ENCORE eCLIP:4161

Experiment Information (Status: Released)

	4161-control	4161
Exp_UID	4161	4161
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR481MVN	ENCSR521GON
ENCODE_alias	gene-yeo:4161-control	gene-yeo:4161
RBP	EXOSC10	EXOSC10
Cell_Line	K562	K562
Batch	batch21	batch21
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB270KRD	ENCAB270KRD
Antibody	A303-987A	A303-987A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	4.358657	4.358657
rescue_GRCh38	1.788433	1.788433
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	537	538

Replicate Information


Rep_UID	4161_01	4161_02	4161_INPUT1	4161_INPUT2
Exp UID	4161	4161	4161	4161
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

	4161-control	4161
Self_consistency_hg38	4.358657	4.358657
rescue_GRCh38	1.788433	1.788433

Replicate QC


Rep_UID	4161_01	4161_02	4161_INPUT1	4161_INPUT2
eCT	11.40	11.40	6.20	6.70
Usable_reads	3405818	1996103	5239965	3318123
Entropy_hg38	0.476493	0.263989

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4161_01	4161_02	4161_INPUT1	4161_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	GGCTCTGA	TATAGCCT	CCTATCCT
i7_barcode	TCCGGAGA	TCCGGAGA	TCCGGAGA	TCCGGAGA

Sequencing Information


Rep_UID	4161_01	4161_02	4161_INPUT1	4161_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
4161_CLIP1_S83_L005_R1_001.fastq.gz	4161_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4161_CLIP2_S65_L004_R1_001.fastq.gz	4161_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4161_IN1_S82_L005_R1_001.fastq.gz	4161_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4161_IN2_S64_L004_R1_001.fastq.gz	4161_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4161_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4161_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4161_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4161_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4161_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4161_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4161_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4161_CLIP1_rep1.vs.4161_CLIP2_rep2.sorted.nh.bb	4161_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4161_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4161_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4161_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4161_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4161_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4161_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4161_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4161_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4161_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4161_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4161_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4161_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4161_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4161_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4161_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4161_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4161_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4161_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:4161-control	ENCSR481MVN	experiment	eCLIP	4161-EXOSC10-K562-control	Released	ENCODE4
gene-yeo:4161	ENCSR521GON	experiment	eCLIP	4161-EXOSC10-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4161_01	ENCLB131HXR	library	eCLIP	4161_01	Released	ENCODE4
gene-yeo:L-K562_102015-4161_02	ENCLB810KHO	library	eCLIP	4161_02	Released	ENCODE4
gene-yeo:L-K562_081815-4161_INPUT1	ENCLB883YNT	library	eCLIP	4161_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4161_INPUT2	ENCLB074UES	library	eCLIP	4161_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4161_CLIP1_S83_L005_R1_001.fastq.gz	ENCFF219AFL	file_fastq	eCLIP	4161_01	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF856GQF	file_bam	eCLIP	4161_01	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF338WDB	file_bam	eCLIP	4161_01	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF541MVG	file_bw	eCLIP	4161_01	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF501LBN	file_bw	eCLIP	4161_01	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF598IUA	file_quantifications	eCLIP	4161_01	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF053PAM	file_bed	eCLIP	4161_01	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF607UEV	file_bb	eCLIP	4161_01	Released	ENCODE4
gene-yeo:4161_CLIP2_S65_L004_R1_001.fastq.gz	ENCFF538WWX	file_fastq	eCLIP	4161_02	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF667MZG	file_bam	eCLIP	4161_02	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF267USI	file_bam	eCLIP	4161_02	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF332TUN	file_bw	eCLIP	4161_02	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF852QAD	file_bw	eCLIP	4161_02	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF587MYC	file_quantifications	eCLIP	4161_02	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF448LBY	file_bed	eCLIP	4161_02	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF486PWI	file_bb	eCLIP	4161_02	Released	ENCODE4
gene-yeo:4161_IN1_S82_L005_R1_001.fastq.gz	ENCFF341UTP	file_fastq	eCLIP	4161_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF052JGT	file_bam	eCLIP	4161_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF020RMT	file_bam	eCLIP	4161_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF793UKM	file_bw	eCLIP	4161_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF080XSM	file_bw	eCLIP	4161_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF631SDU	file_quantifications	eCLIP	4161_INPUT1	Released	ENCODE4
gene-yeo:4161_IN2_S64_L004_R1_001.fastq.gz	ENCFF219CZQ	file_fastq	eCLIP	4161_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF378ACS	file_bam	eCLIP	4161_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF650HUV	file_bam	eCLIP	4161_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF387KLH	file_bw	eCLIP	4161_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF618OJC	file_bw	eCLIP	4161_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4161_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF909IMT	file_quantifications	eCLIP	4161_INPUT2	Released	ENCODE4