ENCORE eCLIP:4146

Experiment Information (Status: Released)

	4146-control	4146
Exp_UID	4146	4146
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR558OKC	ENCSR332LFL
ENCODE_alias	gene-yeo:4146-control	gene-yeo:4146
RBP	DEK	DEK
Cell_Line	HepG2	HepG2
Batch	batch22	batch22
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB872AQT	ENCAB872AQT
Antibody	720215	720215
Lot_num	SD249202	SD249202
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.299043	1.299043
rescue_GRCh38	1.265152	1.265152
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	525	526

Replicate Information


Rep_UID	4146_01	4146_02	4146_INPUT1	4146_INPUT2
Exp UID	4146	4146	4146	4146
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	HepG2_080316	HepG2_080719	HepG2_080316	HepG2_080719
Biosample_ENCODE_Accession	ENCBS133LVQ	ENCBS732SCL	ENCBS133LVQ	ENCBS732SCL
Biosample_ENCODE_Alias	gene-yeo:HepG2_080316	gene-yeo:HepG2_080719	gene-yeo:HepG2_080316	gene-yeo:HepG2_080719
Cell_Line	HepG2	HepG2	HepG2	HepG2
Culture_Start_Date	2016-08-03	2019-08-07	2016-08-03	2019-08-07
Culture_End_Date	2016-08-29	2019-09-07	2016-08-29	2019-09-07
Passage	3	5	3	5

QC Stats

Experiment QC

	4146-control	4146
Self_consistency_hg38	1.299043	1.299043
rescue_GRCh38	1.265152	1.265152

Replicate QC


Rep_UID	4146_01	4146_02	4146_INPUT1	4146_INPUT2
eCT	15.40	15.10	3.90	4.80
Usable_reads	742312	1285334	6525506	5314604
Entropy_hg38	8.292211	6.796755

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4146_01	4146_02	4146_INPUT1	4146_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	GGCTCTGA	TATAGCCT	CCTATCCT
i7_barcode	ATTACTCG	ATTACTCG	ATTACTCG	ATTACTCG

Sequencing Information


Rep_UID	4146_01	4146_02	4146_INPUT1	4146_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
4146_CLIP1_S125_L008_R1_001.fastq.gz	4146_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4146_CLIP2_S127_L008_R1_001.fastq.gz	4146_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4146_IN1_S124_L008_R1_001.fastq.gz	4146_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4146_IN2_S126_L008_R1_001.fastq.gz	4146_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4146_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4146_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4146_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4146_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4146_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4146_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4146_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4146_CLIP1_rep1.vs.4146_CLIP2_rep2.sorted.nh.bb	4146_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4146_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4146_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4146_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4146_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4146_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4146_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4146_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4146_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4146_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4146_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4146_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4146_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4146_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4146_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4146_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4146_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4146_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4146_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:4146-control	ENCSR558OKC	experiment	eCLIP	4146-DEK-HepG2-control	Released	ENCODE4
gene-yeo:4146	ENCSR332LFL	experiment	eCLIP	4146-DEK-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4146_01	ENCLB980LXN	library	eCLIP	4146_01	Released	ENCODE4
gene-yeo:L-HepG2_080719-4146_02	ENCLB637TZS	library	eCLIP	4146_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4146_INPUT1	ENCLB267WRP	library	eCLIP	4146_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_080719-4146_INPUT2	ENCLB922NVI	library	eCLIP	4146_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4146_CLIP1_S125_L008_R1_001.fastq.gz	ENCFF653TSZ	file_fastq	eCLIP	4146_01	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF813JVY	file_bam	eCLIP	4146_01	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF749EYB	file_bam	eCLIP	4146_01	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF612COA	file_bw	eCLIP	4146_01	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF555MTQ	file_bw	eCLIP	4146_01	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF215NNZ	file_quantifications	eCLIP	4146_01	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF144OTO	file_bed	eCLIP	4146_01	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF911LSG	file_bb	eCLIP	4146_01	Released	ENCODE4
gene-yeo:4146_CLIP2_S127_L008_R1_001.fastq.gz	ENCFF994ULB	file_fastq	eCLIP	4146_02	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF661AIR	file_bam	eCLIP	4146_02	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF863DGL	file_bam	eCLIP	4146_02	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF542CVD	file_bw	eCLIP	4146_02	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF971YXU	file_bw	eCLIP	4146_02	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF756YUJ	file_quantifications	eCLIP	4146_02	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF970IXL	file_bed	eCLIP	4146_02	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF363RWL	file_bb	eCLIP	4146_02	Released	ENCODE4
gene-yeo:4146_IN1_S124_L008_R1_001.fastq.gz	ENCFF832KBC	file_fastq	eCLIP	4146_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF517OJL	file_bam	eCLIP	4146_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF180RZC	file_bam	eCLIP	4146_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF659KUS	file_bw	eCLIP	4146_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF683PYI	file_bw	eCLIP	4146_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF637MNH	file_quantifications	eCLIP	4146_INPUT1	Released	ENCODE4
gene-yeo:4146_IN2_S126_L008_R1_001.fastq.gz	ENCFF092POP	file_fastq	eCLIP	4146_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF020QNY	file_bam	eCLIP	4146_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF861TVN	file_bam	eCLIP	4146_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF544QBQ	file_bw	eCLIP	4146_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF627TPQ	file_bw	eCLIP	4146_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4146_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF211YIM	file_quantifications	eCLIP	4146_INPUT2	Released	ENCODE4