ENCORE eCLIP:4137

Experiment Information (Status: Released)

	4137-control	4137
Exp_UID	4137	4137
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR873NGI	ENCSR202LKI
ENCODE_alias	gene-yeo:4137-control	gene-yeo:4137
RBP	ADAR	ADAR
Cell_Line	K562	K562
Batch	batch23	batch23
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB667NOE	ENCAB667NOE
Antibody	14175S	14175S
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.628094	1.628094
rescue_GRCh38	6.749073	6.749073
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	513	514

Replicate Information


Rep_UID	4137_01	4137_02	4137_INPUT1	4137_INPUT2
Exp UID	4137	4137	4137	4137
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

	4137-control	4137
Self_consistency_hg38	1.628094	1.628094
rescue_GRCh38	6.749073	6.749073

Replicate QC


Rep_UID	4137_01	4137_02	4137_INPUT1	4137_INPUT2
eCT	11.10	10.50	8.60	8.10
Usable_reads	19968154	3927314	6001671	7099809
Entropy_hg38	0.294970	0.789147

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4137_01	4137_02	4137_INPUT1	4137_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	AGGCGAAG	AGGCGAAG	GGCTCTGA	GGCTCTGA
i7_barcode	ATTACTCG	TCCGGAGA	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4137_01	4137_02	4137_INPUT1	4137_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
4137_CLIP1_S19_L002_R1_001.fastq.gz	4137_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4137_CLIP2_S21_L002_R1_001.fastq.gz	4137_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4137_INPUT1_S18_L002_R1_001.fastq.gz	4137_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4137_INPUT2_S20_L002_R1_001.fastq.gz	4137_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4137_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4137_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4137_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4137_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4137_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4137_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4137_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4137_CLIP1_rep1.vs.4137_CLIP2_rep2.sorted.nh.bb	4137_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4137_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4137_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4137_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4137_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4137_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4137_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4137_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4137_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4137_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4137_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4137_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4137_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4137_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4137_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4137_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4137_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4137_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4137_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:4137-control	ENCSR873NGI	experiment	eCLIP	4137-ADAR-K562-control	Released	ENCODE4
gene-yeo:4137	ENCSR202LKI	experiment	eCLIP	4137-ADAR-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4137_01	ENCLB705XBM	library	eCLIP	4137_01	Released	ENCODE4
gene-yeo:L-K562_102015-4137_02	ENCLB870CJV	library	eCLIP	4137_02	Released	ENCODE4
gene-yeo:L-K562_081815-4137_INPUT1	ENCLB672CXG	library	eCLIP	4137_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4137_INPUT2	ENCLB487MFJ	library	eCLIP	4137_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4137_CLIP1_S19_L002_R1_001.fastq.gz	ENCFF602KWI	file_fastq	eCLIP	4137_01	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF832UVT	file_bam	eCLIP	4137_01	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF203XCS	file_bam	eCLIP	4137_01	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF946VCQ	file_bw	eCLIP	4137_01	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF902TPF	file_bw	eCLIP	4137_01	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF285WZN	file_quantifications	eCLIP	4137_01	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF665GRX	file_bed	eCLIP	4137_01	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF255EUE	file_bb	eCLIP	4137_01	Released	ENCODE4
gene-yeo:4137_CLIP2_S21_L002_R1_001.fastq.gz	ENCFF543DNL	file_fastq	eCLIP	4137_02	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF021OCT	file_bam	eCLIP	4137_02	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF888PIL	file_bam	eCLIP	4137_02	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF860QWZ	file_bw	eCLIP	4137_02	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF412ZIV	file_bw	eCLIP	4137_02	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF459EDA	file_quantifications	eCLIP	4137_02	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF279GRU	file_bed	eCLIP	4137_02	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF666ZCS	file_bb	eCLIP	4137_02	Released	ENCODE4
gene-yeo:4137_INPUT1_S18_L002_R1_001.fastq.gz	ENCFF420KCV	file_fastq	eCLIP	4137_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF418MOT	file_bam	eCLIP	4137_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF523XSK	file_bam	eCLIP	4137_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF769ZXG	file_bw	eCLIP	4137_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF433SLU	file_bw	eCLIP	4137_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF770SDG	file_quantifications	eCLIP	4137_INPUT1	Released	ENCODE4
gene-yeo:4137_INPUT2_S20_L002_R1_001.fastq.gz	ENCFF601UIL	file_fastq	eCLIP	4137_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF551BTX	file_bam	eCLIP	4137_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF063IFV	file_bam	eCLIP	4137_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF284LPW	file_bw	eCLIP	4137_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF614FIG	file_bw	eCLIP	4137_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4137_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF168QGU	file_quantifications	eCLIP	4137_INPUT2	Released	ENCODE4