ENCORE eCLIP:4001

Experiment Information (Status: Released)

	4001-control	4001
Exp_UID	4001	4001
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR638HPP	ENCSR285QHT
ENCODE_alias	gene-yeo:4001-control	gene-yeo:4001
RBP	NONO	NONO
Cell_Line	K562	K562
Batch	batch2	batch2
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB143JWA	ENCAB143JWA
Antibody	MA3-2024	MA3-2024
Lot_num	TA265182	TA265182
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.990986	1.990986
rescue_GRCh38	2.388040	2.388040
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	557	558

Replicate Information


Rep_UID	4001_01	4001_02	4001_INPUT1	4001_INPUT2
Exp UID	4001	4001	4001	4001
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

	4001-control	4001
Self_consistency_hg38	1.990986	1.990986
rescue_GRCh38	2.388040	2.388040

Replicate QC


Rep_UID	4001_01	4001_02	4001_INPUT1	4001_INPUT2
eCT	11.80	9.70	4.70	1.90
Usable_reads	2660860	3587562	1091357	793680
Entropy_hg38	0.844053	0.405975

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4001_01	4001_02	4001_INPUT1	4001_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	TATAGCCT	TATAGCCT	CCTATCCT
i7_barcode	TCCGGAGA	CGCTCATT	ATTACTCG	CGCTCATT

Sequencing Information


Rep_UID	4001_01	4001_02	4001_INPUT1	4001_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
JM_4001_CLIP1_S18_L007_R1_001.fastq.gz	4001_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
JM_4001_CLIP2_S20_L007_R1_001.fastq.gz	4001_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
JM_4001_INPUT1_S17_L007_R1_001.fastq.gz	4001_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
JM_4001_INPUT2_S19_L007_R1_001.fastq.gz	4001_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4001_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4001_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4001_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4001_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4001_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4001_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4001_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4001_CLIP1_rep1.vs.4001_CLIP2_rep2.sorted.nh.bb	4001_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4001_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4001_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4001_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4001_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4001_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4001_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4001_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4001_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4001_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4001_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4001_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4001_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4001_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4001_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4001_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4001_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4001_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4001_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:4001-control	ENCSR638HPP	experiment	eCLIP	4001-NONO-K562-control	Released	ENCODE4
gene-yeo:4001	ENCSR285QHT	experiment	eCLIP	4001-NONO-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_012016-4001_01	ENCLB469VMB	library	eCLIP	4001_01	Released	ENCODE4
gene-yeo:L-K562_072016-4001_02	ENCLB598SXW	library	eCLIP	4001_02	Released	ENCODE4
gene-yeo:L-K562_012016-4001_INPUT1	ENCLB576JTV	library	eCLIP	4001_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4001_INPUT2	ENCLB906QZW	library	eCLIP	4001_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:JM_4001_CLIP1_S18_L007_R1_001.fastq.gz	ENCFF839YNO	file_fastq	eCLIP	4001_01	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF605EDS	file_bam	eCLIP	4001_01	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF492OOJ	file_bam	eCLIP	4001_01	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF900WOR	file_bw	eCLIP	4001_01	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF128QQV	file_bw	eCLIP	4001_01	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF293RTK	file_quantifications	eCLIP	4001_01	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF692DTT	file_bed	eCLIP	4001_01	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF451PAR	file_bb	eCLIP	4001_01	Released	ENCODE4
gene-yeo:JM_4001_CLIP2_S20_L007_R1_001.fastq.gz	ENCFF060HVC	file_fastq	eCLIP	4001_02	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF698LBS	file_bam	eCLIP	4001_02	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF598UHA	file_bam	eCLIP	4001_02	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF633DEG	file_bw	eCLIP	4001_02	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF123SPE	file_bw	eCLIP	4001_02	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF933CUT	file_quantifications	eCLIP	4001_02	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF381ZLO	file_bed	eCLIP	4001_02	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF247DDQ	file_bb	eCLIP	4001_02	Released	ENCODE4
gene-yeo:JM_4001_INPUT1_S17_L007_R1_001.fastq.gz	ENCFF433GQC	file_fastq	eCLIP	4001_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF020CLU	file_bam	eCLIP	4001_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF949LWL	file_bam	eCLIP	4001_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF260LMV	file_bw	eCLIP	4001_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF446KPT	file_bw	eCLIP	4001_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF737SLU	file_quantifications	eCLIP	4001_INPUT1	Released	ENCODE4
gene-yeo:JM_4001_INPUT2_S19_L007_R1_001.fastq.gz	ENCFF044HDA	file_fastq	eCLIP	4001_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF881XAV	file_bam	eCLIP	4001_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF605HBU	file_bam	eCLIP	4001_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF973WPR	file_bw	eCLIP	4001_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF103BEW	file_bw	eCLIP	4001_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4001_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF452NLY	file_quantifications	eCLIP	4001_INPUT2	Released	ENCODE4