ENCORE eCLIP:4202

Experiment Information (Status: Released)

	4202-control	4202
Exp_UID	4202	4202
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR038SNS	ENCSR678OKJ
ENCODE_alias	gene-yeo:4202-control	gene-yeo:4202
RBP	DHX38	DHX38
Cell_Line	HepG2	HepG2
Batch	batch24	batch24
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB630HFE	ENCAB630HFE
Antibody	A300-858A	A300-858A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.180328	1.180328
rescue_GRCh38	1.768627	1.768627
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	507	508

Replicate Information


Rep_UID	4202_01	4202_02	4202_INPUT1	4202_INPUT2
Exp UID	4202	4202	4202	4202
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

	4202-control	4202
Self_consistency_hg38	1.180328	1.180328
rescue_GRCh38	1.768627	1.768627

Replicate QC


Rep_UID	4202_01	4202_02	4202_INPUT1	4202_INPUT2
eCT	18.40	18.00	12.50	12.10
Usable_reads	770409	869555	5206321	3383329
Entropy_hg38	1.743446	1.002902

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4202_01	4202_02	4202_INPUT1	4202_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	GTACTGAC	AGGCGAAG	CAGGACGT
i7_barcode	GAATTCGT	GAATTCGT	GAATTCGT	GAATTCGT

Sequencing Information


Rep_UID	4202_01	4202_02	4202_INPUT1	4202_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
4202_CLIP1_S95_L006_R1_001.fastq.gz	4202_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4202_CLIP2_S97_L006_R1_001.fastq.gz	4202_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4202_INPUT1_S94_L006_R1_001.fastq.gz	4202_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4202_INPUT2_S96_L006_R1_001.fastq.gz	4202_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4202_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4202_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4202_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4202_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4202_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4202_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4202_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4202_CLIP1_rep1.vs.4202_CLIP2_rep2.sorted.nh.bb	4202_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4202_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4202_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4202_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4202_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4202_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4202_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4202_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4202_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4202_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4202_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4202_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4202_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4202_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4202_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4202_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4202_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4202_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4202_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:4202-control	ENCSR038SNS	experiment	eCLIP	4202-DHX38-HepG2-control	Released	ENCODE4
gene-yeo:4202	ENCSR678OKJ	experiment	eCLIP	4202-DHX38-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4202_01	ENCLB045UTE	library	eCLIP	4202_01	Released	ENCODE4
gene-yeo:L-HepG2_111019-4202_02	ENCLB538QHN	library	eCLIP	4202_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4202_INPUT1	ENCLB325WZF	library	eCLIP	4202_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_111019-4202_INPUT2	ENCLB544BTD	library	eCLIP	4202_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4202_CLIP1_S95_L006_R1_001.fastq.gz	ENCFF302UCJ	file_fastq	eCLIP	4202_01	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF619SVW	file_bam	eCLIP	4202_01	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF072JJJ	file_bam	eCLIP	4202_01	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF968FPA	file_bw	eCLIP	4202_01	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF833GFY	file_bw	eCLIP	4202_01	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF415UWN	file_quantifications	eCLIP	4202_01	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF394EZY	file_bed	eCLIP	4202_01	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF400EIX	file_bb	eCLIP	4202_01	Released	ENCODE4
gene-yeo:4202_CLIP2_S97_L006_R1_001.fastq.gz	ENCFF739SVT	file_fastq	eCLIP	4202_02	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF033LZI	file_bam	eCLIP	4202_02	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF227FPP	file_bam	eCLIP	4202_02	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF579CZG	file_bw	eCLIP	4202_02	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF927PNH	file_bw	eCLIP	4202_02	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF570KJF	file_quantifications	eCLIP	4202_02	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF414KYW	file_bed	eCLIP	4202_02	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF186OIP	file_bb	eCLIP	4202_02	Released	ENCODE4
gene-yeo:4202_INPUT1_S94_L006_R1_001.fastq.gz	ENCFF803WYP	file_fastq	eCLIP	4202_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF639UVB	file_bam	eCLIP	4202_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF662IYW	file_bam	eCLIP	4202_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF908DFY	file_bw	eCLIP	4202_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF219AJW	file_bw	eCLIP	4202_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF944PPO	file_quantifications	eCLIP	4202_INPUT1	Released	ENCODE4
gene-yeo:4202_INPUT2_S96_L006_R1_001.fastq.gz	ENCFF981XZS	file_fastq	eCLIP	4202_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF617MOV	file_bam	eCLIP	4202_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF251SJH	file_bam	eCLIP	4202_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF996TZR	file_bw	eCLIP	4202_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF722VYY	file_bw	eCLIP	4202_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4202_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF564NXT	file_quantifications	eCLIP	4202_INPUT2	Released	ENCODE4