ENCORE eCLIP:4058

Experiment Information (Status: Released)

	4058-control	4058
Exp_UID	4058	4058
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR195PZF	ENCSR124DES
ENCODE_alias	gene-yeo:4058-control	gene-yeo:4058
RBP	SRSF5	SRSF5
Cell_Line	K562	K562
Batch	batch11b	batch11b
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB038XFS	ENCAB038XFS
Antibody	RN082PW	RN082PW
Lot_num	2	2
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	3.081967	3.081967
rescue_GRCh38	2.913462	2.913462
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	593	594

Replicate Information


Rep_UID	4058_01	4058_02	4058_INPUT1	4058_INPUT2
Exp UID	4058	4058	4058	4058
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_072016	K562_111915	K562_072016	K562_111915
Biosample_ENCODE_Accession	ENCBS177POD	ENCBS344MAK	ENCBS177POD	ENCBS344MAK
Biosample_ENCODE_Alias	gene-yeo:K562_072016	gene-yeo:K562_111915	gene-yeo:K562_072016	gene-yeo:K562_111915
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2016-07-20	2015-11-19	2016-07-20	2015-11-19
Culture_End_Date	2016-08-15	2015-12-11	2016-08-15	2015-12-11
Passage	5	4	5	4

QC Stats

Experiment QC

	4058-control	4058
Self_consistency_hg38	3.081967	3.081967
rescue_GRCh38	2.913462	2.913462

Replicate QC


Rep_UID	4058_01	4058_02	4058_INPUT1	4058_INPUT2
eCT	12.70	11.50	4.70	6.20
Usable_reads	1342491	2107415	3211257	2442719
Entropy_hg38	0.203601	0.434666

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4058_01	4058_02	4058_INPUT1	4058_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	ATAGAGGC	TATAGCCT	TATAGCCT
i7_barcode	ATTACTCG	TCCGGAGA	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4058_01	4058_02	4058_INPUT1	4058_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
4058_CLIP1_S95_L006_R1_001.fastq.gz	4058_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4058_CLIP2_S97_L006_R1_001.fastq.gz	4058_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4058_INPUT1_S94_L006_R1_001.fastq.gz	4058_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4058_INPUT2_S96_L006_R1_001.fastq.gz	4058_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4058_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4058_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4058_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4058_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4058_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4058_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4058_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4058_CLIP1_rep1.vs.4058_CLIP2_rep2.sorted.nh.bb	4058_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4058_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4058_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4058_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4058_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4058_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4058_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4058_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4058_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4058_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4058_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4058_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4058_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4058_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4058_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4058_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4058_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11b.4058_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4058_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:4058-control	ENCSR195PZF	experiment	eCLIP	4058-SRSF5-K562-control	Released	ENCODE4
gene-yeo:4058	ENCSR124DES	experiment	eCLIP	4058-SRSF5-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_072016-4058_01	ENCLB326ZIO	library	eCLIP	4058_01	Released	ENCODE4
gene-yeo:L-K562_111915-4058_02	ENCLB462SUL	library	eCLIP	4058_02	Released	ENCODE4
gene-yeo:L-K562_072016-4058_INPUT1	ENCLB296KPY	library	eCLIP	4058_INPUT1	Released	ENCODE4
gene-yeo:L-K562_111915-4058_INPUT2	ENCLB437ZMS	library	eCLIP	4058_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4058_CLIP1_S95_L006_R1_001.fastq.gz	ENCFF734CKL	file_fastq	eCLIP	4058_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF811DAM	file_bam	eCLIP	4058_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF411MNN	file_bam	eCLIP	4058_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF127ANG	file_bw	eCLIP	4058_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF543AMP	file_bw	eCLIP	4058_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF601KQG	file_quantifications	eCLIP	4058_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF175EUU	file_bed	eCLIP	4058_01	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF561QXD	file_bb	eCLIP	4058_01	Released	ENCODE4
gene-yeo:4058_CLIP2_S97_L006_R1_001.fastq.gz	ENCFF347XFC	file_fastq	eCLIP	4058_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF054XDL	file_bam	eCLIP	4058_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF702NBW	file_bam	eCLIP	4058_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF883KHV	file_bw	eCLIP	4058_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF966SFW	file_bw	eCLIP	4058_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF927USJ	file_quantifications	eCLIP	4058_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF041NFR	file_bed	eCLIP	4058_02	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF754GZT	file_bb	eCLIP	4058_02	Released	ENCODE4
gene-yeo:4058_INPUT1_S94_L006_R1_001.fastq.gz	ENCFF061ZNN	file_fastq	eCLIP	4058_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF634EWK	file_bam	eCLIP	4058_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF315DLJ	file_bam	eCLIP	4058_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF306GOA	file_bw	eCLIP	4058_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF486DVU	file_bw	eCLIP	4058_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF961ANS	file_quantifications	eCLIP	4058_INPUT1	Released	ENCODE4
gene-yeo:4058_INPUT2_S96_L006_R1_001.fastq.gz	ENCFF658QZP	file_fastq	eCLIP	4058_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF984YAO	file_bam	eCLIP	4058_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF180BQC	file_bam	eCLIP	4058_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF507RVA	file_bw	eCLIP	4058_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF484YMD	file_bw	eCLIP	4058_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11b.4058_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF951KSM	file_quantifications	eCLIP	4058_INPUT2	Released	ENCODE4