ENCORE eCLIP:4081

Experiment Information (Status: Released)

	4081-control	4081
Exp_UID	4081	4081
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR066WPD	ENCSR554GSW
ENCODE_alias	gene-yeo:4081-control	gene-yeo:4081
RBP	APEX1	APEX1
Cell_Line	HepG2	HepG2
Batch	batch16	batch16
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB328DHC	ENCAB328DHC
Antibody	MA1-440	MA1-440
Lot_num	TB260470	TB260470
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.430723	1.430723
rescue_GRCh38	1.639604	1.639604
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	573	574

Replicate Information


Rep_UID	4081_01	4081_02	4081_INPUT1	4081_INPUT2
Exp UID	4081	4081	4081	4081
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

	4081-control	4081
Self_consistency_hg38	1.430723	1.430723
rescue_GRCh38	1.639604	1.639604

Replicate QC


Rep_UID	4081_01	4081_02	4081_INPUT1	4081_INPUT2
eCT	8.00	6.70	2.50	2.00
Usable_reads	2112669	2616424	4327645	5693264
Entropy_hg38	0.921343	0.430373

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4081_01	4081_02	4081_INPUT1	4081_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	TCCGGAGA	ATTACTCG	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4081_01	4081_02	4081_INPUT1	4081_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
4081_CLIP1_S36_L002_R1_001.fastq.gz	4081_01	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4081_CLIP2_S38_L002_R1_001.fastq.gz	4081_02	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4081_INPUT1_S35_L002_R1_001.fastq.gz	4081_INPUT1	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4081_INPUT2_S37_L002_R1_001.fastq.gz	4081_INPUT2	fastq	reads	single-ended	101	NovaSeq6000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4081_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4081_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4081_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4081_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4081_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4081_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4081_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4081_CLIP1_rep1.vs.4081_CLIP2_rep2.sorted.nh.bb	4081_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4081_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4081_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4081_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4081_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4081_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4081_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4081_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4081_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4081_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4081_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4081_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4081_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4081_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4081_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4081_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4081_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4081_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4081_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:4081-control	ENCSR066WPD	experiment	eCLIP	4081-APEX1-HepG2-control	Released	ENCODE4
gene-yeo:4081	ENCSR554GSW	experiment	eCLIP	4081-APEX1-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4081_01	ENCLB632NAX	library	eCLIP	4081_01	Released	ENCODE4
gene-yeo:L-HepG2_062716-4081_02	ENCLB091EEZ	library	eCLIP	4081_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4081_INPUT1	ENCLB932CVY	library	eCLIP	4081_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_062716-4081_INPUT2	ENCLB667WCK	library	eCLIP	4081_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4081_CLIP1_S36_L002_R1_001.fastq.gz	ENCFF746UYA	file_fastq	eCLIP	4081_01	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF943BHJ	file_bam	eCLIP	4081_01	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF733AZU	file_bam	eCLIP	4081_01	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF211DPF	file_bw	eCLIP	4081_01	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF199ECS	file_bw	eCLIP	4081_01	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF098WWL	file_quantifications	eCLIP	4081_01	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF463ZFZ	file_bed	eCLIP	4081_01	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF349IPQ	file_bb	eCLIP	4081_01	Released	ENCODE4
gene-yeo:4081_CLIP2_S38_L002_R1_001.fastq.gz	ENCFF975RYQ	file_fastq	eCLIP	4081_02	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF661YAR	file_bam	eCLIP	4081_02	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF380JRS	file_bam	eCLIP	4081_02	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF403BJQ	file_bw	eCLIP	4081_02	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF900BQT	file_bw	eCLIP	4081_02	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF406OYY	file_quantifications	eCLIP	4081_02	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF365BPP	file_bed	eCLIP	4081_02	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF610FCL	file_bb	eCLIP	4081_02	Released	ENCODE4
gene-yeo:4081_INPUT1_S35_L002_R1_001.fastq.gz	ENCFF403NBB	file_fastq	eCLIP	4081_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF250JDF	file_bam	eCLIP	4081_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF346ZRP	file_bam	eCLIP	4081_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF902KWS	file_bw	eCLIP	4081_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF759ARI	file_bw	eCLIP	4081_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF604ZMY	file_quantifications	eCLIP	4081_INPUT1	Released	ENCODE4
gene-yeo:4081_INPUT2_S37_L002_R1_001.fastq.gz	ENCFF610QPZ	file_fastq	eCLIP	4081_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF360OHJ	file_bam	eCLIP	4081_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF267KFP	file_bam	eCLIP	4081_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF241GNJ	file_bw	eCLIP	4081_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF232CLE	file_bw	eCLIP	4081_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4081_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF209EMH	file_quantifications	eCLIP	4081_INPUT2	Released	ENCODE4