ENCORE eCLIP:4155

Experiment Information (Status: Released)

	4155-control	4155
Exp_UID	4155	4155
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR255QSR	ENCSR552TNU
ENCODE_alias	gene-yeo:4155-control	gene-yeo:4155
RBP	SNRPD3	SNRPD3
Cell_Line	K562	K562
Batch	batch21	batch21
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB860WEE	ENCAB860WEE
Antibody	A303-954A	A303-954A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.337193	1.337193
rescue_GRCh38	2.467819	2.467819
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	543	544

Replicate Information


Rep_UID	4155_01	4155_02	4155_INPUT1	4155_INPUT2
Exp UID	4155	4155	4155	4155
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_102015	K562_081815	K562_102015	K562_081815
Biosample_ENCODE_Accession	ENCBS592SHU	ENCBS175JIH	ENCBS592SHU	ENCBS175JIH
Biosample_ENCODE_Alias	gene-yeo:K562_102015	gene-yeo:K562_081815	gene-yeo:K562_102015	gene-yeo:K562_081815
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-10-20	2015-08-18	2015-10-20	2015-08-18
Culture_End_Date	2015-11-17	2015-09-08	2015-11-17	2015-09-08
Passage	5	5	5	5

QC Stats

Experiment QC

	4155-control	4155
Self_consistency_hg38	1.337193	1.337193
rescue_GRCh38	2.467819	2.467819

Replicate QC


Rep_UID	4155_01	4155_02	4155_INPUT1	4155_INPUT2
eCT	9.10	9.00	7.00	7.80
Usable_reads	4818008	5582081	1584221	1320141
Entropy_hg38	1.834103	1.148036

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4155_01	4155_02	4155_INPUT1	4155_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	ATTACTCG	TCCGGAGA	ATTACTCG	CGCTCATT

Sequencing Information


Rep_UID	4155_01	4155_02	4155_INPUT1	4155_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
4155_CLIP1_S35_L003_R1_001.fastq.gz	4155_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4155_CLIP2_S37_L003_R1_001.fastq.gz	4155_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4155_IN1_S34_L003_R1_001.fastq.gz	4155_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4155_IN2_S36_L003_R1_001.fastq.gz	4155_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4155_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4155_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4155_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4155_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4155_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4155_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4155_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4155_CLIP1_rep1.vs.4155_CLIP2_rep2.sorted.nh.bb	4155_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4155_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4155_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4155_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4155_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4155_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4155_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4155_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4155_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4155_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4155_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4155_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4155_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4155_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4155_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4155_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4155_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4155_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4155_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:4155-control	ENCSR255QSR	experiment	eCLIP	4155-SNRPD3-K562-control	Released	ENCODE4
gene-yeo:4155	ENCSR552TNU	experiment	eCLIP	4155-SNRPD3-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_102015-4155_01	ENCLB971SGD	library	eCLIP	4155_01	Released	ENCODE4
gene-yeo:L-K562_081815-4155_02	ENCLB968FKU	library	eCLIP	4155_02	Released	ENCODE4
gene-yeo:L-K562_102015-4155_INPUT1	ENCLB106BON	library	eCLIP	4155_INPUT1	Released	ENCODE4
gene-yeo:L-K562_081815-4155_INPUT2	ENCLB962SQF	library	eCLIP	4155_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4155_CLIP1_S35_L003_R1_001.fastq.gz	ENCFF672QML	file_fastq	eCLIP	4155_01	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF331NRS	file_bam	eCLIP	4155_01	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF460HUE	file_bam	eCLIP	4155_01	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF172DWK	file_bw	eCLIP	4155_01	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF149UFA	file_bw	eCLIP	4155_01	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF010HUV	file_quantifications	eCLIP	4155_01	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF009DCV	file_bed	eCLIP	4155_01	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF019NKC	file_bb	eCLIP	4155_01	Released	ENCODE4
gene-yeo:4155_CLIP2_S37_L003_R1_001.fastq.gz	ENCFF411BVQ	file_fastq	eCLIP	4155_02	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF545VBB	file_bam	eCLIP	4155_02	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF065SQD	file_bam	eCLIP	4155_02	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF608MXH	file_bw	eCLIP	4155_02	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF879NTC	file_bw	eCLIP	4155_02	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF213WDC	file_quantifications	eCLIP	4155_02	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF091XOW	file_bed	eCLIP	4155_02	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF802MUT	file_bb	eCLIP	4155_02	Released	ENCODE4
gene-yeo:4155_IN1_S34_L003_R1_001.fastq.gz	ENCFF856ETV	file_fastq	eCLIP	4155_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF042VZW	file_bam	eCLIP	4155_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF316KBW	file_bam	eCLIP	4155_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF990CDH	file_bw	eCLIP	4155_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF864NNO	file_bw	eCLIP	4155_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF996GDS	file_quantifications	eCLIP	4155_INPUT1	Released	ENCODE4
gene-yeo:4155_IN2_S36_L003_R1_001.fastq.gz	ENCFF840ZDL	file_fastq	eCLIP	4155_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF702QGT	file_bam	eCLIP	4155_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF557OFV	file_bam	eCLIP	4155_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF074SQE	file_bw	eCLIP	4155_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF913YYQ	file_bw	eCLIP	4155_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4155_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF778BAK	file_quantifications	eCLIP	4155_INPUT2	Released	ENCODE4