ENCORE eCLIP:4203

Experiment Information (Status: Released)

	4203-control	4203
Exp_UID	4203	4203
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR413TSY	ENCSR203ACR
ENCODE_alias	gene-yeo:4203-control	gene-yeo:4203
RBP	SNRPA1	SNRPA1
Cell_Line	HepG2	HepG2
Batch	batch21	batch21
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB879PIQ	ENCAB879PIQ
Antibody	A303-948A	A303-948A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.607390	1.607390
rescue_GRCh38	1.424528	1.424528
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	541	542

Replicate Information


Rep_UID	4203_01	4203_02	4203_INPUT1	4203_INPUT2
Exp UID	4203	4203	4203	4203
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	HepG2_080316	HepG2_111019	HepG2_080316	HepG2_111019
Biosample_ENCODE_Accession	ENCBS133LVQ	ENCBS766GPS	ENCBS133LVQ	ENCBS766GPS
Biosample_ENCODE_Alias	gene-yeo:HepG2_080316	gene-yeo:HepG2_111019	gene-yeo:HepG2_080316	gene-yeo:HepG2_111019
Cell_Line	HepG2	HepG2	HepG2	HepG2
Culture_Start_Date	2016-08-03	2019-10-23	2016-08-03	2019-10-23
Culture_End_Date	2016-08-29	2019-11-10	2016-08-29	2019-11-10
Passage	3	3	3	3

QC Stats

Experiment QC

	4203-control	4203
Self_consistency_hg38	1.607390	1.607390
rescue_GRCh38	1.424528	1.424528

Replicate QC


Rep_UID	4203_01	4203_02	4203_INPUT1	4203_INPUT2
eCT	18.20	15.70	8.40	8.40
Usable_reads	617851	1956946	5375776	4827232
Entropy_hg38	6.995137	1.587437

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4203_01	4203_02	4203_INPUT1	4203_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	GTACTGAC	AGGCGAAG	CAGGACGT
i7_barcode	CTGAAGCT	CTGAAGCT	CTGAAGCT	CTGAAGCT

Sequencing Information


Rep_UID	4203_01	4203_02	4203_INPUT1	4203_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
4203_CLIP1_R_S43_L003_R1_001.fastq.gz	4203_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4203_CLIP2_R_S45_L003_R1_001.fastq.gz	4203_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4203_IN1_R_S42_L003_R1_001.fastq.gz	4203_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4203_IN2_R_S44_L003_R1_001.fastq.gz	4203_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4203_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4203_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4203_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4203_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4203_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4203_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4203_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4203_CLIP1_rep1.vs.4203_CLIP2_rep2.sorted.nh.bb	4203_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4203_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4203_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4203_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4203_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4203_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4203_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4203_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4203_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4203_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4203_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4203_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4203_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4203_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4203_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4203_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4203_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4203_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4203_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:4203-control	ENCSR413TSY	experiment	eCLIP	4203-SNRPA1-HepG2-control	Released	ENCODE4
gene-yeo:4203	ENCSR203ACR	experiment	eCLIP	4203-SNRPA1-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4203_01	ENCLB459PNI	library	eCLIP	4203_01	Released	ENCODE4
gene-yeo:L-HepG2_111019-4203_02	ENCLB715FLF	library	eCLIP	4203_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4203_INPUT1	ENCLB527URY	library	eCLIP	4203_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_111019-4203_INPUT2	ENCLB608JHE	library	eCLIP	4203_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4203_CLIP1_R_S43_L003_R1_001.fastq.gz	ENCFF935YWA	file_fastq	eCLIP	4203_01	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF138IFT	file_bam	eCLIP	4203_01	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF285QUL	file_bam	eCLIP	4203_01	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF032JZJ	file_bw	eCLIP	4203_01	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF200AUJ	file_bw	eCLIP	4203_01	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF293HBV	file_quantifications	eCLIP	4203_01	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF073MBY	file_bed	eCLIP	4203_01	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF951YVD	file_bb	eCLIP	4203_01	Released	ENCODE4
gene-yeo:4203_CLIP2_R_S45_L003_R1_001.fastq.gz	ENCFF141GNN	file_fastq	eCLIP	4203_02	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF289OQZ	file_bam	eCLIP	4203_02	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF800LOA	file_bam	eCLIP	4203_02	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF560UGL	file_bw	eCLIP	4203_02	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF381XOI	file_bw	eCLIP	4203_02	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF758XNM	file_quantifications	eCLIP	4203_02	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF963WAU	file_bed	eCLIP	4203_02	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF446UAP	file_bb	eCLIP	4203_02	Released	ENCODE4
gene-yeo:4203_IN1_R_S42_L003_R1_001.fastq.gz	ENCFF649LNQ	file_fastq	eCLIP	4203_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF751ONM	file_bam	eCLIP	4203_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF836NWG	file_bam	eCLIP	4203_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF658KLU	file_bw	eCLIP	4203_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF624LJM	file_bw	eCLIP	4203_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF368HNH	file_quantifications	eCLIP	4203_INPUT1	Released	ENCODE4
gene-yeo:4203_IN2_R_S44_L003_R1_001.fastq.gz	ENCFF980OGQ	file_fastq	eCLIP	4203_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF041FXN	file_bam	eCLIP	4203_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF419PJE	file_bam	eCLIP	4203_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF246JPM	file_bw	eCLIP	4203_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF656QOX	file_bw	eCLIP	4203_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4203_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF461CSU	file_quantifications	eCLIP	4203_INPUT2	Released	ENCODE4