ENCORE eCLIP:4212

Experiment Information (Status: Released)

	4212-control	4212
Exp_UID	4212	4212
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR549PMM	ENCSR789YZZ
ENCODE_alias	gene-yeo:4212-control	gene-yeo:4212
RBP	SNRNP200	SNRNP200
Cell_Line	HepG2	HepG2
Batch	batch24	batch24
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB827DRA	ENCAB827DRA
Antibody	A303-454A	A303-454A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	8.316358	8.316358
rescue_GRCh38	6.360166	6.360166
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	511	512

Replicate Information


Rep_UID	4212_01	4212_02	4212_INPUT1	4212_INPUT2
Exp UID	4212	4212	4212	4212
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

	4212-control	4212
Self_consistency_hg38	8.316358	8.316358
rescue_GRCh38	6.360166	6.360166

Replicate QC


Rep_UID	4212_01	4212_02	4212_INPUT1	4212_INPUT2
eCT	16.70	16.80	10.30	11.00
Usable_reads	819745	3061775	7901966	6106512
Entropy_hg38	2.092239	1.342872

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4212_01	4212_02	4212_INPUT1	4212_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	ATAGAGGC	GGCTCTGA	TATAGCCT	CCTATCCT
i7_barcode	GAGATTCC	GAGATTCC	GAGATTCC	GAGATTCC

Sequencing Information


Rep_UID	4212_01	4212_02	4212_INPUT1	4212_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
4212_CLIP1_S76_L005_R1_001.fastq.gz	4212_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4212_CLIP2_S78_L005_R1_001.fastq.gz	4212_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4212_INPUT1_S75_L005_R1_001.fastq.gz	4212_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4212_INPUT2_S77_L005_R1_001.fastq.gz	4212_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4212_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4212_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4212_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4212_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4212_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4212_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4212_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4212_CLIP1_rep1.vs.4212_CLIP2_rep2.sorted.nh.bb	4212_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4212_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4212_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4212_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4212_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4212_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4212_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4212_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4212_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4212_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4212_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4212_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4212_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4212_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4212_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4212_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4212_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4212_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4212_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:4212-control	ENCSR549PMM	experiment	eCLIP	4212-SNRNP200-HepG2-control	Released	ENCODE4
gene-yeo:4212	ENCSR789YZZ	experiment	eCLIP	4212-SNRNP200-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4212_01	ENCLB868KWN	library	eCLIP	4212_01	Released	ENCODE4
gene-yeo:L-HepG2_111019-4212_02	ENCLB101CRJ	library	eCLIP	4212_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4212_INPUT1	ENCLB538LMX	library	eCLIP	4212_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_111019-4212_INPUT2	ENCLB742MRB	library	eCLIP	4212_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4212_CLIP1_S76_L005_R1_001.fastq.gz	ENCFF133QUA	file_fastq	eCLIP	4212_01	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF602XTO	file_bam	eCLIP	4212_01	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF048BKH	file_bam	eCLIP	4212_01	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF434YOX	file_bw	eCLIP	4212_01	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF731QSA	file_bw	eCLIP	4212_01	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF507LIX	file_quantifications	eCLIP	4212_01	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF501LBI	file_bed	eCLIP	4212_01	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF926LGN	file_bb	eCLIP	4212_01	Released	ENCODE4
gene-yeo:4212_CLIP2_S78_L005_R1_001.fastq.gz	ENCFF029XAQ	file_fastq	eCLIP	4212_02	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF964OWA	file_bam	eCLIP	4212_02	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF256RJB	file_bam	eCLIP	4212_02	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF202RTY	file_bw	eCLIP	4212_02	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF279RMA	file_bw	eCLIP	4212_02	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF004GAL	file_quantifications	eCLIP	4212_02	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF661CHQ	file_bed	eCLIP	4212_02	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF160SJB	file_bb	eCLIP	4212_02	Released	ENCODE4
gene-yeo:4212_INPUT1_S75_L005_R1_001.fastq.gz	ENCFF306XZM	file_fastq	eCLIP	4212_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF143RPM	file_bam	eCLIP	4212_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF601BXZ	file_bam	eCLIP	4212_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF858KIB	file_bw	eCLIP	4212_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF534TWM	file_bw	eCLIP	4212_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF445UBT	file_quantifications	eCLIP	4212_INPUT1	Released	ENCODE4
gene-yeo:4212_INPUT2_S77_L005_R1_001.fastq.gz	ENCFF677GTJ	file_fastq	eCLIP	4212_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF593JCG	file_bam	eCLIP	4212_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF566JCT	file_bam	eCLIP	4212_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF988TER	file_bw	eCLIP	4212_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF488KIB	file_bw	eCLIP	4212_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4212_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF769HUF	file_quantifications	eCLIP	4212_INPUT2	Released	ENCODE4