ENCORE eCLIP:4045

Experiment Information (Status: Released)

	4045-control	4045
Exp_UID	4045	4045
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR961NOR	ENCSR321PWZ
ENCODE_alias	gene-yeo:4045-control	gene-yeo:4045
RBP	SRSF1	SRSF1
Cell_Line	K562	K562
Batch	batch11b	batch11b
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB916GNL	ENCAB916GNL
Antibody	32-4500	32-4500
Lot_num	TG273235	TG273235
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.344688	1.344688
rescue_GRCh38	2.314278	2.314278
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	591	592

Replicate Information


Rep_UID	4045_01	4045_02	4045_INPUT1	4045_INPUT2
Exp UID	4045	4045	4045	4045
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

	4045-control	4045
Self_consistency_hg38	1.344688	1.344688
rescue_GRCh38	2.314278	2.314278

Replicate QC


Rep_UID	4045_01	4045_02	4045_INPUT1	4045_INPUT2
eCT	8.70	8.30	5.70	4.60
Usable_reads	6893539	4111692	2384563	2684756
Entropy_hg38	0.502790	0.418026

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4045_01	4045_02	4045_INPUT1	4045_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	ATTCAGAA	GAATTCGT	ATTCAGAA	GAATTCGT

Sequencing Information


Rep_UID	4045_01	4045_02	4045_INPUT1	4045_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
4045_CLIP1_S83_L005_R1_001.fastq.gz	4045_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4045_CLIP2_S85_L005_R1_001.fastq.gz	4045_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4045_INPUT1_S82_L005_R1_001.fastq.gz	4045_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4045_INPUT2_S84_L005_R1_001.fastq.gz	4045_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4045_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4045_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4045_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4045_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4045_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4045_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4045_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4045_CLIP1_rep1.vs.4045_CLIP2_rep2.sorted.nh.bb	4045_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4045_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4045_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4045_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4045_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4045_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4045_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4045_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4045_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4045_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4045_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4045_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4045_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4045_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4045_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4045_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4045_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4045_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4045_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:4045-control	ENCSR961NOR	experiment	eCLIP	4045-SRSF1-K562-control	Released	ENCODE4
gene-yeo:4045	ENCSR321PWZ	experiment	eCLIP	4045-SRSF1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_111915-4045_01	ENCLB509JKW	library	eCLIP	4045_01	Released	ENCODE4
gene-yeo:L-K562_072016-4045_02	ENCLB605NRG	library	eCLIP	4045_02	Released	ENCODE4
gene-yeo:L-K562_111915-4045_INPUT1	ENCLB110CYE	library	eCLIP	4045_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4045_INPUT2	ENCLB304MRR	library	eCLIP	4045_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4045_CLIP1_S83_L005_R1_001.fastq.gz	ENCFF512IIH	file_fastq	eCLIP	4045_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF595NHE	file_bam	eCLIP	4045_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF810FCS	file_bam	eCLIP	4045_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF222PLU	file_bw	eCLIP	4045_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF751DNF	file_bw	eCLIP	4045_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF861ZKG	file_quantifications	eCLIP	4045_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF487OCT	file_bed	eCLIP	4045_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF080NSH	file_bb	eCLIP	4045_01	Released	ENCODE4
gene-yeo:4045_CLIP2_S85_L005_R1_001.fastq.gz	ENCFF882KLC	file_fastq	eCLIP	4045_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF369EUU	file_bam	eCLIP	4045_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF305QSS	file_bam	eCLIP	4045_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF784WKS	file_bw	eCLIP	4045_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF517SBV	file_bw	eCLIP	4045_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF455LQT	file_quantifications	eCLIP	4045_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF969OHE	file_bed	eCLIP	4045_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF126TAF	file_bb	eCLIP	4045_02	Released	ENCODE4
gene-yeo:4045_INPUT1_S82_L005_R1_001.fastq.gz	ENCFF768ZBD	file_fastq	eCLIP	4045_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF508YJF	file_bam	eCLIP	4045_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF241WHP	file_bam	eCLIP	4045_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF988KZA	file_bw	eCLIP	4045_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF165CCT	file_bw	eCLIP	4045_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF072WIQ	file_quantifications	eCLIP	4045_INPUT1	Released	ENCODE4
gene-yeo:4045_INPUT2_S84_L005_R1_001.fastq.gz	ENCFF354CYD	file_fastq	eCLIP	4045_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF089PII	file_bam	eCLIP	4045_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF555ISB	file_bam	eCLIP	4045_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF112MYF	file_bw	eCLIP	4045_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF430HMA	file_bw	eCLIP	4045_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4045_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF014BYC	file_quantifications	eCLIP	4045_INPUT2	Released	ENCODE4