ENCORE eCLIP:4037

Experiment Information (Status: Released)

	4037-control	4037
Exp_UID	4037	4037
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR344GAQ	ENCSR004VIR
ENCODE_alias	gene-yeo:4037-control	gene-yeo:4037
RBP	EEF2	EEF2
Cell_Line	K562	K562
Batch	batch11a	batch11a
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB559BYO	ENCAB559BYO
Antibody	711842	711842
Lot_num	1931156	1931156
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	2.290000	2.290000
rescue_GRCh38	1.692771	1.692771
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	595	596

Replicate Information


Rep_UID	4037_01	4037_02	4037_INPUT1	4037_INPUT2
Exp UID	4037	4037	4037	4037
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

	4037-control	4037
Self_consistency_hg38	2.290000	2.290000
rescue_GRCh38	1.692771	1.692771

Replicate QC


Rep_UID	4037_01	4037_02	4037_INPUT1	4037_INPUT2
eCT	13.40	16.50	8.60	5.20
Usable_reads	1582296	941398	5902693	3874318
Entropy_hg38	0.246574	0.137699

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4037_01	4037_02	4037_INPUT1	4037_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	GAGATTCC	ATTACTCG	GAGATTCC

Sequencing Information


Rep_UID	4037_01	4037_02	4037_INPUT1	4037_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
4037_CLIP1_S6_L001_R1_001.fastq.gz	4037_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4037_CLIP2_S8_L001_R1_001.fastq.gz	4037_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4037_INPUT1_S5_L001_R1_001.fastq.gz	4037_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4037_INPUT2_S7_L001_R1_001.fastq.gz	4037_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4037_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4037_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4037_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4037_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4037_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4037_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4037_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4037_CLIP1_rep1.vs.4037_CLIP2_rep2.sorted.nh.bb	4037_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4037_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4037_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4037_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4037_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4037_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4037_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4037_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4037_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4037_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4037_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4037_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4037_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4037_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4037_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4037_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4037_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4037_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4037_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:4037-control	ENCSR344GAQ	experiment	eCLIP	4037-EEF2-K562-control	Released	ENCODE4
gene-yeo:4037	ENCSR004VIR	experiment	eCLIP	4037-EEF2-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_111915-4037_01	ENCLB383UAZ	library	eCLIP	4037_01	Released	ENCODE4
gene-yeo:L-K562_072016-4037_02	ENCLB340DAE	library	eCLIP	4037_02	Released	ENCODE4
gene-yeo:L-K562_111915-4037_INPUT1	ENCLB416LNL	library	eCLIP	4037_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4037_INPUT2	ENCLB764EDZ	library	eCLIP	4037_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4037_CLIP1_S6_L001_R1_001.fastq.gz	ENCFF930FVO	file_fastq	eCLIP	4037_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF061EAB	file_bam	eCLIP	4037_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF641FYU	file_bam	eCLIP	4037_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF696HGR	file_bw	eCLIP	4037_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF468VOP	file_bw	eCLIP	4037_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF322AZS	file_quantifications	eCLIP	4037_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF431NBT	file_bed	eCLIP	4037_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF810REG	file_bb	eCLIP	4037_01	Released	ENCODE4
gene-yeo:4037_CLIP2_S8_L001_R1_001.fastq.gz	ENCFF928PQT	file_fastq	eCLIP	4037_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF740NJG	file_bam	eCLIP	4037_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF590IGQ	file_bam	eCLIP	4037_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF432QLO	file_bw	eCLIP	4037_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF548NSD	file_bw	eCLIP	4037_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF796RNA	file_quantifications	eCLIP	4037_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF296AYE	file_bed	eCLIP	4037_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF326ZRJ	file_bb	eCLIP	4037_02	Released	ENCODE4
gene-yeo:4037_INPUT1_S5_L001_R1_001.fastq.gz	ENCFF329GEK	file_fastq	eCLIP	4037_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF283UKS	file_bam	eCLIP	4037_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF130MAI	file_bam	eCLIP	4037_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF380JXY	file_bw	eCLIP	4037_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF886NFJ	file_bw	eCLIP	4037_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF317DDE	file_quantifications	eCLIP	4037_INPUT1	Released	ENCODE4
gene-yeo:4037_INPUT2_S7_L001_R1_001.fastq.gz	ENCFF752CAA	file_fastq	eCLIP	4037_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF692SBK	file_bam	eCLIP	4037_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF756QRD	file_bam	eCLIP	4037_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF416FWN	file_bw	eCLIP	4037_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF450KJM	file_bw	eCLIP	4037_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4037_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF887PNA	file_quantifications	eCLIP	4037_INPUT2	Released	ENCODE4