted.nh.bb	4082_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4082_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4082_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4082_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4082_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4082_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4082_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4082_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4082_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4082_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4082_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4082_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4082_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4082_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4082_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4082_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4082_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4082_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4082_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:4082-control	ENCSR729XJN	experiment	eCLIP	4082-EIF4E-HepG2-control	Released	ENCODE4
gene-yeo:4082	ENCSR383BCQ	experiment	eCLIP	4082-EIF4E-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4082_01	ENCLB789XRZ	library	eCLIP	4082_01	Released	ENCODE4
gene-yeo:L-HepG2_062716-4082_02	ENCLB628BOS	library	eCLIP	4082_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4082_INPUT1	ENCLB449SZP	library	eCLIP	4082_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_062716-4082_INPUT2	ENCLB065QIJ	library	eCLIP	4082_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4082_CLIP1_S10_L001_R1_001.fastq.gz	ENCFF964OHP	file_fastq	eCLIP	4082_01	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF011GOV	file_bam	eCLIP	4082_01	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF494OVU	file_bam	eCLIP	4082_01	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF482QGW	file_bw	eCLIP	4082_01	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF943ZTV	file_bw	eCLIP	4082_01	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF388WIV	file_quantifications	eCLIP	4082_01	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF976ZWK	file_bed	eCLIP	4082_01	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF933ALH	file_bb	eCLIP	4082_01	Released	ENCODE4
gene-yeo:4082_CLIP2_S12_L001_R1_001.fastq.gz	ENCFF635WKW	file_fastq	eCLIP	4082_02	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF484FDL	file_bam	eCLIP	4082_02	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF488YEQ	file_bam	eCLIP	4082_02	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF435AET	file_bw	eCLIP	4082_02	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF445OJN	file_bw	eCLIP	4082_02	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF630LFB	file_quantifications	eCLIP	4082_02	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF828FOF	file_bed	eCLIP	4082_02	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF229WGC	file_bb	eCLIP	4082_02	Released	ENCODE4
gene-yeo:4082_INPUT1_S9_L001_R1_001.fastq.gz	ENCFF141FQH	file_fastq	eCLIP	4082_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF865BII	file_bam	eCLIP	4082_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF050QVW	file_bam	eCLIP	4082_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF026SIW	file_bw	eCLIP	4082_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF556FGL	file_bw	eCLIP	4082_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF867MXI	file_quantifications	eCLIP	4082_INPUT1	Released	ENCODE4
gene-yeo:4082_INPUT2_S11_L001_R1_001.fastq.gz	ENCFF320KPP	file_fastq	eCLIP	4082_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF691YJI	file_bam	eCLIP	4082_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF640OAY	file_bam	eCLIP	4082_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF705VQP	file_bw	eCLIP	4082_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF852IXM	file_bw	eCLIP	4082_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4082_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF358DZI	file_quantifications	eCLIP	4082_INPUT2	Released	ENCODE4