ENCORE eCLIP:4149

Experiment Information (Status: Released)

	4149-control	4149
Exp_UID	4149	4149
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR638LZI	ENCSR884RBW
ENCODE_alias	gene-yeo:4149-control	gene-yeo:4149
RBP	PRPF39	PRPF39
Cell_Line	HepG2	HepG2
Batch	batch22	batch22
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	1.217727	1.217727
rescue_GRCh38	1.626758	1.626758
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	529	530

Replicate Information


Rep_UID	4149_01	4149_02	4149_INPUT1	4149_INPUT2
Exp UID	4149	4149	4149	4149
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

	4149-control	4149
Self_consistency_hg38	1.217727	1.217727
rescue_GRCh38	1.626758	1.626758

Replicate QC


Rep_UID	4149_01	4149_02	4149_INPUT1	4149_INPUT2
eCT	12.30	12.90	5.40	4.70
Usable_reads	5038233	6327174	7703281	6153865
Entropy_hg38	0.909924	0.429766

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4149_01	4149_02	4149_INPUT1	4149_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	GAGATTCC	GAGATTCC	GAGATTCC	GAGATTCC

Sequencing Information


Rep_UID	4149_01	4149_02	4149_INPUT1	4149_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
4149_CLIP1_S137_L008_R1_001.fastq.gz	4149_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4149_CLIP2_S139_L008_R1_001.fastq.gz	4149_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4149_IN1_S136_L008_R1_001.fastq.gz	4149_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4149_IN2_S138_L008_R1_001.fastq.gz	4149_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4149_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4149_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4149_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4149_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4149_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4149_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4149_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4149_CLIP1_rep1.vs.4149_CLIP2_rep2.sorted.nh.bb	4149_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4149_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4149_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4149_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4149_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4149_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4149_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4149_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4149_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4149_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4149_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4149_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4149_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4149_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4149_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4149_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4149_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4149_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4149_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:4149-control	ENCSR638LZI	experiment	eCLIP	4149-PRPF39-HepG2-control	Released	ENCODE4
gene-yeo:4149	ENCSR884RBW	experiment	eCLIP	4149-PRPF39-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4149_01	ENCLB299QSL	library	eCLIP	4149_01	Released	ENCODE4
gene-yeo:L-HepG2_080719-4149_02	ENCLB875FZE	library	eCLIP	4149_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4149_INPUT1	ENCLB174VUT	library	eCLIP	4149_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_080719-4149_INPUT2	ENCLB955XDD	library	eCLIP	4149_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4149_CLIP1_S137_L008_R1_001.fastq.gz	ENCFF487RVK	file_fastq	eCLIP	4149_01	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF146JLY	file_bam	eCLIP	4149_01	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF408GLB	file_bam	eCLIP	4149_01	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF830UUP	file_bw	eCLIP	4149_01	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF691RYZ	file_bw	eCLIP	4149_01	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF498ZIT	file_quantifications	eCLIP	4149_01	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF296GSZ	file_bed	eCLIP	4149_01	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF350XQM	file_bb	eCLIP	4149_01	Released	ENCODE4
gene-yeo:4149_CLIP2_S139_L008_R1_001.fastq.gz	ENCFF349OCZ	file_fastq	eCLIP	4149_02	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF654VBH	file_bam	eCLIP	4149_02	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF479PLV	file_bam	eCLIP	4149_02	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF306HFC	file_bw	eCLIP	4149_02	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF016JKR	file_bw	eCLIP	4149_02	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF889UXK	file_quantifications	eCLIP	4149_02	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF569LDW	file_bed	eCLIP	4149_02	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF072WQF	file_bb	eCLIP	4149_02	Released	ENCODE4
gene-yeo:4149_IN1_S136_L008_R1_001.fastq.gz	ENCFF494ESS	file_fastq	eCLIP	4149_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF516VLI	file_bam	eCLIP	4149_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF805GWD	file_bam	eCLIP	4149_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF233LEO	file_bw	eCLIP	4149_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF739SDK	file_bw	eCLIP	4149_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF179JJR	file_quantifications	eCLIP	4149_INPUT1	Released	ENCODE4
gene-yeo:4149_IN2_S138_L008_R1_001.fastq.gz	ENCFF566EEE	file_fastq	eCLIP	4149_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF097GDS	file_bam	eCLIP	4149_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF833BMR	file_bam	eCLIP	4149_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF673ZXU	file_bw	eCLIP	4149_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF118YXJ	file_bw	eCLIP	4149_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4149_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF387SYK	file_quantifications	eCLIP	4149_INPUT2	Released	ENCODE4