ENCORE eCLIP:4104

Experiment Information (Status: Released)

	4104-control	4104
Exp_UID	4104	4104
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR701KRV	ENCSR937RSF
ENCODE_alias	gene-yeo:4104-control	gene-yeo:4104
RBP	RPS10	RPS10
Cell_Line	K562	K562
Batch	batch18	batch18
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB391UDZ	ENCAB391UDZ
Antibody	RN070PW	RN070PW
Lot_num	001	001
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	2.919540	2.919540
rescue_GRCh38	8.840909	8.840909
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	561	562

Replicate Information


Rep_UID	4104_01	4104_02	4104_INPUT1	4104_INPUT2
Exp UID	4104	4104	4104	4104
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_091615	K562_012016	K562_091615	K562_012016
Biosample_ENCODE_Accession	ENCBS505ILK	ENCBS039CVO	ENCBS505ILK	ENCBS039CVO
Biosample_ENCODE_Alias	gene-yeo:K562_091615	gene-yeo:K562_012016	gene-yeo:K562_091615	gene-yeo:K562_012016
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-09-16	2016-01-20	2015-09-16	2016-01-20
Culture_End_Date	2015-10-14	2016-02-17	2015-10-14	2016-02-17
Passage	4	5	4	5

QC Stats

Experiment QC

	4104-control	4104
Self_consistency_hg38	2.919540	2.919540
rescue_GRCh38	8.840909	8.840909

Replicate QC


Rep_UID	4104_01	4104_02	4104_INPUT1	4104_INPUT2
eCT	9.40	11.40	4.60	6.30
Usable_reads	2918096	2430609	1780964	938992
Entropy_hg38	0.038052	0.035485

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4104_01	4104_02	4104_INPUT1	4104_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	ATTCAGAA	GAATTCGT	ATTCAGAA	GAATTCGT

Sequencing Information


Rep_UID	4104_01	4104_02	4104_INPUT1	4104_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
4104_CLIP1_S73_L005_R1_001.fastq.gz	4104_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4104_CLIP2_S75_L005_R1_001.fastq.gz	4104_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4104_INPUT1_S72_L005_R1_001.fastq.gz	4104_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4104_INPUT2_S74_L005_R1_001.fastq.gz	4104_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4104_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4104_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4104_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4104_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4104_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4104_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4104_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4104_CLIP1_rep1.vs.4104_CLIP2_rep2.sorted.nh.bb	4104_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4104_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4104_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4104_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4104_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4104_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4104_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4104_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4104_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4104_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4104_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4104_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4104_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4104_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4104_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4104_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4104_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch18.4104_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4104_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:4104-control	ENCSR701KRV	experiment	eCLIP	4104-RPS10-K562-control	Released	ENCODE4
gene-yeo:4104	ENCSR937RSF	experiment	eCLIP	4104-RPS10-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_091615-4104_01	ENCLB810VQD	library	eCLIP	4104_01	Released	ENCODE4
gene-yeo:L-K562_012016-4104_02	ENCLB219XMW	library	eCLIP	4104_02	Released	ENCODE4
gene-yeo:L-K562_091615-4104_INPUT1	ENCLB885HLI	library	eCLIP	4104_INPUT1	Released	ENCODE4
gene-yeo:L-K562_012016-4104_INPUT2	ENCLB094ANL	library	eCLIP	4104_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4104_CLIP1_S73_L005_R1_001.fastq.gz	ENCFF136QXT	file_fastq	eCLIP	4104_01	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF207WNP	file_bam	eCLIP	4104_01	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF773AYO	file_bam	eCLIP	4104_01	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF252EEK	file_bw	eCLIP	4104_01	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF780EXS	file_bw	eCLIP	4104_01	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF219FMZ	file_quantifications	eCLIP	4104_01	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF586MZN	file_bed	eCLIP	4104_01	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF528GKU	file_bb	eCLIP	4104_01	Released	ENCODE4
gene-yeo:4104_CLIP2_S75_L005_R1_001.fastq.gz	ENCFF101IFB	file_fastq	eCLIP	4104_02	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF384MOC	file_bam	eCLIP	4104_02	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF838AUI	file_bam	eCLIP	4104_02	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF460AVS	file_bw	eCLIP	4104_02	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF045PAR	file_bw	eCLIP	4104_02	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF564AYC	file_quantifications	eCLIP	4104_02	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF338MGY	file_bed	eCLIP	4104_02	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF170RQH	file_bb	eCLIP	4104_02	Released	ENCODE4
gene-yeo:4104_INPUT1_S72_L005_R1_001.fastq.gz	ENCFF644ZWQ	file_fastq	eCLIP	4104_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF791WOY	file_bam	eCLIP	4104_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF009MZM	file_bam	eCLIP	4104_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF093FFL	file_bw	eCLIP	4104_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF390PWQ	file_bw	eCLIP	4104_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF288AKL	file_quantifications	eCLIP	4104_INPUT1	Released	ENCODE4
gene-yeo:4104_INPUT2_S74_L005_R1_001.fastq.gz	ENCFF614IWF	file_fastq	eCLIP	4104_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF060FZC	file_bam	eCLIP	4104_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF512KFR	file_bam	eCLIP	4104_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF923RVS	file_bw	eCLIP	4104_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF355ZZY	file_bw	eCLIP	4104_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch18.4104_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF109BGG	file_quantifications	eCLIP	4104_INPUT2	Released	ENCODE4