ENCORE eCLIP:4036

Experiment Information (Status: Released)

	4036-control	4036
Exp_UID	4036	4036
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR111UKN	ENCSR248TXP
ENCODE_alias	gene-yeo:4036-control	gene-yeo:4036
RBP	FXR1	FXR1
Cell_Line	K562	K562
Batch	batch16	batch16
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB076XDI	ENCAB076XDI
Antibody	702410	702410
Lot_num	2038609	2038609
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	2.859983	2.859983
rescue_GRCh38	1.797597	1.797597
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	581	582

Replicate Information


Rep_UID	4036_01	4036_02	4036_INPUT1	4036_INPUT2
Exp UID	4036	4036	4036	4036
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

	4036-control	4036
Self_consistency_hg38	2.859983	2.859983
rescue_GRCh38	1.797597	1.797597

Replicate QC


Rep_UID	4036_01	4036_02	4036_INPUT1	4036_INPUT2
eCT	11.20	11.20	4.30	4.20
Usable_reads	1276116	1150987	2410697	3476360
Entropy_hg38	1.432648	0.754014

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4036_01	4036_02	4036_INPUT1	4036_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	TCCGGAGA	CGCTCATT	TCCGGAGA

Sequencing Information


Rep_UID	4036_01	4036_02	4036_INPUT1	4036_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
4036_CGCTCATT_TAATCTTA_S25_L001_R1_001.fastq.gz	4036_01	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4036_CLIP2_S8_L001_R1_001.fastq.gz	4036_02	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4036_CGCTCATT_AGGCGAAG_S26_L001_R1_001.fastq.gz	4036_INPUT1	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4036_INPUT2_S7_L001_R1_001.fastq.gz	4036_INPUT2	fastq	reads	single-ended	101	NovaSeq6000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4036_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4036_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4036_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4036_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4036_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4036_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4036_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4036_CLIP1_rep1.vs.4036_CLIP2_rep2.sorted.nh.bb	4036_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4036_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4036_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4036_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4036_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4036_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4036_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4036_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4036_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4036_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4036_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4036_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4036_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4036_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4036_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4036_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4036_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4036_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4036_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:4036-control	ENCSR111UKN	experiment	eCLIP	4036-FXR1-K562-control	Released	ENCODE4
gene-yeo:4036	ENCSR248TXP	experiment	eCLIP	4036-FXR1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_111915-4036_01	ENCLB237AAC	library	eCLIP	4036_01	Released	ENCODE4
gene-yeo:L-K562_072016-4036_02	ENCLB680CKP	library	eCLIP	4036_02	Released	ENCODE4
gene-yeo:L-K562_111915-4036_INPUT1	ENCLB118BRD	library	eCLIP	4036_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4036_INPUT2	ENCLB289ZTR	library	eCLIP	4036_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4036_CGCTCATT_TAATCTTA_S25_L001_R1_001.fastq.gz	ENCFF074ODK	file_fastq	eCLIP	4036_01	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF812FQP	file_bam	eCLIP	4036_01	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF269EKI	file_bam	eCLIP	4036_01	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF805WPQ	file_bw	eCLIP	4036_01	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF630LBY	file_bw	eCLIP	4036_01	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF744FES	file_quantifications	eCLIP	4036_01	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF032HMG	file_bed	eCLIP	4036_01	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF147UIY	file_bb	eCLIP	4036_01	Released	ENCODE4
gene-yeo:4036_CLIP2_S8_L001_R1_001.fastq.gz	ENCFF104LHO	file_fastq	eCLIP	4036_02	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF035ZCH	file_bam	eCLIP	4036_02	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF212YVC	file_bam	eCLIP	4036_02	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF366EQZ	file_bw	eCLIP	4036_02	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF072SZB	file_bw	eCLIP	4036_02	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF585TPA	file_quantifications	eCLIP	4036_02	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF587FOC	file_bed	eCLIP	4036_02	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF568WRV	file_bb	eCLIP	4036_02	Released	ENCODE4
gene-yeo:4036_CGCTCATT_AGGCGAAG_S26_L001_R1_001.fastq.gz	ENCFF991BGJ	file_fastq	eCLIP	4036_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF546TGY	file_bam	eCLIP	4036_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF066WHM	file_bam	eCLIP	4036_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF535QRL	file_bw	eCLIP	4036_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF732CIQ	file_bw	eCLIP	4036_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF455GBF	file_quantifications	eCLIP	4036_INPUT1	Released	ENCODE4
gene-yeo:4036_INPUT2_S7_L001_R1_001.fastq.gz	ENCFF705HGN	file_fastq	eCLIP	4036_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF943UMP	file_bam	eCLIP	4036_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF111AQC	file_bam	eCLIP	4036_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF360IWQ	file_bw	eCLIP	4036_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF592PSI	file_bw	eCLIP	4036_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4036_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF047WLD	file_quantifications	eCLIP	4036_INPUT2	Released	ENCODE4