ENCORE eCLIP:4084

Experiment Information (Status: Released)

	4084-control	4084
Exp_UID	4084	4084
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR363YLC	ENCSR585SMS
ENCODE_alias	gene-yeo:4084-control	gene-yeo:4084
RBP	NONO	NONO
Cell_Line	HepG2	HepG2
Batch	batch18	batch18
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB143JWA	ENCAB143JWA
Antibody	MA3-2024	MA3-2024
Lot_num	TA26182	TA26182
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.247322	1.247322
rescue_GRCh38	2.456653	2.456653
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	559	560

Replicate Information


Rep_UID	4084_01	4084_02	4084_INPUT1	4084_INPUT2
Exp UID	4084	4084	4084	4084
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

	4084-control	4084
Self_consistency_hg38	1.247322	1.247322
rescue_GRCh38	2.456653	2.456653

Replicate QC


Rep_UID	4084_01	4084_02	4084_INPUT1	4084_INPUT2
eCT	4.10	4.00	1.60	1.90
Usable_reads	14425182	7518489	4160444	4913102
Entropy_hg38	0.229157	0.201814

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4084_01	4084_02	4084_INPUT1	4084_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	TCCGGAGA	ATTACTCG	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4084_01	4084_02	4084_INPUT1	4084_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
4084_CLIP1_S52_L004_R1_001.fastq.gz	4084_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4084_CLIP2_S54_L004_R1_001.fastq.gz	4084_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4084_INPUT1_S51_L004_R1_001.fastq.gz	4084_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4084_INPUT2_S53_L004_R1_001.fastq.gz	4084_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4084_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4084_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4084_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4084_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4084_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4084_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4084_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4084_CLIP1_rep1.vs.4084_CLIP2_rep2.sorted.nh.bb	4084_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4084_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4084_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4084_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4084_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4084_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4084_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4084_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4084_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4084_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4084_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4084_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4084_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4084_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4084_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4084_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4084_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4084_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4084_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:4084-control	ENCSR363YLC	experiment	eCLIP	4084-NONO-HepG2-control	Released	ENCODE4
gene-yeo:4084	ENCSR585SMS	experiment	eCLIP	4084-NONO-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4084_01	ENCLB545VDF	library	eCLIP	4084_01	Released	ENCODE4
gene-yeo:L-HepG2_062716-4084_02	ENCLB686LUJ	library	eCLIP	4084_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4084_INPUT1	ENCLB700JKM	library	eCLIP	4084_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_062716-4084_INPUT2	ENCLB672ZKA	library	eCLIP	4084_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4084_CLIP1_S52_L004_R1_001.fastq.gz	ENCFF249GCT	file_fastq	eCLIP	4084_01	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF772WBN	file_bam	eCLIP	4084_01	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF381HOL	file_bam	eCLIP	4084_01	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF799IRF	file_bw	eCLIP	4084_01	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF304HKN	file_bw	eCLIP	4084_01	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF004TSI	file_quantifications	eCLIP	4084_01	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF311KOX	file_bed	eCLIP	4084_01	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF500ZZC	file_bb	eCLIP	4084_01	Released	ENCODE4
gene-yeo:4084_CLIP2_S54_L004_R1_001.fastq.gz	ENCFF711MRT	file_fastq	eCLIP	4084_02	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF357ULL	file_bam	eCLIP	4084_02	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF797FLR	file_bam	eCLIP	4084_02	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF756TZI	file_bw	eCLIP	4084_02	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF181HVR	file_bw	eCLIP	4084_02	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF794QZT	file_quantifications	eCLIP	4084_02	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF133VWV	file_bed	eCLIP	4084_02	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF127YBR	file_bb	eCLIP	4084_02	Released	ENCODE4
gene-yeo:4084_INPUT1_S51_L004_R1_001.fastq.gz	ENCFF401RCG	file_fastq	eCLIP	4084_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF139VQG	file_bam	eCLIP	4084_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF033EEP	file_bam	eCLIP	4084_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF732HBF	file_bw	eCLIP	4084_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF011RWA	file_bw	eCLIP	4084_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF576OWR	file_quantifications	eCLIP	4084_INPUT1	Released	ENCODE4
gene-yeo:4084_INPUT2_S53_L004_R1_001.fastq.gz	ENCFF791JNX	file_fastq	eCLIP	4084_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF383GYN	file_bam	eCLIP	4084_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF345GRN	file_bam	eCLIP	4084_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF373HUY	file_bw	eCLIP	4084_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF269RHL	file_bw	eCLIP	4084_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch18.4084_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF868RLR	file_quantifications	eCLIP	4084_INPUT2	Released	ENCODE4