ENCORE eCLIP:4132

Experiment Information (Status: Released)

	4132-control	4132
Exp_UID	4132	4132
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR219TIG	ENCSR381VNR
ENCODE_alias	gene-yeo:4132-control	gene-yeo:4132
RBP	SRSF9	SRSF9
Cell_Line	K562	K562
Batch	batch21	batch21
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB278ULX	ENCAB278ULX
Antibody	RN081PW	RN081PW
Lot_num	001	001
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.203463	1.203463
rescue_GRCh38	1.885185	1.885185
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	547	548

Replicate Information


Rep_UID	4132_01	4132_02	4132_INPUT1	4132_INPUT2
Exp UID	4132	4132	4132	4132
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_091615	K562_102015	K562_091615	K562_102015
Biosample_ENCODE_Accession	ENCBS505ILK	ENCBS592SHU	ENCBS505ILK	ENCBS592SHU
Biosample_ENCODE_Alias	gene-yeo:K562_091615	gene-yeo:K562_102015	gene-yeo:K562_091615	gene-yeo:K562_102015
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-09-16	2015-10-20	2015-09-16	2015-10-20
Culture_End_Date	2015-10-14	2015-11-17	2015-10-14	2015-11-17
Passage	4	5	4	5

QC Stats

Experiment QC

	4132-control	4132
Self_consistency_hg38	1.203463	1.203463
rescue_GRCh38	1.885185	1.885185

Replicate QC


Rep_UID	4132_01	4132_02	4132_INPUT1	4132_INPUT2
eCT	8.40	9.20	1.10	4.70
Usable_reads	1078579	1000165	1457124	1297752
Entropy_hg38	0.268642	0.344343

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4132_01	4132_02	4132_INPUT1	4132_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	4132_01	4132_02	4132_INPUT1	4132_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
4132_CLIP1_S39_L003_R1_001.fastq.gz	4132_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4132_CLIP2_S41_L003_R1_001.fastq.gz	4132_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4132_IN1_S38_L003_R1_001.fastq.gz	4132_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4132_IN2_S40_L003_R1_001.fastq.gz	4132_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4132_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4132_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4132_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4132_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4132_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4132_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4132_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4132_CLIP1_rep1.vs.4132_CLIP2_rep2.sorted.nh.bb	4132_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4132_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4132_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4132_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4132_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4132_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4132_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4132_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4132_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4132_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4132_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4132_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4132_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4132_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4132_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4132_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4132_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4132_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4132_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:4132-control	ENCSR219TIG	experiment	eCLIP	4132-SRSF9-K562-control	Released	ENCODE4
gene-yeo:4132	ENCSR381VNR	experiment	eCLIP	4132-SRSF9-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_091615-4132_01	ENCLB736IEC	library	eCLIP	4132_01	Released	ENCODE4
gene-yeo:L-K562_102015-4132_02	ENCLB953RHA	library	eCLIP	4132_02	Released	ENCODE4
gene-yeo:L-K562_091615-4132_INPUT1	ENCLB238MYZ	library	eCLIP	4132_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4132_INPUT2	ENCLB558WWD	library	eCLIP	4132_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4132_CLIP1_S39_L003_R1_001.fastq.gz	ENCFF826EHK	file_fastq	eCLIP	4132_01	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF934TLG	file_bam	eCLIP	4132_01	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF870JPN	file_bam	eCLIP	4132_01	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF054DXC	file_bw	eCLIP	4132_01	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF817EMS	file_bw	eCLIP	4132_01	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF706RBS	file_quantifications	eCLIP	4132_01	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF860QZG	file_bed	eCLIP	4132_01	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF392KXS	file_bb	eCLIP	4132_01	Released	ENCODE4
gene-yeo:4132_CLIP2_S41_L003_R1_001.fastq.gz	ENCFF460RIG	file_fastq	eCLIP	4132_02	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF181UTP	file_bam	eCLIP	4132_02	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF937IDV	file_bam	eCLIP	4132_02	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF267JVL	file_bw	eCLIP	4132_02	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF629AZC	file_bw	eCLIP	4132_02	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF476GSP	file_quantifications	eCLIP	4132_02	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF613UUR	file_bed	eCLIP	4132_02	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF580YBK	file_bb	eCLIP	4132_02	Released	ENCODE4
gene-yeo:4132_IN1_S38_L003_R1_001.fastq.gz	ENCFF447ZUQ	file_fastq	eCLIP	4132_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF921NQO	file_bam	eCLIP	4132_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF064HSV	file_bam	eCLIP	4132_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF043PHP	file_bw	eCLIP	4132_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF067FBF	file_bw	eCLIP	4132_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF841DDG	file_quantifications	eCLIP	4132_INPUT1	Released	ENCODE4
gene-yeo:4132_IN2_S40_L003_R1_001.fastq.gz	ENCFF120HCK	file_fastq	eCLIP	4132_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF185LGD	file_bam	eCLIP	4132_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF619YYW	file_bam	eCLIP	4132_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF748CYW	file_bw	eCLIP	4132_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF460SEI	file_bw	eCLIP	4132_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4132_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF575QBN	file_quantifications	eCLIP	4132_INPUT2	Released	ENCODE4