ENCORE eCLIP:4217

Experiment Information (Status: Released)

	4217-control	4217
Exp_UID	4217	4217
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR546JKS	ENCSR750YOM
ENCODE_alias	gene-yeo:4217-control	gene-yeo:4217
RBP	ADAT1	ADAT1
Cell_Line	K562	K562
Batch	batch23	batch23
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB109YPJ	ENCAB109YPJ
Antibody	PA5-98841	PA5-98841
Lot_num	UK2881574	UK2881574
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	3.209901	3.209901
rescue_GRCh38	2.464475	2.464475
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	515	516

Replicate Information


Rep_UID	4217_01	4217_02	4217_INPUT1	4217_INPUT2
Exp UID	4217	4217	4217	4217
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

	4217-control	4217
Self_consistency_hg38	3.209901	3.209901
rescue_GRCh38	2.464475	2.464475

Replicate QC


Rep_UID	4217_01	4217_02	4217_INPUT1	4217_INPUT2
eCT	15.20	14.50	7.30	6.50
Usable_reads	2806432	4585115	5797642	6356620
Entropy_hg38	0.474392	0.459779

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4217_01	4217_02	4217_INPUT1	4217_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	GGCTCTGA	GGCTCTGA	CCTATCCT	CCTATCCT
i7_barcode	ATTACTCG	TCCGGAGA	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4217_01	4217_02	4217_INPUT1	4217_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
4217_CLIP1_S60_L004_R1_001.fastq.gz	4217_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4217_CLIP2_S62_L004_R1_001.fastq.gz	4217_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4217_INPUT1_S59_L004_R1_001.fastq.gz	4217_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4217_INPUT2_S61_L004_R1_001.fastq.gz	4217_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4217_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4217_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4217_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4217_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4217_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4217_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4217_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4217_CLIP1_rep1.vs.4217_CLIP2_rep2.sorted.nh.bb	4217_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4217_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4217_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4217_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4217_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4217_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4217_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4217_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4217_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4217_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4217_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4217_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4217_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4217_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4217_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4217_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4217_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4217_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4217_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:4217-control	ENCSR546JKS	experiment	eCLIP	4217-ADAT1-K562-control	Released	ENCODE4
gene-yeo:4217	ENCSR750YOM	experiment	eCLIP	4217-ADAT1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4217_01	ENCLB579FLB	library	eCLIP	4217_01	Released	ENCODE4
gene-yeo:L-K562_102015-4217_02	ENCLB555KHW	library	eCLIP	4217_02	Released	ENCODE4
gene-yeo:L-K562_081815-4217_INPUT1	ENCLB111DUO	library	eCLIP	4217_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4217_INPUT2	ENCLB169TEE	library	eCLIP	4217_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4217_CLIP1_S60_L004_R1_001.fastq.gz	ENCFF139SOX	file_fastq	eCLIP	4217_01	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF383PNX	file_bam	eCLIP	4217_01	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF863PXE	file_bam	eCLIP	4217_01	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF839HQJ	file_bw	eCLIP	4217_01	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF574XKZ	file_bw	eCLIP	4217_01	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF986BPE	file_quantifications	eCLIP	4217_01	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF050SYC	file_bed	eCLIP	4217_01	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF858HTW	file_bb	eCLIP	4217_01	Released	ENCODE4
gene-yeo:4217_CLIP2_S62_L004_R1_001.fastq.gz	ENCFF306CFO	file_fastq	eCLIP	4217_02	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF082DUL	file_bam	eCLIP	4217_02	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF409XLY	file_bam	eCLIP	4217_02	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF379JWA	file_bw	eCLIP	4217_02	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF398MQC	file_bw	eCLIP	4217_02	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF635DUH	file_quantifications	eCLIP	4217_02	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF770BZW	file_bed	eCLIP	4217_02	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF376PWN	file_bb	eCLIP	4217_02	Released	ENCODE4
gene-yeo:4217_INPUT1_S59_L004_R1_001.fastq.gz	ENCFF806NSC	file_fastq	eCLIP	4217_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF870EGZ	file_bam	eCLIP	4217_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF838PYM	file_bam	eCLIP	4217_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF295DRE	file_bw	eCLIP	4217_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF011UEX	file_bw	eCLIP	4217_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF048JQR	file_quantifications	eCLIP	4217_INPUT1	Released	ENCODE4
gene-yeo:4217_INPUT2_S61_L004_R1_001.fastq.gz	ENCFF718XYW	file_fastq	eCLIP	4217_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF758PHO	file_bam	eCLIP	4217_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF237CPS	file_bam	eCLIP	4217_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF676GEQ	file_bw	eCLIP	4217_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF487NDF	file_bw	eCLIP	4217_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4217_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF331CFN	file_quantifications	eCLIP	4217_INPUT2	Released	ENCODE4