ENCORE eCLIP:4018

Experiment Information (Status: Released)

	4018-control	4018
Exp_UID	4018	4018
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR660DRN	ENCSR391BBA
ENCODE_alias	gene-yeo:4018-control	gene-yeo:4018
RBP	EIF4E	EIF4E
Cell_Line	K562	K562
Batch	batch10	batch10
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB864VOP	ENCAB864VOP
Antibody	MA1-089	MA1-089
Lot_num	TD257774	TD257774
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.858849	1.858849
rescue_GRCh38	1.600559	1.600559
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	603	604

Replicate Information


Rep_UID	4018_01	4018_02	4018_INPUT1	4018_INPUT2
Exp UID	4018	4018	4018	4018
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_111915	K562_072016	K562_111915	K562_072016
Biosample_ENCODE_Accession	ENCBS344MAK	ENCBS177POD	ENCBS344MAK	ENCBS177POD
Biosample_ENCODE_Alias	gene-yeo:K562_111915	gene-yeo:K562_072016	gene-yeo:K562_111915	gene-yeo:K562_072016
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-11-19	2016-07-20	2015-11-19	2016-07-20
Culture_End_Date	2015-12-11	2016-08-15	2015-12-11	2016-08-15
Passage	4	5	4	5

QC Stats

Experiment QC

	4018-control	4018
Self_consistency_hg38	1.858849	1.858849
rescue_GRCh38	1.600559	1.600559

Replicate QC


Rep_UID	4018_01	4018_02	4018_INPUT1	4018_INPUT2
eCT	9.90	8.70	3.70	5.20
Usable_reads	1064023	2354301	2782975	2516728
Entropy_hg38	0.425833	0.568682

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4018_01	4018_02	4018_INPUT1	4018_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	TAATCTTA	AGGCGAAG	AGGCGAAG
i7_barcode	ATTACTCG	TCCGGAGA	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4018_01	4018_02	4018_INPUT1	4018_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
4018_CLIP1_S6_L006_R1_001.fastq.gz	4018_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4018_CLIP2_S8_L006_R1_001.fastq.gz	4018_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4018_INPUT1_S5_L006_R1_001.fastq.gz	4018_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4018_INPUT2_S7_L006_R1_001.fastq.gz	4018_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4018_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4018_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4018_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4018_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4018_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4018_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4018_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4018_CLIP1_rep1.vs.4018_CLIP2_rep2.sorted.nh.bb	4018_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4018_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4018_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4018_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4018_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4018_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4018_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4018_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4018_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4018_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4018_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4018_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4018_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4018_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4018_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4018_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4018_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4018_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4018_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:4018-control	ENCSR660DRN	experiment	eCLIP	4018-EIF4E-K562-control	Released	ENCODE4
gene-yeo:4018	ENCSR391BBA	experiment	eCLIP	4018-EIF4E-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_111915-4018_01	ENCLB950DNW	library	eCLIP	4018_01	Released	ENCODE4
gene-yeo:L-K562_072016-4018_02	ENCLB231NRG	library	eCLIP	4018_02	Released	ENCODE4
gene-yeo:L-K562_111915-4018_INPUT1	ENCLB776DKO	library	eCLIP	4018_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4018_INPUT2	ENCLB690OJP	library	eCLIP	4018_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4018_CLIP1_S6_L006_R1_001.fastq.gz	ENCFF230YKJ	file_fastq	eCLIP	4018_01	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF653YQW	file_bam	eCLIP	4018_01	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF967PSC	file_bam	eCLIP	4018_01	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF327QRW	file_bw	eCLIP	4018_01	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF530DZO	file_bw	eCLIP	4018_01	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF672ABQ	file_quantifications	eCLIP	4018_01	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF412VGD	file_bed	eCLIP	4018_01	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF710OHE	file_bb	eCLIP	4018_01	Released	ENCODE4
gene-yeo:4018_CLIP2_S8_L006_R1_001.fastq.gz	ENCFF497YEF	file_fastq	eCLIP	4018_02	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF992OVY	file_bam	eCLIP	4018_02	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF748VHF	file_bam	eCLIP	4018_02	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF952TZH	file_bw	eCLIP	4018_02	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF069GNZ	file_bw	eCLIP	4018_02	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF856EAY	file_quantifications	eCLIP	4018_02	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF332VUJ	file_bed	eCLIP	4018_02	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF371ZMR	file_bb	eCLIP	4018_02	Released	ENCODE4
gene-yeo:4018_INPUT1_S5_L006_R1_001.fastq.gz	ENCFF740PDL	file_fastq	eCLIP	4018_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF574IHX	file_bam	eCLIP	4018_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF717CGC	file_bam	eCLIP	4018_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF593ZBH	file_bw	eCLIP	4018_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF103XVN	file_bw	eCLIP	4018_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF183RPJ	file_quantifications	eCLIP	4018_INPUT1	Released	ENCODE4
gene-yeo:4018_INPUT2_S7_L006_R1_001.fastq.gz	ENCFF176ITD	file_fastq	eCLIP	4018_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF093ARK	file_bam	eCLIP	4018_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF568VFK	file_bam	eCLIP	4018_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF704QAU	file_bw	eCLIP	4018_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF589QRL	file_bw	eCLIP	4018_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch10.4018_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF041KBV	file_quantifications	eCLIP	4018_INPUT2	Released	ENCODE4