ENCORE eCLIP:4114

Experiment Information (Status: Released)

	4114-control	4114
Exp_UID	4114	4114
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR304BTG	ENCSR348MQL
ENCODE_alias	gene-yeo:4114-control	gene-yeo:4114
RBP	PRPF39	PRPF39
Cell_Line	HepG2	HepG2
Batch	batch17	batch17
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB901VHL	ENCAB901VHL
Antibody	PA5-21627	PA5-21627
Lot_num	UC2743613B	UC2743613B
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.362206	1.362206
rescue_GRCh38	1.446279	1.446279
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	567	568

Replicate Information


Rep_UID	4114_01	4114_02	4114_INPUT1	4114_INPUT2
Exp UID	4114	4114	4114	4114
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

	4114-control	4114
Self_consistency_hg38	1.362206	1.362206
rescue_GRCh38	1.446279	1.446279

Replicate QC


Rep_UID	4114_01	4114_02	4114_INPUT1	4114_INPUT2
eCT	10.10	10.90	4.10	4.60
Usable_reads	5234734	6664420	5776384	5938631
Entropy_hg38	0.871849	1.231898

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4114_01	4114_02	4114_INPUT1	4114_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	TAATCTTA	AGGCGAAG	AGGCGAAG	TAATCTTA
i7_barcode	TCCGGAGA	TCCGGAGA	ATTACTCG	ATTACTCG

Sequencing Information


Rep_UID	4114_01	4114_02	4114_INPUT1	4114_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
4114_CLIP1_S39_L002_R1_001.fastq.gz	4114_01	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4114_CLIP2_S41_L002_R1_001.fastq.gz	4114_02	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4114_INPUT1_S38_L002_R1_001.fastq.gz	4114_INPUT1	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4114_INPUT2_S40_L002_R1_001.fastq.gz	4114_INPUT2	fastq	reads	single-ended	101	NovaSeq6000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4114_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4114_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4114_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4114_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4114_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4114_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4114_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4114_CLIP1_rep1.vs.4114_CLIP2_rep2.sorted.nh.bb	4114_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4114_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4114_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4114_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4114_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4114_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4114_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4114_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4114_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4114_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4114_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4114_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4114_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4114_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4114_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4114_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4114_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4114_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4114_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:4114-control	ENCSR304BTG	experiment	eCLIP	4114-PRPF39-HepG2-control	Released	ENCODE4
gene-yeo:4114	ENCSR348MQL	experiment	eCLIP	4114-PRPF39-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4114_01	ENCLB613OYM	library	eCLIP	4114_01	Released	ENCODE4
gene-yeo:L-HepG2_062716-4114_02	ENCLB793BSU	library	eCLIP	4114_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4114_INPUT1	ENCLB064DDP	library	eCLIP	4114_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_062716-4114_INPUT2	ENCLB346VOL	library	eCLIP	4114_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4114_CLIP1_S39_L002_R1_001.fastq.gz	ENCFF865FYT	file_fastq	eCLIP	4114_01	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF085NPT	file_bam	eCLIP	4114_01	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF805HBA	file_bam	eCLIP	4114_01	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF486MDG	file_bw	eCLIP	4114_01	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF433RVB	file_bw	eCLIP	4114_01	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF510GLT	file_quantifications	eCLIP	4114_01	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF286BHF	file_bed	eCLIP	4114_01	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF467YHM	file_bb	eCLIP	4114_01	Released	ENCODE4
gene-yeo:4114_CLIP2_S41_L002_R1_001.fastq.gz	ENCFF764BHJ	file_fastq	eCLIP	4114_02	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF042RCD	file_bam	eCLIP	4114_02	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF499DGT	file_bam	eCLIP	4114_02	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF951TSV	file_bw	eCLIP	4114_02	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF653VQZ	file_bw	eCLIP	4114_02	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF755DNE	file_quantifications	eCLIP	4114_02	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF872HRS	file_bed	eCLIP	4114_02	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF230YAQ	file_bb	eCLIP	4114_02	Released	ENCODE4
gene-yeo:4114_INPUT1_S38_L002_R1_001.fastq.gz	ENCFF768WIP	file_fastq	eCLIP	4114_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF359EQI	file_bam	eCLIP	4114_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF938IXN	file_bam	eCLIP	4114_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF417UXA	file_bw	eCLIP	4114_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF221KTQ	file_bw	eCLIP	4114_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF912IOB	file_quantifications	eCLIP	4114_INPUT1	Released	ENCODE4
gene-yeo:4114_INPUT2_S40_L002_R1_001.fastq.gz	ENCFF329DRU	file_fastq	eCLIP	4114_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF609RIV	file_bam	eCLIP	4114_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF095UGR	file_bam	eCLIP	4114_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF428XQW	file_bw	eCLIP	4114_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF838XCZ	file_bw	eCLIP	4114_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4114_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF351ISX	file_quantifications	eCLIP	4114_INPUT2	Released	ENCODE4