ENCORE eCLIP:4116

Experiment Information (Status: Released)

	4116-control	4116
Exp_UID	4116	4116
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR108SQZ	ENCSR048YXG
ENCODE_alias	gene-yeo:4116-control	gene-yeo:4116
RBP	AGO2	AGO2
Cell_Line	K562	K562
Batch	batch17	batch17
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB371WEH	ENCAB371WEH
Antibody	sc-53521	sc-53521
Lot_num	H2818	H2818
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.203732	1.203732
rescue_GRCh38	1.562119	1.562119
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	563	564

Replicate Information


Rep_UID	4116_01	4116_02	4116_INPUT1	4116_INPUT2
Exp UID	4116	4116	4116	4116
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_102015	K562_012016	K562_102015	K562_012016
Biosample_ENCODE_Accession	ENCBS592SHU	ENCBS039CVO	ENCBS592SHU	ENCBS039CVO
Biosample_ENCODE_Alias	gene-yeo:K562_102015	gene-yeo:K562_012016	gene-yeo:K562_102015	gene-yeo:K562_012016
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-10-20	2016-01-20	2015-10-20	2016-01-20
Culture_End_Date	2015-11-17	2016-02-17	2015-11-17	2016-02-17
Passage	5	5	5	5

QC Stats

Experiment QC

	4116-control	4116
Self_consistency_hg38	1.203732	1.203732
rescue_GRCh38	1.562119	1.562119

Replicate QC


Rep_UID	4116_01	4116_02	4116_INPUT1	4116_INPUT2
eCT	9.40	9.70	3.90	4.00
Usable_reads	6059825	5658255	3260463	2111321
Entropy_hg38	9.593107	9.489068

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4116_01	4116_02	4116_INPUT1	4116_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	TAATCTTA	TAATCTTA	AGGCGAAG	AGGCGAAG
i7_barcode	CGCTCATT	GAGATTCC	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4116_01	4116_02	4116_INPUT1	4116_INPUT2
seq_read_type	single-ended	single-ended	single-ended	single-ended
read_length	75	75	75	75
machine	NovaSeq6000	NovaSeq6000	NovaSeq6000	NovaSeq6000
flowcell	flowcell	flowcell	flowcell	flowcell
lane	-	-	-	-

File Information

FASTQ

file_name	Sample ID	file_format	output_type	run_type	read_length	platform	assay_type
4116_CLIP1_S43_L002_R1_001.fastq.gz	4116_01	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4116_CLIP2_S45_L002_R1_001.fastq.gz	4116_02	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4116_INPUT1_S42_L002_R1_001.fastq.gz	4116_INPUT1	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4116_INPUT2_S44_L002_R1_001.fastq.gz	4116_INPUT2	fastq	reads	single-ended	101	NovaSeq6000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4116_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4116_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4116_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4116_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4116_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4116_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4116_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4116_CLIP1_rep1.vs.4116_CLIP2_rep2.sorted.nh.bb	4116_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4116_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4116_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4116_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4116_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4116_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4116_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4116_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4116_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4116_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4116_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4116_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4116_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4116_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4116_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4116_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4116_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4116_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4116_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:4116-control	ENCSR108SQZ	experiment	eCLIP	4116-AGO2-K562-control	Released	ENCODE4
gene-yeo:4116	ENCSR048YXG	experiment	eCLIP	4116-AGO2-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_102015-4116_01	ENCLB336IZW	library	eCLIP	4116_01	Released	ENCODE4
gene-yeo:L-K562_012016-4116_02	ENCLB413BLE	library	eCLIP	4116_02	Released	ENCODE4
gene-yeo:L-K562_102015-4116_INPUT1	ENCLB678VWK	library	eCLIP	4116_INPUT1	Released	ENCODE4
gene-yeo:L-K562_012016-4116_INPUT2	ENCLB579ULC	library	eCLIP	4116_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4116_CLIP1_S43_L002_R1_001.fastq.gz	ENCFF417HAO	file_fastq	eCLIP	4116_01	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF708JIN	file_bam	eCLIP	4116_01	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF072MIC	file_bam	eCLIP	4116_01	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF288AQJ	file_bw	eCLIP	4116_01	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF426UZP	file_bw	eCLIP	4116_01	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF346QLD	file_quantifications	eCLIP	4116_01	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF689OAC	file_bed	eCLIP	4116_01	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF601OLY	file_bb	eCLIP	4116_01	Released	ENCODE4
gene-yeo:4116_CLIP2_S45_L002_R1_001.fastq.gz	ENCFF463PDJ	file_fastq	eCLIP	4116_02	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF170ZIN	file_bam	eCLIP	4116_02	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF920OWJ	file_bam	eCLIP	4116_02	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF673YOR	file_bw	eCLIP	4116_02	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF245GCF	file_bw	eCLIP	4116_02	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF234JBS	file_quantifications	eCLIP	4116_02	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF578KGU	file_bed	eCLIP	4116_02	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF454KDP	file_bb	eCLIP	4116_02	Released	ENCODE4
gene-yeo:4116_INPUT1_S42_L002_R1_001.fastq.gz	ENCFF123GGM	file_fastq	eCLIP	4116_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF717BSO	file_bam	eCLIP	4116_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF769EGK	file_bam	eCLIP	4116_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF097VVD	file_bw	eCLIP	4116_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF709ESL	file_bw	eCLIP	4116_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF615ZNU	file_quantifications	eCLIP	4116_INPUT1	Released	ENCODE4
gene-yeo:4116_INPUT2_S44_L002_R1_001.fastq.gz	ENCFF043HUD	file_fastq	eCLIP	4116_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF631FZD	file_bam	eCLIP	4116_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF038DEJ	file_bam	eCLIP	4116_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF602QYO	file_bw	eCLIP	4116_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF310BST	file_bw	eCLIP	4116_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4116_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF956OKY	file_quantifications	eCLIP	4116_INPUT2	Released	ENCODE4