ENCORE eCLIP:4215

Experiment Information (Status: Released)

	4215-control	4215
Exp_UID	4215	4215
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR293CFE	ENCSR379GZS
ENCODE_alias	gene-yeo:4215-control	gene-yeo:4215
RBP	NSUN2	NSUN2
Cell_Line	HepG2	HepG2
Batch	batch26	batch26
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB610PKS	ENCAB610PKS
Antibody	711068	711068
Lot_num	SA245649	SA245649
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.196126	1.196126
rescue_GRCh38	1.703093	1.703093
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	495	496

Replicate Information


Rep_UID	4215_01	4215_02	4215_INPUT1	4215_INPUT2
Exp UID	4215	4215	4215	4215
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	HepG2_080316	HepG2_012220	HepG2_080316	HepG2_012220
Biosample_ENCODE_Accession	ENCBS133LVQ	ENCBS859DVG	ENCBS133LVQ	ENCBS859DVG
Biosample_ENCODE_Alias	gene-yeo:HepG2_080316	gene-yeo:HepG2_012220	gene-yeo:HepG2_080316	gene-yeo:HepG2_012220
Cell_Line	HepG2	HepG2	HepG2	HepG2
Culture_Start_Date	2016-08-03	2020-01-06	2016-08-03	2020-01-06
Culture_End_Date	2016-08-29	2020-01-22	2016-08-29	2020-01-22
Passage	3	3	3	3

QC Stats

Experiment QC

	4215-control	4215
Self_consistency_hg38	1.196126	1.196126
rescue_GRCh38	1.703093	1.703093

Replicate QC


Rep_UID	4215_01	4215_02	4215_INPUT1	4215_INPUT2
eCT	13.90	14.50	8.40	8.90
Usable_reads	2436836	3147715	16219934	8069228
Entropy_hg38	1.028263	0.329764

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4215_01	4215_02	4215_INPUT1	4215_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	GGCTCTGA	GGCTCTGA
i7_barcode	TCCGGAGA	GAGATTCC	ATTACTCG	CGCTCATT

Sequencing Information


Rep_UID	4215_01	4215_02	4215_INPUT1	4215_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
4215_clip1_S60_L008_R1_001.fastq.gz	4215_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4215_clip2_S62_L008_R1_001.fastq.gz	4215_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4215_input1_S59_L008_R1_001.fastq.gz	4215_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4215_input2_S61_L008_R1_001.fastq.gz	4215_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4215_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4215_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4215_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4215_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4215_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4215_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4215_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4215_CLIP1_rep1.vs.4215_CLIP2_rep2.sorted.nh.bb	4215_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4215_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4215_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4215_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4215_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4215_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4215_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4215_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4215_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4215_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4215_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4215_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4215_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4215_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4215_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4215_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4215_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4215_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4215_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:4215-control	ENCSR293CFE	experiment	eCLIP	4215-NSUN2-HepG2-control	Released	ENCODE4
gene-yeo:4215	ENCSR379GZS	experiment	eCLIP	4215-NSUN2-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4215_01	ENCLB890XNW	library	eCLIP	4215_01	Released	ENCODE4
gene-yeo:L-HepG2_012220-4215_02	ENCLB548OUS	library	eCLIP	4215_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4215_INPUT1	ENCLB215KOV	library	eCLIP	4215_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_012220-4215_INPUT2	ENCLB223OWH	library	eCLIP	4215_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4215_clip1_S60_L008_R1_001.fastq.gz	ENCFF311FHF	file_fastq	eCLIP	4215_01	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF553TKS	file_bam	eCLIP	4215_01	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF141HNK	file_bam	eCLIP	4215_01	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF788VGM	file_bw	eCLIP	4215_01	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF765MAJ	file_bw	eCLIP	4215_01	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF546MTC	file_quantifications	eCLIP	4215_01	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF551OMA	file_bed	eCLIP	4215_01	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF593XEF	file_bb	eCLIP	4215_01	Released	ENCODE4
gene-yeo:4215_clip2_S62_L008_R1_001.fastq.gz	ENCFF143ZYE	file_fastq	eCLIP	4215_02	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF960IGR	file_bam	eCLIP	4215_02	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF261FNR	file_bam	eCLIP	4215_02	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF250RWP	file_bw	eCLIP	4215_02	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF937UPG	file_bw	eCLIP	4215_02	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF632DPB	file_quantifications	eCLIP	4215_02	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF823FHE	file_bed	eCLIP	4215_02	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF782AIF	file_bb	eCLIP	4215_02	Released	ENCODE4
gene-yeo:4215_input1_S59_L008_R1_001.fastq.gz	ENCFF388MPI	file_fastq	eCLIP	4215_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF805WTC	file_bam	eCLIP	4215_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF811IEB	file_bam	eCLIP	4215_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF594DPG	file_bw	eCLIP	4215_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF180QZJ	file_bw	eCLIP	4215_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF776LNZ	file_quantifications	eCLIP	4215_INPUT1	Released	ENCODE4
gene-yeo:4215_input2_S61_L008_R1_001.fastq.gz	ENCFF408KFB	file_fastq	eCLIP	4215_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF969GSW	file_bam	eCLIP	4215_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF245SSX	file_bam	eCLIP	4215_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF110JXM	file_bw	eCLIP	4215_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF507QRM	file_bw	eCLIP	4215_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4215_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF554ZER	file_quantifications	eCLIP	4215_INPUT2	Released	ENCODE4