ENCORE eCLIP:4108

Experiment Information (Status: Released)

	4108-control	4108
Exp_UID	4108	4108
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR454AWA	ENCSR181SOG
ENCODE_alias	gene-yeo:4108-control	gene-yeo:4108
RBP	GARS	GARS
Cell_Line	HepG2	HepG2
Batch	batch17	batch17
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB009SWM	ENCAB009SWM
Antibody	MA5-26714	MA5-26714
Lot_num	UA2693064	UA2693064
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.691099	1.691099
rescue_GRCh38	1.418305	1.418305
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	565	566

Replicate Information


Rep_UID	4108_01	4108_02	4108_INPUT1	4108_INPUT2
Exp UID	4108	4108	4108	4108
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

	4108-control	4108
Self_consistency_hg38	1.691099	1.691099
rescue_GRCh38	1.418305	1.418305

Replicate QC


Rep_UID	4108_01	4108_02	4108_INPUT1	4108_INPUT2
eCT	9.40	9.60	2.10	2.60
Usable_reads	2086378	3376254	4254300	4644096
Entropy_hg38	1.386851	1.165899

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4108_01	4108_02	4108_INPUT1	4108_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	GGCTCTGA	GGCTCTGA	CCTATCCT	CCTATCCT
i7_barcode	GAGATTCC	CGCTCATT	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4108_01	4108_02	4108_INPUT1	4108_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
4108_CLIP1_S31_L002_R1_001.fastq.gz	4108_01	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4108_CLIP2_S33_L002_R1_001.fastq.gz	4108_02	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4108_INPUT1_S30_L002_R1_001.fastq.gz	4108_INPUT1	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4108_INPUT2_S32_L002_R1_001.fastq.gz	4108_INPUT2	fastq	reads	single-ended	101	NovaSeq6000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4108_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4108_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4108_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4108_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4108_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4108_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4108_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4108_CLIP1_rep1.vs.4108_CLIP2_rep2.sorted.nh.bb	4108_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4108_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4108_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4108_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4108_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4108_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4108_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4108_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4108_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4108_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4108_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4108_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4108_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4108_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4108_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4108_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4108_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4108_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4108_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:4108-control	ENCSR454AWA	experiment	eCLIP	4108-GARS-HepG2-control	Released	ENCODE4
gene-yeo:4108	ENCSR181SOG	experiment	eCLIP	4108-GARS-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4108_01	ENCLB612CFI	library	eCLIP	4108_01	Released	ENCODE4
gene-yeo:L-HepG2_062716-4108_02	ENCLB375ODW	library	eCLIP	4108_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4108_INPUT1	ENCLB326KKL	library	eCLIP	4108_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_062716-4108_INPUT2	ENCLB931YCK	library	eCLIP	4108_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4108_CLIP1_S31_L002_R1_001.fastq.gz	ENCFF211HPI	file_fastq	eCLIP	4108_01	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF920WRR	file_bam	eCLIP	4108_01	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF351KUC	file_bam	eCLIP	4108_01	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF683NDQ	file_bw	eCLIP	4108_01	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF165UTW	file_bw	eCLIP	4108_01	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF118SDV	file_quantifications	eCLIP	4108_01	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF077STC	file_bed	eCLIP	4108_01	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF306UNE	file_bb	eCLIP	4108_01	Released	ENCODE4
gene-yeo:4108_CLIP2_S33_L002_R1_001.fastq.gz	ENCFF057UEA	file_fastq	eCLIP	4108_02	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF151COU	file_bam	eCLIP	4108_02	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF941ZXJ	file_bam	eCLIP	4108_02	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF687SLO	file_bw	eCLIP	4108_02	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF533RCG	file_bw	eCLIP	4108_02	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF392SHO	file_quantifications	eCLIP	4108_02	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF075LOM	file_bed	eCLIP	4108_02	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF870FSL	file_bb	eCLIP	4108_02	Released	ENCODE4
gene-yeo:4108_INPUT1_S30_L002_R1_001.fastq.gz	ENCFF244WJP	file_fastq	eCLIP	4108_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF815HKP	file_bam	eCLIP	4108_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF387VXM	file_bam	eCLIP	4108_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF738YSO	file_bw	eCLIP	4108_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF952JUV	file_bw	eCLIP	4108_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF090MCI	file_quantifications	eCLIP	4108_INPUT1	Released	ENCODE4
gene-yeo:4108_INPUT2_S32_L002_R1_001.fastq.gz	ENCFF213BIX	file_fastq	eCLIP	4108_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF968GWY	file_bam	eCLIP	4108_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF550ACE	file_bam	eCLIP	4108_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF347OFQ	file_bw	eCLIP	4108_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF963TID	file_bw	eCLIP	4108_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4108_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF741WVJ	file_quantifications	eCLIP	4108_INPUT2	Released	ENCODE4