ENCORE eCLIP:4187

Experiment Information (Status: Released)

	4187-control	4187
Exp_UID	4187	4187
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR981NWK	ENCSR959OKB
ENCODE_alias	gene-yeo:4187-control	gene-yeo:4187
RBP	SNRPC	SNRPC
Cell_Line	HepG2	HepG2
Batch	batch22	batch22
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	1.151199	1.151199
rescue_GRCh38	2.161489	2.161489
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	533	534

Replicate Information


Rep_UID	4187_01	4187_02	4187_INPUT1	4187_INPUT2
Exp UID	4187	4187	4187	4187
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	HepG2_111019	HepG2_080316	HepG2_111019	HepG2_080316
Biosample_ENCODE_Accession	ENCBS766GPS	ENCBS133LVQ	ENCBS766GPS	ENCBS133LVQ
Biosample_ENCODE_Alias	gene-yeo:HepG2_111019	gene-yeo:HepG2_080316	gene-yeo:HepG2_111019	gene-yeo:HepG2_080316
Cell_Line	HepG2	HepG2	HepG2	HepG2
Culture_Start_Date	2019-10-23	2016-08-03	2019-10-23	2016-08-03
Culture_End_Date	2019-11-10	2016-08-29	2019-11-10	2016-08-29
Passage	3	3	3	3

QC Stats

Experiment QC

	4187-control	4187
Self_consistency_hg38	1.151199	1.151199
rescue_GRCh38	2.161489	2.161489

Replicate QC


Rep_UID	4187_01	4187_02	4187_INPUT1	4187_INPUT2
eCT	8.50	10.90	8.40	8.30
Usable_reads	4681291	2984057	3831456	3349625
Entropy_hg38	0.176479	0.346491

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4187_01	4187_02	4187_INPUT1	4187_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	CGCTCATT	GAGATTCC	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4187_01	4187_02	4187_INPUT1	4187_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
4187_CLIP1_S75_L005_R1_001.fastq.gz	4187_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4187_CLIP2_S77_L005_R1_001.fastq.gz	4187_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4187_IN1_S74_L005_R1_001.fastq.gz	4187_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4187_IN2_S76_L005_R1_001.fastq.gz	4187_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4187_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4187_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4187_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4187_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4187_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4187_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4187_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4187_CLIP1_rep1.vs.4187_CLIP2_rep2.sorted.nh.bb	4187_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4187_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4187_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4187_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4187_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4187_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4187_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4187_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4187_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4187_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4187_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4187_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4187_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4187_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4187_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4187_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4187_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4187_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4187_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:4187-control	ENCSR981NWK	experiment	eCLIP	4187-SNRPC-HepG2-control	Released	ENCODE4
gene-yeo:4187	ENCSR959OKB	experiment	eCLIP	4187-SNRPC-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_111019-4187_01	ENCLB914GAL	library	eCLIP	4187_01	Released	ENCODE4
gene-yeo:L-HepG2_080316-4187_02	ENCLB179CAW	library	eCLIP	4187_02	Released	ENCODE4
gene-yeo:L-HepG2_111019-4187_INPUT1	ENCLB884VXG	library	eCLIP	4187_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_080316-4187_INPUT2	ENCLB180KBA	library	eCLIP	4187_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4187_CLIP1_S75_L005_R1_001.fastq.gz	ENCFF797QDP	file_fastq	eCLIP	4187_01	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF737EBL	file_bam	eCLIP	4187_01	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF165TAF	file_bam	eCLIP	4187_01	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF920SVA	file_bw	eCLIP	4187_01	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF715BUD	file_bw	eCLIP	4187_01	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF569MFF	file_quantifications	eCLIP	4187_01	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF677EIS	file_bed	eCLIP	4187_01	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF541FNC	file_bb	eCLIP	4187_01	Released	ENCODE4
gene-yeo:4187_CLIP2_S77_L005_R1_001.fastq.gz	ENCFF977WMX	file_fastq	eCLIP	4187_02	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF310LDP	file_bam	eCLIP	4187_02	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF688DWO	file_bam	eCLIP	4187_02	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF784MJO	file_bw	eCLIP	4187_02	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF543DJR	file_bw	eCLIP	4187_02	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF474RSQ	file_quantifications	eCLIP	4187_02	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF027UFO	file_bed	eCLIP	4187_02	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF077YST	file_bb	eCLIP	4187_02	Released	ENCODE4
gene-yeo:4187_IN1_S74_L005_R1_001.fastq.gz	ENCFF350DBN	file_fastq	eCLIP	4187_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF443MUC	file_bam	eCLIP	4187_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF220WTN	file_bam	eCLIP	4187_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF707WJK	file_bw	eCLIP	4187_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF412XBD	file_bw	eCLIP	4187_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF712PYU	file_quantifications	eCLIP	4187_INPUT1	Released	ENCODE4
gene-yeo:4187_IN2_S76_L005_R1_001.fastq.gz	ENCFF187WGY	file_fastq	eCLIP	4187_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF201FPR	file_bam	eCLIP	4187_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF794HQT	file_bam	eCLIP	4187_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF687HOA	file_bw	eCLIP	4187_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF778EGH	file_bw	eCLIP	4187_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4187_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF158GVB	file_quantifications	eCLIP	4187_INPUT2	Released	ENCODE4