ENCORE eCLIP:4002

Experiment Information (Status: Released)

	4002-control	4002
Exp_UID	4002	4002
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR325HDY	ENCSR767OEY
ENCODE_alias	gene-yeo:4002-control	gene-yeo:4002
RBP	FXR2	FXR2
Cell_Line	K562	K562
Batch	batch2	batch2
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB479NSE	ENCAB479NSE
Antibody	MA1-16767	MA1-16767
Lot_num	SD251451	SD251451
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.068485	1.068485
rescue_GRCh38	2.448632	2.448632
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	555	556

Replicate Information


Rep_UID	4002_01	4002_02	4002_INPUT1	4002_INPUT2
Exp UID	4002	4002	4002	4002
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_012016	K562_072016	K562_012016	K562_072016
Biosample_ENCODE_Accession	ENCBS039CVO	ENCBS177POD	ENCBS039CVO	ENCBS177POD
Biosample_ENCODE_Alias	gene-yeo:K562_012016	gene-yeo:K562_072016	gene-yeo:K562_012016	gene-yeo:K562_072016
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2016-01-20	2016-07-20	2016-01-20	2016-07-20
Culture_End_Date	2016-02-17	2016-08-15	2016-02-17	2016-08-15
Passage	5	5	5	5

QC Stats

Experiment QC

	4002-control	4002
Self_consistency_hg38	1.068485	1.068485
rescue_GRCh38	2.448632	2.448632

Replicate QC


Rep_UID	4002_01	4002_02	4002_INPUT1	4002_INPUT2
eCT	13.30	14.10	10.80	8.50
Usable_reads	1937503	1638345	4012272	5225688
Entropy_hg38	1.185724	2.331680

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4002_01	4002_02	4002_INPUT1	4002_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	TATAGCCT	ATAGAGGC	TATAGCCT	ATAGAGGC
i7_barcode	TCCGGAGA	TCCGGAGA	ATTACTCG	ATTACTCG

Sequencing Information


Rep_UID	4002_01	4002_02	4002_INPUT1	4002_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
4002_CLIP1_S25_L005_R1_001.fastq.gz	4002_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4002_CLIP2_S27_L005_R1_001.fastq.gz	4002_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4002_INPUT1_S24_L005_R1_001.fastq.gz	4002_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4002_INPUT2_S26_L005_R1_001.fastq.gz	4002_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4002_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4002_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4002_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4002_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4002_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4002_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4002_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4002_CLIP1_rep1.vs.4002_CLIP2_rep2.sorted.nh.bb	4002_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4002_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4002_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4002_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4002_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4002_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4002_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4002_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4002_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4002_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4002_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4002_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4002_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4002_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4002_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4002_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4002_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch2.4002_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4002_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:4002-control	ENCSR325HDY	experiment	eCLIP	4002-FXR2-K562-control	Released	ENCODE4
gene-yeo:4002	ENCSR767OEY	experiment	eCLIP	4002-FXR2-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_012016-4002_01	ENCLB478VDG	library	eCLIP	4002_01	Released	ENCODE4
gene-yeo:L-K562_072016-4002_02	ENCLB277ZVY	library	eCLIP	4002_02	Released	ENCODE4
gene-yeo:L-K562_012016-4002_INPUT1	ENCLB133TCR	library	eCLIP	4002_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4002_INPUT2	ENCLB652BNW	library	eCLIP	4002_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4002_CLIP1_S25_L005_R1_001.fastq.gz	ENCFF232ODO	file_fastq	eCLIP	4002_01	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF262HKO	file_bam	eCLIP	4002_01	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF301ANL	file_bam	eCLIP	4002_01	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF209HNC	file_bw	eCLIP	4002_01	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF379JFL	file_bw	eCLIP	4002_01	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF888QOX	file_quantifications	eCLIP	4002_01	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF051IAD	file_bed	eCLIP	4002_01	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF366ZVI	file_bb	eCLIP	4002_01	Released	ENCODE4
gene-yeo:4002_CLIP2_S27_L005_R1_001.fastq.gz	ENCFF581HLQ	file_fastq	eCLIP	4002_02	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF409EJS	file_bam	eCLIP	4002_02	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF272ZMQ	file_bam	eCLIP	4002_02	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF840LRC	file_bw	eCLIP	4002_02	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF730SFB	file_bw	eCLIP	4002_02	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF553NHT	file_quantifications	eCLIP	4002_02	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF210KBV	file_bed	eCLIP	4002_02	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF771QBQ	file_bb	eCLIP	4002_02	Released	ENCODE4
gene-yeo:4002_INPUT1_S24_L005_R1_001.fastq.gz	ENCFF158KAT	file_fastq	eCLIP	4002_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF384YRD	file_bam	eCLIP	4002_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF970KWZ	file_bam	eCLIP	4002_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF145ZRG	file_bw	eCLIP	4002_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF119LVR	file_bw	eCLIP	4002_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF994PAN	file_quantifications	eCLIP	4002_INPUT1	Released	ENCODE4
gene-yeo:4002_INPUT2_S26_L005_R1_001.fastq.gz	ENCFF657IYT	file_fastq	eCLIP	4002_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF594MEU	file_bam	eCLIP	4002_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF909PYJ	file_bam	eCLIP	4002_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF116PBO	file_bw	eCLIP	4002_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF735MLR	file_bw	eCLIP	4002_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch2.4002_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF944REL	file_quantifications	eCLIP	4002_INPUT2	Released	ENCODE4