ENCORE eCLIP:4056

Experiment Information (Status: Released)

	4056-control	4056
Exp_UID	4056	4056
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR060MRW	ENCSR497XZI
ENCODE_alias	gene-yeo:4056-control	gene-yeo:4056
RBP	MBNL1	MBNL1
Cell_Line	K562	K562
Batch	batch11b	batch11b
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB328AVR	ENCAB328AVR
Antibody	PA5-19739	PA5-19739
Lot_num	TK2672742	TK2672742
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.466372	1.466372
rescue_GRCh38	2.318219	2.318219
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	589	590

Replicate Information


Rep_UID	4056_01	4056_02	4056_INPUT1	4056_INPUT2
Exp UID	4056	4056	4056	4056
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_072016	K562_111915	K562_072016	K562_111915
Biosample_ENCODE_Accession	ENCBS177POD	ENCBS344MAK	ENCBS177POD	ENCBS344MAK
Biosample_ENCODE_Alias	gene-yeo:K562_072016	gene-yeo:K562_111915	gene-yeo:K562_072016	gene-yeo:K562_111915
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2016-07-20	2015-11-19	2016-07-20	2015-11-19
Culture_End_Date	2016-08-15	2015-12-11	2016-08-15	2015-12-11
Passage	5	4	5	4

QC Stats

Experiment QC

	4056-control	4056
Self_consistency_hg38	1.466372	1.466372
rescue_GRCh38	2.318219	2.318219

Replicate QC


Rep_UID	4056_01	4056_02	4056_INPUT1	4056_INPUT2
eCT	11.50	9.90	5.80	6.80
Usable_reads	4812040	5407290	4182065	3853323
Entropy_hg38	0.190694	0.211006

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4056_01	4056_02	4056_INPUT1	4056_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	ATTCAGAA	GAATTCGT	ATTCAGAA	GAATTCGT

Sequencing Information


Rep_UID	4056_01	4056_02	4056_INPUT1	4056_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
4056_CLIP1_S99_L006_R1_001.fastq.gz	4056_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4056_CLIP2_S101_L006_R1_001.fastq.gz	4056_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4056_INPUT1_S98_L006_R1_001.fastq.gz	4056_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4056_INPUT2_S100_L006_R1_001.fastq.gz	4056_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4056_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4056_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4056_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4056_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4056_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4056_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4056_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4056_CLIP1_rep1.vs.4056_CLIP2_rep2.sorted.nh.bb	4056_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4056_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4056_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4056_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4056_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4056_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4056_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4056_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4056_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4056_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4056_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4056_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4056_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4056_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4056_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4056_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4056_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4056_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4056_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:4056-control	ENCSR060MRW	experiment	eCLIP	4056-MBNL1-K562-control	Released	ENCODE4
gene-yeo:4056	ENCSR497XZI	experiment	eCLIP	4056-MBNL1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_072016-4056_01	ENCLB313HNH	library	eCLIP	4056_01	Released	ENCODE4
gene-yeo:L-K562_111915-4056_02	ENCLB339JQZ	library	eCLIP	4056_02	Released	ENCODE4
gene-yeo:L-K562_072016-4056_INPUT1	ENCLB475UJU	library	eCLIP	4056_INPUT1	Released	ENCODE4
gene-yeo:L-K562_111915-4056_INPUT2	ENCLB578HCK	library	eCLIP	4056_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4056_CLIP1_S99_L006_R1_001.fastq.gz	ENCFF508CMO	file_fastq	eCLIP	4056_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF060CWR	file_bam	eCLIP	4056_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF452ZSY	file_bam	eCLIP	4056_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF441KZY	file_bw	eCLIP	4056_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF536EQM	file_bw	eCLIP	4056_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF288KYP	file_quantifications	eCLIP	4056_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF099ZBH	file_bed	eCLIP	4056_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF410GFP	file_bb	eCLIP	4056_01	Released	ENCODE4
gene-yeo:4056_CLIP2_S101_L006_R1_001.fastq.gz	ENCFF287XKI	file_fastq	eCLIP	4056_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF400SGM	file_bam	eCLIP	4056_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF380QZK	file_bam	eCLIP	4056_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF917NLI	file_bw	eCLIP	4056_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF424GEO	file_bw	eCLIP	4056_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF520QOD	file_quantifications	eCLIP	4056_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF486BAF	file_bed	eCLIP	4056_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF197KGL	file_bb	eCLIP	4056_02	Released	ENCODE4
gene-yeo:4056_INPUT1_S98_L006_R1_001.fastq.gz	ENCFF020YXZ	file_fastq	eCLIP	4056_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF557YRY	file_bam	eCLIP	4056_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF254JBI	file_bam	eCLIP	4056_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF114ZJZ	file_bw	eCLIP	4056_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF039LIS	file_bw	eCLIP	4056_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF344MXM	file_quantifications	eCLIP	4056_INPUT1	Released	ENCODE4
gene-yeo:4056_INPUT2_S100_L006_R1_001.fastq.gz	ENCFF118MKD	file_fastq	eCLIP	4056_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF465NZH	file_bam	eCLIP	4056_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF762YKX	file_bam	eCLIP	4056_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF768TTR	file_bw	eCLIP	4056_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF580ALJ	file_bw	eCLIP	4056_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4056_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF099MBS	file_quantifications	eCLIP	4056_INPUT2	Released	ENCODE4