ENCORE eCLIP:4224

Experiment Information (Status: Released)

	4224-control	4224
Exp_UID	4224	4224
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR545KBT	ENCSR440MSY
ENCODE_alias	gene-yeo:4224-control	gene-yeo:4224
RBP	ELAC2	ELAC2
Cell_Line	K562	K562
Batch	batch25	batch25
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB519QXK	ENCAB519QXK
Antibody	PA5-78553	PA5-78553
Lot_num	UK2881508	UK2881508
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.058138	1.058138
rescue_GRCh38	1.341482	1.341482
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	505	506

Replicate Information


Rep_UID	4224_01	4224_02	4224_INPUT1	4224_INPUT2
Exp UID	4224	4224	4224	4224
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_081815	K562_102015	K562_081815	K562_102015
Biosample_ENCODE_Accession	ENCBS175JIH	ENCBS592SHU	ENCBS175JIH	ENCBS592SHU
Biosample_ENCODE_Alias	gene-yeo:K562_081815	gene-yeo:K562_102015	gene-yeo:K562_081815	gene-yeo:K562_102015
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-08-18	2015-10-20	2015-08-18	2015-10-20
Culture_End_Date	2015-09-08	2015-11-17	2015-09-08	2015-11-17
Passage	5	5	5	5

QC Stats

Experiment QC

	4224-control	4224
Self_consistency_hg38	1.058138	1.058138
rescue_GRCh38	1.341482	1.341482

Replicate QC


Rep_UID	4224_01	4224_02	4224_INPUT1	4224_INPUT2
eCT	18.40	17.80	11.40	12.00
Usable_reads	8432560	7407326	5606718	10776773
Entropy_hg38	3.747709	2.842145

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4224_01	4224_02	4224_INPUT1	4224_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	TATAGCCT	TATAGCCT
i7_barcode	CGCTCATT	GAGATTCC	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4224_01	4224_02	4224_INPUT1	4224_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
4224_CLIP1_S119_L008_R1_001.fastq.gz	4224_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4224_CLIP2_S121_L008_R1_001.fastq.gz	4224_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4224_INPUT1_S118_L008_R1_001.fastq.gz	4224_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4224_INPUT2_S120_L008_R1_001.fastq.gz	4224_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4224_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4224_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4224_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4224_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4224_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4224_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4224_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4224_CLIP1_rep1.vs.4224_CLIP2_rep2.sorted.nh.bb	4224_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4224_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4224_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4224_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4224_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4224_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4224_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4224_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4224_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4224_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4224_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4224_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4224_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4224_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4224_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4224_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4224_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4224_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4224_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:4224-control	ENCSR545KBT	experiment	eCLIP	4224-ELAC2-K562-control	Released	ENCODE4
gene-yeo:4224	ENCSR440MSY	experiment	eCLIP	4224-ELAC2-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4224_01	ENCLB270TXG	library	eCLIP	4224_01	Released	ENCODE4
gene-yeo:L-K562_102015-4224_02	ENCLB272VSK	library	eCLIP	4224_02	Released	ENCODE4
gene-yeo:L-K562_081815-4224_INPUT1	ENCLB593SRW	library	eCLIP	4224_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4224_INPUT2	ENCLB236HON	library	eCLIP	4224_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4224_CLIP1_S119_L008_R1_001.fastq.gz	ENCFF893MRC	file_fastq	eCLIP	4224_01	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF811PSC	file_bam	eCLIP	4224_01	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF871ZNQ	file_bam	eCLIP	4224_01	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF313HFG	file_bw	eCLIP	4224_01	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF958IRA	file_bw	eCLIP	4224_01	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF257IJD	file_quantifications	eCLIP	4224_01	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF713MUH	file_bed	eCLIP	4224_01	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF454CZU	file_bb	eCLIP	4224_01	Released	ENCODE4
gene-yeo:4224_CLIP2_S121_L008_R1_001.fastq.gz	ENCFF908GRB	file_fastq	eCLIP	4224_02	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF726IYX	file_bam	eCLIP	4224_02	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF121HUI	file_bam	eCLIP	4224_02	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF397BRB	file_bw	eCLIP	4224_02	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF731IGL	file_bw	eCLIP	4224_02	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF382ERX	file_quantifications	eCLIP	4224_02	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF526ZZK	file_bed	eCLIP	4224_02	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF732ZAY	file_bb	eCLIP	4224_02	Released	ENCODE4
gene-yeo:4224_INPUT1_S118_L008_R1_001.fastq.gz	ENCFF676OKA	file_fastq	eCLIP	4224_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF159HOX	file_bam	eCLIP	4224_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF163KLQ	file_bam	eCLIP	4224_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF710WHW	file_bw	eCLIP	4224_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF122OMK	file_bw	eCLIP	4224_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF982BNW	file_quantifications	eCLIP	4224_INPUT1	Released	ENCODE4
gene-yeo:4224_INPUT2_S120_L008_R1_001.fastq.gz	ENCFF021FRQ	file_fastq	eCLIP	4224_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF611ATH	file_bam	eCLIP	4224_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF920UJU	file_bam	eCLIP	4224_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF574NGU	file_bw	eCLIP	4224_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF245MQH	file_bw	eCLIP	4224_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4224_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF063TGC	file_quantifications	eCLIP	4224_INPUT2	Released	ENCODE4