ENCORE eCLIP:4214

Experiment Information (Status: Released)

	4214-control	4214
Exp_UID	4214	4214
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR504UQS	ENCSR352IFB
ENCODE_alias	gene-yeo:4214-control	gene-yeo:4214
RBP	PARP1	PARP1
Cell_Line	HepG2	HepG2
Batch	batch26	batch26
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB316QKO	ENCAB316QKO
Antibody	436400	436400
Lot_num	TE268344	TE268344
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.119658	1.119658
rescue_GRCh38	3.326531	3.326531
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	497	498

Replicate Information


Rep_UID	4214_01	4214_02	4214_INPUT1	4214_INPUT2
Exp UID	4214	4214	4214	4214
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	HepG2_080316	HepG2_012220	HepG2_080316	HepG2_012220
Biosample_ENCODE_Accession	ENCBS133LVQ	ENCBS859DVG	ENCBS133LVQ	ENCBS859DVG
Biosample_ENCODE_Alias	gene-yeo:HepG2_080316	gene-yeo:HepG2_012220	gene-yeo:HepG2_080316	gene-yeo:HepG2_012220
Cell_Line	HepG2	HepG2	HepG2	HepG2
Culture_Start_Date	2016-08-03	2020-01-06	2016-08-03	2020-01-06
Culture_End_Date	2016-08-29	2020-01-22	2016-08-29	2020-01-22
Passage	3	3	3	3

QC Stats

Experiment QC

	4214-control	4214
Self_consistency_hg38	1.119658	1.119658
rescue_GRCh38	3.326531	3.326531

Replicate QC


Rep_UID	4214_01	4214_02	4214_INPUT1	4214_INPUT2
eCT	14.20	13.50	10.20	9.40
Usable_reads	3324073	5026900	5133695	3596111
Entropy_hg38	0.167215	0.029025

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4214_01	4214_02	4214_INPUT1	4214_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	ATAGAGGC	ATAGAGGC
i7_barcode	TCCGGAGA	GAGATTCC	ATTACTCG	CGCTCATT

Sequencing Information


Rep_UID	4214_01	4214_02	4214_INPUT1	4214_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
4214_clip1_S56_L008_R1_001.fastq.gz	4214_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4214_clip2_S58_L008_R1_001.fastq.gz	4214_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4214_input1_S55_L008_R1_001.fastq.gz	4214_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4214_input2_S57_L008_R1_001.fastq.gz	4214_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4214_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4214_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4214_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4214_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4214_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4214_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4214_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4214_CLIP1_rep1.vs.4214_CLIP2_rep2.sorted.nh.bb	4214_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4214_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4214_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4214_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4214_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4214_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4214_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4214_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4214_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4214_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4214_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4214_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4214_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4214_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4214_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4214_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4214_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4214_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4214_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:4214-control	ENCSR504UQS	experiment	eCLIP	4214-PARP1-HepG2-control	Released	ENCODE4
gene-yeo:4214	ENCSR352IFB	experiment	eCLIP	4214-PARP1-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4214_01	ENCLB621ZFJ	library	eCLIP	4214_01	Released	ENCODE4
gene-yeo:L-HepG2_012220-4214_02	ENCLB507DOS	library	eCLIP	4214_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4214_INPUT1	ENCLB915IWA	library	eCLIP	4214_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_012220-4214_INPUT2	ENCLB318AEX	library	eCLIP	4214_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4214_clip1_S56_L008_R1_001.fastq.gz	ENCFF809CRE	file_fastq	eCLIP	4214_01	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF682SBX	file_bam	eCLIP	4214_01	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF835HHO	file_bam	eCLIP	4214_01	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF227GIF	file_bw	eCLIP	4214_01	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF553VKY	file_bw	eCLIP	4214_01	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF545ORG	file_quantifications	eCLIP	4214_01	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF541VZX	file_bed	eCLIP	4214_01	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF778SJK	file_bb	eCLIP	4214_01	Released	ENCODE4
gene-yeo:4214_clip2_S58_L008_R1_001.fastq.gz	ENCFF404CBN	file_fastq	eCLIP	4214_02	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF373SLN	file_bam	eCLIP	4214_02	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF831OOQ	file_bam	eCLIP	4214_02	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF676IQD	file_bw	eCLIP	4214_02	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF598LIU	file_bw	eCLIP	4214_02	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF858KKF	file_quantifications	eCLIP	4214_02	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF950IXS	file_bed	eCLIP	4214_02	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF905EIZ	file_bb	eCLIP	4214_02	Released	ENCODE4
gene-yeo:4214_input1_S55_L008_R1_001.fastq.gz	ENCFF013TKB	file_fastq	eCLIP	4214_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF310DFY	file_bam	eCLIP	4214_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF316XOM	file_bam	eCLIP	4214_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF897XTV	file_bw	eCLIP	4214_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF587DYD	file_bw	eCLIP	4214_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF096ZUO	file_quantifications	eCLIP	4214_INPUT1	Released	ENCODE4
gene-yeo:4214_input2_S57_L008_R1_001.fastq.gz	ENCFF505UNB	file_fastq	eCLIP	4214_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF216JHC	file_bam	eCLIP	4214_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF421VTD	file_bam	eCLIP	4214_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF780UBX	file_bw	eCLIP	4214_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF212LCX	file_bw	eCLIP	4214_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4214_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF421SIL	file_quantifications	eCLIP	4214_INPUT2	Released	ENCODE4