ENCORE eCLIP:4152

Experiment Information (Status: Released)

	4152-control	4152
Exp_UID	4152	4152
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR089LDS	ENCSR280JAB
ENCODE_alias	gene-yeo:4152-control	gene-yeo:4152
RBP	SNRNP200	SNRNP200
Cell_Line	K562	K562
Batch	batch23	batch23
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB827DRA	ENCAB827DRA
Antibody	A303-454A	A303-454A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	25.449198	25.449198
rescue_GRCh38	6.886139	6.886139
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	523	524

Replicate Information


Rep_UID	4152_01	4152_02	4152_INPUT1	4152_INPUT2
Exp UID	4152	4152	4152	4152
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_102015	K562_081815	K562_102015	K562_081815
Biosample_ENCODE_Accession	ENCBS592SHU	ENCBS175JIH	ENCBS592SHU	ENCBS175JIH
Biosample_ENCODE_Alias	gene-yeo:K562_102015	gene-yeo:K562_081815	gene-yeo:K562_102015	gene-yeo:K562_081815
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-10-20	2015-08-18	2015-10-20	2015-08-18
Culture_End_Date	2015-11-17	2015-09-08	2015-11-17	2015-09-08
Passage	5	5	5	5

QC Stats

Experiment QC

	4152-control	4152
Self_consistency_hg38	25.449198	25.449198
rescue_GRCh38	6.886139	6.886139

Replicate QC


Rep_UID	4152_01	4152_02	4152_INPUT1	4152_INPUT2
eCT	14.20	14.70	9.70	11.20
Usable_reads	499033	3807514	4019728	11078075
Entropy_hg38	0.899767	0.737547

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4152_01	4152_02	4152_INPUT1	4152_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	CGCTCATT	GAGATTCC	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4152_01	4152_02	4152_INPUT1	4152_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
4152_CLIP1_S23_L002_R1_001.fastq.gz	4152_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4152_CLIP2_S25_L002_R1_001.fastq.gz	4152_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4152_INPUT1_S22_L002_R1_001.fastq.gz	4152_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4152_INPUT2_S24_L002_R1_001.fastq.gz	4152_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4152_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4152_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4152_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4152_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4152_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4152_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4152_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4152_CLIP1_rep1.vs.4152_CLIP2_rep2.sorted.nh.bb	4152_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4152_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4152_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4152_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4152_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4152_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4152_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4152_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4152_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4152_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4152_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4152_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4152_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4152_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4152_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4152_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4152_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4152_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4152_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:4152-control	ENCSR089LDS	experiment	eCLIP	4152-SNRNP200-K562-control	Released	ENCODE4
gene-yeo:4152	ENCSR280JAB	experiment	eCLIP	4152-SNRNP200-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_102015-4152_01	ENCLB788STC	library	eCLIP	4152_01	Released	ENCODE4
gene-yeo:L-K562_081815-4152_02	ENCLB035UXT	library	eCLIP	4152_02	Released	ENCODE4
gene-yeo:L-K562_102015-4152_INPUT1	ENCLB467QXG	library	eCLIP	4152_INPUT1	Released	ENCODE4
gene-yeo:L-K562_081815-4152_INPUT2	ENCLB120QEB	library	eCLIP	4152_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4152_CLIP1_S23_L002_R1_001.fastq.gz	ENCFF236MAA	file_fastq	eCLIP	4152_01	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF522GXU	file_bam	eCLIP	4152_01	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF724SQO	file_bam	eCLIP	4152_01	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF807VEY	file_bw	eCLIP	4152_01	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF024XZL	file_bw	eCLIP	4152_01	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF815DIV	file_quantifications	eCLIP	4152_01	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF515WSK	file_bed	eCLIP	4152_01	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF567DHM	file_bb	eCLIP	4152_01	Released	ENCODE4
gene-yeo:4152_CLIP2_S25_L002_R1_001.fastq.gz	ENCFF132SYG	file_fastq	eCLIP	4152_02	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF750EUO	file_bam	eCLIP	4152_02	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF156YLP	file_bam	eCLIP	4152_02	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF309YGZ	file_bw	eCLIP	4152_02	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF960QAE	file_bw	eCLIP	4152_02	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF569WHP	file_quantifications	eCLIP	4152_02	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF695EEN	file_bed	eCLIP	4152_02	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF197QBY	file_bb	eCLIP	4152_02	Released	ENCODE4
gene-yeo:4152_INPUT1_S22_L002_R1_001.fastq.gz	ENCFF143IPH	file_fastq	eCLIP	4152_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF193TGB	file_bam	eCLIP	4152_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF839SVS	file_bam	eCLIP	4152_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF310QEQ	file_bw	eCLIP	4152_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF445CRG	file_bw	eCLIP	4152_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF863UQS	file_quantifications	eCLIP	4152_INPUT1	Released	ENCODE4
gene-yeo:4152_INPUT2_S24_L002_R1_001.fastq.gz	ENCFF110XZH	file_fastq	eCLIP	4152_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF312OAZ	file_bam	eCLIP	4152_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF475WZY	file_bam	eCLIP	4152_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF201ZIH	file_bw	eCLIP	4152_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF387QQK	file_bw	eCLIP	4152_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4152_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF793IND	file_quantifications	eCLIP	4152_INPUT2	Released	ENCODE4