ENCORE eCLIP:4006

Experiment Information (Status: Released)

	4006-control	4006
Exp_UID	4006	4006
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR143CTS	ENCSR953ZOA
ENCODE_alias	gene-yeo:4006-control	gene-yeo:4006
RBP	HNRNPK	HNRNPK
Cell_Line	K562	K562
Batch	batch7	batch7
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB309WNL	ENCAB309WNL
Antibody	MA1-087	MA1-087
Lot_num	SA4246066	SA4246066
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.778922	1.778922
rescue_GRCh38	1.889815	1.889815
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	489	490

Replicate Information


Rep_UID	4006_01	4006_02	4006_INPUT1	4006_INPUT2
Exp UID	4006	4006	4006	4006
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

	4006-control	4006
Self_consistency_hg38	1.778922	1.778922
rescue_GRCh38	1.889815	1.889815

Replicate QC


Rep_UID	4006_01	4006_02	4006_INPUT1	4006_INPUT2
eCT	15.80	10.40	5.40	3.90
Usable_reads	3992606	6839526	2957413	3059066
Entropy_hg38	0.674749	0.846974

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4006_01	4006_02	4006_INPUT1	4006_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	CCTATCCT	CCTATCCT	CCTATCCT	CCTATCCT
i7_barcode	GAGATTCC	GAATTCGT	CGCTCATT	ATTCAGAA

Sequencing Information


Rep_UID	4006_01	4006_02	4006_INPUT1	4006_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
4006_CLIP1_S132_L008_R1_001.fastq.gz	4006_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4006_CLIP2_S134_L008_R1_001.fastq.gz	4006_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4006_IN1_S131_L008_R1_001.fastq.gz	4006_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4006_IN2_S133_L008_R1_001.fastq.gz	4006_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4006_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4006_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4006_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4006_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4006_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4006_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4006_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4006_CLIP1_rep1.vs.4006_CLIP2_rep2.sorted.nh.bb	4006_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4006_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4006_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4006_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4006_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4006_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4006_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4006_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4006_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4006_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4006_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4006_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4006_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4006_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4006_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4006_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4006_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch7.4006_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4006_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:4006-control	ENCSR143CTS	experiment	eCLIP	4006-HNRNPK-K562-control	Released	ENCODE4
gene-yeo:4006	ENCSR953ZOA	experiment	eCLIP	4006-HNRNPK-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_012016-4006_01	ENCLB805GYM	library	eCLIP	4006_01	Released	ENCODE4
gene-yeo:L-K562_072016-4006_02	ENCLB382NGG	library	eCLIP	4006_02	Released	ENCODE4
gene-yeo:L-K562_012016-4006_INPUT1	ENCLB550YVG	library	eCLIP	4006_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4006_INPUT2	ENCLB444WJE	library	eCLIP	4006_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4006_CLIP1_S132_L008_R1_001.fastq.gz	ENCFF935EPG	file_fastq	eCLIP	4006_01	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF827GTT	file_bam	eCLIP	4006_01	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF704FID	file_bam	eCLIP	4006_01	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF559GBT	file_bw	eCLIP	4006_01	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF988TCR	file_bw	eCLIP	4006_01	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF210SBQ	file_quantifications	eCLIP	4006_01	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF679HYT	file_bed	eCLIP	4006_01	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF461FMC	file_bb	eCLIP	4006_01	Released	ENCODE4
gene-yeo:4006_CLIP2_S134_L008_R1_001.fastq.gz	ENCFF244ZIB	file_fastq	eCLIP	4006_02	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF826OYP	file_bam	eCLIP	4006_02	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF570EJV	file_bam	eCLIP	4006_02	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF961MIZ	file_bw	eCLIP	4006_02	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF102VWD	file_bw	eCLIP	4006_02	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF276CHG	file_quantifications	eCLIP	4006_02	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF969JDI	file_bed	eCLIP	4006_02	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF148QBJ	file_bb	eCLIP	4006_02	Released	ENCODE4
gene-yeo:4006_IN1_S131_L008_R1_001.fastq.gz	ENCFF560DED	file_fastq	eCLIP	4006_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF980RPI	file_bam	eCLIP	4006_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF571PWT	file_bam	eCLIP	4006_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF102BZO	file_bw	eCLIP	4006_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF709BIQ	file_bw	eCLIP	4006_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF982YSR	file_quantifications	eCLIP	4006_INPUT1	Released	ENCODE4
gene-yeo:4006_IN2_S133_L008_R1_001.fastq.gz	ENCFF398TVO	file_fastq	eCLIP	4006_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF625TPX	file_bam	eCLIP	4006_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF098EUZ	file_bam	eCLIP	4006_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF509GYM	file_bw	eCLIP	4006_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF069HND	file_bw	eCLIP	4006_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch7.4006_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF110CUM	file_quantifications	eCLIP	4006_INPUT2	Released	ENCODE4