ENCORE eCLIP:4164

Experiment Information (Status: Released)

	4164-control	4164
Exp_UID	4164	4164
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR356XVB	ENCSR714FKK
ENCODE_alias	gene-yeo:4164-control	gene-yeo:4164
RBP	SNRPC	SNRPC
Cell_Line	K562	K562
Batch	batch20	batch20
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB311PIH	ENCAB311PIH
Antibody	A303-947A	A303-947A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	4.359107	4.359107
rescue_GRCh38	3.753352	3.753352
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	551	552

Replicate Information


Rep_UID	4164_01	4164_02	4164_INPUT1	4164_INPUT2
Exp UID	4164	4164	4164	4164
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_081815	K562_102015	K562_081815	K562_102015
Biosample_ENCODE_Accession	ENCBS175JIH	ENCBS592SHU	ENCBS175JIH	ENCBS592SHU
Biosample_ENCODE_Alias	gene-yeo:K562_081815	gene-yeo:K562_102015	gene-yeo:K562_081815	gene-yeo:K562_102015
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-08-18	2015-10-20	2015-08-18	2015-10-20
Culture_End_Date	2015-09-08	2015-11-17	2015-09-08	2015-11-17
Passage	5	5	5	5

QC Stats

Experiment QC

	4164-control	4164
Self_consistency_hg38	4.359107	4.359107
rescue_GRCh38	3.753352	3.753352

Replicate QC


Rep_UID	4164_01	4164_02	4164_INPUT1	4164_INPUT2
eCT	8.30	8.40	8.00	6.40
Usable_reads	5668059	4193481	3233443	1868682
Entropy_hg38	0.635059	0.174715

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4164_01	4164_02	4164_INPUT1	4164_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	ATTACTCG	TCCGGAGA	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4164_01	4164_02	4164_INPUT1	4164_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
4164_CLIP1_S31_L002_R1_001.fastq.gz	4164_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4164_CLIP2_S33_L002_R1_001.fastq.gz	4164_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4164_IN1_S30_L002_R1_001.fastq.gz	4164_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4164_IN2_S32_L002_R1_001.fastq.gz	4164_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4164_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4164_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4164_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4164_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4164_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4164_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4164_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4164_CLIP1_rep1.vs.4164_CLIP2_rep2.sorted.nh.bb	4164_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4164_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4164_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4164_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4164_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4164_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4164_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4164_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4164_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4164_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4164_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4164_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4164_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4164_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4164_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4164_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4164_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4164_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4164_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:4164-control	ENCSR356XVB	experiment	eCLIP	4164-SNRPC-K562-control	Released	ENCODE4
gene-yeo:4164	ENCSR714FKK	experiment	eCLIP	4164-SNRPC-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4164_01	ENCLB137DMM	library	eCLIP	4164_01	Released	ENCODE4
gene-yeo:L-K562_102015-4164_02	ENCLB342DOD	library	eCLIP	4164_02	Released	ENCODE4
gene-yeo:L-K562_081815-4164_INPUT1	ENCLB759EWH	library	eCLIP	4164_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4164_INPUT2	ENCLB127RCT	library	eCLIP	4164_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4164_CLIP1_S31_L002_R1_001.fastq.gz	ENCFF825RGY	file_fastq	eCLIP	4164_01	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF435XJI	file_bam	eCLIP	4164_01	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF162QKV	file_bam	eCLIP	4164_01	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF566RXK	file_bw	eCLIP	4164_01	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF605MPF	file_bw	eCLIP	4164_01	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF275WXB	file_quantifications	eCLIP	4164_01	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF925SKU	file_bed	eCLIP	4164_01	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF441CJM	file_bb	eCLIP	4164_01	Released	ENCODE4
gene-yeo:4164_CLIP2_S33_L002_R1_001.fastq.gz	ENCFF416FHZ	file_fastq	eCLIP	4164_02	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF691SCP	file_bam	eCLIP	4164_02	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF403KDR	file_bam	eCLIP	4164_02	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF038GLE	file_bw	eCLIP	4164_02	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF484ISI	file_bw	eCLIP	4164_02	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF332UKK	file_quantifications	eCLIP	4164_02	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF731TGS	file_bed	eCLIP	4164_02	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF250KPS	file_bb	eCLIP	4164_02	Released	ENCODE4
gene-yeo:4164_IN1_S30_L002_R1_001.fastq.gz	ENCFF246QLD	file_fastq	eCLIP	4164_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF934BRY	file_bam	eCLIP	4164_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF506KHH	file_bam	eCLIP	4164_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF669BYS	file_bw	eCLIP	4164_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF754TWB	file_bw	eCLIP	4164_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF944FBN	file_quantifications	eCLIP	4164_INPUT1	Released	ENCODE4
gene-yeo:4164_IN2_S32_L002_R1_001.fastq.gz	ENCFF307RGB	file_fastq	eCLIP	4164_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF627ZYC	file_bam	eCLIP	4164_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF721VRQ	file_bam	eCLIP	4164_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF204ZEM	file_bw	eCLIP	4164_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF041WWB	file_bw	eCLIP	4164_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch20.4164_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF076PYD	file_quantifications	eCLIP	4164_INPUT2	Released	ENCODE4