ENCORE eCLIP:4030

Experiment Information (Status: Released)

	4030-control	4030
Exp_UID	4030	4030
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR856KEU	ENCSR554UVB
ENCODE_alias	gene-yeo:4030-control	gene-yeo:4030
RBP	FMR1	FMR1
Cell_Line	K562	K562
Batch	batch16	batch16
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB650WPE	ENCAB650WPE
Antibody	PA5-34584	PA5-34584
Lot_num	TK2671134	TK2671134
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	2.333333	2.333333
rescue_GRCh38	3.774128	3.774128
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	579	580

Replicate Information


Rep_UID	4030_01	4030_02	4030_INPUT1	4030_INPUT2
Exp UID	4030	4030	4030	4030
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_111915	K562_072016	K562_111915	K562_072016
Biosample_ENCODE_Accession	ENCBS344MAK	ENCBS177POD	ENCBS344MAK	ENCBS177POD
Biosample_ENCODE_Alias	gene-yeo:K562_111915	gene-yeo:K562_072016	gene-yeo:K562_111915	gene-yeo:K562_072016
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-11-19	2016-07-20	2015-11-19	2016-07-20
Culture_End_Date	2015-12-11	2016-08-15	2015-12-11	2016-08-15
Passage	4	5	4	5

QC Stats

Experiment QC

	4030-control	4030
Self_consistency_hg38	2.333333	2.333333
rescue_GRCh38	3.774128	3.774128

Replicate QC


Rep_UID	4030_01	4030_02	4030_INPUT1	4030_INPUT2
eCT	13.40	13.00	7.10	4.40
Usable_reads	1578765	3684684	4393725	1204106
Entropy_hg38	0.945076	1.051809

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4030_01	4030_02	4030_INPUT1	4030_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	GGCTCTGA	TATAGCCT	CCTATCCT
i7_barcode	GAATTCGT	ATTACTCG	GAATTCGT	ATTACTCG

Sequencing Information


Rep_UID	4030_01	4030_02	4030_INPUT1	4030_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
4030_CLIP1_S2_L001_R1_001.fastq.gz	4030_01	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4030_CLIP2_S4_L001_R1_001.fastq.gz	4030_02	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4030_INPUT1_S1_L001_R1_001.fastq.gz	4030_INPUT1	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4030_INPUT2_S3_L001_R1_001.fastq.gz	4030_INPUT2	fastq	reads	single-ended	101	NovaSeq6000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4030_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4030_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4030_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4030_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4030_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4030_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4030_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4030_CLIP1_rep1.vs.4030_CLIP2_rep2.sorted.nh.bb	4030_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4030_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4030_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4030_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4030_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4030_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4030_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4030_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4030_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4030_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4030_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4030_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4030_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4030_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4030_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4030_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4030_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4030_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4030_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:4030-control	ENCSR856KEU	experiment	eCLIP	4030-FMR1-K562-control	Released	ENCODE4
gene-yeo:4030	ENCSR554UVB	experiment	eCLIP	4030-FMR1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_111915-4030_01	ENCLB828AGB	library	eCLIP	4030_01	Released	ENCODE4
gene-yeo:L-K562_072016-4030_02	ENCLB899KZX	library	eCLIP	4030_02	Released	ENCODE4
gene-yeo:L-K562_111915-4030_INPUT1	ENCLB686XOV	library	eCLIP	4030_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4030_INPUT2	ENCLB998HLJ	library	eCLIP	4030_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4030_CLIP1_S2_L001_R1_001.fastq.gz	ENCFF348IRX	file_fastq	eCLIP	4030_01	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF368DCQ	file_bam	eCLIP	4030_01	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF116JQY	file_bam	eCLIP	4030_01	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF524LLU	file_bw	eCLIP	4030_01	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF201KFU	file_bw	eCLIP	4030_01	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF999DYF	file_quantifications	eCLIP	4030_01	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF066LUR	file_bed	eCLIP	4030_01	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF944YNX	file_bb	eCLIP	4030_01	Released	ENCODE4
gene-yeo:4030_CLIP2_S4_L001_R1_001.fastq.gz	ENCFF491YJX	file_fastq	eCLIP	4030_02	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF245BWO	file_bam	eCLIP	4030_02	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF060SQN	file_bam	eCLIP	4030_02	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF271SFW	file_bw	eCLIP	4030_02	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF906CLF	file_bw	eCLIP	4030_02	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF295LNR	file_quantifications	eCLIP	4030_02	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF033DLE	file_bed	eCLIP	4030_02	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF320MZQ	file_bb	eCLIP	4030_02	Released	ENCODE4
gene-yeo:4030_INPUT1_S1_L001_R1_001.fastq.gz	ENCFF588ZBP	file_fastq	eCLIP	4030_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF595FDN	file_bam	eCLIP	4030_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF862NOB	file_bam	eCLIP	4030_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF675RNQ	file_bw	eCLIP	4030_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF662WSD	file_bw	eCLIP	4030_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF213KMR	file_quantifications	eCLIP	4030_INPUT1	Released	ENCODE4
gene-yeo:4030_INPUT2_S3_L001_R1_001.fastq.gz	ENCFF075JTX	file_fastq	eCLIP	4030_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF300SQI	file_bam	eCLIP	4030_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF730RDB	file_bam	eCLIP	4030_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF476GZL	file_bw	eCLIP	4030_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF716YRX	file_bw	eCLIP	4030_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4030_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF224GCI	file_quantifications	eCLIP	4030_INPUT2	Released	ENCODE4