ENCORE eCLIP:4190

Experiment Information (Status: Released)

	4190-control	4190
Exp_UID	4190	4190
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR858DLD	ENCSR150QBS
ENCODE_alias	gene-yeo:4190-control	gene-yeo:4190
RBP	CACTIN	CACTIN
Cell_Line	HepG2	HepG2
Batch	batch23	batch23
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB389VTI	ENCAB389VTI
Antibody	A303-349A	A303-349A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.307927	1.307927
rescue_GRCh38	1.759036	1.759036
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	517	518

Replicate Information


Rep_UID	4190_01	4190_02	4190_INPUT1	4190_INPUT2
Exp UID	4190	4190	4190	4190
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	HepG2_080316	HepG2_111019	HepG2_080316	HepG2_111019
Biosample_ENCODE_Accession	ENCBS133LVQ	ENCBS766GPS	ENCBS133LVQ	ENCBS766GPS
Biosample_ENCODE_Alias	gene-yeo:HepG2_080316	gene-yeo:HepG2_111019	gene-yeo:HepG2_080316	gene-yeo:HepG2_111019
Cell_Line	HepG2	HepG2	HepG2	HepG2
Culture_Start_Date	2016-08-03	2019-10-23	2016-08-03	2019-10-23
Culture_End_Date	2016-08-29	2019-11-10	2016-08-29	2019-11-10
Passage	3	3	3	3

QC Stats

Experiment QC

	4190-control	4190
Self_consistency_hg38	1.307927	1.307927
rescue_GRCh38	1.759036	1.759036

Replicate QC


Rep_UID	4190_01	4190_02	4190_INPUT1	4190_INPUT2
eCT	15.00	14.20	8.60	11.70
Usable_reads	3331753	4844761	7939953	11180814
Entropy_hg38	0.113236	0.053616

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4190_01	4190_02	4190_INPUT1	4190_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	ATTACTCG	TCCGGAGA	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4190_01	4190_02	4190_INPUT1	4190_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
4190_CLIP1_S52_L004_R1_001.fastq.gz	4190_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4190_CLIP2_S54_L004_R1_001.fastq.gz	4190_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4190_INPUT1_S51_L004_R1_001.fastq.gz	4190_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4190_INPUT2_S53_L004_R1_001.fastq.gz	4190_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4190_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4190_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4190_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4190_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4190_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4190_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4190_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4190_CLIP1_rep1.vs.4190_CLIP2_rep2.sorted.nh.bb	4190_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4190_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4190_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4190_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4190_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4190_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4190_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4190_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4190_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4190_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4190_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4190_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4190_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4190_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4190_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4190_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4190_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4190_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4190_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:4190-control	ENCSR858DLD	experiment	eCLIP	4190-CACTIN-HepG2-control	Released	ENCODE4
gene-yeo:4190	ENCSR150QBS	experiment	eCLIP	4190-CACTIN-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4190_01	ENCLB320AQG	library	eCLIP	4190_01	Released	ENCODE4
gene-yeo:L-HepG2_111019-4190_02	ENCLB536GCI	library	eCLIP	4190_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4190_INPUT1	ENCLB692VQJ	library	eCLIP	4190_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_111019-4190_INPUT2	ENCLB585GXD	library	eCLIP	4190_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4190_CLIP1_S52_L004_R1_001.fastq.gz	ENCFF754UAK	file_fastq	eCLIP	4190_01	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF145ZPO	file_bam	eCLIP	4190_01	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF784XRY	file_bam	eCLIP	4190_01	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF028BRZ	file_bw	eCLIP	4190_01	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF708QLV	file_bw	eCLIP	4190_01	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF415OXX	file_quantifications	eCLIP	4190_01	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF722HXZ	file_bed	eCLIP	4190_01	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF642ZAC	file_bb	eCLIP	4190_01	Released	ENCODE4
gene-yeo:4190_CLIP2_S54_L004_R1_001.fastq.gz	ENCFF919JNQ	file_fastq	eCLIP	4190_02	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF191ZAK	file_bam	eCLIP	4190_02	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF994KMC	file_bam	eCLIP	4190_02	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF640YPD	file_bw	eCLIP	4190_02	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF114EMR	file_bw	eCLIP	4190_02	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF424YBR	file_quantifications	eCLIP	4190_02	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF318KBE	file_bed	eCLIP	4190_02	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF768ITK	file_bb	eCLIP	4190_02	Released	ENCODE4
gene-yeo:4190_INPUT1_S51_L004_R1_001.fastq.gz	ENCFF304KIU	file_fastq	eCLIP	4190_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF745BEL	file_bam	eCLIP	4190_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF480PLC	file_bam	eCLIP	4190_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF297JFN	file_bw	eCLIP	4190_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF896DYJ	file_bw	eCLIP	4190_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF918QDT	file_quantifications	eCLIP	4190_INPUT1	Released	ENCODE4
gene-yeo:4190_INPUT2_S53_L004_R1_001.fastq.gz	ENCFF994WSO	file_fastq	eCLIP	4190_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF730GNV	file_bam	eCLIP	4190_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF926MCJ	file_bam	eCLIP	4190_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF092HXS	file_bw	eCLIP	4190_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF932TXZ	file_bw	eCLIP	4190_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4190_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF533JFZ	file_quantifications	eCLIP	4190_INPUT2	Released	ENCODE4