ENCORE eCLIP:4012

Experiment Information (Status: Released)

	4012-control	4012
Exp_UID	4012	4012
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR911RWF	ENCSR100ARZ
ENCODE_alias	gene-yeo:4012-control	gene-yeo:4012
RBP	RPS6	RPS6
Cell_Line	K562	K562
Batch	batch7	batch7
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB305KJD	ENCAB305KJD
Antibody	A300-556A	A300-556A
Lot_num	2	2
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	2.938865	2.938865
rescue_GRCh38	4.431227	4.431227
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	493	494

Replicate Information


Rep_UID	4012_01	4012_02	4012_INPUT1	4012_INPUT2
Exp UID	4012	4012	4012	4012
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_012016	K562_072016	K562_012016	K562_072016
Biosample_ENCODE_Accession	ENCBS039CVO	ENCBS177POD	ENCBS039CVO	ENCBS177POD
Biosample_ENCODE_Alias	gene-yeo:K562_012016	gene-yeo:K562_072016	gene-yeo:K562_012016	gene-yeo:K562_072016
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2016-01-20	2016-07-20	2016-01-20	2016-07-20
Culture_End_Date	2016-02-17	2016-08-15	2016-02-17	2016-08-15
Passage	5	5	5	5

QC Stats

Experiment QC

	4012-control	4012
Self_consistency_hg38	2.938865	2.938865
rescue_GRCh38	4.431227	4.431227

Replicate QC


Rep_UID	4012_01	4012_02	4012_INPUT1	4012_INPUT2
eCT	15.00	14.70	3.60	2.80
Usable_reads	1548928	1225728	796451	1917565
Entropy_hg38	0.185345	0.405271

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4012_01	4012_02	4012_INPUT1	4012_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	TATAGCCT	ATAGAGGC	TATAGCCT	ATAGAGGC
i7_barcode	TCCGGAGA	TCCGGAGA	ATTACTCG	ATTACTCG

Sequencing Information


Rep_UID	4012_01	4012_02	4012_INPUT1	4012_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
4012_CLIP1_S57_L004_R1_001.fastq.gz	4012_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4012_CLIP2_S59_L004_R1_001.fastq.gz	4012_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4012_INPUT1_S56_L004_R1_001.fastq.gz	4012_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4012_INPUT2_S58_L004_R1_001.fastq.gz	4012_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4012_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4012_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4012_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4012_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4012_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4012_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4012_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4012_CLIP1_rep1.vs.4012_CLIP2_rep2.sorted.nh.bb	4012_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4012_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4012_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4012_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4012_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4012_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4012_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4012_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4012_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4012_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4012_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4012_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4012_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4012_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4012_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4012_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4012_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4012_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4012_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:4012-control	ENCSR911RWF	experiment	eCLIP	4012-RPS6-K562-control	Released	ENCODE4
gene-yeo:4012	ENCSR100ARZ	experiment	eCLIP	4012-RPS6-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_012016-4012_01	ENCLB604AQS	library	eCLIP	4012_01	Released	ENCODE4
gene-yeo:L-K562_072016-4012_02	ENCLB076RMX	library	eCLIP	4012_02	Released	ENCODE4
gene-yeo:L-K562_012016-4012_INPUT1	ENCLB354PHR	library	eCLIP	4012_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4012_INPUT2	ENCLB466LVX	library	eCLIP	4012_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4012_CLIP1_S57_L004_R1_001.fastq.gz	ENCFF182GNB	file_fastq	eCLIP	4012_01	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF231YMW	file_bam	eCLIP	4012_01	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF414VIJ	file_bam	eCLIP	4012_01	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF013EJK	file_bw	eCLIP	4012_01	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF457LIU	file_bw	eCLIP	4012_01	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF085EPU	file_quantifications	eCLIP	4012_01	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF338ZYM	file_bed	eCLIP	4012_01	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF368NLU	file_bb	eCLIP	4012_01	Released	ENCODE4
gene-yeo:4012_CLIP2_S59_L004_R1_001.fastq.gz	ENCFF915ASX	file_fastq	eCLIP	4012_02	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF508QDD	file_bam	eCLIP	4012_02	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF931MCZ	file_bam	eCLIP	4012_02	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF929BBP	file_bw	eCLIP	4012_02	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF505QFY	file_bw	eCLIP	4012_02	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF568TFB	file_quantifications	eCLIP	4012_02	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF015KGC	file_bed	eCLIP	4012_02	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF018KHT	file_bb	eCLIP	4012_02	Released	ENCODE4
gene-yeo:4012_INPUT1_S56_L004_R1_001.fastq.gz	ENCFF263CCY	file_fastq	eCLIP	4012_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF932IKG	file_bam	eCLIP	4012_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF498DSL	file_bam	eCLIP	4012_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF623GNO	file_bw	eCLIP	4012_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF949OWM	file_bw	eCLIP	4012_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF593WKS	file_quantifications	eCLIP	4012_INPUT1	Released	ENCODE4
gene-yeo:4012_INPUT2_S58_L004_R1_001.fastq.gz	ENCFF977OER	file_fastq	eCLIP	4012_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF594WLG	file_bam	eCLIP	4012_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF411XRF	file_bam	eCLIP	4012_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF253KMJ	file_bw	eCLIP	4012_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF142SYS	file_bw	eCLIP	4012_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4012_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF463DRZ	file_quantifications	eCLIP	4012_INPUT2	Released	ENCODE4