ENCORE eCLIP:4117

Experiment Information (Status: Released)

	4117-control	4117
Exp_UID	4117	4117
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR618TKA	ENCSR317QOX
ENCODE_alias	gene-yeo:4117-control	gene-yeo:4117
RBP	SF3A1	SF3A1
Cell_Line	HepG2	HepG2
Batch	batch17	batch17
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB549NKF	ENCAB549NKF
Antibody	A301-601A	A301-601A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.000557	1.000557
rescue_GRCh38	1.484878	1.484878
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	569	570

Replicate Information


Rep_UID	4117_01	4117_02	4117_INPUT1	4117_INPUT2
Exp UID	4117	4117	4117	4117
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	HepG2_062716	HepG2_080316	HepG2_062716	HepG2_080316
Biosample_ENCODE_Accession	ENCBS768GCL	ENCBS133LVQ	ENCBS768GCL	ENCBS133LVQ
Biosample_ENCODE_Alias	gene-yeo:HepG2_062716	gene-yeo:HepG2_080316	gene-yeo:HepG2_062716	gene-yeo:HepG2_080316
Cell_Line	HepG2	HepG2	HepG2	HepG2
Culture_Start_Date	2016-06-27	2016-08-03	2016-06-27	2016-08-03
Culture_End_Date	2016-07-25	2016-08-29	2016-07-25	2016-08-29
Passage	3	3	3	3

QC Stats

Experiment QC

	4117-control	4117
Self_consistency_hg38	1.000557	1.000557
rescue_GRCh38	1.484878	1.484878

Replicate QC


Rep_UID	4117_01	4117_02	4117_INPUT1	4117_INPUT2
eCT	10.60	10.80	4.30	4.70
Usable_reads	5694305	5052563	3679039	4688111
Entropy_hg38	5.051834	4.754809

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4117_01	4117_02	4117_INPUT1	4117_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	ATTCAGAA	GAATTCGT	ATTCAGAA	GAATTCGT

Sequencing Information


Rep_UID	4117_01	4117_02	4117_INPUT1	4117_INPUT2
seq_read_type	single-ended	single-ended	single-ended	single-ended
read_length	75	75	75	75
machine	NovaSeq6000	NovaSeq6000	NovaSeq6000	NovaSeq6000
flowcell	flowcell	flowcell	flowcell	flowcell
lane	-	-	-	-

File Information

FASTQ

file_name	Sample ID	file_format	output_type	run_type	read_length	platform	assay_type
4117_CLIP1_S47_L002_R1_001.fastq.gz	4117_01	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4117_CLIP2_S49_L002_R1_001.fastq.gz	4117_02	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4117_INPUT1_S46_L002_R1_001.fastq.gz	4117_INPUT1	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4117_INPUT2_S48_L002_R1_001.fastq.gz	4117_INPUT2	fastq	reads	single-ended	101	NovaSeq6000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4117_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4117_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4117_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4117_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4117_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4117_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4117_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4117_CLIP1_rep1.vs.4117_CLIP2_rep2.sorted.nh.bb	4117_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4117_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4117_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4117_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4117_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4117_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4117_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4117_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4117_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4117_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4117_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4117_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4117_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4117_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4117_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4117_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4117_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch17.4117_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4117_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:4117-control	ENCSR618TKA	experiment	eCLIP	4117-SF3A1-HepG2-control	Released	ENCODE4
gene-yeo:4117	ENCSR317QOX	experiment	eCLIP	4117-SF3A1-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_062716-4117_01	ENCLB215HWE	library	eCLIP	4117_01	Released	ENCODE4
gene-yeo:L-HepG2_080316-4117_02	ENCLB423KJV	library	eCLIP	4117_02	Released	ENCODE4
gene-yeo:L-HepG2_062716-4117_INPUT1	ENCLB394YDA	library	eCLIP	4117_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_080316-4117_INPUT2	ENCLB470CMY	library	eCLIP	4117_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4117_CLIP1_S47_L002_R1_001.fastq.gz	ENCFF767OYS	file_fastq	eCLIP	4117_01	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF056ICL	file_bam	eCLIP	4117_01	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF685NCN	file_bam	eCLIP	4117_01	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF344NRV	file_bw	eCLIP	4117_01	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF266UDI	file_bw	eCLIP	4117_01	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF586TCT	file_quantifications	eCLIP	4117_01	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF530URC	file_bed	eCLIP	4117_01	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF526UJK	file_bb	eCLIP	4117_01	Released	ENCODE4
gene-yeo:4117_CLIP2_S49_L002_R1_001.fastq.gz	ENCFF350YIN	file_fastq	eCLIP	4117_02	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF306ZUJ	file_bam	eCLIP	4117_02	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF152ARZ	file_bam	eCLIP	4117_02	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF076JAG	file_bw	eCLIP	4117_02	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF825VFC	file_bw	eCLIP	4117_02	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF360FGI	file_quantifications	eCLIP	4117_02	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF164EGH	file_bed	eCLIP	4117_02	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF995DEV	file_bb	eCLIP	4117_02	Released	ENCODE4
gene-yeo:4117_INPUT1_S46_L002_R1_001.fastq.gz	ENCFF936YTA	file_fastq	eCLIP	4117_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF896ERP	file_bam	eCLIP	4117_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF150KYP	file_bam	eCLIP	4117_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF634MXD	file_bw	eCLIP	4117_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF145FCZ	file_bw	eCLIP	4117_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF957ZIV	file_quantifications	eCLIP	4117_INPUT1	Released	ENCODE4
gene-yeo:4117_INPUT2_S48_L002_R1_001.fastq.gz	ENCFF320CGU	file_fastq	eCLIP	4117_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF782CSJ	file_bam	eCLIP	4117_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF219NMC	file_bam	eCLIP	4117_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF221GEC	file_bw	eCLIP	4117_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF649VYR	file_bw	eCLIP	4117_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch17.4117_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF748NQV	file_quantifications	eCLIP	4117_INPUT2	Released	ENCODE4